From dan.bolser at gmail.com  Thu Jul  1 05:48:02 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Thu, 1 Jul 2010 10:48:02 +0100
Subject: [Open-bio-l] Best practice for modelling data in GFF
In-Reply-To: <20100601113420.GL1054@sobchak.mgh.harvard.edu>
References: <AANLkTimuku_x7V9RSAERK4f4QxIc4od2zw3qZtdaL4oH@mail.gmail.com>
	<4BFFF7FE.1030004@bioperl.org>
	<685C1029-0E3A-45DD-BBA9-FFA7747810D5@illinois.edu>
	<AANLkTinrTVYODrcY9TUxhznkZKunNRQCvs-bnwgbHdNA@mail.gmail.com>
	<20100601113420.GL1054@sobchak.mgh.harvard.edu>
Message-ID: <AANLkTikcZgIjDlnUUs90IlEXBsvDhtvYq8LESKU9LChu@mail.gmail.com>

On 1 June 2010 12:34, Brad Chapman <chapmanb at 50mail.com> wrote:
> Dan;
> If what you are trying to do is represent your data in a way that the
> most people can parse and reuse it, my suggestion would be to use
> SAM/BAM to represent your alignments. You'll be using a standardized and
> well-supported format specifically designed for this type of data.
>
> While you can do this with GFF, the parser support for correctly
> dealing with match_part or part_of is likely to be less robust.
> As data providers standardize on one way to represent nested
> features, it should become easier to deal with them.

Yeah, I think BAM is a good way to go in this instance.


> Brad
>
>> Thanks all for replies.
>>
>> I'm aware of the GFF spec, and the SO ontology terms. The issue here
>> (as I understand it) is that the feature isn't 'flat', but is a
>> combination of two matching 'reads' that are grouped into a mate-pair
>> depending on their proximity and orientation. As pointed out, not
>> every pair is successfully mapped, specifically one read may be
>> 'missing' from the pair, the pair may span two reference sequences, or
>> the proximity or orientation of the pair may be incorrect.
>>
>> Strictly speaking this can be handled by match and match_part (or
>> read_pair and part_of) terms, however, the question is, does this
>> reflect the biology adequately? (And specifically which terms should
>> be used?)
>>
>> There is a canonical way to model a gene, so I was wondering if it
>> makes sense to describe similar 'biology' (or in this case molecular
>> biology) in standard ways (when the feature isn't simply described by
>> a single line of GFF)?
>>
>> Perhaps I've not understood SO properly, but I'm not sure how its
>> structure is translated into GFF structure ... is there a 1 to 1
>> mapping?
>>
>>
>> Cheers,
>> Dan.
>>
>> On 28 May 2010 18:49, Chris Fields <cjfields at illinois.edu> wrote:
>> > All,
>> >
>> > Appears that link isn't up to date. ?Current GFF3 spec (v. 1.16, updated May 25) here:
>> >
>> > http://www.sequenceontology.org/gff3.shtml
>> >
>> > chris
>> >
>> > On May 28, 2010, at 12:06 PM, Jason Stajich wrote:
>> >
>> >> It's covered in the GFF3 spec as match_part if that helps.
>> >> http://song.sourceforge.net/gff3.shtml
>> >>
>> >> Dan Bolser wrote, On 5/28/10 9:29 AM:
>> >>> Hi guys,
>> >>>
>> >>> Not sure if this is the right forum, but I just thought I'd ask...
>> >>>
>> >>> Where can I find information on 'best practices' for modelling
>> >>> biological data in GFF?
>> >>>
>> >>> For example, I'd like to model paired-end sequence alignments in GFF.
>> >>> One suggestion was to use match/match_part to link each end into a
>> >>> pair. Another option is to use 'read_pair' with 'contig' for the
>> >>> parent feature...
>> >>>
>> >>> Should I just be using SAM/BAM?
>> >>>
>> >>> Seems a shame not to have a standard way to do this in GFF...
>> >>>
>> >>>
>> >>> Cheers,
>> >>> Dan.
>> >>> _______________________________________________
>> >>> Open-Bio-l mailing list
>> >>> Open-Bio-l at lists.open-bio.org
>> >>> http://lists.open-bio.org/mailman/listinfo/open-bio-l
>> >>>
>> >> _______________________________________________
>> >> Open-Bio-l mailing list
>> >> Open-Bio-l at lists.open-bio.org
>> >> http://lists.open-bio.org/mailman/listinfo/open-bio-l
>> >
>> >
>>
>> _______________________________________________
>> Open-Bio-l mailing list
>> Open-Bio-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/open-bio-l
> _______________________________________________
> Open-Bio-l mailing list
> Open-Bio-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/open-bio-l
>


From dan.bolser at gmail.com  Thu Jul  1 06:12:21 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Thu, 1 Jul 2010 11:12:21 +0100
Subject: [Open-bio-l] Best practice for modelling data in GFF
In-Reply-To: <AANLkTinrTVYODrcY9TUxhznkZKunNRQCvs-bnwgbHdNA@mail.gmail.com>
References: <AANLkTimuku_x7V9RSAERK4f4QxIc4od2zw3qZtdaL4oH@mail.gmail.com>
	<4BFFF7FE.1030004@bioperl.org>
	<685C1029-0E3A-45DD-BBA9-FFA7747810D5@illinois.edu>
	<AANLkTinrTVYODrcY9TUxhznkZKunNRQCvs-bnwgbHdNA@mail.gmail.com>
Message-ID: <AANLkTim3OsVC5cwwOlF095A5B6eJ6n03XNc7SpYMZJeV@mail.gmail.com>

On 29 May 2010 00:08, Dan Bolser <dan.bolser at gmail.com> wrote:
> Thanks all for replies.

<snip>

> There is a canonical way to model a gene, so I was wondering if it
> makes sense to describe similar 'biology' (or in this case molecular
> biology) in standard ways (when the feature isn't simply described by
> a single line of GFF)?
>
> Perhaps I've not understood SO properly, but I'm not sure how its
> structure is translated into GFF structure ... is there a 1 to 1
> mapping?

Lack of replies lead me to believe that indeed, the GFF Parent
attribute should reflect (or be strictly determined by) the SO
'relationships' (are they all 'part_of' relationships?)

However, I was trying to get some concepts clear in my head, and I
ended up creating a figure of a 'canonical gene' in SO [1], based on
the one in the GFF docs [2].

[1] http://imagebin.ca/view/Ni9BFbK.html
[2] http://www.sequenceontology.org/gff3.shtml


There is a transitive part_of relationships between 'mRNA' and 'gene',
which explains line 4 to 6 of the canonical gene GFF [2].

However, the figure shows that 'exon' is part_of 'transcript', and not
part_of 'mRNA'. If I got the figure right, and if I understand
correctly, there is no way to transitively infer that exon is part_of
mRNA (line 7 to 11 of the GFF [2]).

This implies that the 'structure' in GFF isn't strictly determined by SO.

Or is it a mistake in SO?


Sorry if this is a 'gotcha' that has been discussed before. Any links
to help me understand would be great.

Dan.

> Cheers,
> Dan.
>
> On 28 May 2010 18:49, Chris Fields <cjfields at illinois.edu> wrote:
>> All,
>>
>> Appears that link isn't up to date. ?Current GFF3 spec (v. 1.16, updated May 25) here:
>>
>> http://www.sequenceontology.org/gff3.shtml
>>
>> chris
>>
>> On May 28, 2010, at 12:06 PM, Jason Stajich wrote:
>>
>>> It's covered in the GFF3 spec as match_part if that helps.
>>> http://song.sourceforge.net/gff3.shtml
>>>
>>> Dan Bolser wrote, On 5/28/10 9:29 AM:
>>>> Hi guys,
>>>>
>>>> Not sure if this is the right forum, but I just thought I'd ask...
>>>>
>>>> Where can I find information on 'best practices' for modelling
>>>> biological data in GFF?
>>>>
>>>> For example, I'd like to model paired-end sequence alignments in GFF.
>>>> One suggestion was to use match/match_part to link each end into a
>>>> pair. Another option is to use 'read_pair' with 'contig' for the
>>>> parent feature...
>>>>
>>>> Should I just be using SAM/BAM?
>>>>
>>>> Seems a shame not to have a standard way to do this in GFF...
>>>>
>>>>
>>>> Cheers,
>>>> Dan.
>>>> _______________________________________________
>>>> Open-Bio-l mailing list
>>>> Open-Bio-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/open-bio-l
>>>>
>>> _______________________________________________
>>> Open-Bio-l mailing list
>>> Open-Bio-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/open-bio-l
>>
>>
>


From cjfields at illinois.edu  Fri Jul  2 09:27:46 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 2 Jul 2010 08:27:46 -0500
Subject: [Open-bio-l] GitHub Organizations
Message-ID: <6C174734-0D66-422F-89F2-C724C9BE6BE9@illinois.edu>

I will likely switch the bioperl repository over to an Organization account on GitHub in the next couple of days.  I don't believe this will change anything (git clone address, etc) but will check into it prior to making the switch.

Have any other Bio* on GitHub made this switch yet?

chris

From cjfields at illinois.edu  Fri Jul  2 09:45:43 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 2 Jul 2010 08:45:43 -0500
Subject: [Open-bio-l] GitHub Organizations
In-Reply-To: <6C174734-0D66-422F-89F2-C724C9BE6BE9@illinois.edu>
References: <6C174734-0D66-422F-89F2-C724C9BE6BE9@illinois.edu>
Message-ID: <BDCB990F-4612-40F2-93D3-71E79BCC8502@illinois.edu>

On Jul 2, 2010, at 8:27 AM, Chris Fields wrote:

> I will likely switch the bioperl repository over to an Organization account on GitHub in the next couple of days.  

Um, amend that to 'now'.  It's very nice!

> I don't believe this will change anything (git clone address, etc) but will check into it prior to making the switch.
> 
> Have any other Bio* on GitHub made this switch yet?
> 
> chris

The org setup has teams, so you can now assign the same team to multiple projects as needed.  The GitHub folk had hinted this was coming, glad to see it now!

chris

From p.j.a.cock at googlemail.com  Fri Jul  2 10:03:44 2010
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 2 Jul 2010 15:03:44 +0100
Subject: [Open-bio-l] GitHub Organizations
In-Reply-To: <BDCB990F-4612-40F2-93D3-71E79BCC8502@illinois.edu>
References: <6C174734-0D66-422F-89F2-C724C9BE6BE9@illinois.edu>
	<BDCB990F-4612-40F2-93D3-71E79BCC8502@illinois.edu>
Message-ID: <AANLkTin2DgDCRPn6E7OsQQIPGUbtQTYloZStDvNepz_R@mail.gmail.com>

On Fri, Jul 2, 2010 at 2:45 PM, Chris Fields <cjfields at illinois.edu> wrote:
> On Jul 2, 2010, at 8:27 AM, Chris Fields wrote:
>
>> I will likely switch the bioperl repository over to an Organization account on GitHub in the next couple of days.
>
> Um, amend that to 'now'. ?It's very nice!
>
>> I don't believe this will change anything (git clone address, etc) but will check into it prior to making the switch.
>>
>> Have any other Bio* on GitHub made this switch yet?
>>
>> chris
>
> The org setup has teams, so you can now assign the same team to multiple projects as needed. ?The GitHub folk had hinted this was coming, glad to see it now!
>
> chris

No - I wasn't aware this was available yet. I should check... thanks
for the heads up!

Peter


From chapmanb at 50mail.com  Fri Jul  2 09:38:22 2010
From: chapmanb at 50mail.com (Brad Chapman)
Date: Fri, 2 Jul 2010 09:38:22 -0400
Subject: [Open-bio-l] Codefest 2010: Final details
Message-ID: <20100702133822.GA8735@sobchak.mgh.harvard.edu>

Hi all;
Codefest 2010 is finally here: next Wednesday and Thursday at
Harvard Medical School and Massachusetts General Hospital in
beautiful Boston. All of the logistics, directions and details 
are on the wiki page:

http://www.open-bio.org/wiki/Codefest_2010

If you want the short version: show up at Harvard Medical School on
Wednesday at 10am and we'll take care of the rest. Thanks to the
hard work of Oliver, Kimberly, Leah, Toshiaki, and Mitsuteru we'll
have coffee, lunches and internet. Thanks to Steffen and Ntino,
we'll have Amazon credits to utilize. And of course, there will be 
BBQ and drinking on Thursday night when we are finished.

I'm looking forward to a fun and productive time. The general plan
will be to spend a bit of time on Wednesday morning organizing 
ourselves into like minded groups of folks, and then commence with
coding and collaborating.

If you aren't able to make it and you're listed on the wiki page under
participants, please do cross your name off so we have a good idea of
final numbers. Likewise, if you are coming but haven't put your name up
there please add it.

If you are interested in helping with making software and data
available on shared cloud resources, here are the latest Amazon
AMIs, snapshots, and the code base:

Cloud BioLinux images:
64bit: ami-d62cc4bf
32bit: ami-5423cb3d

An EBS public snapshot with indexed genomes:
snap-67446d0f

Infrastructure:
http://github.com/chapmanb/bcbb/tree/master/ec2/biolinux/

Send an e-mail with any questions, thoughts or concerns. My phone
number is 617-447-8586 in case you end up hopelessly lost somewhere
in Boston and are desperate to begin programming.

Looking forward to seeing everyone next Wednesday,
Brad

From maizemu at gmail.com  Sat Jul  3 01:36:48 2010
From: maizemu at gmail.com (Christopher Bottoms)
Date: Sat, 3 Jul 2010 00:36:48 -0500
Subject: [Open-bio-l] Codefest 2010: Final details
In-Reply-To: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
Message-ID: <AANLkTilM3_kEu9BWx2CIUaS2lklP1ULVKLhlKHtukgk2@mail.gmail.com>

Hi all,

I was originally planning on working on cloud computing at the Codefest.
However, the 2-day cloud computing tutorial that I was going to attend in
mid June was canceled. Does anyone have any programming that they would like
help with? I have experience with Perl 5, including Moose, and I am starting
to dabble in Perl 6. I have also programmed in Java in the past. I hear
Python is easy to learn, so I'd be open to working on a Python project as
well.

Thanks,
Christopher Bottoms

On Fri, Jul 2, 2010 at 8:38 AM, Brad Chapman <chapmanb at 50mail.com> wrote:

> Hi all;
> Codefest 2010 is finally here: next Wednesday and Thursday at
> Harvard Medical School and Massachusetts General Hospital in
> beautiful Boston. All of the logistics, directions and details
> are on the wiki page:
>
> http://www.open-bio.org/wiki/Codefest_2010
>
> If you want the short version: show up at Harvard Medical School on
> Wednesday at 10am and we'll take care of the rest. Thanks to the
> hard work of Oliver, Kimberly, Leah, Toshiaki, and Mitsuteru we'll
> have coffee, lunches and internet. Thanks to Steffen and Ntino,
> we'll have Amazon credits to utilize. And of course, there will be
> BBQ and drinking on Thursday night when we are finished.
>
> I'm looking forward to a fun and productive time. The general plan
> will be to spend a bit of time on Wednesday morning organizing
> ourselves into like minded groups of folks, and then commence with
> coding and collaborating.
>
> If you aren't able to make it and you're listed on the wiki page under
> participants, please do cross your name off so we have a good idea of
> final numbers. Likewise, if you are coming but haven't put your name up
> there please add it.
>
> If you are interested in helping with making software and data
> available on shared cloud resources, here are the latest Amazon
> AMIs, snapshots, and the code base:
>
> Cloud BioLinux images:
> 64bit: ami-d62cc4bf
> 32bit: ami-5423cb3d
>
> An EBS public snapshot with indexed genomes:
> snap-67446d0f
>
> Infrastructure:
> http://github.com/chapmanb/bcbb/tree/master/ec2/biolinux/
>
> Send an e-mail with any questions, thoughts or concerns. My phone
> number is 617-447-8586 in case you end up hopelessly lost somewhere
> in Boston and are desperate to begin programming.
>
> Looking forward to seeing everyone next Wednesday,
> Brad
>

From heikki.lehvaslaiho at gmail.com  Sat Jul  3 01:44:23 2010
From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho)
Date: Sat, 3 Jul 2010 08:44:23 +0300
Subject: [Open-bio-l] Codefest 2010: Final details
In-Reply-To: <AANLkTilM3_kEu9BWx2CIUaS2lklP1ULVKLhlKHtukgk2@mail.gmail.com>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu> 
	<AANLkTilM3_kEu9BWx2CIUaS2lklP1ULVKLhlKHtukgk2@mail.gmail.com>
Message-ID: <AANLkTiku8rxnLRFf0JULsAYvz5D07FeZR9ejKBZHQrCQ@mail.gmail.com>

Chris,

I do not have too much experience on cloud computing, either. There
will be quite a few people from BioPerl . We'll meet and  come up with
a plan first thing in the morning. Unless someone has a very good one
ready for sharing...

     -Heikki

Heikki Lehvaslaiho - skype:heikki_lehvaslaiho
cell: +966 545 595 849  office: +966 2 808 2429

Computational Bioscience Research Centre (CBRC), Building #2, Office #4216
4700 King Abdullah University of Science and Technology (KAUST)
Thuwal 23955-6900, Kingdom of Saudi Arabia




On 3 July 2010 08:36, Christopher Bottoms <maizemu at gmail.com> wrote:
> Hi all,
>
> I was originally planning on working on cloud computing at the Codefest.
> However, the 2-day cloud computing tutorial that I was going to attend in
> mid June was canceled. Does anyone have any programming that they would like
> help with? I have experience with Perl 5, including Moose, and I am starting
> to dabble in Perl 6. I have also programmed in Java in the past. I hear
> Python is easy to learn, so I'd be open to working on a Python project as
> well.
>
> Thanks,
> Christopher Bottoms
>
> On Fri, Jul 2, 2010 at 8:38 AM, Brad Chapman <chapmanb at 50mail.com> wrote:
>>
>> Hi all;
>> Codefest 2010 is finally here: next Wednesday and Thursday at
>> Harvard Medical School and Massachusetts General Hospital in
>> beautiful Boston. All of the logistics, directions and details
>> are on the wiki page:
>>
>> http://www.open-bio.org/wiki/Codefest_2010
>>
>> If you want the short version: show up at Harvard Medical School on
>> Wednesday at 10am and we'll take care of the rest. Thanks to the
>> hard work of Oliver, Kimberly, Leah, Toshiaki, and Mitsuteru we'll
>> have coffee, lunches and internet. Thanks to Steffen and Ntino,
>> we'll have Amazon credits to utilize. And of course, there will be
>> BBQ and drinking on Thursday night when we are finished.
>>
>> I'm looking forward to a fun and productive time. The general plan
>> will be to spend a bit of time on Wednesday morning organizing
>> ourselves into like minded groups of folks, and then commence with
>> coding and collaborating.
>>
>> If you aren't able to make it and you're listed on the wiki page under
>> participants, please do cross your name off so we have a good idea of
>> final numbers. Likewise, if you are coming but haven't put your name up
>> there please add it.
>>
>> If you are interested in helping with making software and data
>> available on shared cloud resources, here are the latest Amazon
>> AMIs, snapshots, and the code base:
>>
>> Cloud BioLinux images:
>> 64bit: ami-d62cc4bf
>> 32bit: ami-5423cb3d
>>
>> An EBS public snapshot with indexed genomes:
>> snap-67446d0f
>>
>> Infrastructure:
>> http://github.com/chapmanb/bcbb/tree/master/ec2/biolinux/
>>
>> Send an e-mail with any questions, thoughts or concerns. My phone
>> number is 617-447-8586 in case you end up hopelessly lost somewhere
>> in Boston and are desperate to begin programming.
>>
>> Looking forward to seeing everyone next Wednesday,
>> Brad
>
>

From cjfields at illinois.edu  Sat Jul  3 10:15:18 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Sat, 3 Jul 2010 09:15:18 -0500
Subject: [Open-bio-l] Codefest 2010: Final details
In-Reply-To: <AANLkTiku8rxnLRFf0JULsAYvz5D07FeZR9ejKBZHQrCQ@mail.gmail.com>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTilM3_kEu9BWx2CIUaS2lklP1ULVKLhlKHtukgk2@mail.gmail.com>
	<AANLkTiku8rxnLRFf0JULsAYvz5D07FeZR9ejKBZHQrCQ@mail.gmail.com>
Message-ID: <EEB50E10-CC46-43C7-928B-3CE8FC074315@illinois.edu>

I will be there on the afternoon of the 7th.  There are a couple of projects one can look into for Moose and Perl 6 (Biome and BioPerl6).  I think Hilmar was to do some DBIx::Class stuff for BioSQL at one point, not sure where that is (might be surplanted by SQLite work?).  Would be nice to talk with Mark re: the wrapper system for BioPerl as well.

So lots of stuff to think over and plan for.  Maybe we should move this to open-bio-l, or bioperl-l?

chris (fields)

On Jul 3, 2010, at 12:44 AM, Heikki Lehvaslaiho wrote:

> Chris,
> 
> I do not have too much experience on cloud computing, either. There
> will be quite a few people from BioPerl . We'll meet and  come up with
> a plan first thing in the morning. Unless someone has a very good one
> ready for sharing...
> 
>     -Heikki
> 
> Heikki Lehvaslaiho - skype:heikki_lehvaslaiho
> cell: +966 545 595 849  office: +966 2 808 2429
> 
> Computational Bioscience Research Centre (CBRC), Building #2, Office #4216
> 4700 King Abdullah University of Science and Technology (KAUST)
> Thuwal 23955-6900, Kingdom of Saudi Arabia
> 
> 
> 
> 
> On 3 July 2010 08:36, Christopher Bottoms <maizemu at gmail.com> wrote:
>> Hi all,
>> 
>> I was originally planning on working on cloud computing at the Codefest.
>> However, the 2-day cloud computing tutorial that I was going to attend in
>> mid June was canceled. Does anyone have any programming that they would like
>> help with? I have experience with Perl 5, including Moose, and I am starting
>> to dabble in Perl 6. I have also programmed in Java in the past. I hear
>> Python is easy to learn, so I'd be open to working on a Python project as
>> well.
>> 
>> Thanks,
>> Christopher Bottoms
>> 
>> On Fri, Jul 2, 2010 at 8:38 AM, Brad Chapman <chapmanb at 50mail.com> wrote:
>>> 
>>> Hi all;
>>> Codefest 2010 is finally here: next Wednesday and Thursday at
>>> Harvard Medical School and Massachusetts General Hospital in
>>> beautiful Boston. All of the logistics, directions and details
>>> are on the wiki page:
>>> 
>>> http://www.open-bio.org/wiki/Codefest_2010
>>> 
>>> If you want the short version: show up at Harvard Medical School on
>>> Wednesday at 10am and we'll take care of the rest. Thanks to the
>>> hard work of Oliver, Kimberly, Leah, Toshiaki, and Mitsuteru we'll
>>> have coffee, lunches and internet. Thanks to Steffen and Ntino,
>>> we'll have Amazon credits to utilize. And of course, there will be
>>> BBQ and drinking on Thursday night when we are finished.
>>> 
>>> I'm looking forward to a fun and productive time. The general plan
>>> will be to spend a bit of time on Wednesday morning organizing
>>> ourselves into like minded groups of folks, and then commence with
>>> coding and collaborating.
>>> 
>>> If you aren't able to make it and you're listed on the wiki page under
>>> participants, please do cross your name off so we have a good idea of
>>> final numbers. Likewise, if you are coming but haven't put your name up
>>> there please add it.
>>> 
>>> If you are interested in helping with making software and data
>>> available on shared cloud resources, here are the latest Amazon
>>> AMIs, snapshots, and the code base:
>>> 
>>> Cloud BioLinux images:
>>> 64bit: ami-d62cc4bf
>>> 32bit: ami-5423cb3d
>>> 
>>> An EBS public snapshot with indexed genomes:
>>> snap-67446d0f
>>> 
>>> Infrastructure:
>>> http://github.com/chapmanb/bcbb/tree/master/ec2/biolinux/
>>> 
>>> Send an e-mail with any questions, thoughts or concerns. My phone
>>> number is 617-447-8586 in case you end up hopelessly lost somewhere
>>> in Boston and are desperate to begin programming.
>>> 
>>> Looking forward to seeing everyone next Wednesday,
>>> Brad
>> 
>> 



From hlapp at nescent.org  Sat Jul  3 14:36:21 2010
From: hlapp at nescent.org (Hilmar Lapp)
Date: Sat, 3 Jul 2010 14:36:21 -0400
Subject: [Open-bio-l] Codefest 2010: Final details
In-Reply-To: <EEB50E10-CC46-43C7-928B-3CE8FC074315@illinois.edu>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTilM3_kEu9BWx2CIUaS2lklP1ULVKLhlKHtukgk2@mail.gmail.com>
	<AANLkTiku8rxnLRFf0JULsAYvz5D07FeZR9ejKBZHQrCQ@mail.gmail.com>
	<EEB50E10-CC46-43C7-928B-3CE8FC074315@illinois.edu>
Message-ID: <F9E2FEB5-B7C9-4F27-A572-0D66261CC925@nescent.org>


On Jul 3, 2010, at 10:15 AM, Chris Fields wrote:

> I think Hilmar was to do some DBIx::Class stuff for BioSQL at one  
> point

Yes, would love to look into that.

> not sure where that is (might be surplanted by SQLite work?).

I hope SQLite won't take all or even a majority of my time there.

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================




From cjfields at illinois.edu  Sat Jul  3 15:11:50 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Sat, 3 Jul 2010 14:11:50 -0500
Subject: [Open-bio-l] Codefest 2010: Final details
In-Reply-To: <F9E2FEB5-B7C9-4F27-A572-0D66261CC925@nescent.org>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTilM3_kEu9BWx2CIUaS2lklP1ULVKLhlKHtukgk2@mail.gmail.com>
	<AANLkTiku8rxnLRFf0JULsAYvz5D07FeZR9ejKBZHQrCQ@mail.gmail.com>
	<EEB50E10-CC46-43C7-928B-3CE8FC074315@illinois.edu>
	<F9E2FEB5-B7C9-4F27-A572-0D66261CC925@nescent.org>
Message-ID: <E3F893B2-221F-4120-A3CF-905261186C37@illinois.edu>

On Jul 3, 2010, at 1:36 PM, Hilmar Lapp wrote:

> On Jul 3, 2010, at 10:15 AM, Chris Fields wrote:
> 
>> I think Hilmar was to do some DBIx::Class stuff for BioSQL at one point
> 
> Yes, would love to look into that.
> 
>> not sure where that is (might be surplanted by SQLite work?).
> 
> I hope SQLite won't take all or even a majority of my time there.
> 
> 	-hilmar

Would be nice to emphasize DBIx::Class, which abstracts the DB backend.  Not sure if Rob Buels will be there, might be a good contact person on that re: his work with DBIx::Class and Bio::Schema::Chado.

chris



From chapmanb at 50mail.com  Sun Jul  4 14:51:55 2010
From: chapmanb at 50mail.com (Brad Chapman)
Date: Sun, 4 Jul 2010 14:51:55 -0400
Subject: [Open-bio-l] Codefest 2010: Final details
In-Reply-To: <EEB50E10-CC46-43C7-928B-3CE8FC074315@illinois.edu>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTilM3_kEu9BWx2CIUaS2lklP1ULVKLhlKHtukgk2@mail.gmail.com>
	<AANLkTiku8rxnLRFf0JULsAYvz5D07FeZR9ejKBZHQrCQ@mail.gmail.com>
	<EEB50E10-CC46-43C7-928B-3CE8FC074315@illinois.edu>
Message-ID: <20100704185155.GB24102@kunkel>

Christopher, Chris, Heikki and Hilmar;
Nice discussion. If you have an overview of what you are hoping
to tackle on the BioPerl side, please add it on the wiki page. The
getting started part of the coding sessions is always the hardest
part, so it'll be a huge help if we can stand up at the beginning,
describe the project ideas, and then let people break into groups:

http://www.open-bio.org/wiki/Codefest_2010#ToDo_List

Edit away and this'll point us all in the right direction.
Looking forward to next week,
Brad

> I will be there on the afternoon of the 7th.  There are a couple of projects one can look into for Moose and Perl 6 (Biome and BioPerl6).  I think Hilmar was to do some DBIx::Class stuff for BioSQL at one point, not sure where that is (might be surplanted by SQLite work?).  Would be nice to talk with Mark re: the wrapper system for BioPerl as well.
> 
> So lots of stuff to think over and plan for.  Maybe we should move this to open-bio-l, or bioperl-l?
> 
> chris (fields)
> 
> On Jul 3, 2010, at 12:44 AM, Heikki Lehvaslaiho wrote:
> 
> > Chris,
> > 
> > I do not have too much experience on cloud computing, either. There
> > will be quite a few people from BioPerl . We'll meet and  come up with
> > a plan first thing in the morning. Unless someone has a very good one
> > ready for sharing...
> > 
> >     -Heikki
> > 
> > Heikki Lehvaslaiho - skype:heikki_lehvaslaiho
> > cell: +966 545 595 849  office: +966 2 808 2429
> > 
> > Computational Bioscience Research Centre (CBRC), Building #2, Office #4216
> > 4700 King Abdullah University of Science and Technology (KAUST)
> > Thuwal 23955-6900, Kingdom of Saudi Arabia
> > 
> > 
> > 
> > 
> > On 3 July 2010 08:36, Christopher Bottoms <maizemu at gmail.com> wrote:
> >> Hi all,
> >> 
> >> I was originally planning on working on cloud computing at the Codefest.
> >> However, the 2-day cloud computing tutorial that I was going to attend in
> >> mid June was canceled. Does anyone have any programming that they would like
> >> help with? I have experience with Perl 5, including Moose, and I am starting
> >> to dabble in Perl 6. I have also programmed in Java in the past. I hear
> >> Python is easy to learn, so I'd be open to working on a Python project as
> >> well.
> >> 
> >> Thanks,
> >> Christopher Bottoms
> >> 
> >> On Fri, Jul 2, 2010 at 8:38 AM, Brad Chapman <chapmanb at 50mail.com> wrote:
> >>> 
> >>> Hi all;
> >>> Codefest 2010 is finally here: next Wednesday and Thursday at
> >>> Harvard Medical School and Massachusetts General Hospital in
> >>> beautiful Boston. All of the logistics, directions and details
> >>> are on the wiki page:
> >>> 
> >>> http://www.open-bio.org/wiki/Codefest_2010
> >>> 
> >>> If you want the short version: show up at Harvard Medical School on
> >>> Wednesday at 10am and we'll take care of the rest. Thanks to the
> >>> hard work of Oliver, Kimberly, Leah, Toshiaki, and Mitsuteru we'll
> >>> have coffee, lunches and internet. Thanks to Steffen and Ntino,
> >>> we'll have Amazon credits to utilize. And of course, there will be
> >>> BBQ and drinking on Thursday night when we are finished.
> >>> 
> >>> I'm looking forward to a fun and productive time. The general plan
> >>> will be to spend a bit of time on Wednesday morning organizing
> >>> ourselves into like minded groups of folks, and then commence with
> >>> coding and collaborating.
> >>> 
> >>> If you aren't able to make it and you're listed on the wiki page under
> >>> participants, please do cross your name off so we have a good idea of
> >>> final numbers. Likewise, if you are coming but haven't put your name up
> >>> there please add it.
> >>> 
> >>> If you are interested in helping with making software and data
> >>> available on shared cloud resources, here are the latest Amazon
> >>> AMIs, snapshots, and the code base:
> >>> 
> >>> Cloud BioLinux images:
> >>> 64bit: ami-d62cc4bf
> >>> 32bit: ami-5423cb3d
> >>> 
> >>> An EBS public snapshot with indexed genomes:
> >>> snap-67446d0f
> >>> 
> >>> Infrastructure:
> >>> http://github.com/chapmanb/bcbb/tree/master/ec2/biolinux/
> >>> 
> >>> Send an e-mail with any questions, thoughts or concerns. My phone
> >>> number is 617-447-8586 in case you end up hopelessly lost somewhere
> >>> in Boston and are desperate to begin programming.
> >>> 
> >>> Looking forward to seeing everyone next Wednesday,
> >>> Brad
> >> 
> >> 
> 

From heikki.lehvaslaiho at gmail.com  Mon Jul  5 13:57:14 2010
From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho)
Date: Mon, 5 Jul 2010 20:57:14 +0300
Subject: [Open-bio-l] Codefest 2010: Final details
In-Reply-To: <20100704185155.GB24102@kunkel>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu> 
	<AANLkTilM3_kEu9BWx2CIUaS2lklP1ULVKLhlKHtukgk2@mail.gmail.com> 
	<AANLkTiku8rxnLRFf0JULsAYvz5D07FeZR9ejKBZHQrCQ@mail.gmail.com> 
	<EEB50E10-CC46-43C7-928B-3CE8FC074315@illinois.edu>
	<20100704185155.GB24102@kunkel>
Message-ID: <AANLkTikSyTOZ3DpqHjCVirQePX3mg4T27qOruO8fDs1W@mail.gmail.com>

Chris,

I'd love to hear an overview of Biome project (bioperl in perl6) and
design decisions you have taken there. That would help me understand
it better. Do you think you could do that?

     -Heikki

Heikki Lehvaslaiho - skype:heikki_lehvaslaiho
cell: +966 545 595 849  office: +966 2 808 2429

Computational Bioscience Research Centre (CBRC), Building #2, Office #4216
4700 King Abdullah University of Science and Technology (KAUST)
Thuwal 23955-6900, Kingdom of Saudi Arabia




On 4 July 2010 21:51, Brad Chapman <chapmanb at 50mail.com> wrote:
> Christopher, Chris, Heikki and Hilmar;
> Nice discussion. If you have an overview of what you are hoping
> to tackle on the BioPerl side, please add it on the wiki page. The
> getting started part of the coding sessions is always the hardest
> part, so it'll be a huge help if we can stand up at the beginning,
> describe the project ideas, and then let people break into groups:
>
> http://www.open-bio.org/wiki/Codefest_2010#ToDo_List
>
> Edit away and this'll point us all in the right direction.
> Looking forward to next week,
> Brad
>
>> I will be there on the afternoon of the 7th. ?There are a couple of projects one can look into for Moose and Perl 6 (Biome and BioPerl6). ?I think Hilmar was to do some DBIx::Class stuff for BioSQL at one point, not sure where that is (might be surplanted by SQLite work?). ?Would be nice to talk with Mark re: the wrapper system for BioPerl as well.
>>
>> So lots of stuff to think over and plan for. ?Maybe we should move this to open-bio-l, or bioperl-l?
>>
>> chris (fields)
>>
>> On Jul 3, 2010, at 12:44 AM, Heikki Lehvaslaiho wrote:
>>
>> > Chris,
>> >
>> > I do not have too much experience on cloud computing, either. There
>> > will be quite a few people from BioPerl . We'll meet and ?come up with
>> > a plan first thing in the morning. Unless someone has a very good one
>> > ready for sharing...
>> >
>> > ? ? -Heikki
>> >
>> > Heikki Lehvaslaiho - skype:heikki_lehvaslaiho
>> > cell: +966 545 595 849 ?office: +966 2 808 2429
>> >
>> > Computational Bioscience Research Centre (CBRC), Building #2, Office #4216
>> > 4700 King Abdullah University of Science and Technology (KAUST)
>> > Thuwal 23955-6900, Kingdom of Saudi Arabia
>> >
>> >
>> >
>> >
>> > On 3 July 2010 08:36, Christopher Bottoms <maizemu at gmail.com> wrote:
>> >> Hi all,
>> >>
>> >> I was originally planning on working on cloud computing at the Codefest.
>> >> However, the 2-day cloud computing tutorial that I was going to attend in
>> >> mid June was canceled. Does anyone have any programming that they would like
>> >> help with? I have experience with Perl 5, including Moose, and I am starting
>> >> to dabble in Perl 6. I have also programmed in Java in the past. I hear
>> >> Python is easy to learn, so I'd be open to working on a Python project as
>> >> well.
>> >>
>> >> Thanks,
>> >> Christopher Bottoms
>> >>
>> >> On Fri, Jul 2, 2010 at 8:38 AM, Brad Chapman <chapmanb at 50mail.com> wrote:
>> >>>
>> >>> Hi all;
>> >>> Codefest 2010 is finally here: next Wednesday and Thursday at
>> >>> Harvard Medical School and Massachusetts General Hospital in
>> >>> beautiful Boston. All of the logistics, directions and details
>> >>> are on the wiki page:
>> >>>
>> >>> http://www.open-bio.org/wiki/Codefest_2010
>> >>>
>> >>> If you want the short version: show up at Harvard Medical School on
>> >>> Wednesday at 10am and we'll take care of the rest. Thanks to the
>> >>> hard work of Oliver, Kimberly, Leah, Toshiaki, and Mitsuteru we'll
>> >>> have coffee, lunches and internet. Thanks to Steffen and Ntino,
>> >>> we'll have Amazon credits to utilize. And of course, there will be
>> >>> BBQ and drinking on Thursday night when we are finished.
>> >>>
>> >>> I'm looking forward to a fun and productive time. The general plan
>> >>> will be to spend a bit of time on Wednesday morning organizing
>> >>> ourselves into like minded groups of folks, and then commence with
>> >>> coding and collaborating.
>> >>>
>> >>> If you aren't able to make it and you're listed on the wiki page under
>> >>> participants, please do cross your name off so we have a good idea of
>> >>> final numbers. Likewise, if you are coming but haven't put your name up
>> >>> there please add it.
>> >>>
>> >>> If you are interested in helping with making software and data
>> >>> available on shared cloud resources, here are the latest Amazon
>> >>> AMIs, snapshots, and the code base:
>> >>>
>> >>> Cloud BioLinux images:
>> >>> 64bit: ami-d62cc4bf
>> >>> 32bit: ami-5423cb3d
>> >>>
>> >>> An EBS public snapshot with indexed genomes:
>> >>> snap-67446d0f
>> >>>
>> >>> Infrastructure:
>> >>> http://github.com/chapmanb/bcbb/tree/master/ec2/biolinux/
>> >>>
>> >>> Send an e-mail with any questions, thoughts or concerns. My phone
>> >>> number is 617-447-8586 in case you end up hopelessly lost somewhere
>> >>> in Boston and are desperate to begin programming.
>> >>>
>> >>> Looking forward to seeing everyone next Wednesday,
>> >>> Brad
>> >>
>> >>
>>
>


From cjfields at illinois.edu  Mon Jul  5 15:02:10 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 5 Jul 2010 14:02:10 -0500
Subject: [Open-bio-l] Codefest 2010: Final details
In-Reply-To: <B790F1F8-59DF-4F80-84F5-10676261DA6C@nescent.org>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTilM3_kEu9BWx2CIUaS2lklP1ULVKLhlKHtukgk2@mail.gmail.com>
	<AANLkTiku8rxnLRFf0JULsAYvz5D07FeZR9ejKBZHQrCQ@mail.gmail.com>
	<EEB50E10-CC46-43C7-928B-3CE8FC074315@illinois.edu>
	<20100704185155.GB24102@kunkel>
	<AANLkTikSyTOZ3DpqHjCVirQePX3mg4T27qOruO8fDs1W@mail.gmail.com>
	<B790F1F8-59DF-4F80-84F5-10676261DA6C@nescent.org>
Message-ID: <3896D350-324A-426D-BD82-74C4D437400F@illinois.edu>

I can probably come up with something (I have a few slides).  The design for both Biome and bioperl6 is fairly straightforward (interfaces -> roles), but it would be nice to sit down with those interested to see what would be the best path to take design-wise regarding future development, mistakes learned, etc.

chris

On Jul 5, 2010, at 1:51 PM, Hilmar Lapp wrote:

> I agree that would be great!
> 
> 	-hilmar
> 
> On Jul 5, 2010, at 1:57 PM, Heikki Lehvaslaiho wrote:
> 
>> Chris,
>> 
>> I'd love to hear an overview of Biome project (bioperl in perl6) and
>> design decisions you have taken there. That would help me understand
>> it better. Do you think you could do that?
>> 
>>    -Heikki
>> 
>> Heikki Lehvaslaiho - skype:heikki_lehvaslaiho
>> cell: +966 545 595 849  office: +966 2 808 2429
>> 
>> Computational Bioscience Research Centre (CBRC), Building #2, Office #4216
>> 4700 King Abdullah University of Science and Technology (KAUST)
>> Thuwal 23955-6900, Kingdom of Saudi Arabia
>> 
>> 
>> 
>> 
>> On 4 July 2010 21:51, Brad Chapman <chapmanb at 50mail.com> wrote:
>>> Christopher, Chris, Heikki and Hilmar;
>>> Nice discussion. If you have an overview of what you are hoping
>>> to tackle on the BioPerl side, please add it on the wiki page. The
>>> getting started part of the coding sessions is always the hardest
>>> part, so it'll be a huge help if we can stand up at the beginning,
>>> describe the project ideas, and then let people break into groups:
>>> 
>>> http://www.open-bio.org/wiki/Codefest_2010#ToDo_List
>>> 
>>> Edit away and this'll point us all in the right direction.
>>> Looking forward to next week,
>>> Brad
>>> 
>>>> I will be there on the afternoon of the 7th.  There are a couple of projects one can look into for Moose and Perl 6 (Biome and BioPerl6).  I think Hilmar was to do some DBIx::Class stuff for BioSQL at one point, not sure where that is (might be surplanted by SQLite work?).  Would be nice to talk with Mark re: the wrapper system for BioPerl as well.
>>>> 
>>>> So lots of stuff to think over and plan for.  Maybe we should move this to open-bio-l, or bioperl-l?
>>>> 
>>>> chris (fields)
>>>> 
>>>> On Jul 3, 2010, at 12:44 AM, Heikki Lehvaslaiho wrote:
>>>> 
>>>>> Chris,
>>>>> 
>>>>> I do not have too much experience on cloud computing, either. There
>>>>> will be quite a few people from BioPerl . We'll meet and  come up with
>>>>> a plan first thing in the morning. Unless someone has a very good one
>>>>> ready for sharing...
>>>>> 
>>>>>    -Heikki
>>>>> 
>>>>> Heikki Lehvaslaiho - skype:heikki_lehvaslaiho
>>>>> cell: +966 545 595 849  office: +966 2 808 2429
>>>>> 
>>>>> Computational Bioscience Research Centre (CBRC), Building #2, Office #4216
>>>>> 4700 King Abdullah University of Science and Technology (KAUST)
>>>>> Thuwal 23955-6900, Kingdom of Saudi Arabia
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> On 3 July 2010 08:36, Christopher Bottoms <maizemu at gmail.com> wrote:
>>>>>> Hi all,
>>>>>> 
>>>>>> I was originally planning on working on cloud computing at the Codefest.
>>>>>> However, the 2-day cloud computing tutorial that I was going to attend in
>>>>>> mid June was canceled. Does anyone have any programming that they would like
>>>>>> help with? I have experience with Perl 5, including Moose, and I am starting
>>>>>> to dabble in Perl 6. I have also programmed in Java in the past. I hear
>>>>>> Python is easy to learn, so I'd be open to working on a Python project as
>>>>>> well.
>>>>>> 
>>>>>> Thanks,
>>>>>> Christopher Bottoms
>>>>>> 
>>>>>> On Fri, Jul 2, 2010 at 8:38 AM, Brad Chapman <chapmanb at 50mail.com> wrote:
>>>>>>> 
>>>>>>> Hi all;
>>>>>>> Codefest 2010 is finally here: next Wednesday and Thursday at
>>>>>>> Harvard Medical School and Massachusetts General Hospital in
>>>>>>> beautiful Boston. All of the logistics, directions and details
>>>>>>> are on the wiki page:
>>>>>>> 
>>>>>>> http://www.open-bio.org/wiki/Codefest_2010
>>>>>>> 
>>>>>>> If you want the short version: show up at Harvard Medical School on
>>>>>>> Wednesday at 10am and we'll take care of the rest. Thanks to the
>>>>>>> hard work of Oliver, Kimberly, Leah, Toshiaki, and Mitsuteru we'll
>>>>>>> have coffee, lunches and internet. Thanks to Steffen and Ntino,
>>>>>>> we'll have Amazon credits to utilize. And of course, there will be
>>>>>>> BBQ and drinking on Thursday night when we are finished.
>>>>>>> 
>>>>>>> I'm looking forward to a fun and productive time. The general plan
>>>>>>> will be to spend a bit of time on Wednesday morning organizing
>>>>>>> ourselves into like minded groups of folks, and then commence with
>>>>>>> coding and collaborating.
>>>>>>> 
>>>>>>> If you aren't able to make it and you're listed on the wiki page under
>>>>>>> participants, please do cross your name off so we have a good idea of
>>>>>>> final numbers. Likewise, if you are coming but haven't put your name up
>>>>>>> there please add it.
>>>>>>> 
>>>>>>> If you are interested in helping with making software and data
>>>>>>> available on shared cloud resources, here are the latest Amazon
>>>>>>> AMIs, snapshots, and the code base:
>>>>>>> 
>>>>>>> Cloud BioLinux images:
>>>>>>> 64bit: ami-d62cc4bf
>>>>>>> 32bit: ami-5423cb3d
>>>>>>> 
>>>>>>> An EBS public snapshot with indexed genomes:
>>>>>>> snap-67446d0f
>>>>>>> 
>>>>>>> Infrastructure:
>>>>>>> http://github.com/chapmanb/bcbb/tree/master/ec2/biolinux/
>>>>>>> 
>>>>>>> Send an e-mail with any questions, thoughts or concerns. My phone
>>>>>>> number is 617-447-8586 in case you end up hopelessly lost somewhere
>>>>>>> in Boston and are desperate to begin programming.
>>>>>>> 
>>>>>>> Looking forward to seeing everyone next Wednesday,
>>>>>>> Brad
>>>>>> 
>>>>>> 
>>>> 
>>> 
> 
> -- 
> ===========================================================
> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
> ===========================================================
> 
> 
> 



From maj at fortinbras.us  Mon Jul  5 15:34:09 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Mon, 5 Jul 2010 15:34:09 -0400
Subject: [Open-bio-l] Codefest 2010: Final details
In-Reply-To: <3896D350-324A-426D-BD82-74C4D437400F@illinois.edu>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTilM3_kEu9BWx2CIUaS2lklP1ULVKLhlKHtukgk2@mail.gmail.com>
	<AANLkTiku8rxnLRFf0JULsAYvz5D07FeZR9ejKBZHQrCQ@mail.gmail.com>
	<EEB50E10-CC46-43C7-928B-3CE8FC074315@illinois.edu>
	<20100704185155.GB24102@kunkel>
	<AANLkTikSyTOZ3DpqHjCVirQePX3mg4T27qOruO8fDs1W@mail.gmail.com>
	<B790F1F8-59DF-4F80-84F5-10676261DA6C@nescent.org>
	<3896D350-324A-426D-BD82-74C4D437400F@illinois.edu>
Message-ID: <6903B53BB0B24235AFDA7313E6845FBC@NewLife>

[so straightforward that 3 or 4 introductory slides couldn't possibly hurt?]
----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Hilmar Lapp" <hlapp at nescent.org>
Cc: "Heikki Lehvaslaiho" <heikki.lehvaslaiho at gmail.com>; "Brad Chapman" 
<chapmanb at 50mail.com>; "Christopher Bottoms" <maizemu at gmail.com>; 
<open-bio-l at lists.open-bio.org>; "Oliver Hofmann" <ohofmann at hsph.harvard.edu>; 
"Kimberly Begley" <Kimberly at fisciconsulting.com>; "Michael Heuer" 
<heuermh at acm.org>; "Eric Talevich" <eric.talevich at gmail.com>; "James Taylor" 
<james.taylor at emory.edu>; "Enis Afgan" <eafgan at emory.edu>; "Dannon Baker" 
<dannonbaker at me.com>; "Ntino Krampis" <agbiotec at gmail.com>; "Tim Booth" 
<tbooth at ceh.ac.uk>; "Richard Holland" <holland at eaglegenomics.com>; "Mark Jensen" 
<maj at fortinbras.us>; "Kam Dahlquist" <kdahlquist at lmu.edu>; "John David N. 
Dionisio" <dondi at lmu.edu>; "Steffen M?ller" <steffen_moeller at gmx.de>; "Bela 
Tiwari" <btiwari at ceh.ac.uk>; "Dominique Belhachemi" <domibel at cs.tu-berlin.de>; 
"Toshiaki Katayama" <ktym at hgc.jp>; "Mitsuteru Nakao" <mn at dbcls.jp>; "Dave 
Messina" <David.Messina at sbc.su.se>; "Christian Zmasek" <czmasek at burnham.org>; 
"Akira KINJO" <akinjo at protein.osaka-u.ac.jp>; "Naohisa Goto" <ng at bioruby.org>; 
"Yasunori Yamamoto" <yy at dbcls.jp>; "Raoul J.P. Bonnal" <bonnalraoul at ingm.it>; 
"Atsuko Yamaguchi" <atsuko at dbcls.jp>
Sent: Monday, July 05, 2010 3:02 PM
Subject: Re: Codefest 2010: Final details


I can probably come up with something (I have a few slides).  The design for 
both Biome and bioperl6 is fairly straightforward (interfaces -> roles), but it 
would be nice to sit down with those interested to see what would be the best 
path to take design-wise regarding future development, mistakes learned, etc.

chris

On Jul 5, 2010, at 1:51 PM, Hilmar Lapp wrote:

> I agree that would be great!
>
> -hilmar
>
> On Jul 5, 2010, at 1:57 PM, Heikki Lehvaslaiho wrote:
>
>> Chris,
>>
>> I'd love to hear an overview of Biome project (bioperl in perl6) and
>> design decisions you have taken there. That would help me understand
>> it better. Do you think you could do that?
>>
>>    -Heikki
>>
>> Heikki Lehvaslaiho - skype:heikki_lehvaslaiho
>> cell: +966 545 595 849  office: +966 2 808 2429
>>
>> Computational Bioscience Research Centre (CBRC), Building #2, Office #4216
>> 4700 King Abdullah University of Science and Technology (KAUST)
>> Thuwal 23955-6900, Kingdom of Saudi Arabia
>>
>>
>>
>>
>> On 4 July 2010 21:51, Brad Chapman <chapmanb at 50mail.com> wrote:
>>> Christopher, Chris, Heikki and Hilmar;
>>> Nice discussion. If you have an overview of what you are hoping
>>> to tackle on the BioPerl side, please add it on the wiki page. The
>>> getting started part of the coding sessions is always the hardest
>>> part, so it'll be a huge help if we can stand up at the beginning,
>>> describe the project ideas, and then let people break into groups:
>>>
>>> http://www.open-bio.org/wiki/Codefest_2010#ToDo_List
>>>
>>> Edit away and this'll point us all in the right direction.
>>> Looking forward to next week,
>>> Brad
>>>
>>>> I will be there on the afternoon of the 7th.  There are a couple of 
>>>> projects one can look into for Moose and Perl 6 (Biome and BioPerl6).  I 
>>>> think Hilmar was to do some DBIx::Class stuff for BioSQL at one point, not 
>>>> sure where that is (might be surplanted by SQLite work?).  Would be nice to 
>>>> talk with Mark re: the wrapper system for BioPerl as well.
>>>>
>>>> So lots of stuff to think over and plan for.  Maybe we should move this to 
>>>> open-bio-l, or bioperl-l?
>>>>
>>>> chris (fields)
>>>>
>>>> On Jul 3, 2010, at 12:44 AM, Heikki Lehvaslaiho wrote:
>>>>
>>>>> Chris,
>>>>>
>>>>> I do not have too much experience on cloud computing, either. There
>>>>> will be quite a few people from BioPerl . We'll meet and  come up with
>>>>> a plan first thing in the morning. Unless someone has a very good one
>>>>> ready for sharing...
>>>>>
>>>>>    -Heikki
>>>>>
>>>>> Heikki Lehvaslaiho - skype:heikki_lehvaslaiho
>>>>> cell: +966 545 595 849  office: +966 2 808 2429
>>>>>
>>>>> Computational Bioscience Research Centre (CBRC), Building #2, Office #4216
>>>>> 4700 King Abdullah University of Science and Technology (KAUST)
>>>>> Thuwal 23955-6900, Kingdom of Saudi Arabia
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On 3 July 2010 08:36, Christopher Bottoms <maizemu at gmail.com> wrote:
>>>>>> Hi all,
>>>>>>
>>>>>> I was originally planning on working on cloud computing at the Codefest.
>>>>>> However, the 2-day cloud computing tutorial that I was going to attend in
>>>>>> mid June was canceled. Does anyone have any programming that they would 
>>>>>> like
>>>>>> help with? I have experience with Perl 5, including Moose, and I am 
>>>>>> starting
>>>>>> to dabble in Perl 6. I have also programmed in Java in the past. I hear
>>>>>> Python is easy to learn, so I'd be open to working on a Python project as
>>>>>> well.
>>>>>>
>>>>>> Thanks,
>>>>>> Christopher Bottoms
>>>>>>
>>>>>> On Fri, Jul 2, 2010 at 8:38 AM, Brad Chapman <chapmanb at 50mail.com> wrote:
>>>>>>>
>>>>>>> Hi all;
>>>>>>> Codefest 2010 is finally here: next Wednesday and Thursday at
>>>>>>> Harvard Medical School and Massachusetts General Hospital in
>>>>>>> beautiful Boston. All of the logistics, directions and details
>>>>>>> are on the wiki page:
>>>>>>>
>>>>>>> http://www.open-bio.org/wiki/Codefest_2010
>>>>>>>
>>>>>>> If you want the short version: show up at Harvard Medical School on
>>>>>>> Wednesday at 10am and we'll take care of the rest. Thanks to the
>>>>>>> hard work of Oliver, Kimberly, Leah, Toshiaki, and Mitsuteru we'll
>>>>>>> have coffee, lunches and internet. Thanks to Steffen and Ntino,
>>>>>>> we'll have Amazon credits to utilize. And of course, there will be
>>>>>>> BBQ and drinking on Thursday night when we are finished.
>>>>>>>
>>>>>>> I'm looking forward to a fun and productive time. The general plan
>>>>>>> will be to spend a bit of time on Wednesday morning organizing
>>>>>>> ourselves into like minded groups of folks, and then commence with
>>>>>>> coding and collaborating.
>>>>>>>
>>>>>>> If you aren't able to make it and you're listed on the wiki page under
>>>>>>> participants, please do cross your name off so we have a good idea of
>>>>>>> final numbers. Likewise, if you are coming but haven't put your name up
>>>>>>> there please add it.
>>>>>>>
>>>>>>> If you are interested in helping with making software and data
>>>>>>> available on shared cloud resources, here are the latest Amazon
>>>>>>> AMIs, snapshots, and the code base:
>>>>>>>
>>>>>>> Cloud BioLinux images:
>>>>>>> 64bit: ami-d62cc4bf
>>>>>>> 32bit: ami-5423cb3d
>>>>>>>
>>>>>>> An EBS public snapshot with indexed genomes:
>>>>>>> snap-67446d0f
>>>>>>>
>>>>>>> Infrastructure:
>>>>>>> http://github.com/chapmanb/bcbb/tree/master/ec2/biolinux/
>>>>>>>
>>>>>>> Send an e-mail with any questions, thoughts or concerns. My phone
>>>>>>> number is 617-447-8586 in case you end up hopelessly lost somewhere
>>>>>>> in Boston and are desperate to begin programming.
>>>>>>>
>>>>>>> Looking forward to seeing everyone next Wednesday,
>>>>>>> Brad
>>>>>>
>>>>>>
>>>>
>>>
>
> -- 
> ===========================================================
> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
> ===========================================================
>
>
>




From dan.bolser at gmail.com  Tue Jul  6 06:10:51 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Tue, 6 Jul 2010 11:10:51 +0100
Subject: [Open-bio-l] Best practice for modelling data in GFF
In-Reply-To: <AANLkTim3OsVC5cwwOlF095A5B6eJ6n03XNc7SpYMZJeV@mail.gmail.com>
References: <AANLkTimuku_x7V9RSAERK4f4QxIc4od2zw3qZtdaL4oH@mail.gmail.com>
	<4BFFF7FE.1030004@bioperl.org>
	<685C1029-0E3A-45DD-BBA9-FFA7747810D5@illinois.edu>
	<AANLkTinrTVYODrcY9TUxhznkZKunNRQCvs-bnwgbHdNA@mail.gmail.com>
	<AANLkTim3OsVC5cwwOlF095A5B6eJ6n03XNc7SpYMZJeV@mail.gmail.com>
Message-ID: <AANLkTim20_VVGZbChnU1F5OmqKhAdbmoGGgAYuSSG2Kj@mail.gmail.com>

When you don't get a reply, you never know if your question was too
dumb, too smart, or totally off topic.

Any hints?

Cheers,
Dan.

On 1 July 2010 11:12, Dan Bolser <dan.bolser at gmail.com> wrote:
> On 29 May 2010 00:08, Dan Bolser <dan.bolser at gmail.com> wrote:
>> Thanks all for replies.
>
> <snip>
>
>> There is a canonical way to model a gene, so I was wondering if it
>> makes sense to describe similar 'biology' (or in this case molecular
>> biology) in standard ways (when the feature isn't simply described by
>> a single line of GFF)?
>>
>> Perhaps I've not understood SO properly, but I'm not sure how its
>> structure is translated into GFF structure ... is there a 1 to 1
>> mapping?
>
> Lack of replies lead me to believe that indeed, the GFF Parent
> attribute should reflect (or be strictly determined by) the SO
> 'relationships' (are they all 'part_of' relationships?)
>
> However, I was trying to get some concepts clear in my head, and I
> ended up creating a figure of a 'canonical gene' in SO [1], based on
> the one in the GFF docs [2].
>
> [1] http://imagebin.ca/view/Ni9BFbK.html
> [2] http://www.sequenceontology.org/gff3.shtml
>
>
> There is a transitive part_of relationships between 'mRNA' and 'gene',
> which explains line 4 to 6 of the canonical gene GFF [2].
>
> However, the figure shows that 'exon' is part_of 'transcript', and not
> part_of 'mRNA'. If I got the figure right, and if I understand
> correctly, there is no way to transitively infer that exon is part_of
> mRNA (line 7 to 11 of the GFF [2]).
>
> This implies that the 'structure' in GFF isn't strictly determined by SO.
>
> Or is it a mistake in SO?
>
>
> Sorry if this is a 'gotcha' that has been discussed before. Any links
> to help me understand would be great.
>
> Dan.

From lpritc at scri.ac.uk  Tue Jul  6 06:58:44 2010
From: lpritc at scri.ac.uk (Leighton Pritchard)
Date: Tue, 06 Jul 2010 11:58:44 +0100
Subject: [Open-bio-l] Best practice for modelling data in GFF
In-Reply-To: <AANLkTim20_VVGZbChnU1F5OmqKhAdbmoGGgAYuSSG2Kj@mail.gmail.com>
Message-ID: <C858CAF4.3867D%lpritc@scri.ac.uk>

Hi Dan,

GFF3 is just a file format, capable of representing the SO's hierarchical
subfeatures.  You can represent other things (including other ontologies) in
the same format.  How strictly you choose to stick to the SO's hierarchy is
up to you, whether you use GFF3 to represent your data or not: you are free
to be as canonical or noncanonical as you like.  You are not constrained to
having mRNA be the parent of a CDS by the file format - you can happily
create a model that has things the other way round and represent it in valid
GFF3.  It will be biological nonsense and not SO-compliant, but you can do
it:

broken  .   CDS 100 1100    .   +   0   ID=cds01
broken  .   mRNA    0   1500    .   +   .   ID=mRNA01;Parent=cds01

Putting your model into GFF3 is a separate issue to building the model, so
long as GFF3 is capable of representing your model.  And if the package
you're loading your GFF3 into doesn't care about ontologies and
relationships, you'll get away with it.

So yes, if you want to build a SO-compatible gene model, you had better make
sure the parent-child relationships correspond to the hierarchy in the SO.
This is true whether you want to represent the model in GFF3 or not.

Now, for your specific question about the exon/mRNA terms: an exon is_a
transcript_region, and a transcript_region is part_of a transcript.  [And a
transcript is_a gene_member_region, and a gene_member_region is a member_of
a gene.]

Now, an mRNA is_a mature_transcript, which is_a transcript.  The exon that
is part_of a transcript can therefore be part_of an mRNA, because an mRNA is
a transcript.

So in the model at http://www.sequenceontology.org/gff3.shtml the transcript
you're looking for is the mRNA.  The same would be true if the parent
feature was a monocistronic_mRNA, which is_a mRNA, and also is_a
monocistronic_transcript, which is_a transcript.

Have you had a look at OBO-Edit?  It's a useful learning tool for getting
your head around these things, and you can browse through the SO in it.

Cheers,

L.


On 06/07/2010 Tuesday, July 6, 11:10, "Dan Bolser" <dan.bolser at gmail.com>
wrote:

> When you don't get a reply, you never know if your question was too
> dumb, too smart, or totally off topic.
> 
> Any hints?
> 
> Cheers,
> Dan.
> 
> On 1 July 2010 11:12, Dan Bolser <dan.bolser at gmail.com> wrote:
>> On 29 May 2010 00:08, Dan Bolser <dan.bolser at gmail.com> wrote:
>>> Thanks all for replies.
>> 
>> <snip>
>> 
>>> There is a canonical way to model a gene, so I was wondering if it
>>> makes sense to describe similar 'biology' (or in this case molecular
>>> biology) in standard ways (when the feature isn't simply described by
>>> a single line of GFF)?
>>> 
>>> Perhaps I've not understood SO properly, but I'm not sure how its
>>> structure is translated into GFF structure ... is there a 1 to 1
>>> mapping?
>> 
>> Lack of replies lead me to believe that indeed, the GFF Parent
>> attribute should reflect (or be strictly determined by) the SO
>> 'relationships' (are they all 'part_of' relationships?)
>> 
>> However, I was trying to get some concepts clear in my head, and I
>> ended up creating a figure of a 'canonical gene' in SO [1], based on
>> the one in the GFF docs [2].
>> 
>> [1] http://imagebin.ca/view/Ni9BFbK.html
>> [2] http://www.sequenceontology.org/gff3.shtml
>> 
>> 
>> There is a transitive part_of relationships between 'mRNA' and 'gene',
>> which explains line 4 to 6 of the canonical gene GFF [2].
>> 
>> However, the figure shows that 'exon' is part_of 'transcript', and not
>> part_of 'mRNA'. If I got the figure right, and if I understand
>> correctly, there is no way to transitively infer that exon is part_of
>> mRNA (line 7 to 11 of the GFF [2]).
>> 
>> This implies that the 'structure' in GFF isn't strictly determined by SO.
>> 
>> Or is it a mistake in SO?
>> 
>> 
>> Sorry if this is a 'gotcha' that has been discussed before. Any links
>> to help me understand would be great.
>> 
>> Dan.
> _______________________________________________
> Open-Bio-l mailing list
> Open-Bio-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/open-bio-l
> 
> ______________________________________________________________________
> This email has been scanned by the MessageLabs Email Security System.
> For more information please visit http://www.messagelabs.com/email
> ______________________________________________________________________

-- 
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405


______________________________________________________
SCRI, Invergowrie, Dundee, DD2 5DA.  
The Scottish Crop Research Institute is a charitable company limited by guarantee. 
Registered in Scotland No: SC 29367.
Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.


DISCLAIMER:

This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries.  This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed.  It may not be disclosed or used by any other than that addressee.
If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify postmaster at scri.ac.uk quoting the name of the sender and delete the email from your system.

Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any).
______________________________________________________

From dan.bolser at gmail.com  Tue Jul  6 08:11:54 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Tue, 6 Jul 2010 13:11:54 +0100
Subject: [Open-bio-l] Best practice for modelling data in GFF
In-Reply-To: <C858CAF4.3867D%lpritc@scri.ac.uk>
References: <AANLkTim20_VVGZbChnU1F5OmqKhAdbmoGGgAYuSSG2Kj@mail.gmail.com>
	<C858CAF4.3867D%lpritc@scri.ac.uk>
Message-ID: <AANLkTilX_vVX2nHmX4IOCVcsmvopJpNLFRRE-v4oqN1f@mail.gmail.com>

On 6 July 2010 11:58, Leighton Pritchard <lpritc at scri.ac.uk> wrote:
> Hi Dan,
>
> GFF3 is just a file format, capable of representing the SO's hierarchical
> subfeatures. ?You can represent other things (including other ontologies) in
> the same format. ?How strictly you choose to stick to the SO's hierarchy is
> up to you,

<snip>

OK, I understand. So the answer to my original question "Where can I
find information on 'best practices' for modelling biological data in
GFF?" was just, "work out where your data fits in the Sequence
Ontology model".

:-)


> So yes, if you want to build a SO-compatible gene model, you had better make
> sure the parent-child relationships correspond to the hierarchy in the SO.
> This is true whether you want to represent the model in GFF3 or not.

OK


> Now, for your specific question about the exon/mRNA terms: an exon is_a
> transcript_region, and a transcript_region is part_of a transcript. ?[And a
> transcript is_a gene_member_region, and a gene_member_region is a member_of
> a gene.]
>
> Now, an mRNA is_a mature_transcript, which is_a transcript. ?The exon that
> is part_of a transcript can therefore be part_of an mRNA, because an mRNA is
> a transcript.

I see... I guess this only applies because of the specific 'is_a'
relationship. i.e. just because a nose is part_of a face and a mouth
is part_of a face, you can't make inferences about relationships
between nose and mouth.

I guess I'm confused because I can't see the link types in miso.


> So in the model at http://www.sequenceontology.org/gff3.shtml the transcript
> you're looking for is the mRNA. ?The same would be true if the parent
> feature was a monocistronic_mRNA, which is_a mRNA, and also is_a
> monocistronic_transcript, which is_a transcript.
>
> Have you had a look at OBO-Edit? ?It's a useful learning tool for getting
> your head around these things, and you can browse through the SO in it.

I'll have a look.


Thanks very much for taking the time to provide such a detailed reply,
and sorry for the dumb questions.

All the best,
Dan.


> Cheers,
>
> L.
>
>
> On 06/07/2010 Tuesday, July 6, 11:10, "Dan Bolser" <dan.bolser at gmail.com>
> wrote:
>
>> When you don't get a reply, you never know if your question was too
>> dumb, too smart, or totally off topic.
>>
>> Any hints?
>>
>> Cheers,
>> Dan.
>>
>> On 1 July 2010 11:12, Dan Bolser <dan.bolser at gmail.com> wrote:
>>> On 29 May 2010 00:08, Dan Bolser <dan.bolser at gmail.com> wrote:
>>>> Thanks all for replies.
>>>
>>> <snip>
>>>
>>>> There is a canonical way to model a gene, so I was wondering if it
>>>> makes sense to describe similar 'biology' (or in this case molecular
>>>> biology) in standard ways (when the feature isn't simply described by
>>>> a single line of GFF)?
>>>>
>>>> Perhaps I've not understood SO properly, but I'm not sure how its
>>>> structure is translated into GFF structure ... is there a 1 to 1
>>>> mapping?
>>>
>>> Lack of replies lead me to believe that indeed, the GFF Parent
>>> attribute should reflect (or be strictly determined by) the SO
>>> 'relationships' (are they all 'part_of' relationships?)
>>>
>>> However, I was trying to get some concepts clear in my head, and I
>>> ended up creating a figure of a 'canonical gene' in SO [1], based on
>>> the one in the GFF docs [2].
>>>
>>> [1] http://imagebin.ca/view/Ni9BFbK.html
>>> [2] http://www.sequenceontology.org/gff3.shtml
>>>
>>>
>>> There is a transitive part_of relationships between 'mRNA' and 'gene',
>>> which explains line 4 to 6 of the canonical gene GFF [2].
>>>
>>> However, the figure shows that 'exon' is part_of 'transcript', and not
>>> part_of 'mRNA'. If I got the figure right, and if I understand
>>> correctly, there is no way to transitively infer that exon is part_of
>>> mRNA (line 7 to 11 of the GFF [2]).
>>>
>>> This implies that the 'structure' in GFF isn't strictly determined by SO.
>>>
>>> Or is it a mistake in SO?
>>>
>>>
>>> Sorry if this is a 'gotcha' that has been discussed before. Any links
>>> to help me understand would be great.
>>>
>>> Dan.
>> _______________________________________________
>> Open-Bio-l mailing list
>> Open-Bio-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/open-bio-l
>>
>> ______________________________________________________________________
>> This email has been scanned by the MessageLabs Email Security System.
>> For more information please visit http://www.messagelabs.com/email
>> ______________________________________________________________________
>
> --
> Dr Leighton Pritchard MRSC
> D131, Plant Pathology Programme, SCRI
> Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
> e:lpritc at scri.ac.uk ? ? ? w:http://www.scri.ac.uk/staff/leightonpritchard
> gpg/pgp: 0xFEFC205C ? ? ? tel:+44(0)1382 562731 x2405
>
>
> ______________________________________________________
> SCRI, Invergowrie, Dundee, DD2 5DA.
> The Scottish Crop Research Institute is a charitable company limited by guarantee.
> Registered in Scotland No: SC 29367.
> Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.
>
>
> DISCLAIMER:
>
> This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries. ?This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed. ?It may not be disclosed or used by any other than that addressee.
> If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify postmaster at scri.ac.uk quoting the name of the sender and delete the email from your system.
>
> Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any).
> ______________________________________________________
>


From lpritc at scri.ac.uk  Tue Jul  6 10:29:35 2010
From: lpritc at scri.ac.uk (Leighton Pritchard)
Date: Tue, 06 Jul 2010 15:29:35 +0100
Subject: [Open-bio-l] Best practice for modelling data in GFF
In-Reply-To: <AANLkTilX_vVX2nHmX4IOCVcsmvopJpNLFRRE-v4oqN1f@mail.gmail.com>
Message-ID: <C858FC5F.386A1%lpritc@scri.ac.uk>

On 06/07/2010 Tuesday, July 6, 13:11, "Dan Bolser" <dan.bolser at gmail.com>
wrote:

> I see... I guess this only applies because of the specific 'is_a'
> relationship. i.e. just because a nose is part_of a face and a mouth
> is part_of a face, you can't make inferences about relationships
> between nose and mouth.

Sounds like you get it.  To extend that analogy you can infer things about
nostrils and earholes, such as that putting a biro in a nostril is valid,
whether it's a left_nostril or a right_nostril, because nostril is_a orifice
- and that's why you can stick a biro in your ear, as well ;)
 
> Thanks very much for taking the time to provide such a detailed reply,
> and sorry for the dumb questions.

They weren't dumb questions.  I recently had a similar issue where I was
wondering how to represent sub-parts of protein domains that span exons in a
chromosomal reference frame.  It didn't seem right to have them span an
intron, as they derive from the polypeptide, but the ontology terms don't
have explicit subfeatures.  Happily the polypeptide_region feature provides
enough flexibility to get around this.

Cheers,

L.

-- 
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405


______________________________________________________
SCRI, Invergowrie, Dundee, DD2 5DA.  
The Scottish Crop Research Institute is a charitable company limited by guarantee. 
Registered in Scotland No: SC 29367.
Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.


DISCLAIMER:

This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries.  This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed.  It may not be disclosed or used by any other than that addressee.
If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify postmaster at scri.ac.uk quoting the name of the sender and delete the email from your system.

Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any).
______________________________________________________

From dan.bolser at gmail.com  Tue Jul  6 10:36:40 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Tue, 6 Jul 2010 15:36:40 +0100
Subject: [Open-bio-l] Best practice for modelling data in GFF
In-Reply-To: <C858FC5F.386A1%lpritc@scri.ac.uk>
References: <AANLkTilX_vVX2nHmX4IOCVcsmvopJpNLFRRE-v4oqN1f@mail.gmail.com>
	<C858FC5F.386A1%lpritc@scri.ac.uk>
Message-ID: <AANLkTikle3Qo2R2B8gqdZNj1qlo5CyZ5jt7IYRVsbkfC@mail.gmail.com>

On 6 July 2010 15:29, Leighton Pritchard <lpritc at scri.ac.uk> wrote:
> On 06/07/2010 Tuesday, July 6, 13:11, "Dan Bolser" <dan.bolser at gmail.com>
> wrote:
>
>> I see... I guess this only applies because of the specific 'is_a'
>> relationship. i.e. just because a nose is part_of a face and a mouth
>> is part_of a face, you can't make inferences about relationships
>> between nose and mouth.
>
> Sounds like you get it. ?To extend that analogy you can infer things about
> nostrils and earholes, such as that putting a biro in a nostril is valid,
> whether it's a left_nostril or a right_nostril, because nostril is_a orifice
> - and that's why you can stick a biro in your ear, as well ;)
>
>> Thanks very much for taking the time to provide such a detailed reply,
>> and sorry for the dumb questions.
>
> They weren't dumb questions. ?I recently had a similar issue where I was
> wondering how to represent sub-parts of protein domains that span exons in a
> chromosomal reference frame. ?It didn't seem right to have them span an
> intron, as they derive from the polypeptide, but the ontology terms don't
> have explicit subfeatures. ?Happily the polypeptide_region feature provides
> enough flexibility to get around this.

Perhaps there is scope for a 'best practices' catalogue after all?

P.S. How did you know (about the biro that is).

Dan.


> Cheers,
>
> L.
>
> --
> Dr Leighton Pritchard MRSC
> D131, Plant Pathology Programme, SCRI
> Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
> e:lpritc at scri.ac.uk ? ? ? w:http://www.scri.ac.uk/staff/leightonpritchard
> gpg/pgp: 0xFEFC205C ? ? ? tel:+44(0)1382 562731 x2405
>
>
> ______________________________________________________
> SCRI, Invergowrie, Dundee, DD2 5DA.
> The Scottish Crop Research Institute is a charitable company limited by guarantee.
> Registered in Scotland No: SC 29367.
> Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.
>
>
> DISCLAIMER:
>
> This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries. ?This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed. ?It may not be disclosed or used by any other than that addressee.
> If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify postmaster at scri.ac.uk quoting the name of the sender and delete the email from your system.
>
> Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any).
> ______________________________________________________
>


From biopython at maubp.freeserve.co.uk  Tue Jul 27 11:31:38 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 27 Jul 2010 16:31:38 +0100
Subject: [Open-bio-l] Agreed name for UniProt XML file format
Message-ID: <AANLkTikPq-dfFQphUEKJircwbAyJdXEADXKU4FZrUo=k@mail.gmail.com>

Dear all,

BioPerl, Biopython and EMBOSS all have a set of sequence file format
names (as strings), used as arguments to their SeqIO modules or as
command line arguments in EMBOSS. I understand that in BioRuby
and BioJava you have named classes instead(?). We currently have
reasonably consistent existing names. For the FASTQ files formats
we managed to agree consistent naming for the Sanger, Solexa and
Illumina 1.3+ variants. Now for the next "new" format...

Andrea Pierlenoin (CC'd) has been working on parsing the UniProt
XML file format in Biopython - this is essentially an XML replacement
for the old SwissProt plain text file format which is called "swiss" in
BioPerl, Biopython and EMBOSS (although EMBOSS also allows
"sw" and "swissprot" as well).

We were originally suggesting calling this new format "uniprot",
http://bioperl.org/pipermail/open-bio-l/2010-January/000609.html

Andrea has since pointed out that in the EBI REST services the file
format is referred as "uniprot-xml" which is also less ambiguous
(after all the old "swiss" plain text format might equally be referred
to as the plain text UniProt format).

So, what do people feel about standardising on "uniprot" and/or
"uniprot-xml" as the format name in Biopython, BioPerl & EMBOSS?

Thanks,

Peter

P.S. Chris, am I right in thinking that if BioPerl were to support this
file format under the name "uniprot-xml" this would be equivalent
to accepting format="uniprot" and variant="xml"? And furthermore
and assuming you regard this as the default/only variant, Bio::SeqIO
would also just accept format="uniprot"?

From hlapp at drycafe.net  Tue Jul 27 11:49:21 2010
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Tue, 27 Jul 2010 11:49:21 -0400
Subject: [Open-bio-l] Agreed name for UniProt XML file format
In-Reply-To: <AANLkTikPq-dfFQphUEKJircwbAyJdXEADXKU4FZrUo=k@mail.gmail.com>
References: <AANLkTikPq-dfFQphUEKJircwbAyJdXEADXKU4FZrUo=k@mail.gmail.com>
Message-ID: <DD9EDBAD-67DE-44F3-8917-CFBA145C0A6C@drycafe.net>


On Jul 27, 2010, at 11:31 AM, Peter wrote:

> So, what do people feel about standardising on "uniprot" and/or
> "uniprot-xml" as the format name in Biopython, BioPerl & EMBOSS?


uniprot-xml

It is clear and unambiguous, unlike uniprot alone, which might easily  
be mistaken to refer to the swissprot format of UniProt entries.

	-hilmar
-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================





From rmb32 at cornell.edu  Tue Jul 27 12:10:50 2010
From: rmb32 at cornell.edu (Robert Buels)
Date: Tue, 27 Jul 2010 09:10:50 -0700
Subject: [Open-bio-l] Agreed name for UniProt XML file format
In-Reply-To: <DD9EDBAD-67DE-44F3-8917-CFBA145C0A6C@drycafe.net>
References: <AANLkTikPq-dfFQphUEKJircwbAyJdXEADXKU4FZrUo=k@mail.gmail.com>
	<DD9EDBAD-67DE-44F3-8917-CFBA145C0A6C@drycafe.net>
Message-ID: <4C4F050A.70208@cornell.edu>

Hilmar Lapp wrote:
> uniprot-xml

+1

From biopython at maubp.freeserve.co.uk  Tue Jul 27 12:27:53 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 27 Jul 2010 17:27:53 +0100
Subject: [Open-bio-l] Agreed name for UniProt XML file format
In-Reply-To: <AD9A2A32-0F8B-4F81-A21F-C42039DDA627@illinois.edu>
References: <AANLkTikPq-dfFQphUEKJircwbAyJdXEADXKU4FZrUo=k@mail.gmail.com>
	<AD9A2A32-0F8B-4F81-A21F-C42039DDA627@illinois.edu>
Message-ID: <AANLkTi=x1tALUFBUThmafD8Wq6zzqh+LN+=5Nm_g0JM+@mail.gmail.com>

On Tue, Jul 27, 2010 at 5:14 PM, Chris Fields <cjfields at illinois.edu> wrote:
>
> On Jul 27, 2010, at 10:31 AM, Peter wrote:
>
>> Andrea has since pointed out that in the EBI REST services the file
>> format is referred as "uniprot-xml" which is also less ambiguous
>> (after all the old "swiss" plain text format might equally be referred
>> to as the plain text UniProt format).
>>
>> So, what do people feel about standardising on "uniprot" and/or
>> "uniprot-xml" as the format name in Biopython, BioPerl & EMBOSS?
>
> Agree with hilmar, 'uniprot-xml'.

That looks like a consensus (so far). Thank you all.

>> P.S. Chris, am I right in thinking that if BioPerl were to support this
>> file format under the name "uniprot-xml" this would be equivalent
>> to accepting format="uniprot" and variant="xml"? And furthermore
>> and assuming you regard this as the default/only variant, Bio::SeqIO
>> would also just accept format="uniprot"?
>
> In cases where 'uniprot' is passed, we could handle it either way:
> delegate to 'swiss' if xml isn't specified (so 'uniprot' is just an alias
> of 'swiss'), or always use the XML handler for 'uniprot' and ignore
> the variant argument. ?Either way is fine with us.

Or raise an error as it is ambiguous? But that wouldn't be in the spirit
of Perl though would it? ;)

Peter


From cjfields at illinois.edu  Tue Jul 27 12:14:41 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 27 Jul 2010 11:14:41 -0500
Subject: [Open-bio-l] Agreed name for UniProt XML file format
In-Reply-To: <AANLkTikPq-dfFQphUEKJircwbAyJdXEADXKU4FZrUo=k@mail.gmail.com>
References: <AANLkTikPq-dfFQphUEKJircwbAyJdXEADXKU4FZrUo=k@mail.gmail.com>
Message-ID: <AD9A2A32-0F8B-4F81-A21F-C42039DDA627@illinois.edu>


On Jul 27, 2010, at 10:31 AM, Peter wrote:

> Dear all,
> 
> BioPerl, Biopython and EMBOSS all have a set of sequence file format
> names (as strings), used as arguments to their SeqIO modules or as
> command line arguments in EMBOSS. I understand that in BioRuby
> and BioJava you have named classes instead(?). We currently have
> reasonably consistent existing names. For the FASTQ files formats
> we managed to agree consistent naming for the Sanger, Solexa and
> Illumina 1.3+ variants. Now for the next "new" format...
> 
> Andrea Pierlenoin (CC'd) has been working on parsing the UniProt
> XML file format in Biopython - this is essentially an XML replacement
> for the old SwissProt plain text file format which is called "swiss" in
> BioPerl, Biopython and EMBOSS (although EMBOSS also allows
> "sw" and "swissprot" as well).
> 
> We were originally suggesting calling this new format "uniprot",
> http://bioperl.org/pipermail/open-bio-l/2010-January/000609.html
> 
> Andrea has since pointed out that in the EBI REST services the file
> format is referred as "uniprot-xml" which is also less ambiguous
> (after all the old "swiss" plain text format might equally be referred
> to as the plain text UniProt format).
> 
> So, what do people feel about standardising on "uniprot" and/or
> "uniprot-xml" as the format name in Biopython, BioPerl & EMBOSS?

Agree with hilmar, 'uniprot-xml'.

> Thanks,
> 
> Peter
> 
> P.S. Chris, am I right in thinking that if BioPerl were to support this
> file format under the name "uniprot-xml" this would be equivalent
> to accepting format="uniprot" and variant="xml"? And furthermore
> and assuming you regard this as the default/only variant, Bio::SeqIO
> would also just accept format="uniprot"?

In cases where 'uniprot' is passed, we could handle it either way: delegate to 'swiss' if xml isn't specified (so 'uniprot' is just an alias of 'swiss'), or always use the XML handler for 'uniprot' and ignore the variant argument.  Either way is fine with us.

chris





From David.Messina at sbc.su.se  Tue Jul 27 12:58:12 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Tue, 27 Jul 2010 10:58:12 -0600
Subject: [Open-bio-l] Agreed name for UniProt XML file format
In-Reply-To: <AANLkTi=x1tALUFBUThmafD8Wq6zzqh+LN+=5Nm_g0JM+@mail.gmail.com>
References: <AANLkTikPq-dfFQphUEKJircwbAyJdXEADXKU4FZrUo=k@mail.gmail.com>
	<AD9A2A32-0F8B-4F81-A21F-C42039DDA627@illinois.edu>
	<AANLkTi=x1tALUFBUThmafD8Wq6zzqh+LN+=5Nm_g0JM+@mail.gmail.com>
Message-ID: <B4AF6005-1B12-457A-A2B4-A6A52D19881B@sbc.su.se>

> Or raise an error as it is ambiguous? But that wouldn't be in the spirit
> of Perl though would it? ;)

Perly or not :), I like this idea.

It has the advantage that when (if?) plaintext uniprot stops being used, and that ambiguity disappears, we can make 'uniprot' an alias of 'uniprot-xml'.


Dave

(or an alias to 'swiss', in the apocalyptic event that XML is abandoned.) 

From cjfields at illinois.edu  Tue Jul 27 12:51:07 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 27 Jul 2010 11:51:07 -0500
Subject: [Open-bio-l] Agreed name for UniProt XML file format
In-Reply-To: <AANLkTi=x1tALUFBUThmafD8Wq6zzqh+LN+=5Nm_g0JM+@mail.gmail.com>
References: <AANLkTikPq-dfFQphUEKJircwbAyJdXEADXKU4FZrUo=k@mail.gmail.com>
	<AD9A2A32-0F8B-4F81-A21F-C42039DDA627@illinois.edu>
	<AANLkTi=x1tALUFBUThmafD8Wq6zzqh+LN+=5Nm_g0JM+@mail.gmail.com>
Message-ID: <35FDA04E-F141-4166-9DD2-424B788D65FC@illinois.edu>


On Jul 27, 2010, at 11:27 AM, Peter wrote:

> On Tue, Jul 27, 2010 at 5:14 PM, Chris Fields <cjfields at illinois.edu> wrote:
>> 
>> On Jul 27, 2010, at 10:31 AM, Peter wrote:
>> 
>>> Andrea has since pointed out that in the EBI REST services the file
>>> format is referred as "uniprot-xml" which is also less ambiguous
>>> (after all the old "swiss" plain text format might equally be referred
>>> to as the plain text UniProt format).
>>> 
>>> So, what do people feel about standardising on "uniprot" and/or
>>> "uniprot-xml" as the format name in Biopython, BioPerl & EMBOSS?
>> 
>> Agree with hilmar, 'uniprot-xml'.
> 
> That looks like a consensus (so far). Thank you all.
> 
>>> P.S. Chris, am I right in thinking that if BioPerl were to support this
>>> file format under the name "uniprot-xml" this would be equivalent
>>> to accepting format="uniprot" and variant="xml"? And furthermore
>>> and assuming you regard this as the default/only variant, Bio::SeqIO
>>> would also just accept format="uniprot"?
>> 
>> In cases where 'uniprot' is passed, we could handle it either way:
>> delegate to 'swiss' if xml isn't specified (so 'uniprot' is just an alias
>> of 'swiss'), or always use the XML handler for 'uniprot' and ignore
>> the variant argument.  Either way is fine with us.
> 
> Or raise an error as it is ambiguous? But that wouldn't be in the spirit
> of Perl though would it? ;)
> 
> Peter

An error is fine by me as well.  

chrus



From hlapp at drycafe.net  Tue Jul 27 14:57:33 2010
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Tue, 27 Jul 2010 14:57:33 -0400
Subject: [Open-bio-l] Agreed name for UniProt XML file format
In-Reply-To: <AD9A2A32-0F8B-4F81-A21F-C42039DDA627@illinois.edu>
References: <AANLkTikPq-dfFQphUEKJircwbAyJdXEADXKU4FZrUo=k@mail.gmail.com>
	<AD9A2A32-0F8B-4F81-A21F-C42039DDA627@illinois.edu>
Message-ID: <29A06AD7-A202-4C54-8DEE-8629B600A07B@drycafe.net>


On Jul 27, 2010, at 12:14 PM, Chris Fields wrote:

>> P.S. Chris, am I right in thinking that if BioPerl were to support  
>> this
>> file format under the name "uniprot-xml" this would be equivalent
>> to accepting format="uniprot" and variant="xml"? And furthermore
>> and assuming you regard this as the default/only variant, Bio::SeqIO
>> would also just accept format="uniprot"?
>
> In cases where 'uniprot' is passed, we could handle it either way:  
> delegate to 'swiss' if xml isn't specified (so 'uniprot' is just an  
> alias of 'swiss'), or always use the XML handler for 'uniprot' and  
> ignore the variant argument.  Either way is fine with us.


Frankly I'm afraid to most people uniprot as a format name is  
synonymous with swiss(prot). So that should probably be the default  
(rule: the default should always be the least surprising choice).

Alternatively, can we auto-detect whether it is XML without messing up  
an XML parser if the input is coming from a pipe?

	-hilmar
-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================





From pmr at ebi.ac.uk  Wed Jul 28 03:35:38 2010
From: pmr at ebi.ac.uk (Peter Rice)
Date: Wed, 28 Jul 2010 08:35:38 +0100
Subject: [Open-bio-l] Agreed name for UniProt XML file format
In-Reply-To: <AANLkTikPq-dfFQphUEKJircwbAyJdXEADXKU4FZrUo=k@mail.gmail.com>
References: <AANLkTikPq-dfFQphUEKJircwbAyJdXEADXKU4FZrUo=k@mail.gmail.com>
Message-ID: <4C4FDDCA.7010709@ebi.ac.uk>

On 27/07/2010 16:31, Peter C. wrote:

> So, what do people feel about standardising on "uniprot" and/or
> "uniprot-xml" as the format name in Biopython, BioPerl&  EMBOSS?

The name is good for EMBOSS. We do not hav ethis format yet ... but will 
add it under whatever name is agreed.

regards,

Peter Rice

From bonnalraoul at ingm.it  Tue Jul 13 09:15:14 2010
From: bonnalraoul at ingm.it (Raoul Bonnal)
Date: Tue, 13 Jul 2010 13:15:14 -0000
Subject: [Open-bio-l]  Code fest 2010: thinking to '11
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTikqs9a7BX_Db7UhhGI34onixjwMDbWcx3isp-V5@mail.gmail.com>
Message-ID: <0edae1b2-c20e-4a01-8dec-d3b233f795b6@ingm.it>

Dear All,
Codefest 2010 is finished and I think it has been a great success. 
I was so happy to do what I like to do more, coding, meeting people (it's better with a beer) and coding again.
Codefest +1

I'd like to have a BOSC more... like a round table than just presentations which are for sure very useful but not enough in my idea. 
Bosc +1-

As requested by many people @ BBQ, I'm just wondering how it could be having a Codefest in Italy, that would be definetely amazing. If you like the idea, in the next months I'll try to figure out how to make it possible. Keep in mind that my working place is in Milan.
Codefest at Milan +1

Then, I realized that is very important to be on the same boat and I'd like to join the OBF in a more active way, how to start ?

Chrees.
--
Raoul J.P. Bonnal
Life Science Informatics
Integrative Biology Program
Fondazione INGM
Via F. Sforza 28
20122 Milano, IT
phone: +39 02 006 623  26
fax: +39 02 006 623 46
http://www.ingm.it



From bonnalraoul at ingm.it  Mon Jul 19 05:45:06 2010
From: bonnalraoul at ingm.it (Raoul Bonnal)
Date: Mon, 19 Jul 2010 09:45:06 -0000
Subject: [Open-bio-l] R:  Code fest 2010: thinking to '11
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTikqs9a7BX_Db7UhhGI34onixjwMDbWcx3isp-V5@mail.gmail.com>
	<0edae1b2-c20e-4a01-8dec-d3b233f795b6@ingm.it>
	<4C410BE9.7040203@burnham.org>
	<8E65215F-FC4B-4E8E-B755-570FFEDBF644@eaglegenomics.com>
	<20100719090451.GA14892@thebird.nl> <4C441993.1020707@gmx.de>
Message-ID: <e74ca971-c182-4360-9bae-dbb6edad2b20@ingm.it>

About Milano, 
I don't want to push Milano, it was just an idea born during the BBQ. I know that it would require a lot of travel. It was to collect your opinion on that...

If there is a chance to have R guys join us, probably is better to find out a place in Vienna. If we want to stay in Vienna and no one can provide a room we could look for places used by gamers for their lan-parties or some other OpenSource community

    * Linux User Group at the Technical University of Vienna

City: 	Vienna 	Web Site: 	http://lll.ins.at/
Contact: 	Arno Belohlavek 	Email: 	bodi at cslab.tuwien.ac.at
Click here for more information
 

    * Linux User Group Austria (LUGA)

City: 	Vienna 	Web Site: 	http://www.luga.at/
Contact: 	N/A 	Email: 	office at luga.at
Click here for more information

Regards

--
Raoul J.P. Bonnal
Life Science Informatics
Integrative Biology Program
Fondazione INGM
Via F. Sforza 28
20122 Milano, IT
phone: +39 02 006 623  26
fax: +39 02 006 623 46
http://www.ingm.it

> -----Messaggio originale-----
> Da: Steffen M?ller [mailto:steffen_moeller at gmx.de]
> Inviato: luned? 19 luglio 2010 11:24
> A: Pjotr Prins
> Cc: Richard Holland; Christian M Zmasek; Raoul Bonnal; 'Brad Chapman';
> open-bio-l at lists.open-bio.org; 'Akira KINJO'; 'Eric Talevich'; 'Tim
> Booth'; 'Yasunori Yamamoto'; 'Christopher Bottoms'; 'Atsuko Yamaguchi';
> 'Kimberly Begley'; 'James Taylor'; 'Michael Heuer'; 'Kam Dahlquist';
> 'Hilmar Lapp'; 'Bela Tiwari'; 'Mitsuteru Nakao'; 'Toshiaki Katayama';
> 'Heikki Lehvaslaiho'; 'Dannon Baker'; 'Naohisa Goto'; 'Enis Afgan';
> Christian Zmasek; 'Ntino Krampis'; 'Oliver Hofmann'; 'John David N.
> Dionisio'; 'Dominique Belhachemi'; 'Lincoln Stein'
> Oggetto: Re: [Open-bio-l] Code fest 2010: thinking to '11
> 
> On 07/19/2010 11:04 AM, Pjotr Prins wrote:
> > On Sat, Jul 17, 2010 at 03:09:07PM +0100, Richard Holland wrote:
> >
> >> Should be possible to organise something in Vienna itself I would
> >> have thought? There's bound to be an institute there somewhere who
> >> could offer to help by providing a room for us to work in?
> >>
> > Vienna is also nice (I hear),
> it is
> > though maybe not as nice as Milano.
> >
> er, I'd say Milano already loses against the neighbouring Bergamo, but
> let's fight over this :)
> > ISMB/BOSC was also in Vienna in 2007 - so the organisers may be able
> > to give ideas.
> >
> > But amongst ourselves, who knows people in Vienna? We only need a
> > room with Internet, right?
> >
> I have someone to ask. Also we should contact the BioConductor
> folks (R is exceptionally strong in Vienna) to join in, which possibly
> solves all our problems :)
> > Clifford (of RockLinux fame - though he may frown on our coding -
> > http://www.clifford.at/frame.cgi?style.html and author of
> > http://openscad.org/) is in Vienna. I can try and ask him. But it is
> a
> > bit early now.
> >
> But Milano (and let me just mention Luebeck again) was thought
> as a meeting between the meetings, no?
> 
> Many greetings
> 
> Steffen




From bonnalraoul at ingm.it  Mon Jul 19 10:05:08 2010
From: bonnalraoul at ingm.it (Raoul Bonnal)
Date: Mon, 19 Jul 2010 14:05:08 -0000
Subject: [Open-bio-l] R: R:  Code fest 2010: thinking to '11
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTikqs9a7BX_Db7UhhGI34onixjwMDbWcx3isp-V5@mail.gmail.com>
	<0edae1b2-c20e-4a01-8dec-d3b233f795b6@ingm.it>
	<4C410BE9.7040203@burnham.org>
	<8E65215F-FC4B-4E8E-B755-570FFEDBF644@eaglegenomics.com>
	<20100719090451.GA14892@thebird.nl> <4C441993.1020707@gmx.de>
	<e74ca971-c182-4360-9bae-dbb6edad2b20@ingm.it>
	<20100719123836.GL16399@sobchak.mgh.harvard.e
	du> <81D91BED-8C74-495D-8A43-F10B37BBD181@eaglegenomics.com>
	<4C44519C.3060808@gmx.de>
Message-ID: <ad6de416-eed4-45ce-a209-0882b63a63c1@ingm.it>





> -----Messaggio originale-----
> Da: Steffen M?ller [mailto:steffen_moeller at gmx.de]
> There is the annual supercomputing conference May-Juneish in
> neighbouring
> Hamburg, diverse clinical events, nothing that really fits and I'd be
> aware of.
> We could create a summer or winter school ourselves, actually. We
> should
> meet more towards the Winter, I think, wherever it is. I suggest
> December,
> then we have the Xmas market as an event, and we should really think
> about
> financing ourselves with a cloud winter school.
> http://www.asc-
> luebeck.de/files/images/Luebeck%20Weihnachtsmarkt.preview.jpg
I like this idea.

+1 Winter


> >> There were also some great ideas about BOSC itself. I helped
> >> with the organizing this last year for the first time, and Kam is
> >> really open to letting organizers try and shape the conference
> >> goals. When Kam makes the announcements about organizing, which
> >> should be near the end of the year, definitely get involved and
> >> mention these ideas. It would be cool to see us try out some new
> >> notions of what BOSC can provide for attendees.
> >>
> +1
+1

--
Raoul J.P. Bonnal
Life Science Informatics
Integrative Biology Program
Fondazione INGM
Via F. Sforza 28
20122 Milano, IT
phone: +39 02 006 623  26
fax: +39 02 006 623 46
http://www.ingm.it



From rmb32 at cornell.edu  Tue Jul  6 16:06:36 2010
From: rmb32 at cornell.edu (Robert Buels)
Date: Tue, 06 Jul 2010 20:06:36 -0000
Subject: [Open-bio-l] Codefest 2010: Final details
In-Reply-To: <E3F893B2-221F-4120-A3CF-905261186C37@illinois.edu>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>	<AANLkTilM3_kEu9BWx2CIUaS2lklP1ULVKLhlKHtukgk2@mail.gmail.com>	<AANLkTiku8rxnLRFf0JULsAYvz5D07FeZR9ejKBZHQrCQ@mail.gmail.com>	<EEB50E10-CC46-43C7-928B-3CE8FC074315@illinois.edu>	<F9E2FEB5-B7C9-4F27-A572-0D66261CC925@nescent.org>
	<E3F893B2-221F-4120-A3CF-905261186C37@illinois.edu>
Message-ID: <4C3385D0.1020000@cornell.edu>

Chris Fields wrote:
> Would be nice to emphasize DBIx::Class, which abstracts the DB backend.  Not sure if Rob Buels will be there, might be a good contact person on that re: his work with DBIx::Class and Bio::Schema::Chado.

Gah, I won't be there, which is kind of driving me up the wall.  :-( 
Sorry guys!

Rob


From hlapp at nescent.org  Wed Jul  7 06:21:33 2010
From: hlapp at nescent.org (Hilmar Lapp)
Date: Wed, 07 Jul 2010 10:21:33 -0000
Subject: [Open-bio-l] Codefest 2010: Final details
In-Reply-To: <20100704185155.GB24102@kunkel>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTilM3_kEu9BWx2CIUaS2lklP1ULVKLhlKHtukgk2@mail.gmail.com>
	<AANLkTiku8rxnLRFf0JULsAYvz5D07FeZR9ejKBZHQrCQ@mail.gmail.com>
	<EEB50E10-CC46-43C7-928B-3CE8FC074315@illinois.edu>
	<20100704185155.GB24102@kunkel>
Message-ID: <9E077631-BDBB-45F2-8FC5-7BD3A3D1F6D7@nescent.org>

FYI, I'll be delayed by 2.5 hrs, so won't be there before 11am. Sorry about that.

-hilmar

Sent from away

On Jul 4, 2010, at 2:51 PM, Brad Chapman <chapmanb at 50mail.com> wrote:

> Christopher, Chris, Heikki and Hilmar;
> Nice discussion. If you have an overview of what you are hoping
> to tackle on the BioPerl side, please add it on the wiki page. The
> getting started part of the coding sessions is always the hardest
> part, so it'll be a huge help if we can stand up at the beginning,
> describe the project ideas, and then let people break into groups:
> 
> http://www.open-bio.org/wiki/Codefest_2010#ToDo_List
> 
> Edit away and this'll point us all in the right direction.
> Looking forward to next week,
> Brad
> 
>> I will be there on the afternoon of the 7th.  There are a couple of projects one can look into for Moose and Perl 6 (Biome and BioPerl6).  I think Hilmar was to do some DBIx::Class stuff for BioSQL at one point, not sure where that is (might be surplanted by SQLite work?).  Would be nice to talk with Mark re: the wrapper system for BioPerl as well.
>> 
>> So lots of stuff to think over and plan for.  Maybe we should move this to open-bio-l, or bioperl-l?
>> 
>> chris (fields)
>> 
>> On Jul 3, 2010, at 12:44 AM, Heikki Lehvaslaiho wrote:
>> 
>>> Chris,
>>> 
>>> I do not have too much experience on cloud computing, either. There
>>> will be quite a few people from BioPerl . We'll meet and  come up with
>>> a plan first thing in the morning. Unless someone has a very good one
>>> ready for sharing...
>>> 
>>>    -Heikki
>>> 
>>> Heikki Lehvaslaiho - skype:heikki_lehvaslaiho
>>> cell: +966 545 595 849  office: +966 2 808 2429
>>> 
>>> Computational Bioscience Research Centre (CBRC), Building #2, Office #4216
>>> 4700 King Abdullah University of Science and Technology (KAUST)
>>> Thuwal 23955-6900, Kingdom of Saudi Arabia
>>> 
>>> 
>>> 
>>> 
>>> On 3 July 2010 08:36, Christopher Bottoms <maizemu at gmail.com> wrote:
>>>> Hi all,
>>>> 
>>>> I was originally planning on working on cloud computing at the Codefest.
>>>> However, the 2-day cloud computing tutorial that I was going to attend in
>>>> mid June was canceled. Does anyone have any programming that they would like
>>>> help with? I have experience with Perl 5, including Moose, and I am starting
>>>> to dabble in Perl 6. I have also programmed in Java in the past. I hear
>>>> Python is easy to learn, so I'd be open to working on a Python project as
>>>> well.
>>>> 
>>>> Thanks,
>>>> Christopher Bottoms
>>>> 
>>>> On Fri, Jul 2, 2010 at 8:38 AM, Brad Chapman <chapmanb at 50mail.com> wrote:
>>>>> 
>>>>> Hi all;
>>>>> Codefest 2010 is finally here: next Wednesday and Thursday at
>>>>> Harvard Medical School and Massachusetts General Hospital in
>>>>> beautiful Boston. All of the logistics, directions and details
>>>>> are on the wiki page:
>>>>> 
>>>>> http://www.open-bio.org/wiki/Codefest_2010
>>>>> 
>>>>> If you want the short version: show up at Harvard Medical School on
>>>>> Wednesday at 10am and we'll take care of the rest. Thanks to the
>>>>> hard work of Oliver, Kimberly, Leah, Toshiaki, and Mitsuteru we'll
>>>>> have coffee, lunches and internet. Thanks to Steffen and Ntino,
>>>>> we'll have Amazon credits to utilize. And of course, there will be
>>>>> BBQ and drinking on Thursday night when we are finished.
>>>>> 
>>>>> I'm looking forward to a fun and productive time. The general plan
>>>>> will be to spend a bit of time on Wednesday morning organizing
>>>>> ourselves into like minded groups of folks, and then commence with
>>>>> coding and collaborating.
>>>>> 
>>>>> If you aren't able to make it and you're listed on the wiki page under
>>>>> participants, please do cross your name off so we have a good idea of
>>>>> final numbers. Likewise, if you are coming but haven't put your name up
>>>>> there please add it.
>>>>> 
>>>>> If you are interested in helping with making software and data
>>>>> available on shared cloud resources, here are the latest Amazon
>>>>> AMIs, snapshots, and the code base:
>>>>> 
>>>>> Cloud BioLinux images:
>>>>> 64bit: ami-d62cc4bf
>>>>> 32bit: ami-5423cb3d
>>>>> 
>>>>> An EBS public snapshot with indexed genomes:
>>>>> snap-67446d0f
>>>>> 
>>>>> Infrastructure:
>>>>> http://github.com/chapmanb/bcbb/tree/master/ec2/biolinux/
>>>>> 
>>>>> Send an e-mail with any questions, thoughts or concerns. My phone
>>>>> number is 617-447-8586 in case you end up hopelessly lost somewhere
>>>>> in Boston and are desperate to begin programming.
>>>>> 
>>>>> Looking forward to seeing everyone next Wednesday,
>>>>> Brad
>>>> 
>>>> 
>> 


From steffen_moeller at gmx.de  Tue Jul 13 09:55:07 2010
From: steffen_moeller at gmx.de (=?ISO-8859-1?Q?Steffen_M=F6ller?=)
Date: Tue, 13 Jul 2010 13:55:07 -0000
Subject: [Open-bio-l] Code fest 2010: thinking to '11
In-Reply-To: <0edae1b2-c20e-4a01-8dec-d3b233f795b6@ingm.it>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTikqs9a7BX_Db7UhhGI34onixjwMDbWcx3isp-V5@mail.gmail.com>
	<0edae1b2-c20e-4a01-8dec-d3b233f795b6@ingm.it>
Message-ID: <4C3C6B62.6060209@gmx.de>

Hi Raoul,

On 07/13/2010 03:01 PM, Raoul Bonnal wrote:
> Codefest 2010 is finished and I think it has been a great success. 
> I was so happy to do what I like to do more, coding, meeting people (it's better with a beer) and coding again.
> Codefest +1
>   
+1 , the "no question asked" series of presentations at BOSC was kind of
strange. But sure, all questions you would want to ask to BioPerl etc
you would have asked a while ago, not at the conference.
> I'd like to have a BOSC more... like a round table than just presentations which are for sure very useful but not enough in my idea. 
> Bosc +1-
>   
+1  - these doing-something-together meetings are good.
> As requested by many people @ BBQ, I'm just wondering how it could be having a Codefest in Italy, that would be definetely amazing. If you like the idea, in the next months I'll try to figure out how to make it possible. Keep in mind that my working place is in Milan.
> Codefest at Milan +1
>   
The problem is with the funding of the travel, which again would speak
for an increased regionalisation of the efforts and the integration of
others via the net.
A conference nearby does not really help if you don't also have a paper
on it :)
> Then, I realized that is very important to be on the same boat and I'd like to join the OBF in a more active way, how to start ?
>   
Well, we'd need the OBF for an OK to call it BOSC Hackathon, or BOSCF
(for BOSCloudFest). But the meeting we could plan rightaway. I can offer
the same for Luebeck, literally at the beach. Consider a free room
settled, accomodation is about 45 Euros per night. The nearest airports
would be the 50 miles apart Hamburg (Northern Germany) or Luebeck itself
with direct RyanAir flights from around Europe (Bergamo, Pisa, Stansted,
Barcelona, Edinburgh, "Stockholm", Gdansk and probably others).
Actually, Richard and Dominique already plan to come, maybe we could
synchronise things a bit.

Many greetings

Steffen

From holland at eaglegenomics.com  Tue Jul 13 10:44:12 2010
From: holland at eaglegenomics.com (Richard Holland)
Date: Tue, 13 Jul 2010 14:44:12 -0000
Subject: [Open-bio-l] Code fest 2010: thinking to '11
In-Reply-To: <4C3C6B62.6060209@gmx.de>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTikqs9a7BX_Db7UhhGI34onixjwMDbWcx3isp-V5@mail.gmail.com>
	<0edae1b2-c20e-4a01-8dec-d3b233f795b6@ingm.it>
	<4C3C6B62.6060209@gmx.de>
Message-ID: <ED49C5C3-D612-424C-900C-637D6C507FC2@eaglegenomics.com>

Hello all,

Speaking now strictly in my personal/OBF-member role now and not with my company hat on.

On 13 Jul 2010, at 09:34, Steffen M?ller wrote:

> Hi Raoul,
> 
> On 07/13/2010 03:01 PM, Raoul Bonnal wrote:
>> Codefest 2010 is finished and I think it has been a great success. 
>> I was so happy to do what I like to do more, coding, meeting people (it's better with a beer) and coding again.
>> Codefest +1
>> 
> +1 , the "no question asked" series of presentations at BOSC was kind of
> strange. But sure, all questions you would want to ask to BioPerl etc
> you would have asked a while ago, not at the conference.

+1, The question then arises, what is BOSC for. The Bio* projects function perfectly well these days without needing to present, and the audience tends to be made up of the already converted so they are not really attracting any extra users there. The hackathons/codefests are a much better and more useful event for the Bio* projects in my mind. The remaining talks about specific bits of software are very interesting but its not always obvious what the biological problem is that they're trying to solve - or whether it really is a problem unique to biological informatics or if they would be better off in a more generic informatics conference (where their code and design practices would also come under much closer scrutiny!).

>> I'd like to have a BOSC more... like a round table than just presentations which are for sure very useful but not enough in my idea. 
>> Bosc +1-
>> 
> +1  - these doing-something-together meetings are good.

+1 yes agreed, despite advances in comms technology still nothing beats a few beers at the pub with your laptops.

>> As requested by many people @ BBQ, I'm just wondering how it could be having a Codefest in Italy, that would be definetely amazing. If you like the idea, in the next months I'll try to figure out how to make it possible. Keep in mind that my working place is in Milan.
>> Codefest at Milan +1
>> 
> The problem is with the funding of the travel, which again would speak
> for an increased regionalisation of the efforts and the integration of
> others via the net.
> A conference nearby does not really help if you don't also have a paper
> on it :)

Indeed. I think regional efforts are going to be unavoidable because of this, so you'll need a key core of people at each one to keep the momentum going. e.g. a 'management team' at each Bio* project that has a knowledgeable senior member in every region that is able to lead these meetings when they take place.

>> Then, I realized that is very important to be on the same boat and I'd like to join the OBF in a more active way, how to start ?
>> 
> Well, we'd need the OBF for an OK to call it BOSC Hackathon, or BOSCF
> (for BOSCloudFest). But the meeting we could plan rightaway. I can offer
> the same for Luebeck, literally at the beach. Consider a free room
> settled, accomodation is about 45 Euros per night. The nearest airports
> would be the 50 miles apart Hamburg (Northern Germany) or Luebeck itself
> with direct RyanAir flights from around Europe (Bergamo, Pisa, Stansted,
> Barcelona, Edinburgh, "Stockholm", Gdansk and probably others).
> Actually, Richard and Dominique already plan to come, maybe we could
> synchronise things a bit.

Yup, definitely planning on coming to the Luebeck thing if it happens. In future, we can offer similar facilities in Cambridge (actually Babraham really, but close enough) - nearest airport Stansted, unfortunately no beach.

cheers,
Richard

> Many greetings
> 
> Steffen

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/



From czmasek at burnham.org  Fri Jul 16 21:58:18 2010
From: czmasek at burnham.org (Christian M Zmasek)
Date: Sat, 17 Jul 2010 01:58:18 -0000
Subject: [Open-bio-l] Code fest 2010: thinking to '11
In-Reply-To: <0edae1b2-c20e-4a01-8dec-d3b233f795b6@ingm.it>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTikqs9a7BX_Db7UhhGI34onixjwMDbWcx3isp-V5@mail.gmail.com>
	<0edae1b2-c20e-4a01-8dec-d3b233f795b6@ingm.it>
Message-ID: <4C410BE9.7040203@burnham.org>

Hi, Raoul:

While having a "codefest" in Italy sounds (very) tempting, I recommend 
to first get a rough estimate of the number of people who actually might 
be able/willing to travel to Italy from Vienna, before making any 
serious plans.

I think part of the reason why codefest 2010 was a success was because 
it was very convenient to combine it with BOSC 2010 (same hotels, no 
additional travel, etc.).

Clearly, for some (including me) additional travel might be a plus, but 
maybe not for everyone...

Good luck, in any case!

Christian





Raoul Bonnal wrote:
> Dear All,
> Codefest 2010 is finished and I think it has been a great success. 
> I was so happy to do what I like to do more, coding, meeting people (it's better with a beer) and coding again.
> Codefest +1
> 
> I'd like to have a BOSC more... like a round table than just presentations which are for sure very useful but not enough in my idea. 
> Bosc +1-
> 
> As requested by many people @ BBQ, I'm just wondering how it could be having a Codefest in Italy, that would be definetely amazing. If you like the idea, in the next months I'll try to figure out how to make it possible. Keep in mind that my working place is in Milan.
> Codefest at Milan +1
> 
> Then, I realized that is very important to be on the same boat and I'd like to join the OBF in a more active way, how to start ?
> 
> Chrees.
> --
> Raoul J.P. Bonnal
> Life Science Informatics
> Integrative Biology Program
> Fondazione INGM
> Via F. Sforza 28
> 20122 Milano, IT
> phone: +39 02 006 623  26
> fax: +39 02 006 623 46
> http://www.ingm.it
> 


From holland at eaglegenomics.com  Sat Jul 17 10:53:56 2010
From: holland at eaglegenomics.com (Richard Holland)
Date: Sat, 17 Jul 2010 14:53:56 -0000
Subject: [Open-bio-l] Code fest 2010: thinking to '11
In-Reply-To: <4C410BE9.7040203@burnham.org>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTikqs9a7BX_Db7UhhGI34onixjwMDbWcx3isp-V5@mail.gmail.com>
	<0edae1b2-c20e-4a01-8dec-d3b233f795b6@ingm.it>
	<4C410BE9.7040203@burnham.org>
Message-ID: <8E65215F-FC4B-4E8E-B755-570FFEDBF644@eaglegenomics.com>

The combined purpose trip was definitely a big part of the decision to attend. I could only do Italy if it was really cheap to get there from Vienna, otherwise couldn't justify the extra cost. Unless there was something else going on in Italy to go to as well at the same time?

Should be possible to organise something in Vienna itself I would have thought? There's bound to be an institute there somewhere who could offer to help by providing a room for us to work in?

On 17 Jul 2010, at 02:48, Christian M Zmasek wrote:

> Hi, Raoul:
> 
> While having a "codefest" in Italy sounds (very) tempting, I recommend to first get a rough estimate of the number of people who actually might be able/willing to travel to Italy from Vienna, before making any serious plans.
> 
> I think part of the reason why codefest 2010 was a success was because it was very convenient to combine it with BOSC 2010 (same hotels, no additional travel, etc.).
> 
> Clearly, for some (including me) additional travel might be a plus, but maybe not for everyone...
> 
> Good luck, in any case!
> 
> Christian
> 
> 
> 
> 
> 
> Raoul Bonnal wrote:
>> Dear All,
>> Codefest 2010 is finished and I think it has been a great success. I was so happy to do what I like to do more, coding, meeting people (it's better with a beer) and coding again.
>> Codefest +1
>> I'd like to have a BOSC more... like a round table than just presentations which are for sure very useful but not enough in my idea. Bosc +1-
>> As requested by many people @ BBQ, I'm just wondering how it could be having a Codefest in Italy, that would be definetely amazing. If you like the idea, in the next months I'll try to figure out how to make it possible. Keep in mind that my working place is in Milan.
>> Codefest at Milan +1
>> Then, I realized that is very important to be on the same boat and I'd like to join the OBF in a more active way, how to start ?
>> Chrees.
>> --
>> Raoul J.P. Bonnal
>> Life Science Informatics
>> Integrative Biology Program
>> Fondazione INGM
>> Via F. Sforza 28
>> 20122 Milano, IT
>> phone: +39 02 006 623  26
>> fax: +39 02 006 623 46
>> http://www.ingm.it
> 

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/



From pjotr.public14 at thebird.nl  Mon Jul 19 05:11:25 2010
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Mon, 19 Jul 2010 09:11:25 -0000
Subject: [Open-bio-l] Code fest 2010: thinking to '11
In-Reply-To: <8E65215F-FC4B-4E8E-B755-570FFEDBF644@eaglegenomics.com>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTikqs9a7BX_Db7UhhGI34onixjwMDbWcx3isp-V5@mail.gmail.com>
	<0edae1b2-c20e-4a01-8dec-d3b233f795b6@ingm.it>
	<4C410BE9.7040203@burnham.org>
	<8E65215F-FC4B-4E8E-B755-570FFEDBF644@eaglegenomics.com>
Message-ID: <20100719090451.GA14892@thebird.nl>

On Sat, Jul 17, 2010 at 03:09:07PM +0100, Richard Holland wrote:
> Should be possible to organise something in Vienna itself I would
> have thought? There's bound to be an institute there somewhere who
> could offer to help by providing a room for us to work in?

Vienna is also nice (I hear), though maybe not as nice as Milano.

ISMB/BOSC was also in Vienna in 2007 - so the organisers may be able
to give ideas.

But amongst ourselves, who knows people in Vienna? We only need a
room with Internet, right? 

Clifford (of RockLinux fame - though he may frown on our coding -
http://www.clifford.at/frame.cgi?style.html and author of
http://openscad.org/) is in Vienna. I can try and ask him. But it is a
bit early now.

Pj.

From steffen_moeller at gmx.de  Mon Jul 19 05:23:44 2010
From: steffen_moeller at gmx.de (=?ISO-8859-1?Q?Steffen_M=F6ller?=)
Date: Mon, 19 Jul 2010 09:23:44 -0000
Subject: [Open-bio-l] Code fest 2010: thinking to '11
In-Reply-To: <20100719090451.GA14892@thebird.nl>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTikqs9a7BX_Db7UhhGI34onixjwMDbWcx3isp-V5@mail.gmail.com>
	<0edae1b2-c20e-4a01-8dec-d3b233f795b6@ingm.it>
	<4C410BE9.7040203@burnham.org>
	<8E65215F-FC4B-4E8E-B755-570FFEDBF644@eaglegenomics.com>
	<20100719090451.GA14892@thebird.nl>
Message-ID: <4C441993.1020707@gmx.de>

On 07/19/2010 11:04 AM, Pjotr Prins wrote:
> On Sat, Jul 17, 2010 at 03:09:07PM +0100, Richard Holland wrote:
>   
>> Should be possible to organise something in Vienna itself I would
>> have thought? There's bound to be an institute there somewhere who
>> could offer to help by providing a room for us to work in?
>>     
> Vienna is also nice (I hear),
it is
> though maybe not as nice as Milano.
>   
er, I'd say Milano already loses against the neighbouring Bergamo, but
let's fight over this :)
> ISMB/BOSC was also in Vienna in 2007 - so the organisers may be able
> to give ideas.
>
> But amongst ourselves, who knows people in Vienna? We only need a
> room with Internet, right? 
>   
I have someone to ask. Also we should contact the BioConductor
folks (R is exceptionally strong in Vienna) to join in, which possibly
solves all our problems :)  
> Clifford (of RockLinux fame - though he may frown on our coding -
> http://www.clifford.at/frame.cgi?style.html and author of
> http://openscad.org/) is in Vienna. I can try and ask him. But it is a
> bit early now.
>   
But Milano (and let me just mention Luebeck again) was thought
as a meeting between the meetings, no?

Many greetings

Steffen


From holland at eaglegenomics.com  Mon Jul 19 08:45:45 2010
From: holland at eaglegenomics.com (Richard Holland)
Date: Mon, 19 Jul 2010 12:45:45 -0000
Subject: [Open-bio-l] R:  Code fest 2010: thinking to '11
In-Reply-To: <20100719123836.GL16399@sobchak.mgh.harvard.edu>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTikqs9a7BX_Db7UhhGI34onixjwMDbWcx3isp-V5@mail.gmail.com>
	<0edae1b2-c20e-4a01-8dec-d3b233f795b6@ingm.it>
	<4C410BE9.7040203@burnham.org>
	<8E65215F-FC4B-4E8E-B755-570FFEDBF644@eaglegenomics.com>
	<20100719090451.GA14892@thebird.nl> <4C441993.1020707@gmx.de>
	<e74ca971-c182-4360-9bae-dbb6edad2b20@ingm.it>
	<20100719123836.GL16399@sobchak.mgh.harvard.edu>
Message-ID: <81D91BED-8C74-495D-8A43-F10B37BBD181@eaglegenomics.com>

With regard to point 2 about other conferences - ECCB is in Ghent (Belgium) this year, in September. This is the conference that ISMB pairs with every time it is in Europe so could be a good excuse for an attached codefest. However my network of Belgian bioinformaticians is about as good as my network of Viennese ones. :)

cheers,
Richard

On 19 Jul 2010, at 13:38, Brad Chapman wrote:

> Hey all;
> It's awesome to see so much interest in continuing the informal
> Codefests; this is a great discussion. Raoul, thanks for kicking 
> it off.
> 
> To try and summarize the thoughts so far, we have 2 different
> ideas floating about regarding future Codefest sessions:
> 
> 1. Another Codefest next year in conjunction with BOSC and ISMB in
> Vienna. So far we have proposals for either Milano or Vienna itself.
> The key aspect here is to figure out the logistics: if we wanted to
> do Milano what is the transport situation to Vienna afterwards? If
> we want to have it in Vienna can we find someone locally who is
> willing to do the on the ground work to ensure we have space,
> internet and power?
> 
> Although the work of actually organizing is not especially taxing,
> we do need to have someone committed locally as there are lots of
> little things that need a person willing to handle them. It's
> not too early to try and identify folks who might be interested and
> get them integrated into the community. Although we wouldn't need to
> book a room a year out, we would want to ensure that anyone
> interested in hosting would get enough out of the coding session to
> make it worth their time to help with the organization. Can anyone
> who knows people in Vienna who might be interested get in contact
> for at least an informal discussion? Then we can start to enumerate
> the specifics so we can compare our options.
> 
> 2. Intermediate, potentially regional, Codefests between BOSC. These
> sound like a good idea, and I would second Richard's point about
> associating these with conferences to help encourage attendance. It
> is a lot easier to justing budgeting out time and travel money if
> there is a relevant more "official" event happening in conjunction
> with the coding session. It's good to keep in mind that not
> everyone, and their bosses, are entirely altruistic and to think
> about how we can also satisfy professional needs while getting in
> some coding time. Steffen, are there any conferences or near Luebeck
> that it would make sense to coordinate with?
> 
> There were also some great ideas about BOSC itself. I helped
> with the organizing this last year for the first time, and Kam is
> really open to letting organizers try and shape the conference
> goals. When Kam makes the announcements about organizing, which
> should be near the end of the year, definitely get involved and
> mention these ideas. It would be cool to see us try out some new
> notions of what BOSC can provide for attendees.
> 
> Finally, thanks again to everyone for coming to Codefest this year.
> It was a great turnout and looking forward to doing it again,
> Brad

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/



From chapmanb at 50mail.com  Mon Jul 19 08:46:06 2010
From: chapmanb at 50mail.com (Brad Chapman)
Date: Mon, 19 Jul 2010 12:46:06 -0000
Subject: [Open-bio-l] R:  Code fest 2010: thinking to '11
In-Reply-To: <e74ca971-c182-4360-9bae-dbb6edad2b20@ingm.it>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTikqs9a7BX_Db7UhhGI34onixjwMDbWcx3isp-V5@mail.gmail.com>
	<0edae1b2-c20e-4a01-8dec-d3b233f795b6@ingm.it>
	<4C410BE9.7040203@burnham.org>
	<8E65215F-FC4B-4E8E-B755-570FFEDBF644@eaglegenomics.com>
	<20100719090451.GA14892@thebird.nl> <4C441993.1020707@gmx.de>
	<e74ca971-c182-4360-9bae-dbb6edad2b20@ingm.it>
Message-ID: <20100719123836.GL16399@sobchak.mgh.harvard.edu>

Hey all;
It's awesome to see so much interest in continuing the informal
Codefests; this is a great discussion. Raoul, thanks for kicking 
it off.

To try and summarize the thoughts so far, we have 2 different
ideas floating about regarding future Codefest sessions:

1. Another Codefest next year in conjunction with BOSC and ISMB in
Vienna. So far we have proposals for either Milano or Vienna itself.
The key aspect here is to figure out the logistics: if we wanted to
do Milano what is the transport situation to Vienna afterwards? If
we want to have it in Vienna can we find someone locally who is
willing to do the on the ground work to ensure we have space,
internet and power?

Although the work of actually organizing is not especially taxing,
we do need to have someone committed locally as there are lots of
little things that need a person willing to handle them. It's
not too early to try and identify folks who might be interested and
get them integrated into the community. Although we wouldn't need to
book a room a year out, we would want to ensure that anyone
interested in hosting would get enough out of the coding session to
make it worth their time to help with the organization. Can anyone
who knows people in Vienna who might be interested get in contact
for at least an informal discussion? Then we can start to enumerate
the specifics so we can compare our options.

2. Intermediate, potentially regional, Codefests between BOSC. These
sound like a good idea, and I would second Richard's point about
associating these with conferences to help encourage attendance. It
is a lot easier to justing budgeting out time and travel money if
there is a relevant more "official" event happening in conjunction
with the coding session. It's good to keep in mind that not
everyone, and their bosses, are entirely altruistic and to think
about how we can also satisfy professional needs while getting in
some coding time. Steffen, are there any conferences or near Luebeck
that it would make sense to coordinate with?

There were also some great ideas about BOSC itself. I helped
with the organizing this last year for the first time, and Kam is
really open to letting organizers try and shape the conference
goals. When Kam makes the announcements about organizing, which
should be near the end of the year, definitely get involved and
mention these ideas. It would be cool to see us try out some new
notions of what BOSC can provide for attendees.

Finally, thanks again to everyone for coming to Codefest this year.
It was a great turnout and looking forward to doing it again,
Brad

From steffen_moeller at gmx.de  Mon Jul 19 09:22:50 2010
From: steffen_moeller at gmx.de (=?ISO-8859-1?Q?Steffen_M=F6ller?=)
Date: Mon, 19 Jul 2010 13:22:50 -0000
Subject: [Open-bio-l] R:  Code fest 2010: thinking to '11
In-Reply-To: <81D91BED-8C74-495D-8A43-F10B37BBD181@eaglegenomics.com>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTikqs9a7BX_Db7UhhGI34onixjwMDbWcx3isp-V5@mail.gmail.com>
	<0edae1b2-c20e-4a01-8dec-d3b233f795b6@ingm.it>
	<4C410BE9.7040203@burnham.org>
	<8E65215F-FC4B-4E8E-B755-570FFEDBF644@eaglegenomics.com>
	<20100719090451.GA14892@thebird.nl> <4C441993.1020707@gmx.de>
	<e74ca971-c182-4360-9bae-dbb6edad2b20@ingm.it>
	<20100719123836.GL16399@sobchak.mgh.harvard.edu>
	<81D91BED-8C74-495D-8A43-F10B37BBD181@eaglegenomics.com>
Message-ID: <4C44519C.3060808@gmx.de>

Hello,

On 07/19/2010 02:44 PM, Richard Holland wrote:
> With regard to point 2 about other conferences - ECCB is in Ghent (Belgium) this year, in September. This is the conference that ISMB pairs with every time it is in Europe so could be a good excuse for an attached codefest. However my network of Belgian bioinformaticians is about as good as my network of Viennese ones. :)
>   
I like the idea, but September is a bit too soonish for me as we
basically have just met.

> On 19 Jul 2010, at 13:38, Brad Chapman wrote
>> Hey all;
>> It's awesome to see so much interest in continuing the informal
>> Codefests; this is a great discussion. Raoul, thanks for kicking 
>> it off.
>>
>> To try and summarize the thoughts so far, we have 2 different
>> ideas floating about regarding future Codefest sessions:
>>
>> 1. Another Codefest next year in conjunction with BOSC and ISMB in
>> Vienna. So far we have proposals for either Milano or Vienna itself.
>> The key aspect here is to figure out the logistics: if we wanted to
>> do Milano what is the transport situation to Vienna afterwards? If
>> we want to have it in Vienna can we find someone locally who is
>> willing to do the on the ground work to ensure we have space,
>> internet and power?
>>     
I expect to be at the ISMB and could prepare for that.
But there is no point in separating the CodeFest from BOSC, really.
And it certainly was not meant that way. It should be in Vienna.
>> Although the work of actually organizing is not especially taxing,
>> we do need to have someone committed locally as there are lots of
>> little things that need a person willing to handle them. It's
>> not too early to try and identify folks who might be interested and
>> get them integrated into the community. Although we wouldn't need to
>> book a room a year out, we would want to ensure that anyone
>> interested in hosting would get enough out of the coding session to
>> make it worth their time to help with the organization. Can anyone
>> who knows people in Vienna who might be interested get in contact
>> for at least an informal discussion? Then we can start to enumerate
>> the specifics so we can compare our options.
>>     
I'd ask a few individuals and then see what they say. Am I right presuming
that we cannot pay anything?
>> 2. Intermediate, potentially regional, Codefests between BOSC. These
>> sound like a good idea, and I would second Richard's point about
>> associating these with conferences to help encourage attendance.
Right. But not everyone needs to attend every meeting. In the contrary,
I think that it would be the major achievement of the cloud environments
that we can stay where we are and nonetheless somehow feel involved.
>> It
>> is a lot easier to justing budgeting out time and travel money if
>> there is a relevant more "official" event happening in conjunction
>> with the coding session. It's good to keep in mind that not
>> everyone, and their bosses, are entirely altruistic and to think
>> about how we can also satisfy professional needs while getting in
>> some coding time. Steffen, are there any conferences or near Luebeck
>> that it would make sense to coordinate with?
>>     
There is the annual supercomputing conference May-Juneish in neighbouring
Hamburg, diverse clinical events, nothing that really fits and I'd be
aware of.
We could create a summer or winter school ourselves, actually. We should
meet more towards the Winter, I think, wherever it is. I suggest December,
then we have the Xmas market as an event, and we should really think about
financing ourselves with a cloud winter school.
http://www.asc-luebeck.de/files/images/Luebeck%20Weihnachtsmarkt.preview.jpg

>> There were also some great ideas about BOSC itself. I helped
>> with the organizing this last year for the first time, and Kam is
>> really open to letting organizers try and shape the conference
>> goals. When Kam makes the announcements about organizing, which
>> should be near the end of the year, definitely get involved and
>> mention these ideas. It would be cool to see us try out some new
>> notions of what BOSC can provide for attendees.
>>     
+1

Many greetings

Steffen



From hlapp at drycafe.net  Fri Jul 23 13:05:50 2010
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Fri, 23 Jul 2010 17:05:50 -0000
Subject: [Open-bio-l] Code fest 2010: thinking to '11
In-Reply-To: <20100719090451.GA14892@thebird.nl>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTikqs9a7BX_Db7UhhGI34onixjwMDbWcx3isp-V5@mail.gmail.com>
	<0edae1b2-c20e-4a01-8dec-d3b233f795b6@ingm.it>
	<4C410BE9.7040203@burnham.org>
	<8E65215F-FC4B-4E8E-B755-570FFEDBF644@eaglegenomics.com>
	<20100719090451.GA14892@thebird.nl>
Message-ID: <BFF24009-397B-4938-9A4F-63D805231445@drycafe.net>


On Jul 19, 2010, at 5:04 AM, Pjotr Prins wrote:

> Vienna is also nice (I hear), though maybe not as nice as Milano.

I think it is nicer. But I'm biased :-)

> But amongst ourselves, who knows people in Vienna? We only need a
> room with Internet, right?

Right. I know people at the IMP (http://www.imp.ac.at/) and another  
center in the same building, and they might be able and willing to  
organize something. I have not asked yet, though.

> Clifford (of RockLinux fame - though he may frown on our coding -
> http://www.clifford.at/frame.cgi?style.html and author of
> http://openscad.org/) is in Vienna.

What might actually be a really interesting and cool location is the  
Metalab:
http://metalab.at/wiki/Info_Folder

(Click on "English Version" if you don't understand German)

I also know someone at the KLIVV, though I don't know how inclined  
they'd be to entertain the idea of hosting us:
http://www.oeaw.ac.at/klivv/

Other cool locations:
IST: http://www.ist.ac.at (Nick Barton just moved there)
IIASA (International Institute for Applied Systems Analysis): http://www.iiasa.ac.at 
  (They are in the Laxenburg Castle - *really* gorgeous place  
actually: http://www.iiasa.ac.at/docs/IIASA_Tour.html?sb=6)

	-hilmar
-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================





From dan.bolser at gmail.com  Thu Jul  1 09:48:02 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Thu, 1 Jul 2010 10:48:02 +0100
Subject: [Open-bio-l] Best practice for modelling data in GFF
In-Reply-To: <20100601113420.GL1054@sobchak.mgh.harvard.edu>
References: <AANLkTimuku_x7V9RSAERK4f4QxIc4od2zw3qZtdaL4oH@mail.gmail.com>
	<4BFFF7FE.1030004@bioperl.org>
	<685C1029-0E3A-45DD-BBA9-FFA7747810D5@illinois.edu>
	<AANLkTinrTVYODrcY9TUxhznkZKunNRQCvs-bnwgbHdNA@mail.gmail.com>
	<20100601113420.GL1054@sobchak.mgh.harvard.edu>
Message-ID: <AANLkTikcZgIjDlnUUs90IlEXBsvDhtvYq8LESKU9LChu@mail.gmail.com>

On 1 June 2010 12:34, Brad Chapman <chapmanb at 50mail.com> wrote:
> Dan;
> If what you are trying to do is represent your data in a way that the
> most people can parse and reuse it, my suggestion would be to use
> SAM/BAM to represent your alignments. You'll be using a standardized and
> well-supported format specifically designed for this type of data.
>
> While you can do this with GFF, the parser support for correctly
> dealing with match_part or part_of is likely to be less robust.
> As data providers standardize on one way to represent nested
> features, it should become easier to deal with them.

Yeah, I think BAM is a good way to go in this instance.


> Brad
>
>> Thanks all for replies.
>>
>> I'm aware of the GFF spec, and the SO ontology terms. The issue here
>> (as I understand it) is that the feature isn't 'flat', but is a
>> combination of two matching 'reads' that are grouped into a mate-pair
>> depending on their proximity and orientation. As pointed out, not
>> every pair is successfully mapped, specifically one read may be
>> 'missing' from the pair, the pair may span two reference sequences, or
>> the proximity or orientation of the pair may be incorrect.
>>
>> Strictly speaking this can be handled by match and match_part (or
>> read_pair and part_of) terms, however, the question is, does this
>> reflect the biology adequately? (And specifically which terms should
>> be used?)
>>
>> There is a canonical way to model a gene, so I was wondering if it
>> makes sense to describe similar 'biology' (or in this case molecular
>> biology) in standard ways (when the feature isn't simply described by
>> a single line of GFF)?
>>
>> Perhaps I've not understood SO properly, but I'm not sure how its
>> structure is translated into GFF structure ... is there a 1 to 1
>> mapping?
>>
>>
>> Cheers,
>> Dan.
>>
>> On 28 May 2010 18:49, Chris Fields <cjfields at illinois.edu> wrote:
>> > All,
>> >
>> > Appears that link isn't up to date. ?Current GFF3 spec (v. 1.16, updated May 25) here:
>> >
>> > http://www.sequenceontology.org/gff3.shtml
>> >
>> > chris
>> >
>> > On May 28, 2010, at 12:06 PM, Jason Stajich wrote:
>> >
>> >> It's covered in the GFF3 spec as match_part if that helps.
>> >> http://song.sourceforge.net/gff3.shtml
>> >>
>> >> Dan Bolser wrote, On 5/28/10 9:29 AM:
>> >>> Hi guys,
>> >>>
>> >>> Not sure if this is the right forum, but I just thought I'd ask...
>> >>>
>> >>> Where can I find information on 'best practices' for modelling
>> >>> biological data in GFF?
>> >>>
>> >>> For example, I'd like to model paired-end sequence alignments in GFF.
>> >>> One suggestion was to use match/match_part to link each end into a
>> >>> pair. Another option is to use 'read_pair' with 'contig' for the
>> >>> parent feature...
>> >>>
>> >>> Should I just be using SAM/BAM?
>> >>>
>> >>> Seems a shame not to have a standard way to do this in GFF...
>> >>>
>> >>>
>> >>> Cheers,
>> >>> Dan.
>> >>> _______________________________________________
>> >>> Open-Bio-l mailing list
>> >>> Open-Bio-l at lists.open-bio.org
>> >>> http://lists.open-bio.org/mailman/listinfo/open-bio-l
>> >>>
>> >> _______________________________________________
>> >> Open-Bio-l mailing list
>> >> Open-Bio-l at lists.open-bio.org
>> >> http://lists.open-bio.org/mailman/listinfo/open-bio-l
>> >
>> >
>>
>> _______________________________________________
>> Open-Bio-l mailing list
>> Open-Bio-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/open-bio-l
> _______________________________________________
> Open-Bio-l mailing list
> Open-Bio-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/open-bio-l
>



From dan.bolser at gmail.com  Thu Jul  1 10:12:21 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Thu, 1 Jul 2010 11:12:21 +0100
Subject: [Open-bio-l] Best practice for modelling data in GFF
In-Reply-To: <AANLkTinrTVYODrcY9TUxhznkZKunNRQCvs-bnwgbHdNA@mail.gmail.com>
References: <AANLkTimuku_x7V9RSAERK4f4QxIc4od2zw3qZtdaL4oH@mail.gmail.com>
	<4BFFF7FE.1030004@bioperl.org>
	<685C1029-0E3A-45DD-BBA9-FFA7747810D5@illinois.edu>
	<AANLkTinrTVYODrcY9TUxhznkZKunNRQCvs-bnwgbHdNA@mail.gmail.com>
Message-ID: <AANLkTim3OsVC5cwwOlF095A5B6eJ6n03XNc7SpYMZJeV@mail.gmail.com>

On 29 May 2010 00:08, Dan Bolser <dan.bolser at gmail.com> wrote:
> Thanks all for replies.

<snip>

> There is a canonical way to model a gene, so I was wondering if it
> makes sense to describe similar 'biology' (or in this case molecular
> biology) in standard ways (when the feature isn't simply described by
> a single line of GFF)?
>
> Perhaps I've not understood SO properly, but I'm not sure how its
> structure is translated into GFF structure ... is there a 1 to 1
> mapping?

Lack of replies lead me to believe that indeed, the GFF Parent
attribute should reflect (or be strictly determined by) the SO
'relationships' (are they all 'part_of' relationships?)

However, I was trying to get some concepts clear in my head, and I
ended up creating a figure of a 'canonical gene' in SO [1], based on
the one in the GFF docs [2].

[1] http://imagebin.ca/view/Ni9BFbK.html
[2] http://www.sequenceontology.org/gff3.shtml


There is a transitive part_of relationships between 'mRNA' and 'gene',
which explains line 4 to 6 of the canonical gene GFF [2].

However, the figure shows that 'exon' is part_of 'transcript', and not
part_of 'mRNA'. If I got the figure right, and if I understand
correctly, there is no way to transitively infer that exon is part_of
mRNA (line 7 to 11 of the GFF [2]).

This implies that the 'structure' in GFF isn't strictly determined by SO.

Or is it a mistake in SO?


Sorry if this is a 'gotcha' that has been discussed before. Any links
to help me understand would be great.

Dan.

> Cheers,
> Dan.
>
> On 28 May 2010 18:49, Chris Fields <cjfields at illinois.edu> wrote:
>> All,
>>
>> Appears that link isn't up to date. ?Current GFF3 spec (v. 1.16, updated May 25) here:
>>
>> http://www.sequenceontology.org/gff3.shtml
>>
>> chris
>>
>> On May 28, 2010, at 12:06 PM, Jason Stajich wrote:
>>
>>> It's covered in the GFF3 spec as match_part if that helps.
>>> http://song.sourceforge.net/gff3.shtml
>>>
>>> Dan Bolser wrote, On 5/28/10 9:29 AM:
>>>> Hi guys,
>>>>
>>>> Not sure if this is the right forum, but I just thought I'd ask...
>>>>
>>>> Where can I find information on 'best practices' for modelling
>>>> biological data in GFF?
>>>>
>>>> For example, I'd like to model paired-end sequence alignments in GFF.
>>>> One suggestion was to use match/match_part to link each end into a
>>>> pair. Another option is to use 'read_pair' with 'contig' for the
>>>> parent feature...
>>>>
>>>> Should I just be using SAM/BAM?
>>>>
>>>> Seems a shame not to have a standard way to do this in GFF...
>>>>
>>>>
>>>> Cheers,
>>>> Dan.
>>>> _______________________________________________
>>>> Open-Bio-l mailing list
>>>> Open-Bio-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/open-bio-l
>>>>
>>> _______________________________________________
>>> Open-Bio-l mailing list
>>> Open-Bio-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/open-bio-l
>>
>>
>



From cjfields at illinois.edu  Fri Jul  2 13:27:46 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 2 Jul 2010 08:27:46 -0500
Subject: [Open-bio-l] GitHub Organizations
Message-ID: <6C174734-0D66-422F-89F2-C724C9BE6BE9@illinois.edu>

I will likely switch the bioperl repository over to an Organization account on GitHub in the next couple of days.  I don't believe this will change anything (git clone address, etc) but will check into it prior to making the switch.

Have any other Bio* on GitHub made this switch yet?

chris


From cjfields at illinois.edu  Fri Jul  2 13:45:43 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 2 Jul 2010 08:45:43 -0500
Subject: [Open-bio-l] GitHub Organizations
In-Reply-To: <6C174734-0D66-422F-89F2-C724C9BE6BE9@illinois.edu>
References: <6C174734-0D66-422F-89F2-C724C9BE6BE9@illinois.edu>
Message-ID: <BDCB990F-4612-40F2-93D3-71E79BCC8502@illinois.edu>

On Jul 2, 2010, at 8:27 AM, Chris Fields wrote:

> I will likely switch the bioperl repository over to an Organization account on GitHub in the next couple of days.  

Um, amend that to 'now'.  It's very nice!

> I don't believe this will change anything (git clone address, etc) but will check into it prior to making the switch.
> 
> Have any other Bio* on GitHub made this switch yet?
> 
> chris

The org setup has teams, so you can now assign the same team to multiple projects as needed.  The GitHub folk had hinted this was coming, glad to see it now!

chris


From p.j.a.cock at googlemail.com  Fri Jul  2 14:03:44 2010
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 2 Jul 2010 15:03:44 +0100
Subject: [Open-bio-l] GitHub Organizations
In-Reply-To: <BDCB990F-4612-40F2-93D3-71E79BCC8502@illinois.edu>
References: <6C174734-0D66-422F-89F2-C724C9BE6BE9@illinois.edu>
	<BDCB990F-4612-40F2-93D3-71E79BCC8502@illinois.edu>
Message-ID: <AANLkTin2DgDCRPn6E7OsQQIPGUbtQTYloZStDvNepz_R@mail.gmail.com>

On Fri, Jul 2, 2010 at 2:45 PM, Chris Fields <cjfields at illinois.edu> wrote:
> On Jul 2, 2010, at 8:27 AM, Chris Fields wrote:
>
>> I will likely switch the bioperl repository over to an Organization account on GitHub in the next couple of days.
>
> Um, amend that to 'now'. ?It's very nice!
>
>> I don't believe this will change anything (git clone address, etc) but will check into it prior to making the switch.
>>
>> Have any other Bio* on GitHub made this switch yet?
>>
>> chris
>
> The org setup has teams, so you can now assign the same team to multiple projects as needed. ?The GitHub folk had hinted this was coming, glad to see it now!
>
> chris

No - I wasn't aware this was available yet. I should check... thanks
for the heads up!

Peter



From chapmanb at 50mail.com  Fri Jul  2 13:38:22 2010
From: chapmanb at 50mail.com (Brad Chapman)
Date: Fri, 2 Jul 2010 09:38:22 -0400
Subject: [Open-bio-l] Codefest 2010: Final details
Message-ID: <20100702133822.GA8735@sobchak.mgh.harvard.edu>

Hi all;
Codefest 2010 is finally here: next Wednesday and Thursday at
Harvard Medical School and Massachusetts General Hospital in
beautiful Boston. All of the logistics, directions and details 
are on the wiki page:

http://www.open-bio.org/wiki/Codefest_2010

If you want the short version: show up at Harvard Medical School on
Wednesday at 10am and we'll take care of the rest. Thanks to the
hard work of Oliver, Kimberly, Leah, Toshiaki, and Mitsuteru we'll
have coffee, lunches and internet. Thanks to Steffen and Ntino,
we'll have Amazon credits to utilize. And of course, there will be 
BBQ and drinking on Thursday night when we are finished.

I'm looking forward to a fun and productive time. The general plan
will be to spend a bit of time on Wednesday morning organizing 
ourselves into like minded groups of folks, and then commence with
coding and collaborating.

If you aren't able to make it and you're listed on the wiki page under
participants, please do cross your name off so we have a good idea of
final numbers. Likewise, if you are coming but haven't put your name up
there please add it.

If you are interested in helping with making software and data
available on shared cloud resources, here are the latest Amazon
AMIs, snapshots, and the code base:

Cloud BioLinux images:
64bit: ami-d62cc4bf
32bit: ami-5423cb3d

An EBS public snapshot with indexed genomes:
snap-67446d0f

Infrastructure:
http://github.com/chapmanb/bcbb/tree/master/ec2/biolinux/

Send an e-mail with any questions, thoughts or concerns. My phone
number is 617-447-8586 in case you end up hopelessly lost somewhere
in Boston and are desperate to begin programming.

Looking forward to seeing everyone next Wednesday,
Brad


From maizemu at gmail.com  Sat Jul  3 05:36:48 2010
From: maizemu at gmail.com (Christopher Bottoms)
Date: Sat, 3 Jul 2010 00:36:48 -0500
Subject: [Open-bio-l] Codefest 2010: Final details
In-Reply-To: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
Message-ID: <AANLkTilM3_kEu9BWx2CIUaS2lklP1ULVKLhlKHtukgk2@mail.gmail.com>

Hi all,

I was originally planning on working on cloud computing at the Codefest.
However, the 2-day cloud computing tutorial that I was going to attend in
mid June was canceled. Does anyone have any programming that they would like
help with? I have experience with Perl 5, including Moose, and I am starting
to dabble in Perl 6. I have also programmed in Java in the past. I hear
Python is easy to learn, so I'd be open to working on a Python project as
well.

Thanks,
Christopher Bottoms

On Fri, Jul 2, 2010 at 8:38 AM, Brad Chapman <chapmanb at 50mail.com> wrote:

> Hi all;
> Codefest 2010 is finally here: next Wednesday and Thursday at
> Harvard Medical School and Massachusetts General Hospital in
> beautiful Boston. All of the logistics, directions and details
> are on the wiki page:
>
> http://www.open-bio.org/wiki/Codefest_2010
>
> If you want the short version: show up at Harvard Medical School on
> Wednesday at 10am and we'll take care of the rest. Thanks to the
> hard work of Oliver, Kimberly, Leah, Toshiaki, and Mitsuteru we'll
> have coffee, lunches and internet. Thanks to Steffen and Ntino,
> we'll have Amazon credits to utilize. And of course, there will be
> BBQ and drinking on Thursday night when we are finished.
>
> I'm looking forward to a fun and productive time. The general plan
> will be to spend a bit of time on Wednesday morning organizing
> ourselves into like minded groups of folks, and then commence with
> coding and collaborating.
>
> If you aren't able to make it and you're listed on the wiki page under
> participants, please do cross your name off so we have a good idea of
> final numbers. Likewise, if you are coming but haven't put your name up
> there please add it.
>
> If you are interested in helping with making software and data
> available on shared cloud resources, here are the latest Amazon
> AMIs, snapshots, and the code base:
>
> Cloud BioLinux images:
> 64bit: ami-d62cc4bf
> 32bit: ami-5423cb3d
>
> An EBS public snapshot with indexed genomes:
> snap-67446d0f
>
> Infrastructure:
> http://github.com/chapmanb/bcbb/tree/master/ec2/biolinux/
>
> Send an e-mail with any questions, thoughts or concerns. My phone
> number is 617-447-8586 in case you end up hopelessly lost somewhere
> in Boston and are desperate to begin programming.
>
> Looking forward to seeing everyone next Wednesday,
> Brad
>


From heikki.lehvaslaiho at gmail.com  Sat Jul  3 05:44:23 2010
From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho)
Date: Sat, 3 Jul 2010 08:44:23 +0300
Subject: [Open-bio-l] Codefest 2010: Final details
In-Reply-To: <AANLkTilM3_kEu9BWx2CIUaS2lklP1ULVKLhlKHtukgk2@mail.gmail.com>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu> 
	<AANLkTilM3_kEu9BWx2CIUaS2lklP1ULVKLhlKHtukgk2@mail.gmail.com>
Message-ID: <AANLkTiku8rxnLRFf0JULsAYvz5D07FeZR9ejKBZHQrCQ@mail.gmail.com>

Chris,

I do not have too much experience on cloud computing, either. There
will be quite a few people from BioPerl . We'll meet and  come up with
a plan first thing in the morning. Unless someone has a very good one
ready for sharing...

     -Heikki

Heikki Lehvaslaiho - skype:heikki_lehvaslaiho
cell: +966 545 595 849  office: +966 2 808 2429

Computational Bioscience Research Centre (CBRC), Building #2, Office #4216
4700 King Abdullah University of Science and Technology (KAUST)
Thuwal 23955-6900, Kingdom of Saudi Arabia




On 3 July 2010 08:36, Christopher Bottoms <maizemu at gmail.com> wrote:
> Hi all,
>
> I was originally planning on working on cloud computing at the Codefest.
> However, the 2-day cloud computing tutorial that I was going to attend in
> mid June was canceled. Does anyone have any programming that they would like
> help with? I have experience with Perl 5, including Moose, and I am starting
> to dabble in Perl 6. I have also programmed in Java in the past. I hear
> Python is easy to learn, so I'd be open to working on a Python project as
> well.
>
> Thanks,
> Christopher Bottoms
>
> On Fri, Jul 2, 2010 at 8:38 AM, Brad Chapman <chapmanb at 50mail.com> wrote:
>>
>> Hi all;
>> Codefest 2010 is finally here: next Wednesday and Thursday at
>> Harvard Medical School and Massachusetts General Hospital in
>> beautiful Boston. All of the logistics, directions and details
>> are on the wiki page:
>>
>> http://www.open-bio.org/wiki/Codefest_2010
>>
>> If you want the short version: show up at Harvard Medical School on
>> Wednesday at 10am and we'll take care of the rest. Thanks to the
>> hard work of Oliver, Kimberly, Leah, Toshiaki, and Mitsuteru we'll
>> have coffee, lunches and internet. Thanks to Steffen and Ntino,
>> we'll have Amazon credits to utilize. And of course, there will be
>> BBQ and drinking on Thursday night when we are finished.
>>
>> I'm looking forward to a fun and productive time. The general plan
>> will be to spend a bit of time on Wednesday morning organizing
>> ourselves into like minded groups of folks, and then commence with
>> coding and collaborating.
>>
>> If you aren't able to make it and you're listed on the wiki page under
>> participants, please do cross your name off so we have a good idea of
>> final numbers. Likewise, if you are coming but haven't put your name up
>> there please add it.
>>
>> If you are interested in helping with making software and data
>> available on shared cloud resources, here are the latest Amazon
>> AMIs, snapshots, and the code base:
>>
>> Cloud BioLinux images:
>> 64bit: ami-d62cc4bf
>> 32bit: ami-5423cb3d
>>
>> An EBS public snapshot with indexed genomes:
>> snap-67446d0f
>>
>> Infrastructure:
>> http://github.com/chapmanb/bcbb/tree/master/ec2/biolinux/
>>
>> Send an e-mail with any questions, thoughts or concerns. My phone
>> number is 617-447-8586 in case you end up hopelessly lost somewhere
>> in Boston and are desperate to begin programming.
>>
>> Looking forward to seeing everyone next Wednesday,
>> Brad
>
>


From cjfields at illinois.edu  Sat Jul  3 14:15:18 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Sat, 3 Jul 2010 09:15:18 -0500
Subject: [Open-bio-l] Codefest 2010: Final details
In-Reply-To: <AANLkTiku8rxnLRFf0JULsAYvz5D07FeZR9ejKBZHQrCQ@mail.gmail.com>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTilM3_kEu9BWx2CIUaS2lklP1ULVKLhlKHtukgk2@mail.gmail.com>
	<AANLkTiku8rxnLRFf0JULsAYvz5D07FeZR9ejKBZHQrCQ@mail.gmail.com>
Message-ID: <EEB50E10-CC46-43C7-928B-3CE8FC074315@illinois.edu>

I will be there on the afternoon of the 7th.  There are a couple of projects one can look into for Moose and Perl 6 (Biome and BioPerl6).  I think Hilmar was to do some DBIx::Class stuff for BioSQL at one point, not sure where that is (might be surplanted by SQLite work?).  Would be nice to talk with Mark re: the wrapper system for BioPerl as well.

So lots of stuff to think over and plan for.  Maybe we should move this to open-bio-l, or bioperl-l?

chris (fields)

On Jul 3, 2010, at 12:44 AM, Heikki Lehvaslaiho wrote:

> Chris,
> 
> I do not have too much experience on cloud computing, either. There
> will be quite a few people from BioPerl . We'll meet and  come up with
> a plan first thing in the morning. Unless someone has a very good one
> ready for sharing...
> 
>     -Heikki
> 
> Heikki Lehvaslaiho - skype:heikki_lehvaslaiho
> cell: +966 545 595 849  office: +966 2 808 2429
> 
> Computational Bioscience Research Centre (CBRC), Building #2, Office #4216
> 4700 King Abdullah University of Science and Technology (KAUST)
> Thuwal 23955-6900, Kingdom of Saudi Arabia
> 
> 
> 
> 
> On 3 July 2010 08:36, Christopher Bottoms <maizemu at gmail.com> wrote:
>> Hi all,
>> 
>> I was originally planning on working on cloud computing at the Codefest.
>> However, the 2-day cloud computing tutorial that I was going to attend in
>> mid June was canceled. Does anyone have any programming that they would like
>> help with? I have experience with Perl 5, including Moose, and I am starting
>> to dabble in Perl 6. I have also programmed in Java in the past. I hear
>> Python is easy to learn, so I'd be open to working on a Python project as
>> well.
>> 
>> Thanks,
>> Christopher Bottoms
>> 
>> On Fri, Jul 2, 2010 at 8:38 AM, Brad Chapman <chapmanb at 50mail.com> wrote:
>>> 
>>> Hi all;
>>> Codefest 2010 is finally here: next Wednesday and Thursday at
>>> Harvard Medical School and Massachusetts General Hospital in
>>> beautiful Boston. All of the logistics, directions and details
>>> are on the wiki page:
>>> 
>>> http://www.open-bio.org/wiki/Codefest_2010
>>> 
>>> If you want the short version: show up at Harvard Medical School on
>>> Wednesday at 10am and we'll take care of the rest. Thanks to the
>>> hard work of Oliver, Kimberly, Leah, Toshiaki, and Mitsuteru we'll
>>> have coffee, lunches and internet. Thanks to Steffen and Ntino,
>>> we'll have Amazon credits to utilize. And of course, there will be
>>> BBQ and drinking on Thursday night when we are finished.
>>> 
>>> I'm looking forward to a fun and productive time. The general plan
>>> will be to spend a bit of time on Wednesday morning organizing
>>> ourselves into like minded groups of folks, and then commence with
>>> coding and collaborating.
>>> 
>>> If you aren't able to make it and you're listed on the wiki page under
>>> participants, please do cross your name off so we have a good idea of
>>> final numbers. Likewise, if you are coming but haven't put your name up
>>> there please add it.
>>> 
>>> If you are interested in helping with making software and data
>>> available on shared cloud resources, here are the latest Amazon
>>> AMIs, snapshots, and the code base:
>>> 
>>> Cloud BioLinux images:
>>> 64bit: ami-d62cc4bf
>>> 32bit: ami-5423cb3d
>>> 
>>> An EBS public snapshot with indexed genomes:
>>> snap-67446d0f
>>> 
>>> Infrastructure:
>>> http://github.com/chapmanb/bcbb/tree/master/ec2/biolinux/
>>> 
>>> Send an e-mail with any questions, thoughts or concerns. My phone
>>> number is 617-447-8586 in case you end up hopelessly lost somewhere
>>> in Boston and are desperate to begin programming.
>>> 
>>> Looking forward to seeing everyone next Wednesday,
>>> Brad
>> 
>> 




From hlapp at nescent.org  Sat Jul  3 18:36:21 2010
From: hlapp at nescent.org (Hilmar Lapp)
Date: Sat, 3 Jul 2010 14:36:21 -0400
Subject: [Open-bio-l] Codefest 2010: Final details
In-Reply-To: <EEB50E10-CC46-43C7-928B-3CE8FC074315@illinois.edu>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTilM3_kEu9BWx2CIUaS2lklP1ULVKLhlKHtukgk2@mail.gmail.com>
	<AANLkTiku8rxnLRFf0JULsAYvz5D07FeZR9ejKBZHQrCQ@mail.gmail.com>
	<EEB50E10-CC46-43C7-928B-3CE8FC074315@illinois.edu>
Message-ID: <F9E2FEB5-B7C9-4F27-A572-0D66261CC925@nescent.org>


On Jul 3, 2010, at 10:15 AM, Chris Fields wrote:

> I think Hilmar was to do some DBIx::Class stuff for BioSQL at one  
> point

Yes, would love to look into that.

> not sure where that is (might be surplanted by SQLite work?).

I hope SQLite won't take all or even a majority of my time there.

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================





From cjfields at illinois.edu  Sat Jul  3 19:11:50 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Sat, 3 Jul 2010 14:11:50 -0500
Subject: [Open-bio-l] Codefest 2010: Final details
In-Reply-To: <F9E2FEB5-B7C9-4F27-A572-0D66261CC925@nescent.org>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTilM3_kEu9BWx2CIUaS2lklP1ULVKLhlKHtukgk2@mail.gmail.com>
	<AANLkTiku8rxnLRFf0JULsAYvz5D07FeZR9ejKBZHQrCQ@mail.gmail.com>
	<EEB50E10-CC46-43C7-928B-3CE8FC074315@illinois.edu>
	<F9E2FEB5-B7C9-4F27-A572-0D66261CC925@nescent.org>
Message-ID: <E3F893B2-221F-4120-A3CF-905261186C37@illinois.edu>

On Jul 3, 2010, at 1:36 PM, Hilmar Lapp wrote:

> On Jul 3, 2010, at 10:15 AM, Chris Fields wrote:
> 
>> I think Hilmar was to do some DBIx::Class stuff for BioSQL at one point
> 
> Yes, would love to look into that.
> 
>> not sure where that is (might be surplanted by SQLite work?).
> 
> I hope SQLite won't take all or even a majority of my time there.
> 
> 	-hilmar

Would be nice to emphasize DBIx::Class, which abstracts the DB backend.  Not sure if Rob Buels will be there, might be a good contact person on that re: his work with DBIx::Class and Bio::Schema::Chado.

chris




From chapmanb at 50mail.com  Sun Jul  4 18:51:55 2010
From: chapmanb at 50mail.com (Brad Chapman)
Date: Sun, 4 Jul 2010 14:51:55 -0400
Subject: [Open-bio-l] Codefest 2010: Final details
In-Reply-To: <EEB50E10-CC46-43C7-928B-3CE8FC074315@illinois.edu>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTilM3_kEu9BWx2CIUaS2lklP1ULVKLhlKHtukgk2@mail.gmail.com>
	<AANLkTiku8rxnLRFf0JULsAYvz5D07FeZR9ejKBZHQrCQ@mail.gmail.com>
	<EEB50E10-CC46-43C7-928B-3CE8FC074315@illinois.edu>
Message-ID: <20100704185155.GB24102@kunkel>

Christopher, Chris, Heikki and Hilmar;
Nice discussion. If you have an overview of what you are hoping
to tackle on the BioPerl side, please add it on the wiki page. The
getting started part of the coding sessions is always the hardest
part, so it'll be a huge help if we can stand up at the beginning,
describe the project ideas, and then let people break into groups:

http://www.open-bio.org/wiki/Codefest_2010#ToDo_List

Edit away and this'll point us all in the right direction.
Looking forward to next week,
Brad

> I will be there on the afternoon of the 7th.  There are a couple of projects one can look into for Moose and Perl 6 (Biome and BioPerl6).  I think Hilmar was to do some DBIx::Class stuff for BioSQL at one point, not sure where that is (might be surplanted by SQLite work?).  Would be nice to talk with Mark re: the wrapper system for BioPerl as well.
> 
> So lots of stuff to think over and plan for.  Maybe we should move this to open-bio-l, or bioperl-l?
> 
> chris (fields)
> 
> On Jul 3, 2010, at 12:44 AM, Heikki Lehvaslaiho wrote:
> 
> > Chris,
> > 
> > I do not have too much experience on cloud computing, either. There
> > will be quite a few people from BioPerl . We'll meet and  come up with
> > a plan first thing in the morning. Unless someone has a very good one
> > ready for sharing...
> > 
> >     -Heikki
> > 
> > Heikki Lehvaslaiho - skype:heikki_lehvaslaiho
> > cell: +966 545 595 849  office: +966 2 808 2429
> > 
> > Computational Bioscience Research Centre (CBRC), Building #2, Office #4216
> > 4700 King Abdullah University of Science and Technology (KAUST)
> > Thuwal 23955-6900, Kingdom of Saudi Arabia
> > 
> > 
> > 
> > 
> > On 3 July 2010 08:36, Christopher Bottoms <maizemu at gmail.com> wrote:
> >> Hi all,
> >> 
> >> I was originally planning on working on cloud computing at the Codefest.
> >> However, the 2-day cloud computing tutorial that I was going to attend in
> >> mid June was canceled. Does anyone have any programming that they would like
> >> help with? I have experience with Perl 5, including Moose, and I am starting
> >> to dabble in Perl 6. I have also programmed in Java in the past. I hear
> >> Python is easy to learn, so I'd be open to working on a Python project as
> >> well.
> >> 
> >> Thanks,
> >> Christopher Bottoms
> >> 
> >> On Fri, Jul 2, 2010 at 8:38 AM, Brad Chapman <chapmanb at 50mail.com> wrote:
> >>> 
> >>> Hi all;
> >>> Codefest 2010 is finally here: next Wednesday and Thursday at
> >>> Harvard Medical School and Massachusetts General Hospital in
> >>> beautiful Boston. All of the logistics, directions and details
> >>> are on the wiki page:
> >>> 
> >>> http://www.open-bio.org/wiki/Codefest_2010
> >>> 
> >>> If you want the short version: show up at Harvard Medical School on
> >>> Wednesday at 10am and we'll take care of the rest. Thanks to the
> >>> hard work of Oliver, Kimberly, Leah, Toshiaki, and Mitsuteru we'll
> >>> have coffee, lunches and internet. Thanks to Steffen and Ntino,
> >>> we'll have Amazon credits to utilize. And of course, there will be
> >>> BBQ and drinking on Thursday night when we are finished.
> >>> 
> >>> I'm looking forward to a fun and productive time. The general plan
> >>> will be to spend a bit of time on Wednesday morning organizing
> >>> ourselves into like minded groups of folks, and then commence with
> >>> coding and collaborating.
> >>> 
> >>> If you aren't able to make it and you're listed on the wiki page under
> >>> participants, please do cross your name off so we have a good idea of
> >>> final numbers. Likewise, if you are coming but haven't put your name up
> >>> there please add it.
> >>> 
> >>> If you are interested in helping with making software and data
> >>> available on shared cloud resources, here are the latest Amazon
> >>> AMIs, snapshots, and the code base:
> >>> 
> >>> Cloud BioLinux images:
> >>> 64bit: ami-d62cc4bf
> >>> 32bit: ami-5423cb3d
> >>> 
> >>> An EBS public snapshot with indexed genomes:
> >>> snap-67446d0f
> >>> 
> >>> Infrastructure:
> >>> http://github.com/chapmanb/bcbb/tree/master/ec2/biolinux/
> >>> 
> >>> Send an e-mail with any questions, thoughts or concerns. My phone
> >>> number is 617-447-8586 in case you end up hopelessly lost somewhere
> >>> in Boston and are desperate to begin programming.
> >>> 
> >>> Looking forward to seeing everyone next Wednesday,
> >>> Brad
> >> 
> >> 
> 


From heikki.lehvaslaiho at gmail.com  Mon Jul  5 17:57:14 2010
From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho)
Date: Mon, 5 Jul 2010 20:57:14 +0300
Subject: [Open-bio-l] Codefest 2010: Final details
In-Reply-To: <20100704185155.GB24102@kunkel>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu> 
	<AANLkTilM3_kEu9BWx2CIUaS2lklP1ULVKLhlKHtukgk2@mail.gmail.com> 
	<AANLkTiku8rxnLRFf0JULsAYvz5D07FeZR9ejKBZHQrCQ@mail.gmail.com> 
	<EEB50E10-CC46-43C7-928B-3CE8FC074315@illinois.edu>
	<20100704185155.GB24102@kunkel>
Message-ID: <AANLkTikSyTOZ3DpqHjCVirQePX3mg4T27qOruO8fDs1W@mail.gmail.com>

Chris,

I'd love to hear an overview of Biome project (bioperl in perl6) and
design decisions you have taken there. That would help me understand
it better. Do you think you could do that?

     -Heikki

Heikki Lehvaslaiho - skype:heikki_lehvaslaiho
cell: +966 545 595 849  office: +966 2 808 2429

Computational Bioscience Research Centre (CBRC), Building #2, Office #4216
4700 King Abdullah University of Science and Technology (KAUST)
Thuwal 23955-6900, Kingdom of Saudi Arabia




On 4 July 2010 21:51, Brad Chapman <chapmanb at 50mail.com> wrote:
> Christopher, Chris, Heikki and Hilmar;
> Nice discussion. If you have an overview of what you are hoping
> to tackle on the BioPerl side, please add it on the wiki page. The
> getting started part of the coding sessions is always the hardest
> part, so it'll be a huge help if we can stand up at the beginning,
> describe the project ideas, and then let people break into groups:
>
> http://www.open-bio.org/wiki/Codefest_2010#ToDo_List
>
> Edit away and this'll point us all in the right direction.
> Looking forward to next week,
> Brad
>
>> I will be there on the afternoon of the 7th. ?There are a couple of projects one can look into for Moose and Perl 6 (Biome and BioPerl6). ?I think Hilmar was to do some DBIx::Class stuff for BioSQL at one point, not sure where that is (might be surplanted by SQLite work?). ?Would be nice to talk with Mark re: the wrapper system for BioPerl as well.
>>
>> So lots of stuff to think over and plan for. ?Maybe we should move this to open-bio-l, or bioperl-l?
>>
>> chris (fields)
>>
>> On Jul 3, 2010, at 12:44 AM, Heikki Lehvaslaiho wrote:
>>
>> > Chris,
>> >
>> > I do not have too much experience on cloud computing, either. There
>> > will be quite a few people from BioPerl . We'll meet and ?come up with
>> > a plan first thing in the morning. Unless someone has a very good one
>> > ready for sharing...
>> >
>> > ? ? -Heikki
>> >
>> > Heikki Lehvaslaiho - skype:heikki_lehvaslaiho
>> > cell: +966 545 595 849 ?office: +966 2 808 2429
>> >
>> > Computational Bioscience Research Centre (CBRC), Building #2, Office #4216
>> > 4700 King Abdullah University of Science and Technology (KAUST)
>> > Thuwal 23955-6900, Kingdom of Saudi Arabia
>> >
>> >
>> >
>> >
>> > On 3 July 2010 08:36, Christopher Bottoms <maizemu at gmail.com> wrote:
>> >> Hi all,
>> >>
>> >> I was originally planning on working on cloud computing at the Codefest.
>> >> However, the 2-day cloud computing tutorial that I was going to attend in
>> >> mid June was canceled. Does anyone have any programming that they would like
>> >> help with? I have experience with Perl 5, including Moose, and I am starting
>> >> to dabble in Perl 6. I have also programmed in Java in the past. I hear
>> >> Python is easy to learn, so I'd be open to working on a Python project as
>> >> well.
>> >>
>> >> Thanks,
>> >> Christopher Bottoms
>> >>
>> >> On Fri, Jul 2, 2010 at 8:38 AM, Brad Chapman <chapmanb at 50mail.com> wrote:
>> >>>
>> >>> Hi all;
>> >>> Codefest 2010 is finally here: next Wednesday and Thursday at
>> >>> Harvard Medical School and Massachusetts General Hospital in
>> >>> beautiful Boston. All of the logistics, directions and details
>> >>> are on the wiki page:
>> >>>
>> >>> http://www.open-bio.org/wiki/Codefest_2010
>> >>>
>> >>> If you want the short version: show up at Harvard Medical School on
>> >>> Wednesday at 10am and we'll take care of the rest. Thanks to the
>> >>> hard work of Oliver, Kimberly, Leah, Toshiaki, and Mitsuteru we'll
>> >>> have coffee, lunches and internet. Thanks to Steffen and Ntino,
>> >>> we'll have Amazon credits to utilize. And of course, there will be
>> >>> BBQ and drinking on Thursday night when we are finished.
>> >>>
>> >>> I'm looking forward to a fun and productive time. The general plan
>> >>> will be to spend a bit of time on Wednesday morning organizing
>> >>> ourselves into like minded groups of folks, and then commence with
>> >>> coding and collaborating.
>> >>>
>> >>> If you aren't able to make it and you're listed on the wiki page under
>> >>> participants, please do cross your name off so we have a good idea of
>> >>> final numbers. Likewise, if you are coming but haven't put your name up
>> >>> there please add it.
>> >>>
>> >>> If you are interested in helping with making software and data
>> >>> available on shared cloud resources, here are the latest Amazon
>> >>> AMIs, snapshots, and the code base:
>> >>>
>> >>> Cloud BioLinux images:
>> >>> 64bit: ami-d62cc4bf
>> >>> 32bit: ami-5423cb3d
>> >>>
>> >>> An EBS public snapshot with indexed genomes:
>> >>> snap-67446d0f
>> >>>
>> >>> Infrastructure:
>> >>> http://github.com/chapmanb/bcbb/tree/master/ec2/biolinux/
>> >>>
>> >>> Send an e-mail with any questions, thoughts or concerns. My phone
>> >>> number is 617-447-8586 in case you end up hopelessly lost somewhere
>> >>> in Boston and are desperate to begin programming.
>> >>>
>> >>> Looking forward to seeing everyone next Wednesday,
>> >>> Brad
>> >>
>> >>
>>
>



From cjfields at illinois.edu  Mon Jul  5 19:02:10 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 5 Jul 2010 14:02:10 -0500
Subject: [Open-bio-l] Codefest 2010: Final details
In-Reply-To: <B790F1F8-59DF-4F80-84F5-10676261DA6C@nescent.org>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTilM3_kEu9BWx2CIUaS2lklP1ULVKLhlKHtukgk2@mail.gmail.com>
	<AANLkTiku8rxnLRFf0JULsAYvz5D07FeZR9ejKBZHQrCQ@mail.gmail.com>
	<EEB50E10-CC46-43C7-928B-3CE8FC074315@illinois.edu>
	<20100704185155.GB24102@kunkel>
	<AANLkTikSyTOZ3DpqHjCVirQePX3mg4T27qOruO8fDs1W@mail.gmail.com>
	<B790F1F8-59DF-4F80-84F5-10676261DA6C@nescent.org>
Message-ID: <3896D350-324A-426D-BD82-74C4D437400F@illinois.edu>

I can probably come up with something (I have a few slides).  The design for both Biome and bioperl6 is fairly straightforward (interfaces -> roles), but it would be nice to sit down with those interested to see what would be the best path to take design-wise regarding future development, mistakes learned, etc.

chris

On Jul 5, 2010, at 1:51 PM, Hilmar Lapp wrote:

> I agree that would be great!
> 
> 	-hilmar
> 
> On Jul 5, 2010, at 1:57 PM, Heikki Lehvaslaiho wrote:
> 
>> Chris,
>> 
>> I'd love to hear an overview of Biome project (bioperl in perl6) and
>> design decisions you have taken there. That would help me understand
>> it better. Do you think you could do that?
>> 
>>    -Heikki
>> 
>> Heikki Lehvaslaiho - skype:heikki_lehvaslaiho
>> cell: +966 545 595 849  office: +966 2 808 2429
>> 
>> Computational Bioscience Research Centre (CBRC), Building #2, Office #4216
>> 4700 King Abdullah University of Science and Technology (KAUST)
>> Thuwal 23955-6900, Kingdom of Saudi Arabia
>> 
>> 
>> 
>> 
>> On 4 July 2010 21:51, Brad Chapman <chapmanb at 50mail.com> wrote:
>>> Christopher, Chris, Heikki and Hilmar;
>>> Nice discussion. If you have an overview of what you are hoping
>>> to tackle on the BioPerl side, please add it on the wiki page. The
>>> getting started part of the coding sessions is always the hardest
>>> part, so it'll be a huge help if we can stand up at the beginning,
>>> describe the project ideas, and then let people break into groups:
>>> 
>>> http://www.open-bio.org/wiki/Codefest_2010#ToDo_List
>>> 
>>> Edit away and this'll point us all in the right direction.
>>> Looking forward to next week,
>>> Brad
>>> 
>>>> I will be there on the afternoon of the 7th.  There are a couple of projects one can look into for Moose and Perl 6 (Biome and BioPerl6).  I think Hilmar was to do some DBIx::Class stuff for BioSQL at one point, not sure where that is (might be surplanted by SQLite work?).  Would be nice to talk with Mark re: the wrapper system for BioPerl as well.
>>>> 
>>>> So lots of stuff to think over and plan for.  Maybe we should move this to open-bio-l, or bioperl-l?
>>>> 
>>>> chris (fields)
>>>> 
>>>> On Jul 3, 2010, at 12:44 AM, Heikki Lehvaslaiho wrote:
>>>> 
>>>>> Chris,
>>>>> 
>>>>> I do not have too much experience on cloud computing, either. There
>>>>> will be quite a few people from BioPerl . We'll meet and  come up with
>>>>> a plan first thing in the morning. Unless someone has a very good one
>>>>> ready for sharing...
>>>>> 
>>>>>    -Heikki
>>>>> 
>>>>> Heikki Lehvaslaiho - skype:heikki_lehvaslaiho
>>>>> cell: +966 545 595 849  office: +966 2 808 2429
>>>>> 
>>>>> Computational Bioscience Research Centre (CBRC), Building #2, Office #4216
>>>>> 4700 King Abdullah University of Science and Technology (KAUST)
>>>>> Thuwal 23955-6900, Kingdom of Saudi Arabia
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> On 3 July 2010 08:36, Christopher Bottoms <maizemu at gmail.com> wrote:
>>>>>> Hi all,
>>>>>> 
>>>>>> I was originally planning on working on cloud computing at the Codefest.
>>>>>> However, the 2-day cloud computing tutorial that I was going to attend in
>>>>>> mid June was canceled. Does anyone have any programming that they would like
>>>>>> help with? I have experience with Perl 5, including Moose, and I am starting
>>>>>> to dabble in Perl 6. I have also programmed in Java in the past. I hear
>>>>>> Python is easy to learn, so I'd be open to working on a Python project as
>>>>>> well.
>>>>>> 
>>>>>> Thanks,
>>>>>> Christopher Bottoms
>>>>>> 
>>>>>> On Fri, Jul 2, 2010 at 8:38 AM, Brad Chapman <chapmanb at 50mail.com> wrote:
>>>>>>> 
>>>>>>> Hi all;
>>>>>>> Codefest 2010 is finally here: next Wednesday and Thursday at
>>>>>>> Harvard Medical School and Massachusetts General Hospital in
>>>>>>> beautiful Boston. All of the logistics, directions and details
>>>>>>> are on the wiki page:
>>>>>>> 
>>>>>>> http://www.open-bio.org/wiki/Codefest_2010
>>>>>>> 
>>>>>>> If you want the short version: show up at Harvard Medical School on
>>>>>>> Wednesday at 10am and we'll take care of the rest. Thanks to the
>>>>>>> hard work of Oliver, Kimberly, Leah, Toshiaki, and Mitsuteru we'll
>>>>>>> have coffee, lunches and internet. Thanks to Steffen and Ntino,
>>>>>>> we'll have Amazon credits to utilize. And of course, there will be
>>>>>>> BBQ and drinking on Thursday night when we are finished.
>>>>>>> 
>>>>>>> I'm looking forward to a fun and productive time. The general plan
>>>>>>> will be to spend a bit of time on Wednesday morning organizing
>>>>>>> ourselves into like minded groups of folks, and then commence with
>>>>>>> coding and collaborating.
>>>>>>> 
>>>>>>> If you aren't able to make it and you're listed on the wiki page under
>>>>>>> participants, please do cross your name off so we have a good idea of
>>>>>>> final numbers. Likewise, if you are coming but haven't put your name up
>>>>>>> there please add it.
>>>>>>> 
>>>>>>> If you are interested in helping with making software and data
>>>>>>> available on shared cloud resources, here are the latest Amazon
>>>>>>> AMIs, snapshots, and the code base:
>>>>>>> 
>>>>>>> Cloud BioLinux images:
>>>>>>> 64bit: ami-d62cc4bf
>>>>>>> 32bit: ami-5423cb3d
>>>>>>> 
>>>>>>> An EBS public snapshot with indexed genomes:
>>>>>>> snap-67446d0f
>>>>>>> 
>>>>>>> Infrastructure:
>>>>>>> http://github.com/chapmanb/bcbb/tree/master/ec2/biolinux/
>>>>>>> 
>>>>>>> Send an e-mail with any questions, thoughts or concerns. My phone
>>>>>>> number is 617-447-8586 in case you end up hopelessly lost somewhere
>>>>>>> in Boston and are desperate to begin programming.
>>>>>>> 
>>>>>>> Looking forward to seeing everyone next Wednesday,
>>>>>>> Brad
>>>>>> 
>>>>>> 
>>>> 
>>> 
> 
> -- 
> ===========================================================
> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
> ===========================================================
> 
> 
> 




From maj at fortinbras.us  Mon Jul  5 19:34:09 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Mon, 5 Jul 2010 15:34:09 -0400
Subject: [Open-bio-l] Codefest 2010: Final details
In-Reply-To: <3896D350-324A-426D-BD82-74C4D437400F@illinois.edu>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTilM3_kEu9BWx2CIUaS2lklP1ULVKLhlKHtukgk2@mail.gmail.com>
	<AANLkTiku8rxnLRFf0JULsAYvz5D07FeZR9ejKBZHQrCQ@mail.gmail.com>
	<EEB50E10-CC46-43C7-928B-3CE8FC074315@illinois.edu>
	<20100704185155.GB24102@kunkel>
	<AANLkTikSyTOZ3DpqHjCVirQePX3mg4T27qOruO8fDs1W@mail.gmail.com>
	<B790F1F8-59DF-4F80-84F5-10676261DA6C@nescent.org>
	<3896D350-324A-426D-BD82-74C4D437400F@illinois.edu>
Message-ID: <6903B53BB0B24235AFDA7313E6845FBC@NewLife>

[so straightforward that 3 or 4 introductory slides couldn't possibly hurt?]
----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Hilmar Lapp" <hlapp at nescent.org>
Cc: "Heikki Lehvaslaiho" <heikki.lehvaslaiho at gmail.com>; "Brad Chapman" 
<chapmanb at 50mail.com>; "Christopher Bottoms" <maizemu at gmail.com>; 
<open-bio-l at lists.open-bio.org>; "Oliver Hofmann" <ohofmann at hsph.harvard.edu>; 
"Kimberly Begley" <Kimberly at fisciconsulting.com>; "Michael Heuer" 
<heuermh at acm.org>; "Eric Talevich" <eric.talevich at gmail.com>; "James Taylor" 
<james.taylor at emory.edu>; "Enis Afgan" <eafgan at emory.edu>; "Dannon Baker" 
<dannonbaker at me.com>; "Ntino Krampis" <agbiotec at gmail.com>; "Tim Booth" 
<tbooth at ceh.ac.uk>; "Richard Holland" <holland at eaglegenomics.com>; "Mark Jensen" 
<maj at fortinbras.us>; "Kam Dahlquist" <kdahlquist at lmu.edu>; "John David N. 
Dionisio" <dondi at lmu.edu>; "Steffen M?ller" <steffen_moeller at gmx.de>; "Bela 
Tiwari" <btiwari at ceh.ac.uk>; "Dominique Belhachemi" <domibel at cs.tu-berlin.de>; 
"Toshiaki Katayama" <ktym at hgc.jp>; "Mitsuteru Nakao" <mn at dbcls.jp>; "Dave 
Messina" <David.Messina at sbc.su.se>; "Christian Zmasek" <czmasek at burnham.org>; 
"Akira KINJO" <akinjo at protein.osaka-u.ac.jp>; "Naohisa Goto" <ng at bioruby.org>; 
"Yasunori Yamamoto" <yy at dbcls.jp>; "Raoul J.P. Bonnal" <bonnalraoul at ingm.it>; 
"Atsuko Yamaguchi" <atsuko at dbcls.jp>
Sent: Monday, July 05, 2010 3:02 PM
Subject: Re: Codefest 2010: Final details


I can probably come up with something (I have a few slides).  The design for 
both Biome and bioperl6 is fairly straightforward (interfaces -> roles), but it 
would be nice to sit down with those interested to see what would be the best 
path to take design-wise regarding future development, mistakes learned, etc.

chris

On Jul 5, 2010, at 1:51 PM, Hilmar Lapp wrote:

> I agree that would be great!
>
> -hilmar
>
> On Jul 5, 2010, at 1:57 PM, Heikki Lehvaslaiho wrote:
>
>> Chris,
>>
>> I'd love to hear an overview of Biome project (bioperl in perl6) and
>> design decisions you have taken there. That would help me understand
>> it better. Do you think you could do that?
>>
>>    -Heikki
>>
>> Heikki Lehvaslaiho - skype:heikki_lehvaslaiho
>> cell: +966 545 595 849  office: +966 2 808 2429
>>
>> Computational Bioscience Research Centre (CBRC), Building #2, Office #4216
>> 4700 King Abdullah University of Science and Technology (KAUST)
>> Thuwal 23955-6900, Kingdom of Saudi Arabia
>>
>>
>>
>>
>> On 4 July 2010 21:51, Brad Chapman <chapmanb at 50mail.com> wrote:
>>> Christopher, Chris, Heikki and Hilmar;
>>> Nice discussion. If you have an overview of what you are hoping
>>> to tackle on the BioPerl side, please add it on the wiki page. The
>>> getting started part of the coding sessions is always the hardest
>>> part, so it'll be a huge help if we can stand up at the beginning,
>>> describe the project ideas, and then let people break into groups:
>>>
>>> http://www.open-bio.org/wiki/Codefest_2010#ToDo_List
>>>
>>> Edit away and this'll point us all in the right direction.
>>> Looking forward to next week,
>>> Brad
>>>
>>>> I will be there on the afternoon of the 7th.  There are a couple of 
>>>> projects one can look into for Moose and Perl 6 (Biome and BioPerl6).  I 
>>>> think Hilmar was to do some DBIx::Class stuff for BioSQL at one point, not 
>>>> sure where that is (might be surplanted by SQLite work?).  Would be nice to 
>>>> talk with Mark re: the wrapper system for BioPerl as well.
>>>>
>>>> So lots of stuff to think over and plan for.  Maybe we should move this to 
>>>> open-bio-l, or bioperl-l?
>>>>
>>>> chris (fields)
>>>>
>>>> On Jul 3, 2010, at 12:44 AM, Heikki Lehvaslaiho wrote:
>>>>
>>>>> Chris,
>>>>>
>>>>> I do not have too much experience on cloud computing, either. There
>>>>> will be quite a few people from BioPerl . We'll meet and  come up with
>>>>> a plan first thing in the morning. Unless someone has a very good one
>>>>> ready for sharing...
>>>>>
>>>>>    -Heikki
>>>>>
>>>>> Heikki Lehvaslaiho - skype:heikki_lehvaslaiho
>>>>> cell: +966 545 595 849  office: +966 2 808 2429
>>>>>
>>>>> Computational Bioscience Research Centre (CBRC), Building #2, Office #4216
>>>>> 4700 King Abdullah University of Science and Technology (KAUST)
>>>>> Thuwal 23955-6900, Kingdom of Saudi Arabia
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On 3 July 2010 08:36, Christopher Bottoms <maizemu at gmail.com> wrote:
>>>>>> Hi all,
>>>>>>
>>>>>> I was originally planning on working on cloud computing at the Codefest.
>>>>>> However, the 2-day cloud computing tutorial that I was going to attend in
>>>>>> mid June was canceled. Does anyone have any programming that they would 
>>>>>> like
>>>>>> help with? I have experience with Perl 5, including Moose, and I am 
>>>>>> starting
>>>>>> to dabble in Perl 6. I have also programmed in Java in the past. I hear
>>>>>> Python is easy to learn, so I'd be open to working on a Python project as
>>>>>> well.
>>>>>>
>>>>>> Thanks,
>>>>>> Christopher Bottoms
>>>>>>
>>>>>> On Fri, Jul 2, 2010 at 8:38 AM, Brad Chapman <chapmanb at 50mail.com> wrote:
>>>>>>>
>>>>>>> Hi all;
>>>>>>> Codefest 2010 is finally here: next Wednesday and Thursday at
>>>>>>> Harvard Medical School and Massachusetts General Hospital in
>>>>>>> beautiful Boston. All of the logistics, directions and details
>>>>>>> are on the wiki page:
>>>>>>>
>>>>>>> http://www.open-bio.org/wiki/Codefest_2010
>>>>>>>
>>>>>>> If you want the short version: show up at Harvard Medical School on
>>>>>>> Wednesday at 10am and we'll take care of the rest. Thanks to the
>>>>>>> hard work of Oliver, Kimberly, Leah, Toshiaki, and Mitsuteru we'll
>>>>>>> have coffee, lunches and internet. Thanks to Steffen and Ntino,
>>>>>>> we'll have Amazon credits to utilize. And of course, there will be
>>>>>>> BBQ and drinking on Thursday night when we are finished.
>>>>>>>
>>>>>>> I'm looking forward to a fun and productive time. The general plan
>>>>>>> will be to spend a bit of time on Wednesday morning organizing
>>>>>>> ourselves into like minded groups of folks, and then commence with
>>>>>>> coding and collaborating.
>>>>>>>
>>>>>>> If you aren't able to make it and you're listed on the wiki page under
>>>>>>> participants, please do cross your name off so we have a good idea of
>>>>>>> final numbers. Likewise, if you are coming but haven't put your name up
>>>>>>> there please add it.
>>>>>>>
>>>>>>> If you are interested in helping with making software and data
>>>>>>> available on shared cloud resources, here are the latest Amazon
>>>>>>> AMIs, snapshots, and the code base:
>>>>>>>
>>>>>>> Cloud BioLinux images:
>>>>>>> 64bit: ami-d62cc4bf
>>>>>>> 32bit: ami-5423cb3d
>>>>>>>
>>>>>>> An EBS public snapshot with indexed genomes:
>>>>>>> snap-67446d0f
>>>>>>>
>>>>>>> Infrastructure:
>>>>>>> http://github.com/chapmanb/bcbb/tree/master/ec2/biolinux/
>>>>>>>
>>>>>>> Send an e-mail with any questions, thoughts or concerns. My phone
>>>>>>> number is 617-447-8586 in case you end up hopelessly lost somewhere
>>>>>>> in Boston and are desperate to begin programming.
>>>>>>>
>>>>>>> Looking forward to seeing everyone next Wednesday,
>>>>>>> Brad
>>>>>>
>>>>>>
>>>>
>>>
>
> -- 
> ===========================================================
> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
> ===========================================================
>
>
>





From dan.bolser at gmail.com  Tue Jul  6 10:10:51 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Tue, 6 Jul 2010 11:10:51 +0100
Subject: [Open-bio-l] Best practice for modelling data in GFF
In-Reply-To: <AANLkTim3OsVC5cwwOlF095A5B6eJ6n03XNc7SpYMZJeV@mail.gmail.com>
References: <AANLkTimuku_x7V9RSAERK4f4QxIc4od2zw3qZtdaL4oH@mail.gmail.com>
	<4BFFF7FE.1030004@bioperl.org>
	<685C1029-0E3A-45DD-BBA9-FFA7747810D5@illinois.edu>
	<AANLkTinrTVYODrcY9TUxhznkZKunNRQCvs-bnwgbHdNA@mail.gmail.com>
	<AANLkTim3OsVC5cwwOlF095A5B6eJ6n03XNc7SpYMZJeV@mail.gmail.com>
Message-ID: <AANLkTim20_VVGZbChnU1F5OmqKhAdbmoGGgAYuSSG2Kj@mail.gmail.com>

When you don't get a reply, you never know if your question was too
dumb, too smart, or totally off topic.

Any hints?

Cheers,
Dan.

On 1 July 2010 11:12, Dan Bolser <dan.bolser at gmail.com> wrote:
> On 29 May 2010 00:08, Dan Bolser <dan.bolser at gmail.com> wrote:
>> Thanks all for replies.
>
> <snip>
>
>> There is a canonical way to model a gene, so I was wondering if it
>> makes sense to describe similar 'biology' (or in this case molecular
>> biology) in standard ways (when the feature isn't simply described by
>> a single line of GFF)?
>>
>> Perhaps I've not understood SO properly, but I'm not sure how its
>> structure is translated into GFF structure ... is there a 1 to 1
>> mapping?
>
> Lack of replies lead me to believe that indeed, the GFF Parent
> attribute should reflect (or be strictly determined by) the SO
> 'relationships' (are they all 'part_of' relationships?)
>
> However, I was trying to get some concepts clear in my head, and I
> ended up creating a figure of a 'canonical gene' in SO [1], based on
> the one in the GFF docs [2].
>
> [1] http://imagebin.ca/view/Ni9BFbK.html
> [2] http://www.sequenceontology.org/gff3.shtml
>
>
> There is a transitive part_of relationships between 'mRNA' and 'gene',
> which explains line 4 to 6 of the canonical gene GFF [2].
>
> However, the figure shows that 'exon' is part_of 'transcript', and not
> part_of 'mRNA'. If I got the figure right, and if I understand
> correctly, there is no way to transitively infer that exon is part_of
> mRNA (line 7 to 11 of the GFF [2]).
>
> This implies that the 'structure' in GFF isn't strictly determined by SO.
>
> Or is it a mistake in SO?
>
>
> Sorry if this is a 'gotcha' that has been discussed before. Any links
> to help me understand would be great.
>
> Dan.


From lpritc at scri.ac.uk  Tue Jul  6 10:58:44 2010
From: lpritc at scri.ac.uk (Leighton Pritchard)
Date: Tue, 06 Jul 2010 11:58:44 +0100
Subject: [Open-bio-l] Best practice for modelling data in GFF
In-Reply-To: <AANLkTim20_VVGZbChnU1F5OmqKhAdbmoGGgAYuSSG2Kj@mail.gmail.com>
Message-ID: <C858CAF4.3867D%lpritc@scri.ac.uk>

Hi Dan,

GFF3 is just a file format, capable of representing the SO's hierarchical
subfeatures.  You can represent other things (including other ontologies) in
the same format.  How strictly you choose to stick to the SO's hierarchy is
up to you, whether you use GFF3 to represent your data or not: you are free
to be as canonical or noncanonical as you like.  You are not constrained to
having mRNA be the parent of a CDS by the file format - you can happily
create a model that has things the other way round and represent it in valid
GFF3.  It will be biological nonsense and not SO-compliant, but you can do
it:

broken  .   CDS 100 1100    .   +   0   ID=cds01
broken  .   mRNA    0   1500    .   +   .   ID=mRNA01;Parent=cds01

Putting your model into GFF3 is a separate issue to building the model, so
long as GFF3 is capable of representing your model.  And if the package
you're loading your GFF3 into doesn't care about ontologies and
relationships, you'll get away with it.

So yes, if you want to build a SO-compatible gene model, you had better make
sure the parent-child relationships correspond to the hierarchy in the SO.
This is true whether you want to represent the model in GFF3 or not.

Now, for your specific question about the exon/mRNA terms: an exon is_a
transcript_region, and a transcript_region is part_of a transcript.  [And a
transcript is_a gene_member_region, and a gene_member_region is a member_of
a gene.]

Now, an mRNA is_a mature_transcript, which is_a transcript.  The exon that
is part_of a transcript can therefore be part_of an mRNA, because an mRNA is
a transcript.

So in the model at http://www.sequenceontology.org/gff3.shtml the transcript
you're looking for is the mRNA.  The same would be true if the parent
feature was a monocistronic_mRNA, which is_a mRNA, and also is_a
monocistronic_transcript, which is_a transcript.

Have you had a look at OBO-Edit?  It's a useful learning tool for getting
your head around these things, and you can browse through the SO in it.

Cheers,

L.


On 06/07/2010 Tuesday, July 6, 11:10, "Dan Bolser" <dan.bolser at gmail.com>
wrote:

> When you don't get a reply, you never know if your question was too
> dumb, too smart, or totally off topic.
> 
> Any hints?
> 
> Cheers,
> Dan.
> 
> On 1 July 2010 11:12, Dan Bolser <dan.bolser at gmail.com> wrote:
>> On 29 May 2010 00:08, Dan Bolser <dan.bolser at gmail.com> wrote:
>>> Thanks all for replies.
>> 
>> <snip>
>> 
>>> There is a canonical way to model a gene, so I was wondering if it
>>> makes sense to describe similar 'biology' (or in this case molecular
>>> biology) in standard ways (when the feature isn't simply described by
>>> a single line of GFF)?
>>> 
>>> Perhaps I've not understood SO properly, but I'm not sure how its
>>> structure is translated into GFF structure ... is there a 1 to 1
>>> mapping?
>> 
>> Lack of replies lead me to believe that indeed, the GFF Parent
>> attribute should reflect (or be strictly determined by) the SO
>> 'relationships' (are they all 'part_of' relationships?)
>> 
>> However, I was trying to get some concepts clear in my head, and I
>> ended up creating a figure of a 'canonical gene' in SO [1], based on
>> the one in the GFF docs [2].
>> 
>> [1] http://imagebin.ca/view/Ni9BFbK.html
>> [2] http://www.sequenceontology.org/gff3.shtml
>> 
>> 
>> There is a transitive part_of relationships between 'mRNA' and 'gene',
>> which explains line 4 to 6 of the canonical gene GFF [2].
>> 
>> However, the figure shows that 'exon' is part_of 'transcript', and not
>> part_of 'mRNA'. If I got the figure right, and if I understand
>> correctly, there is no way to transitively infer that exon is part_of
>> mRNA (line 7 to 11 of the GFF [2]).
>> 
>> This implies that the 'structure' in GFF isn't strictly determined by SO.
>> 
>> Or is it a mistake in SO?
>> 
>> 
>> Sorry if this is a 'gotcha' that has been discussed before. Any links
>> to help me understand would be great.
>> 
>> Dan.
> _______________________________________________
> Open-Bio-l mailing list
> Open-Bio-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/open-bio-l
> 
> ______________________________________________________________________
> This email has been scanned by the MessageLabs Email Security System.
> For more information please visit http://www.messagelabs.com/email
> ______________________________________________________________________

-- 
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405


______________________________________________________
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From dan.bolser at gmail.com  Tue Jul  6 12:11:54 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Tue, 6 Jul 2010 13:11:54 +0100
Subject: [Open-bio-l] Best practice for modelling data in GFF
In-Reply-To: <C858CAF4.3867D%lpritc@scri.ac.uk>
References: <AANLkTim20_VVGZbChnU1F5OmqKhAdbmoGGgAYuSSG2Kj@mail.gmail.com>
	<C858CAF4.3867D%lpritc@scri.ac.uk>
Message-ID: <AANLkTilX_vVX2nHmX4IOCVcsmvopJpNLFRRE-v4oqN1f@mail.gmail.com>

On 6 July 2010 11:58, Leighton Pritchard <lpritc at scri.ac.uk> wrote:
> Hi Dan,
>
> GFF3 is just a file format, capable of representing the SO's hierarchical
> subfeatures. ?You can represent other things (including other ontologies) in
> the same format. ?How strictly you choose to stick to the SO's hierarchy is
> up to you,

<snip>

OK, I understand. So the answer to my original question "Where can I
find information on 'best practices' for modelling biological data in
GFF?" was just, "work out where your data fits in the Sequence
Ontology model".

:-)


> So yes, if you want to build a SO-compatible gene model, you had better make
> sure the parent-child relationships correspond to the hierarchy in the SO.
> This is true whether you want to represent the model in GFF3 or not.

OK


> Now, for your specific question about the exon/mRNA terms: an exon is_a
> transcript_region, and a transcript_region is part_of a transcript. ?[And a
> transcript is_a gene_member_region, and a gene_member_region is a member_of
> a gene.]
>
> Now, an mRNA is_a mature_transcript, which is_a transcript. ?The exon that
> is part_of a transcript can therefore be part_of an mRNA, because an mRNA is
> a transcript.

I see... I guess this only applies because of the specific 'is_a'
relationship. i.e. just because a nose is part_of a face and a mouth
is part_of a face, you can't make inferences about relationships
between nose and mouth.

I guess I'm confused because I can't see the link types in miso.


> So in the model at http://www.sequenceontology.org/gff3.shtml the transcript
> you're looking for is the mRNA. ?The same would be true if the parent
> feature was a monocistronic_mRNA, which is_a mRNA, and also is_a
> monocistronic_transcript, which is_a transcript.
>
> Have you had a look at OBO-Edit? ?It's a useful learning tool for getting
> your head around these things, and you can browse through the SO in it.

I'll have a look.


Thanks very much for taking the time to provide such a detailed reply,
and sorry for the dumb questions.

All the best,
Dan.


> Cheers,
>
> L.
>
>
> On 06/07/2010 Tuesday, July 6, 11:10, "Dan Bolser" <dan.bolser at gmail.com>
> wrote:
>
>> When you don't get a reply, you never know if your question was too
>> dumb, too smart, or totally off topic.
>>
>> Any hints?
>>
>> Cheers,
>> Dan.
>>
>> On 1 July 2010 11:12, Dan Bolser <dan.bolser at gmail.com> wrote:
>>> On 29 May 2010 00:08, Dan Bolser <dan.bolser at gmail.com> wrote:
>>>> Thanks all for replies.
>>>
>>> <snip>
>>>
>>>> There is a canonical way to model a gene, so I was wondering if it
>>>> makes sense to describe similar 'biology' (or in this case molecular
>>>> biology) in standard ways (when the feature isn't simply described by
>>>> a single line of GFF)?
>>>>
>>>> Perhaps I've not understood SO properly, but I'm not sure how its
>>>> structure is translated into GFF structure ... is there a 1 to 1
>>>> mapping?
>>>
>>> Lack of replies lead me to believe that indeed, the GFF Parent
>>> attribute should reflect (or be strictly determined by) the SO
>>> 'relationships' (are they all 'part_of' relationships?)
>>>
>>> However, I was trying to get some concepts clear in my head, and I
>>> ended up creating a figure of a 'canonical gene' in SO [1], based on
>>> the one in the GFF docs [2].
>>>
>>> [1] http://imagebin.ca/view/Ni9BFbK.html
>>> [2] http://www.sequenceontology.org/gff3.shtml
>>>
>>>
>>> There is a transitive part_of relationships between 'mRNA' and 'gene',
>>> which explains line 4 to 6 of the canonical gene GFF [2].
>>>
>>> However, the figure shows that 'exon' is part_of 'transcript', and not
>>> part_of 'mRNA'. If I got the figure right, and if I understand
>>> correctly, there is no way to transitively infer that exon is part_of
>>> mRNA (line 7 to 11 of the GFF [2]).
>>>
>>> This implies that the 'structure' in GFF isn't strictly determined by SO.
>>>
>>> Or is it a mistake in SO?
>>>
>>>
>>> Sorry if this is a 'gotcha' that has been discussed before. Any links
>>> to help me understand would be great.
>>>
>>> Dan.
>> _______________________________________________
>> Open-Bio-l mailing list
>> Open-Bio-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/open-bio-l
>>
>> ______________________________________________________________________
>> This email has been scanned by the MessageLabs Email Security System.
>> For more information please visit http://www.messagelabs.com/email
>> ______________________________________________________________________
>
> --
> Dr Leighton Pritchard MRSC
> D131, Plant Pathology Programme, SCRI
> Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
> e:lpritc at scri.ac.uk ? ? ? w:http://www.scri.ac.uk/staff/leightonpritchard
> gpg/pgp: 0xFEFC205C ? ? ? tel:+44(0)1382 562731 x2405
>
>
> ______________________________________________________
> SCRI, Invergowrie, Dundee, DD2 5DA.
> The Scottish Crop Research Institute is a charitable company limited by guarantee.
> Registered in Scotland No: SC 29367.
> Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.
>
>
> DISCLAIMER:
>
> This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries. ?This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed. ?It may not be disclosed or used by any other than that addressee.
> If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify postmaster at scri.ac.uk quoting the name of the sender and delete the email from your system.
>
> Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any).
> ______________________________________________________
>



From lpritc at scri.ac.uk  Tue Jul  6 14:29:35 2010
From: lpritc at scri.ac.uk (Leighton Pritchard)
Date: Tue, 06 Jul 2010 15:29:35 +0100
Subject: [Open-bio-l] Best practice for modelling data in GFF
In-Reply-To: <AANLkTilX_vVX2nHmX4IOCVcsmvopJpNLFRRE-v4oqN1f@mail.gmail.com>
Message-ID: <C858FC5F.386A1%lpritc@scri.ac.uk>

On 06/07/2010 Tuesday, July 6, 13:11, "Dan Bolser" <dan.bolser at gmail.com>
wrote:

> I see... I guess this only applies because of the specific 'is_a'
> relationship. i.e. just because a nose is part_of a face and a mouth
> is part_of a face, you can't make inferences about relationships
> between nose and mouth.

Sounds like you get it.  To extend that analogy you can infer things about
nostrils and earholes, such as that putting a biro in a nostril is valid,
whether it's a left_nostril or a right_nostril, because nostril is_a orifice
- and that's why you can stick a biro in your ear, as well ;)
 
> Thanks very much for taking the time to provide such a detailed reply,
> and sorry for the dumb questions.

They weren't dumb questions.  I recently had a similar issue where I was
wondering how to represent sub-parts of protein domains that span exons in a
chromosomal reference frame.  It didn't seem right to have them span an
intron, as they derive from the polypeptide, but the ontology terms don't
have explicit subfeatures.  Happily the polypeptide_region feature provides
enough flexibility to get around this.

Cheers,

L.

-- 
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405


______________________________________________________
SCRI, Invergowrie, Dundee, DD2 5DA.  
The Scottish Crop Research Institute is a charitable company limited by guarantee. 
Registered in Scotland No: SC 29367.
Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.


DISCLAIMER:

This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries.  This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed.  It may not be disclosed or used by any other than that addressee.
If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify postmaster at scri.ac.uk quoting the name of the sender and delete the email from your system.

Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any).
______________________________________________________


From dan.bolser at gmail.com  Tue Jul  6 14:36:40 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Tue, 6 Jul 2010 15:36:40 +0100
Subject: [Open-bio-l] Best practice for modelling data in GFF
In-Reply-To: <C858FC5F.386A1%lpritc@scri.ac.uk>
References: <AANLkTilX_vVX2nHmX4IOCVcsmvopJpNLFRRE-v4oqN1f@mail.gmail.com>
	<C858FC5F.386A1%lpritc@scri.ac.uk>
Message-ID: <AANLkTikle3Qo2R2B8gqdZNj1qlo5CyZ5jt7IYRVsbkfC@mail.gmail.com>

On 6 July 2010 15:29, Leighton Pritchard <lpritc at scri.ac.uk> wrote:
> On 06/07/2010 Tuesday, July 6, 13:11, "Dan Bolser" <dan.bolser at gmail.com>
> wrote:
>
>> I see... I guess this only applies because of the specific 'is_a'
>> relationship. i.e. just because a nose is part_of a face and a mouth
>> is part_of a face, you can't make inferences about relationships
>> between nose and mouth.
>
> Sounds like you get it. ?To extend that analogy you can infer things about
> nostrils and earholes, such as that putting a biro in a nostril is valid,
> whether it's a left_nostril or a right_nostril, because nostril is_a orifice
> - and that's why you can stick a biro in your ear, as well ;)
>
>> Thanks very much for taking the time to provide such a detailed reply,
>> and sorry for the dumb questions.
>
> They weren't dumb questions. ?I recently had a similar issue where I was
> wondering how to represent sub-parts of protein domains that span exons in a
> chromosomal reference frame. ?It didn't seem right to have them span an
> intron, as they derive from the polypeptide, but the ontology terms don't
> have explicit subfeatures. ?Happily the polypeptide_region feature provides
> enough flexibility to get around this.

Perhaps there is scope for a 'best practices' catalogue after all?

P.S. How did you know (about the biro that is).

Dan.


> Cheers,
>
> L.
>
> --
> Dr Leighton Pritchard MRSC
> D131, Plant Pathology Programme, SCRI
> Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
> e:lpritc at scri.ac.uk ? ? ? w:http://www.scri.ac.uk/staff/leightonpritchard
> gpg/pgp: 0xFEFC205C ? ? ? tel:+44(0)1382 562731 x2405
>
>
> ______________________________________________________
> SCRI, Invergowrie, Dundee, DD2 5DA.
> The Scottish Crop Research Institute is a charitable company limited by guarantee.
> Registered in Scotland No: SC 29367.
> Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.
>
>
> DISCLAIMER:
>
> This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries. ?This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed. ?It may not be disclosed or used by any other than that addressee.
> If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify postmaster at scri.ac.uk quoting the name of the sender and delete the email from your system.
>
> Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any).
> ______________________________________________________
>



From biopython at maubp.freeserve.co.uk  Tue Jul 27 15:31:38 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 27 Jul 2010 16:31:38 +0100
Subject: [Open-bio-l] Agreed name for UniProt XML file format
Message-ID: <AANLkTikPq-dfFQphUEKJircwbAyJdXEADXKU4FZrUo=k@mail.gmail.com>

Dear all,

BioPerl, Biopython and EMBOSS all have a set of sequence file format
names (as strings), used as arguments to their SeqIO modules or as
command line arguments in EMBOSS. I understand that in BioRuby
and BioJava you have named classes instead(?). We currently have
reasonably consistent existing names. For the FASTQ files formats
we managed to agree consistent naming for the Sanger, Solexa and
Illumina 1.3+ variants. Now for the next "new" format...

Andrea Pierlenoin (CC'd) has been working on parsing the UniProt
XML file format in Biopython - this is essentially an XML replacement
for the old SwissProt plain text file format which is called "swiss" in
BioPerl, Biopython and EMBOSS (although EMBOSS also allows
"sw" and "swissprot" as well).

We were originally suggesting calling this new format "uniprot",
http://bioperl.org/pipermail/open-bio-l/2010-January/000609.html

Andrea has since pointed out that in the EBI REST services the file
format is referred as "uniprot-xml" which is also less ambiguous
(after all the old "swiss" plain text format might equally be referred
to as the plain text UniProt format).

So, what do people feel about standardising on "uniprot" and/or
"uniprot-xml" as the format name in Biopython, BioPerl & EMBOSS?

Thanks,

Peter

P.S. Chris, am I right in thinking that if BioPerl were to support this
file format under the name "uniprot-xml" this would be equivalent
to accepting format="uniprot" and variant="xml"? And furthermore
and assuming you regard this as the default/only variant, Bio::SeqIO
would also just accept format="uniprot"?


From hlapp at drycafe.net  Tue Jul 27 15:49:21 2010
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Tue, 27 Jul 2010 11:49:21 -0400
Subject: [Open-bio-l] Agreed name for UniProt XML file format
In-Reply-To: <AANLkTikPq-dfFQphUEKJircwbAyJdXEADXKU4FZrUo=k@mail.gmail.com>
References: <AANLkTikPq-dfFQphUEKJircwbAyJdXEADXKU4FZrUo=k@mail.gmail.com>
Message-ID: <DD9EDBAD-67DE-44F3-8917-CFBA145C0A6C@drycafe.net>


On Jul 27, 2010, at 11:31 AM, Peter wrote:

> So, what do people feel about standardising on "uniprot" and/or
> "uniprot-xml" as the format name in Biopython, BioPerl & EMBOSS?


uniprot-xml

It is clear and unambiguous, unlike uniprot alone, which might easily  
be mistaken to refer to the swissprot format of UniProt entries.

	-hilmar
-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From rmb32 at cornell.edu  Tue Jul 27 16:10:50 2010
From: rmb32 at cornell.edu (Robert Buels)
Date: Tue, 27 Jul 2010 09:10:50 -0700
Subject: [Open-bio-l] Agreed name for UniProt XML file format
In-Reply-To: <DD9EDBAD-67DE-44F3-8917-CFBA145C0A6C@drycafe.net>
References: <AANLkTikPq-dfFQphUEKJircwbAyJdXEADXKU4FZrUo=k@mail.gmail.com>
	<DD9EDBAD-67DE-44F3-8917-CFBA145C0A6C@drycafe.net>
Message-ID: <4C4F050A.70208@cornell.edu>

Hilmar Lapp wrote:
> uniprot-xml

+1


From biopython at maubp.freeserve.co.uk  Tue Jul 27 16:27:53 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 27 Jul 2010 17:27:53 +0100
Subject: [Open-bio-l] Agreed name for UniProt XML file format
In-Reply-To: <AD9A2A32-0F8B-4F81-A21F-C42039DDA627@illinois.edu>
References: <AANLkTikPq-dfFQphUEKJircwbAyJdXEADXKU4FZrUo=k@mail.gmail.com>
	<AD9A2A32-0F8B-4F81-A21F-C42039DDA627@illinois.edu>
Message-ID: <AANLkTi=x1tALUFBUThmafD8Wq6zzqh+LN+=5Nm_g0JM+@mail.gmail.com>

On Tue, Jul 27, 2010 at 5:14 PM, Chris Fields <cjfields at illinois.edu> wrote:
>
> On Jul 27, 2010, at 10:31 AM, Peter wrote:
>
>> Andrea has since pointed out that in the EBI REST services the file
>> format is referred as "uniprot-xml" which is also less ambiguous
>> (after all the old "swiss" plain text format might equally be referred
>> to as the plain text UniProt format).
>>
>> So, what do people feel about standardising on "uniprot" and/or
>> "uniprot-xml" as the format name in Biopython, BioPerl & EMBOSS?
>
> Agree with hilmar, 'uniprot-xml'.

That looks like a consensus (so far). Thank you all.

>> P.S. Chris, am I right in thinking that if BioPerl were to support this
>> file format under the name "uniprot-xml" this would be equivalent
>> to accepting format="uniprot" and variant="xml"? And furthermore
>> and assuming you regard this as the default/only variant, Bio::SeqIO
>> would also just accept format="uniprot"?
>
> In cases where 'uniprot' is passed, we could handle it either way:
> delegate to 'swiss' if xml isn't specified (so 'uniprot' is just an alias
> of 'swiss'), or always use the XML handler for 'uniprot' and ignore
> the variant argument. ?Either way is fine with us.

Or raise an error as it is ambiguous? But that wouldn't be in the spirit
of Perl though would it? ;)

Peter



From cjfields at illinois.edu  Tue Jul 27 16:14:41 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 27 Jul 2010 11:14:41 -0500
Subject: [Open-bio-l] Agreed name for UniProt XML file format
In-Reply-To: <AANLkTikPq-dfFQphUEKJircwbAyJdXEADXKU4FZrUo=k@mail.gmail.com>
References: <AANLkTikPq-dfFQphUEKJircwbAyJdXEADXKU4FZrUo=k@mail.gmail.com>
Message-ID: <AD9A2A32-0F8B-4F81-A21F-C42039DDA627@illinois.edu>


On Jul 27, 2010, at 10:31 AM, Peter wrote:

> Dear all,
> 
> BioPerl, Biopython and EMBOSS all have a set of sequence file format
> names (as strings), used as arguments to their SeqIO modules or as
> command line arguments in EMBOSS. I understand that in BioRuby
> and BioJava you have named classes instead(?). We currently have
> reasonably consistent existing names. For the FASTQ files formats
> we managed to agree consistent naming for the Sanger, Solexa and
> Illumina 1.3+ variants. Now for the next "new" format...
> 
> Andrea Pierlenoin (CC'd) has been working on parsing the UniProt
> XML file format in Biopython - this is essentially an XML replacement
> for the old SwissProt plain text file format which is called "swiss" in
> BioPerl, Biopython and EMBOSS (although EMBOSS also allows
> "sw" and "swissprot" as well).
> 
> We were originally suggesting calling this new format "uniprot",
> http://bioperl.org/pipermail/open-bio-l/2010-January/000609.html
> 
> Andrea has since pointed out that in the EBI REST services the file
> format is referred as "uniprot-xml" which is also less ambiguous
> (after all the old "swiss" plain text format might equally be referred
> to as the plain text UniProt format).
> 
> So, what do people feel about standardising on "uniprot" and/or
> "uniprot-xml" as the format name in Biopython, BioPerl & EMBOSS?

Agree with hilmar, 'uniprot-xml'.

> Thanks,
> 
> Peter
> 
> P.S. Chris, am I right in thinking that if BioPerl were to support this
> file format under the name "uniprot-xml" this would be equivalent
> to accepting format="uniprot" and variant="xml"? And furthermore
> and assuming you regard this as the default/only variant, Bio::SeqIO
> would also just accept format="uniprot"?

In cases where 'uniprot' is passed, we could handle it either way: delegate to 'swiss' if xml isn't specified (so 'uniprot' is just an alias of 'swiss'), or always use the XML handler for 'uniprot' and ignore the variant argument.  Either way is fine with us.

chris






From David.Messina at sbc.su.se  Tue Jul 27 16:58:12 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Tue, 27 Jul 2010 10:58:12 -0600
Subject: [Open-bio-l] Agreed name for UniProt XML file format
In-Reply-To: <AANLkTi=x1tALUFBUThmafD8Wq6zzqh+LN+=5Nm_g0JM+@mail.gmail.com>
References: <AANLkTikPq-dfFQphUEKJircwbAyJdXEADXKU4FZrUo=k@mail.gmail.com>
	<AD9A2A32-0F8B-4F81-A21F-C42039DDA627@illinois.edu>
	<AANLkTi=x1tALUFBUThmafD8Wq6zzqh+LN+=5Nm_g0JM+@mail.gmail.com>
Message-ID: <B4AF6005-1B12-457A-A2B4-A6A52D19881B@sbc.su.se>

> Or raise an error as it is ambiguous? But that wouldn't be in the spirit
> of Perl though would it? ;)

Perly or not :), I like this idea.

It has the advantage that when (if?) plaintext uniprot stops being used, and that ambiguity disappears, we can make 'uniprot' an alias of 'uniprot-xml'.


Dave

(or an alias to 'swiss', in the apocalyptic event that XML is abandoned.) 


From cjfields at illinois.edu  Tue Jul 27 16:51:07 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 27 Jul 2010 11:51:07 -0500
Subject: [Open-bio-l] Agreed name for UniProt XML file format
In-Reply-To: <AANLkTi=x1tALUFBUThmafD8Wq6zzqh+LN+=5Nm_g0JM+@mail.gmail.com>
References: <AANLkTikPq-dfFQphUEKJircwbAyJdXEADXKU4FZrUo=k@mail.gmail.com>
	<AD9A2A32-0F8B-4F81-A21F-C42039DDA627@illinois.edu>
	<AANLkTi=x1tALUFBUThmafD8Wq6zzqh+LN+=5Nm_g0JM+@mail.gmail.com>
Message-ID: <35FDA04E-F141-4166-9DD2-424B788D65FC@illinois.edu>


On Jul 27, 2010, at 11:27 AM, Peter wrote:

> On Tue, Jul 27, 2010 at 5:14 PM, Chris Fields <cjfields at illinois.edu> wrote:
>> 
>> On Jul 27, 2010, at 10:31 AM, Peter wrote:
>> 
>>> Andrea has since pointed out that in the EBI REST services the file
>>> format is referred as "uniprot-xml" which is also less ambiguous
>>> (after all the old "swiss" plain text format might equally be referred
>>> to as the plain text UniProt format).
>>> 
>>> So, what do people feel about standardising on "uniprot" and/or
>>> "uniprot-xml" as the format name in Biopython, BioPerl & EMBOSS?
>> 
>> Agree with hilmar, 'uniprot-xml'.
> 
> That looks like a consensus (so far). Thank you all.
> 
>>> P.S. Chris, am I right in thinking that if BioPerl were to support this
>>> file format under the name "uniprot-xml" this would be equivalent
>>> to accepting format="uniprot" and variant="xml"? And furthermore
>>> and assuming you regard this as the default/only variant, Bio::SeqIO
>>> would also just accept format="uniprot"?
>> 
>> In cases where 'uniprot' is passed, we could handle it either way:
>> delegate to 'swiss' if xml isn't specified (so 'uniprot' is just an alias
>> of 'swiss'), or always use the XML handler for 'uniprot' and ignore
>> the variant argument.  Either way is fine with us.
> 
> Or raise an error as it is ambiguous? But that wouldn't be in the spirit
> of Perl though would it? ;)
> 
> Peter

An error is fine by me as well.  

chrus




From hlapp at drycafe.net  Tue Jul 27 18:57:33 2010
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Tue, 27 Jul 2010 14:57:33 -0400
Subject: [Open-bio-l] Agreed name for UniProt XML file format
In-Reply-To: <AD9A2A32-0F8B-4F81-A21F-C42039DDA627@illinois.edu>
References: <AANLkTikPq-dfFQphUEKJircwbAyJdXEADXKU4FZrUo=k@mail.gmail.com>
	<AD9A2A32-0F8B-4F81-A21F-C42039DDA627@illinois.edu>
Message-ID: <29A06AD7-A202-4C54-8DEE-8629B600A07B@drycafe.net>


On Jul 27, 2010, at 12:14 PM, Chris Fields wrote:

>> P.S. Chris, am I right in thinking that if BioPerl were to support  
>> this
>> file format under the name "uniprot-xml" this would be equivalent
>> to accepting format="uniprot" and variant="xml"? And furthermore
>> and assuming you regard this as the default/only variant, Bio::SeqIO
>> would also just accept format="uniprot"?
>
> In cases where 'uniprot' is passed, we could handle it either way:  
> delegate to 'swiss' if xml isn't specified (so 'uniprot' is just an  
> alias of 'swiss'), or always use the XML handler for 'uniprot' and  
> ignore the variant argument.  Either way is fine with us.


Frankly I'm afraid to most people uniprot as a format name is  
synonymous with swiss(prot). So that should probably be the default  
(rule: the default should always be the least surprising choice).

Alternatively, can we auto-detect whether it is XML without messing up  
an XML parser if the input is coming from a pipe?

	-hilmar
-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From pmr at ebi.ac.uk  Wed Jul 28 07:35:38 2010
From: pmr at ebi.ac.uk (Peter Rice)
Date: Wed, 28 Jul 2010 08:35:38 +0100
Subject: [Open-bio-l] Agreed name for UniProt XML file format
In-Reply-To: <AANLkTikPq-dfFQphUEKJircwbAyJdXEADXKU4FZrUo=k@mail.gmail.com>
References: <AANLkTikPq-dfFQphUEKJircwbAyJdXEADXKU4FZrUo=k@mail.gmail.com>
Message-ID: <4C4FDDCA.7010709@ebi.ac.uk>

On 27/07/2010 16:31, Peter C. wrote:

> So, what do people feel about standardising on "uniprot" and/or
> "uniprot-xml" as the format name in Biopython, BioPerl&  EMBOSS?

The name is good for EMBOSS. We do not hav ethis format yet ... but will 
add it under whatever name is agreed.

regards,

Peter Rice


From bonnalraoul at ingm.it  Tue Jul 13 13:15:14 2010
From: bonnalraoul at ingm.it (Raoul Bonnal)
Date: Tue, 13 Jul 2010 13:15:14 -0000
Subject: [Open-bio-l]  Code fest 2010: thinking to '11
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTikqs9a7BX_Db7UhhGI34onixjwMDbWcx3isp-V5@mail.gmail.com>
Message-ID: <0edae1b2-c20e-4a01-8dec-d3b233f795b6@ingm.it>

Dear All,
Codefest 2010 is finished and I think it has been a great success. 
I was so happy to do what I like to do more, coding, meeting people (it's better with a beer) and coding again.
Codefest +1

I'd like to have a BOSC more... like a round table than just presentations which are for sure very useful but not enough in my idea. 
Bosc +1-

As requested by many people @ BBQ, I'm just wondering how it could be having a Codefest in Italy, that would be definetely amazing. If you like the idea, in the next months I'll try to figure out how to make it possible. Keep in mind that my working place is in Milan.
Codefest at Milan +1

Then, I realized that is very important to be on the same boat and I'd like to join the OBF in a more active way, how to start ?

Chrees.
--
Raoul J.P. Bonnal
Life Science Informatics
Integrative Biology Program
Fondazione INGM
Via F. Sforza 28
20122 Milano, IT
phone: +39 02 006 623  26
fax: +39 02 006 623 46
http://www.ingm.it




From bonnalraoul at ingm.it  Mon Jul 19 09:45:06 2010
From: bonnalraoul at ingm.it (Raoul Bonnal)
Date: Mon, 19 Jul 2010 09:45:06 -0000
Subject: [Open-bio-l] R:  Code fest 2010: thinking to '11
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTikqs9a7BX_Db7UhhGI34onixjwMDbWcx3isp-V5@mail.gmail.com>
	<0edae1b2-c20e-4a01-8dec-d3b233f795b6@ingm.it>
	<4C410BE9.7040203@burnham.org>
	<8E65215F-FC4B-4E8E-B755-570FFEDBF644@eaglegenomics.com>
	<20100719090451.GA14892@thebird.nl> <4C441993.1020707@gmx.de>
Message-ID: <e74ca971-c182-4360-9bae-dbb6edad2b20@ingm.it>

About Milano, 
I don't want to push Milano, it was just an idea born during the BBQ. I know that it would require a lot of travel. It was to collect your opinion on that...

If there is a chance to have R guys join us, probably is better to find out a place in Vienna. If we want to stay in Vienna and no one can provide a room we could look for places used by gamers for their lan-parties or some other OpenSource community

    * Linux User Group at the Technical University of Vienna

City: 	Vienna 	Web Site: 	http://lll.ins.at/
Contact: 	Arno Belohlavek 	Email: 	bodi at cslab.tuwien.ac.at
Click here for more information
 

    * Linux User Group Austria (LUGA)

City: 	Vienna 	Web Site: 	http://www.luga.at/
Contact: 	N/A 	Email: 	office at luga.at
Click here for more information

Regards

--
Raoul J.P. Bonnal
Life Science Informatics
Integrative Biology Program
Fondazione INGM
Via F. Sforza 28
20122 Milano, IT
phone: +39 02 006 623  26
fax: +39 02 006 623 46
http://www.ingm.it

> -----Messaggio originale-----
> Da: Steffen M?ller [mailto:steffen_moeller at gmx.de]
> Inviato: luned? 19 luglio 2010 11:24
> A: Pjotr Prins
> Cc: Richard Holland; Christian M Zmasek; Raoul Bonnal; 'Brad Chapman';
> open-bio-l at lists.open-bio.org; 'Akira KINJO'; 'Eric Talevich'; 'Tim
> Booth'; 'Yasunori Yamamoto'; 'Christopher Bottoms'; 'Atsuko Yamaguchi';
> 'Kimberly Begley'; 'James Taylor'; 'Michael Heuer'; 'Kam Dahlquist';
> 'Hilmar Lapp'; 'Bela Tiwari'; 'Mitsuteru Nakao'; 'Toshiaki Katayama';
> 'Heikki Lehvaslaiho'; 'Dannon Baker'; 'Naohisa Goto'; 'Enis Afgan';
> Christian Zmasek; 'Ntino Krampis'; 'Oliver Hofmann'; 'John David N.
> Dionisio'; 'Dominique Belhachemi'; 'Lincoln Stein'
> Oggetto: Re: [Open-bio-l] Code fest 2010: thinking to '11
> 
> On 07/19/2010 11:04 AM, Pjotr Prins wrote:
> > On Sat, Jul 17, 2010 at 03:09:07PM +0100, Richard Holland wrote:
> >
> >> Should be possible to organise something in Vienna itself I would
> >> have thought? There's bound to be an institute there somewhere who
> >> could offer to help by providing a room for us to work in?
> >>
> > Vienna is also nice (I hear),
> it is
> > though maybe not as nice as Milano.
> >
> er, I'd say Milano already loses against the neighbouring Bergamo, but
> let's fight over this :)
> > ISMB/BOSC was also in Vienna in 2007 - so the organisers may be able
> > to give ideas.
> >
> > But amongst ourselves, who knows people in Vienna? We only need a
> > room with Internet, right?
> >
> I have someone to ask. Also we should contact the BioConductor
> folks (R is exceptionally strong in Vienna) to join in, which possibly
> solves all our problems :)
> > Clifford (of RockLinux fame - though he may frown on our coding -
> > http://www.clifford.at/frame.cgi?style.html and author of
> > http://openscad.org/) is in Vienna. I can try and ask him. But it is
> a
> > bit early now.
> >
> But Milano (and let me just mention Luebeck again) was thought
> as a meeting between the meetings, no?
> 
> Many greetings
> 
> Steffen





From bonnalraoul at ingm.it  Mon Jul 19 14:05:08 2010
From: bonnalraoul at ingm.it (Raoul Bonnal)
Date: Mon, 19 Jul 2010 14:05:08 -0000
Subject: [Open-bio-l] R: R:  Code fest 2010: thinking to '11
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTikqs9a7BX_Db7UhhGI34onixjwMDbWcx3isp-V5@mail.gmail.com>
	<0edae1b2-c20e-4a01-8dec-d3b233f795b6@ingm.it>
	<4C410BE9.7040203@burnham.org>
	<8E65215F-FC4B-4E8E-B755-570FFEDBF644@eaglegenomics.com>
	<20100719090451.GA14892@thebird.nl> <4C441993.1020707@gmx.de>
	<e74ca971-c182-4360-9bae-dbb6edad2b20@ingm.it>
	<20100719123836.GL16399@sobchak.mgh.harvard.e
	du> <81D91BED-8C74-495D-8A43-F10B37BBD181@eaglegenomics.com>
	<4C44519C.3060808@gmx.de>
Message-ID: <ad6de416-eed4-45ce-a209-0882b63a63c1@ingm.it>





> -----Messaggio originale-----
> Da: Steffen M?ller [mailto:steffen_moeller at gmx.de]
> There is the annual supercomputing conference May-Juneish in
> neighbouring
> Hamburg, diverse clinical events, nothing that really fits and I'd be
> aware of.
> We could create a summer or winter school ourselves, actually. We
> should
> meet more towards the Winter, I think, wherever it is. I suggest
> December,
> then we have the Xmas market as an event, and we should really think
> about
> financing ourselves with a cloud winter school.
> http://www.asc-
> luebeck.de/files/images/Luebeck%20Weihnachtsmarkt.preview.jpg
I like this idea.

+1 Winter


> >> There were also some great ideas about BOSC itself. I helped
> >> with the organizing this last year for the first time, and Kam is
> >> really open to letting organizers try and shape the conference
> >> goals. When Kam makes the announcements about organizing, which
> >> should be near the end of the year, definitely get involved and
> >> mention these ideas. It would be cool to see us try out some new
> >> notions of what BOSC can provide for attendees.
> >>
> +1
+1

--
Raoul J.P. Bonnal
Life Science Informatics
Integrative Biology Program
Fondazione INGM
Via F. Sforza 28
20122 Milano, IT
phone: +39 02 006 623  26
fax: +39 02 006 623 46
http://www.ingm.it




From rmb32 at cornell.edu  Tue Jul  6 20:06:36 2010
From: rmb32 at cornell.edu (Robert Buels)
Date: Tue, 06 Jul 2010 20:06:36 -0000
Subject: [Open-bio-l] Codefest 2010: Final details
In-Reply-To: <E3F893B2-221F-4120-A3CF-905261186C37@illinois.edu>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>	<AANLkTilM3_kEu9BWx2CIUaS2lklP1ULVKLhlKHtukgk2@mail.gmail.com>	<AANLkTiku8rxnLRFf0JULsAYvz5D07FeZR9ejKBZHQrCQ@mail.gmail.com>	<EEB50E10-CC46-43C7-928B-3CE8FC074315@illinois.edu>	<F9E2FEB5-B7C9-4F27-A572-0D66261CC925@nescent.org>
	<E3F893B2-221F-4120-A3CF-905261186C37@illinois.edu>
Message-ID: <4C3385D0.1020000@cornell.edu>

Chris Fields wrote:
> Would be nice to emphasize DBIx::Class, which abstracts the DB backend.  Not sure if Rob Buels will be there, might be a good contact person on that re: his work with DBIx::Class and Bio::Schema::Chado.

Gah, I won't be there, which is kind of driving me up the wall.  :-( 
Sorry guys!

Rob



From hlapp at nescent.org  Wed Jul  7 10:21:33 2010
From: hlapp at nescent.org (Hilmar Lapp)
Date: Wed, 07 Jul 2010 10:21:33 -0000
Subject: [Open-bio-l] Codefest 2010: Final details
In-Reply-To: <20100704185155.GB24102@kunkel>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTilM3_kEu9BWx2CIUaS2lklP1ULVKLhlKHtukgk2@mail.gmail.com>
	<AANLkTiku8rxnLRFf0JULsAYvz5D07FeZR9ejKBZHQrCQ@mail.gmail.com>
	<EEB50E10-CC46-43C7-928B-3CE8FC074315@illinois.edu>
	<20100704185155.GB24102@kunkel>
Message-ID: <9E077631-BDBB-45F2-8FC5-7BD3A3D1F6D7@nescent.org>

FYI, I'll be delayed by 2.5 hrs, so won't be there before 11am. Sorry about that.

-hilmar

Sent from away

On Jul 4, 2010, at 2:51 PM, Brad Chapman <chapmanb at 50mail.com> wrote:

> Christopher, Chris, Heikki and Hilmar;
> Nice discussion. If you have an overview of what you are hoping
> to tackle on the BioPerl side, please add it on the wiki page. The
> getting started part of the coding sessions is always the hardest
> part, so it'll be a huge help if we can stand up at the beginning,
> describe the project ideas, and then let people break into groups:
> 
> http://www.open-bio.org/wiki/Codefest_2010#ToDo_List
> 
> Edit away and this'll point us all in the right direction.
> Looking forward to next week,
> Brad
> 
>> I will be there on the afternoon of the 7th.  There are a couple of projects one can look into for Moose and Perl 6 (Biome and BioPerl6).  I think Hilmar was to do some DBIx::Class stuff for BioSQL at one point, not sure where that is (might be surplanted by SQLite work?).  Would be nice to talk with Mark re: the wrapper system for BioPerl as well.
>> 
>> So lots of stuff to think over and plan for.  Maybe we should move this to open-bio-l, or bioperl-l?
>> 
>> chris (fields)
>> 
>> On Jul 3, 2010, at 12:44 AM, Heikki Lehvaslaiho wrote:
>> 
>>> Chris,
>>> 
>>> I do not have too much experience on cloud computing, either. There
>>> will be quite a few people from BioPerl . We'll meet and  come up with
>>> a plan first thing in the morning. Unless someone has a very good one
>>> ready for sharing...
>>> 
>>>    -Heikki
>>> 
>>> Heikki Lehvaslaiho - skype:heikki_lehvaslaiho
>>> cell: +966 545 595 849  office: +966 2 808 2429
>>> 
>>> Computational Bioscience Research Centre (CBRC), Building #2, Office #4216
>>> 4700 King Abdullah University of Science and Technology (KAUST)
>>> Thuwal 23955-6900, Kingdom of Saudi Arabia
>>> 
>>> 
>>> 
>>> 
>>> On 3 July 2010 08:36, Christopher Bottoms <maizemu at gmail.com> wrote:
>>>> Hi all,
>>>> 
>>>> I was originally planning on working on cloud computing at the Codefest.
>>>> However, the 2-day cloud computing tutorial that I was going to attend in
>>>> mid June was canceled. Does anyone have any programming that they would like
>>>> help with? I have experience with Perl 5, including Moose, and I am starting
>>>> to dabble in Perl 6. I have also programmed in Java in the past. I hear
>>>> Python is easy to learn, so I'd be open to working on a Python project as
>>>> well.
>>>> 
>>>> Thanks,
>>>> Christopher Bottoms
>>>> 
>>>> On Fri, Jul 2, 2010 at 8:38 AM, Brad Chapman <chapmanb at 50mail.com> wrote:
>>>>> 
>>>>> Hi all;
>>>>> Codefest 2010 is finally here: next Wednesday and Thursday at
>>>>> Harvard Medical School and Massachusetts General Hospital in
>>>>> beautiful Boston. All of the logistics, directions and details
>>>>> are on the wiki page:
>>>>> 
>>>>> http://www.open-bio.org/wiki/Codefest_2010
>>>>> 
>>>>> If you want the short version: show up at Harvard Medical School on
>>>>> Wednesday at 10am and we'll take care of the rest. Thanks to the
>>>>> hard work of Oliver, Kimberly, Leah, Toshiaki, and Mitsuteru we'll
>>>>> have coffee, lunches and internet. Thanks to Steffen and Ntino,
>>>>> we'll have Amazon credits to utilize. And of course, there will be
>>>>> BBQ and drinking on Thursday night when we are finished.
>>>>> 
>>>>> I'm looking forward to a fun and productive time. The general plan
>>>>> will be to spend a bit of time on Wednesday morning organizing
>>>>> ourselves into like minded groups of folks, and then commence with
>>>>> coding and collaborating.
>>>>> 
>>>>> If you aren't able to make it and you're listed on the wiki page under
>>>>> participants, please do cross your name off so we have a good idea of
>>>>> final numbers. Likewise, if you are coming but haven't put your name up
>>>>> there please add it.
>>>>> 
>>>>> If you are interested in helping with making software and data
>>>>> available on shared cloud resources, here are the latest Amazon
>>>>> AMIs, snapshots, and the code base:
>>>>> 
>>>>> Cloud BioLinux images:
>>>>> 64bit: ami-d62cc4bf
>>>>> 32bit: ami-5423cb3d
>>>>> 
>>>>> An EBS public snapshot with indexed genomes:
>>>>> snap-67446d0f
>>>>> 
>>>>> Infrastructure:
>>>>> http://github.com/chapmanb/bcbb/tree/master/ec2/biolinux/
>>>>> 
>>>>> Send an e-mail with any questions, thoughts or concerns. My phone
>>>>> number is 617-447-8586 in case you end up hopelessly lost somewhere
>>>>> in Boston and are desperate to begin programming.
>>>>> 
>>>>> Looking forward to seeing everyone next Wednesday,
>>>>> Brad
>>>> 
>>>> 
>> 



From steffen_moeller at gmx.de  Tue Jul 13 13:55:07 2010
From: steffen_moeller at gmx.de (=?ISO-8859-1?Q?Steffen_M=F6ller?=)
Date: Tue, 13 Jul 2010 13:55:07 -0000
Subject: [Open-bio-l] Code fest 2010: thinking to '11
In-Reply-To: <0edae1b2-c20e-4a01-8dec-d3b233f795b6@ingm.it>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTikqs9a7BX_Db7UhhGI34onixjwMDbWcx3isp-V5@mail.gmail.com>
	<0edae1b2-c20e-4a01-8dec-d3b233f795b6@ingm.it>
Message-ID: <4C3C6B62.6060209@gmx.de>

Hi Raoul,

On 07/13/2010 03:01 PM, Raoul Bonnal wrote:
> Codefest 2010 is finished and I think it has been a great success. 
> I was so happy to do what I like to do more, coding, meeting people (it's better with a beer) and coding again.
> Codefest +1
>   
+1 , the "no question asked" series of presentations at BOSC was kind of
strange. But sure, all questions you would want to ask to BioPerl etc
you would have asked a while ago, not at the conference.
> I'd like to have a BOSC more... like a round table than just presentations which are for sure very useful but not enough in my idea. 
> Bosc +1-
>   
+1  - these doing-something-together meetings are good.
> As requested by many people @ BBQ, I'm just wondering how it could be having a Codefest in Italy, that would be definetely amazing. If you like the idea, in the next months I'll try to figure out how to make it possible. Keep in mind that my working place is in Milan.
> Codefest at Milan +1
>   
The problem is with the funding of the travel, which again would speak
for an increased regionalisation of the efforts and the integration of
others via the net.
A conference nearby does not really help if you don't also have a paper
on it :)
> Then, I realized that is very important to be on the same boat and I'd like to join the OBF in a more active way, how to start ?
>   
Well, we'd need the OBF for an OK to call it BOSC Hackathon, or BOSCF
(for BOSCloudFest). But the meeting we could plan rightaway. I can offer
the same for Luebeck, literally at the beach. Consider a free room
settled, accomodation is about 45 Euros per night. The nearest airports
would be the 50 miles apart Hamburg (Northern Germany) or Luebeck itself
with direct RyanAir flights from around Europe (Bergamo, Pisa, Stansted,
Barcelona, Edinburgh, "Stockholm", Gdansk and probably others).
Actually, Richard and Dominique already plan to come, maybe we could
synchronise things a bit.

Many greetings

Steffen


From holland at eaglegenomics.com  Tue Jul 13 14:44:12 2010
From: holland at eaglegenomics.com (Richard Holland)
Date: Tue, 13 Jul 2010 14:44:12 -0000
Subject: [Open-bio-l] Code fest 2010: thinking to '11
In-Reply-To: <4C3C6B62.6060209@gmx.de>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTikqs9a7BX_Db7UhhGI34onixjwMDbWcx3isp-V5@mail.gmail.com>
	<0edae1b2-c20e-4a01-8dec-d3b233f795b6@ingm.it>
	<4C3C6B62.6060209@gmx.de>
Message-ID: <ED49C5C3-D612-424C-900C-637D6C507FC2@eaglegenomics.com>

Hello all,

Speaking now strictly in my personal/OBF-member role now and not with my company hat on.

On 13 Jul 2010, at 09:34, Steffen M?ller wrote:

> Hi Raoul,
> 
> On 07/13/2010 03:01 PM, Raoul Bonnal wrote:
>> Codefest 2010 is finished and I think it has been a great success. 
>> I was so happy to do what I like to do more, coding, meeting people (it's better with a beer) and coding again.
>> Codefest +1
>> 
> +1 , the "no question asked" series of presentations at BOSC was kind of
> strange. But sure, all questions you would want to ask to BioPerl etc
> you would have asked a while ago, not at the conference.

+1, The question then arises, what is BOSC for. The Bio* projects function perfectly well these days without needing to present, and the audience tends to be made up of the already converted so they are not really attracting any extra users there. The hackathons/codefests are a much better and more useful event for the Bio* projects in my mind. The remaining talks about specific bits of software are very interesting but its not always obvious what the biological problem is that they're trying to solve - or whether it really is a problem unique to biological informatics or if they would be better off in a more generic informatics conference (where their code and design practices would also come under much closer scrutiny!).

>> I'd like to have a BOSC more... like a round table than just presentations which are for sure very useful but not enough in my idea. 
>> Bosc +1-
>> 
> +1  - these doing-something-together meetings are good.

+1 yes agreed, despite advances in comms technology still nothing beats a few beers at the pub with your laptops.

>> As requested by many people @ BBQ, I'm just wondering how it could be having a Codefest in Italy, that would be definetely amazing. If you like the idea, in the next months I'll try to figure out how to make it possible. Keep in mind that my working place is in Milan.
>> Codefest at Milan +1
>> 
> The problem is with the funding of the travel, which again would speak
> for an increased regionalisation of the efforts and the integration of
> others via the net.
> A conference nearby does not really help if you don't also have a paper
> on it :)

Indeed. I think regional efforts are going to be unavoidable because of this, so you'll need a key core of people at each one to keep the momentum going. e.g. a 'management team' at each Bio* project that has a knowledgeable senior member in every region that is able to lead these meetings when they take place.

>> Then, I realized that is very important to be on the same boat and I'd like to join the OBF in a more active way, how to start ?
>> 
> Well, we'd need the OBF for an OK to call it BOSC Hackathon, or BOSCF
> (for BOSCloudFest). But the meeting we could plan rightaway. I can offer
> the same for Luebeck, literally at the beach. Consider a free room
> settled, accomodation is about 45 Euros per night. The nearest airports
> would be the 50 miles apart Hamburg (Northern Germany) or Luebeck itself
> with direct RyanAir flights from around Europe (Bergamo, Pisa, Stansted,
> Barcelona, Edinburgh, "Stockholm", Gdansk and probably others).
> Actually, Richard and Dominique already plan to come, maybe we could
> synchronise things a bit.

Yup, definitely planning on coming to the Luebeck thing if it happens. In future, we can offer similar facilities in Cambridge (actually Babraham really, but close enough) - nearest airport Stansted, unfortunately no beach.

cheers,
Richard

> Many greetings
> 
> Steffen

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/




From czmasek at burnham.org  Sat Jul 17 01:58:18 2010
From: czmasek at burnham.org (Christian M Zmasek)
Date: Sat, 17 Jul 2010 01:58:18 -0000
Subject: [Open-bio-l] Code fest 2010: thinking to '11
In-Reply-To: <0edae1b2-c20e-4a01-8dec-d3b233f795b6@ingm.it>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTikqs9a7BX_Db7UhhGI34onixjwMDbWcx3isp-V5@mail.gmail.com>
	<0edae1b2-c20e-4a01-8dec-d3b233f795b6@ingm.it>
Message-ID: <4C410BE9.7040203@burnham.org>

Hi, Raoul:

While having a "codefest" in Italy sounds (very) tempting, I recommend 
to first get a rough estimate of the number of people who actually might 
be able/willing to travel to Italy from Vienna, before making any 
serious plans.

I think part of the reason why codefest 2010 was a success was because 
it was very convenient to combine it with BOSC 2010 (same hotels, no 
additional travel, etc.).

Clearly, for some (including me) additional travel might be a plus, but 
maybe not for everyone...

Good luck, in any case!

Christian





Raoul Bonnal wrote:
> Dear All,
> Codefest 2010 is finished and I think it has been a great success. 
> I was so happy to do what I like to do more, coding, meeting people (it's better with a beer) and coding again.
> Codefest +1
> 
> I'd like to have a BOSC more... like a round table than just presentations which are for sure very useful but not enough in my idea. 
> Bosc +1-
> 
> As requested by many people @ BBQ, I'm just wondering how it could be having a Codefest in Italy, that would be definetely amazing. If you like the idea, in the next months I'll try to figure out how to make it possible. Keep in mind that my working place is in Milan.
> Codefest at Milan +1
> 
> Then, I realized that is very important to be on the same boat and I'd like to join the OBF in a more active way, how to start ?
> 
> Chrees.
> --
> Raoul J.P. Bonnal
> Life Science Informatics
> Integrative Biology Program
> Fondazione INGM
> Via F. Sforza 28
> 20122 Milano, IT
> phone: +39 02 006 623  26
> fax: +39 02 006 623 46
> http://www.ingm.it
> 



From holland at eaglegenomics.com  Sat Jul 17 14:53:56 2010
From: holland at eaglegenomics.com (Richard Holland)
Date: Sat, 17 Jul 2010 14:53:56 -0000
Subject: [Open-bio-l] Code fest 2010: thinking to '11
In-Reply-To: <4C410BE9.7040203@burnham.org>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTikqs9a7BX_Db7UhhGI34onixjwMDbWcx3isp-V5@mail.gmail.com>
	<0edae1b2-c20e-4a01-8dec-d3b233f795b6@ingm.it>
	<4C410BE9.7040203@burnham.org>
Message-ID: <8E65215F-FC4B-4E8E-B755-570FFEDBF644@eaglegenomics.com>

The combined purpose trip was definitely a big part of the decision to attend. I could only do Italy if it was really cheap to get there from Vienna, otherwise couldn't justify the extra cost. Unless there was something else going on in Italy to go to as well at the same time?

Should be possible to organise something in Vienna itself I would have thought? There's bound to be an institute there somewhere who could offer to help by providing a room for us to work in?

On 17 Jul 2010, at 02:48, Christian M Zmasek wrote:

> Hi, Raoul:
> 
> While having a "codefest" in Italy sounds (very) tempting, I recommend to first get a rough estimate of the number of people who actually might be able/willing to travel to Italy from Vienna, before making any serious plans.
> 
> I think part of the reason why codefest 2010 was a success was because it was very convenient to combine it with BOSC 2010 (same hotels, no additional travel, etc.).
> 
> Clearly, for some (including me) additional travel might be a plus, but maybe not for everyone...
> 
> Good luck, in any case!
> 
> Christian
> 
> 
> 
> 
> 
> Raoul Bonnal wrote:
>> Dear All,
>> Codefest 2010 is finished and I think it has been a great success. I was so happy to do what I like to do more, coding, meeting people (it's better with a beer) and coding again.
>> Codefest +1
>> I'd like to have a BOSC more... like a round table than just presentations which are for sure very useful but not enough in my idea. Bosc +1-
>> As requested by many people @ BBQ, I'm just wondering how it could be having a Codefest in Italy, that would be definetely amazing. If you like the idea, in the next months I'll try to figure out how to make it possible. Keep in mind that my working place is in Milan.
>> Codefest at Milan +1
>> Then, I realized that is very important to be on the same boat and I'd like to join the OBF in a more active way, how to start ?
>> Chrees.
>> --
>> Raoul J.P. Bonnal
>> Life Science Informatics
>> Integrative Biology Program
>> Fondazione INGM
>> Via F. Sforza 28
>> 20122 Milano, IT
>> phone: +39 02 006 623  26
>> fax: +39 02 006 623 46
>> http://www.ingm.it
> 

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/




From pjotr.public14 at thebird.nl  Mon Jul 19 09:11:25 2010
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Mon, 19 Jul 2010 09:11:25 -0000
Subject: [Open-bio-l] Code fest 2010: thinking to '11
In-Reply-To: <8E65215F-FC4B-4E8E-B755-570FFEDBF644@eaglegenomics.com>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTikqs9a7BX_Db7UhhGI34onixjwMDbWcx3isp-V5@mail.gmail.com>
	<0edae1b2-c20e-4a01-8dec-d3b233f795b6@ingm.it>
	<4C410BE9.7040203@burnham.org>
	<8E65215F-FC4B-4E8E-B755-570FFEDBF644@eaglegenomics.com>
Message-ID: <20100719090451.GA14892@thebird.nl>

On Sat, Jul 17, 2010 at 03:09:07PM +0100, Richard Holland wrote:
> Should be possible to organise something in Vienna itself I would
> have thought? There's bound to be an institute there somewhere who
> could offer to help by providing a room for us to work in?

Vienna is also nice (I hear), though maybe not as nice as Milano.

ISMB/BOSC was also in Vienna in 2007 - so the organisers may be able
to give ideas.

But amongst ourselves, who knows people in Vienna? We only need a
room with Internet, right? 

Clifford (of RockLinux fame - though he may frown on our coding -
http://www.clifford.at/frame.cgi?style.html and author of
http://openscad.org/) is in Vienna. I can try and ask him. But it is a
bit early now.

Pj.


From steffen_moeller at gmx.de  Mon Jul 19 09:23:44 2010
From: steffen_moeller at gmx.de (=?ISO-8859-1?Q?Steffen_M=F6ller?=)
Date: Mon, 19 Jul 2010 09:23:44 -0000
Subject: [Open-bio-l] Code fest 2010: thinking to '11
In-Reply-To: <20100719090451.GA14892@thebird.nl>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTikqs9a7BX_Db7UhhGI34onixjwMDbWcx3isp-V5@mail.gmail.com>
	<0edae1b2-c20e-4a01-8dec-d3b233f795b6@ingm.it>
	<4C410BE9.7040203@burnham.org>
	<8E65215F-FC4B-4E8E-B755-570FFEDBF644@eaglegenomics.com>
	<20100719090451.GA14892@thebird.nl>
Message-ID: <4C441993.1020707@gmx.de>

On 07/19/2010 11:04 AM, Pjotr Prins wrote:
> On Sat, Jul 17, 2010 at 03:09:07PM +0100, Richard Holland wrote:
>   
>> Should be possible to organise something in Vienna itself I would
>> have thought? There's bound to be an institute there somewhere who
>> could offer to help by providing a room for us to work in?
>>     
> Vienna is also nice (I hear),
it is
> though maybe not as nice as Milano.
>   
er, I'd say Milano already loses against the neighbouring Bergamo, but
let's fight over this :)
> ISMB/BOSC was also in Vienna in 2007 - so the organisers may be able
> to give ideas.
>
> But amongst ourselves, who knows people in Vienna? We only need a
> room with Internet, right? 
>   
I have someone to ask. Also we should contact the BioConductor
folks (R is exceptionally strong in Vienna) to join in, which possibly
solves all our problems :)  
> Clifford (of RockLinux fame - though he may frown on our coding -
> http://www.clifford.at/frame.cgi?style.html and author of
> http://openscad.org/) is in Vienna. I can try and ask him. But it is a
> bit early now.
>   
But Milano (and let me just mention Luebeck again) was thought
as a meeting between the meetings, no?

Many greetings

Steffen



From holland at eaglegenomics.com  Mon Jul 19 12:45:45 2010
From: holland at eaglegenomics.com (Richard Holland)
Date: Mon, 19 Jul 2010 12:45:45 -0000
Subject: [Open-bio-l] R:  Code fest 2010: thinking to '11
In-Reply-To: <20100719123836.GL16399@sobchak.mgh.harvard.edu>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTikqs9a7BX_Db7UhhGI34onixjwMDbWcx3isp-V5@mail.gmail.com>
	<0edae1b2-c20e-4a01-8dec-d3b233f795b6@ingm.it>
	<4C410BE9.7040203@burnham.org>
	<8E65215F-FC4B-4E8E-B755-570FFEDBF644@eaglegenomics.com>
	<20100719090451.GA14892@thebird.nl> <4C441993.1020707@gmx.de>
	<e74ca971-c182-4360-9bae-dbb6edad2b20@ingm.it>
	<20100719123836.GL16399@sobchak.mgh.harvard.edu>
Message-ID: <81D91BED-8C74-495D-8A43-F10B37BBD181@eaglegenomics.com>

With regard to point 2 about other conferences - ECCB is in Ghent (Belgium) this year, in September. This is the conference that ISMB pairs with every time it is in Europe so could be a good excuse for an attached codefest. However my network of Belgian bioinformaticians is about as good as my network of Viennese ones. :)

cheers,
Richard

On 19 Jul 2010, at 13:38, Brad Chapman wrote:

> Hey all;
> It's awesome to see so much interest in continuing the informal
> Codefests; this is a great discussion. Raoul, thanks for kicking 
> it off.
> 
> To try and summarize the thoughts so far, we have 2 different
> ideas floating about regarding future Codefest sessions:
> 
> 1. Another Codefest next year in conjunction with BOSC and ISMB in
> Vienna. So far we have proposals for either Milano or Vienna itself.
> The key aspect here is to figure out the logistics: if we wanted to
> do Milano what is the transport situation to Vienna afterwards? If
> we want to have it in Vienna can we find someone locally who is
> willing to do the on the ground work to ensure we have space,
> internet and power?
> 
> Although the work of actually organizing is not especially taxing,
> we do need to have someone committed locally as there are lots of
> little things that need a person willing to handle them. It's
> not too early to try and identify folks who might be interested and
> get them integrated into the community. Although we wouldn't need to
> book a room a year out, we would want to ensure that anyone
> interested in hosting would get enough out of the coding session to
> make it worth their time to help with the organization. Can anyone
> who knows people in Vienna who might be interested get in contact
> for at least an informal discussion? Then we can start to enumerate
> the specifics so we can compare our options.
> 
> 2. Intermediate, potentially regional, Codefests between BOSC. These
> sound like a good idea, and I would second Richard's point about
> associating these with conferences to help encourage attendance. It
> is a lot easier to justing budgeting out time and travel money if
> there is a relevant more "official" event happening in conjunction
> with the coding session. It's good to keep in mind that not
> everyone, and their bosses, are entirely altruistic and to think
> about how we can also satisfy professional needs while getting in
> some coding time. Steffen, are there any conferences or near Luebeck
> that it would make sense to coordinate with?
> 
> There were also some great ideas about BOSC itself. I helped
> with the organizing this last year for the first time, and Kam is
> really open to letting organizers try and shape the conference
> goals. When Kam makes the announcements about organizing, which
> should be near the end of the year, definitely get involved and
> mention these ideas. It would be cool to see us try out some new
> notions of what BOSC can provide for attendees.
> 
> Finally, thanks again to everyone for coming to Codefest this year.
> It was a great turnout and looking forward to doing it again,
> Brad

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/




From chapmanb at 50mail.com  Mon Jul 19 12:46:06 2010
From: chapmanb at 50mail.com (Brad Chapman)
Date: Mon, 19 Jul 2010 12:46:06 -0000
Subject: [Open-bio-l] R:  Code fest 2010: thinking to '11
In-Reply-To: <e74ca971-c182-4360-9bae-dbb6edad2b20@ingm.it>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTikqs9a7BX_Db7UhhGI34onixjwMDbWcx3isp-V5@mail.gmail.com>
	<0edae1b2-c20e-4a01-8dec-d3b233f795b6@ingm.it>
	<4C410BE9.7040203@burnham.org>
	<8E65215F-FC4B-4E8E-B755-570FFEDBF644@eaglegenomics.com>
	<20100719090451.GA14892@thebird.nl> <4C441993.1020707@gmx.de>
	<e74ca971-c182-4360-9bae-dbb6edad2b20@ingm.it>
Message-ID: <20100719123836.GL16399@sobchak.mgh.harvard.edu>

Hey all;
It's awesome to see so much interest in continuing the informal
Codefests; this is a great discussion. Raoul, thanks for kicking 
it off.

To try and summarize the thoughts so far, we have 2 different
ideas floating about regarding future Codefest sessions:

1. Another Codefest next year in conjunction with BOSC and ISMB in
Vienna. So far we have proposals for either Milano or Vienna itself.
The key aspect here is to figure out the logistics: if we wanted to
do Milano what is the transport situation to Vienna afterwards? If
we want to have it in Vienna can we find someone locally who is
willing to do the on the ground work to ensure we have space,
internet and power?

Although the work of actually organizing is not especially taxing,
we do need to have someone committed locally as there are lots of
little things that need a person willing to handle them. It's
not too early to try and identify folks who might be interested and
get them integrated into the community. Although we wouldn't need to
book a room a year out, we would want to ensure that anyone
interested in hosting would get enough out of the coding session to
make it worth their time to help with the organization. Can anyone
who knows people in Vienna who might be interested get in contact
for at least an informal discussion? Then we can start to enumerate
the specifics so we can compare our options.

2. Intermediate, potentially regional, Codefests between BOSC. These
sound like a good idea, and I would second Richard's point about
associating these with conferences to help encourage attendance. It
is a lot easier to justing budgeting out time and travel money if
there is a relevant more "official" event happening in conjunction
with the coding session. It's good to keep in mind that not
everyone, and their bosses, are entirely altruistic and to think
about how we can also satisfy professional needs while getting in
some coding time. Steffen, are there any conferences or near Luebeck
that it would make sense to coordinate with?

There were also some great ideas about BOSC itself. I helped
with the organizing this last year for the first time, and Kam is
really open to letting organizers try and shape the conference
goals. When Kam makes the announcements about organizing, which
should be near the end of the year, definitely get involved and
mention these ideas. It would be cool to see us try out some new
notions of what BOSC can provide for attendees.

Finally, thanks again to everyone for coming to Codefest this year.
It was a great turnout and looking forward to doing it again,
Brad


From steffen_moeller at gmx.de  Mon Jul 19 13:22:50 2010
From: steffen_moeller at gmx.de (=?ISO-8859-1?Q?Steffen_M=F6ller?=)
Date: Mon, 19 Jul 2010 13:22:50 -0000
Subject: [Open-bio-l] R:  Code fest 2010: thinking to '11
In-Reply-To: <81D91BED-8C74-495D-8A43-F10B37BBD181@eaglegenomics.com>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTikqs9a7BX_Db7UhhGI34onixjwMDbWcx3isp-V5@mail.gmail.com>
	<0edae1b2-c20e-4a01-8dec-d3b233f795b6@ingm.it>
	<4C410BE9.7040203@burnham.org>
	<8E65215F-FC4B-4E8E-B755-570FFEDBF644@eaglegenomics.com>
	<20100719090451.GA14892@thebird.nl> <4C441993.1020707@gmx.de>
	<e74ca971-c182-4360-9bae-dbb6edad2b20@ingm.it>
	<20100719123836.GL16399@sobchak.mgh.harvard.edu>
	<81D91BED-8C74-495D-8A43-F10B37BBD181@eaglegenomics.com>
Message-ID: <4C44519C.3060808@gmx.de>

Hello,

On 07/19/2010 02:44 PM, Richard Holland wrote:
> With regard to point 2 about other conferences - ECCB is in Ghent (Belgium) this year, in September. This is the conference that ISMB pairs with every time it is in Europe so could be a good excuse for an attached codefest. However my network of Belgian bioinformaticians is about as good as my network of Viennese ones. :)
>   
I like the idea, but September is a bit too soonish for me as we
basically have just met.

> On 19 Jul 2010, at 13:38, Brad Chapman wrote
>> Hey all;
>> It's awesome to see so much interest in continuing the informal
>> Codefests; this is a great discussion. Raoul, thanks for kicking 
>> it off.
>>
>> To try and summarize the thoughts so far, we have 2 different
>> ideas floating about regarding future Codefest sessions:
>>
>> 1. Another Codefest next year in conjunction with BOSC and ISMB in
>> Vienna. So far we have proposals for either Milano or Vienna itself.
>> The key aspect here is to figure out the logistics: if we wanted to
>> do Milano what is the transport situation to Vienna afterwards? If
>> we want to have it in Vienna can we find someone locally who is
>> willing to do the on the ground work to ensure we have space,
>> internet and power?
>>     
I expect to be at the ISMB and could prepare for that.
But there is no point in separating the CodeFest from BOSC, really.
And it certainly was not meant that way. It should be in Vienna.
>> Although the work of actually organizing is not especially taxing,
>> we do need to have someone committed locally as there are lots of
>> little things that need a person willing to handle them. It's
>> not too early to try and identify folks who might be interested and
>> get them integrated into the community. Although we wouldn't need to
>> book a room a year out, we would want to ensure that anyone
>> interested in hosting would get enough out of the coding session to
>> make it worth their time to help with the organization. Can anyone
>> who knows people in Vienna who might be interested get in contact
>> for at least an informal discussion? Then we can start to enumerate
>> the specifics so we can compare our options.
>>     
I'd ask a few individuals and then see what they say. Am I right presuming
that we cannot pay anything?
>> 2. Intermediate, potentially regional, Codefests between BOSC. These
>> sound like a good idea, and I would second Richard's point about
>> associating these with conferences to help encourage attendance.
Right. But not everyone needs to attend every meeting. In the contrary,
I think that it would be the major achievement of the cloud environments
that we can stay where we are and nonetheless somehow feel involved.
>> It
>> is a lot easier to justing budgeting out time and travel money if
>> there is a relevant more "official" event happening in conjunction
>> with the coding session. It's good to keep in mind that not
>> everyone, and their bosses, are entirely altruistic and to think
>> about how we can also satisfy professional needs while getting in
>> some coding time. Steffen, are there any conferences or near Luebeck
>> that it would make sense to coordinate with?
>>     
There is the annual supercomputing conference May-Juneish in neighbouring
Hamburg, diverse clinical events, nothing that really fits and I'd be
aware of.
We could create a summer or winter school ourselves, actually. We should
meet more towards the Winter, I think, wherever it is. I suggest December,
then we have the Xmas market as an event, and we should really think about
financing ourselves with a cloud winter school.
http://www.asc-luebeck.de/files/images/Luebeck%20Weihnachtsmarkt.preview.jpg

>> There were also some great ideas about BOSC itself. I helped
>> with the organizing this last year for the first time, and Kam is
>> really open to letting organizers try and shape the conference
>> goals. When Kam makes the announcements about organizing, which
>> should be near the end of the year, definitely get involved and
>> mention these ideas. It would be cool to see us try out some new
>> notions of what BOSC can provide for attendees.
>>     
+1

Many greetings

Steffen




From hlapp at drycafe.net  Fri Jul 23 17:05:50 2010
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Fri, 23 Jul 2010 17:05:50 -0000
Subject: [Open-bio-l] Code fest 2010: thinking to '11
In-Reply-To: <20100719090451.GA14892@thebird.nl>
References: <20100702133822.GA8735@sobchak.mgh.harvard.edu>
	<AANLkTikqs9a7BX_Db7UhhGI34onixjwMDbWcx3isp-V5@mail.gmail.com>
	<0edae1b2-c20e-4a01-8dec-d3b233f795b6@ingm.it>
	<4C410BE9.7040203@burnham.org>
	<8E65215F-FC4B-4E8E-B755-570FFEDBF644@eaglegenomics.com>
	<20100719090451.GA14892@thebird.nl>
Message-ID: <BFF24009-397B-4938-9A4F-63D805231445@drycafe.net>


On Jul 19, 2010, at 5:04 AM, Pjotr Prins wrote:

> Vienna is also nice (I hear), though maybe not as nice as Milano.

I think it is nicer. But I'm biased :-)

> But amongst ourselves, who knows people in Vienna? We only need a
> room with Internet, right?

Right. I know people at the IMP (http://www.imp.ac.at/) and another  
center in the same building, and they might be able and willing to  
organize something. I have not asked yet, though.

> Clifford (of RockLinux fame - though he may frown on our coding -
> http://www.clifford.at/frame.cgi?style.html and author of
> http://openscad.org/) is in Vienna.

What might actually be a really interesting and cool location is the  
Metalab:
http://metalab.at/wiki/Info_Folder

(Click on "English Version" if you don't understand German)

I also know someone at the KLIVV, though I don't know how inclined  
they'd be to entertain the idea of hosting us:
http://www.oeaw.ac.at/klivv/

Other cool locations:
IST: http://www.ist.ac.at (Nick Barton just moved there)
IIASA (International Institute for Applied Systems Analysis): http://www.iiasa.ac.at 
  (They are in the Laxenburg Castle - *really* gorgeous place  
actually: http://www.iiasa.ac.at/docs/IIASA_Tour.html?sb=6)

	-hilmar
-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================