From p.j.a.cock at googlemail.com  Mon Mar  2 23:07:34 2015
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 2 Mar 2015 23:07:34 +0000
Subject: [Biopython-dev] Experimenting with migrating wiki to GitHub pages
Message-ID: <CAKVJ-_50F0OkGLZ3wMw-Y+iXg4uM1pLqsgdpMCEj4K4_Zur_Og@mail.gmail.com>

Dear all,

Those of you who have contributed to the Biopython wiki
in the past, and who have a GitHub account, might have
spotted this new repository:

https://github.com/peterjc/peterjc.github.io

I am experimenting with migrating the MediaWiki content
on biopython.org into MarkDown files (using pandoc, and
saving each wiki revision as a git commit), for display as
a webpage via GitHub Pages using Jekyll.

https://github.com/peterjc/mediawiki_to_git_md

The mapping from wiki user accounts to GitHub accounts
was done by hand. Please email me directly if I made a
mistake with your contributions. If I continue this effort I
will be re-running the migration script in future.

This conversion may not prove practical, and is not yet pretty
or even functional, but potentially could one day ofter an
alternative approach - and means we (the OBF) wouldn't
need to maintain a server running MediaWiki and Apache.

Note I'm not going to make any sudden changes to the
current biopython.org site without any warning or discussion.

Regards,

Peter

From p.j.a.cock at googlemail.com  Tue Mar  3 15:25:08 2015
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 3 Mar 2015 15:25:08 +0000
Subject: [Biopython-dev] [GSoC] Project Proposal for Google Summer of
	Code
In-Reply-To: <CAFZWoGZjEpajLSH+gHA6n-drD2DLFVN=SmysQr8VC2YtbjqYsA@mail.gmail.com>
References: <CAFZWoGZjEpajLSH+gHA6n-drD2DLFVN=SmysQr8VC2YtbjqYsA@mail.gmail.com>
Message-ID: <CAKVJ-_48Gnpda8BVbPwqee894xRW2FqAvC635dGdRZyAAo0NXg@mail.gmail.com>

Hi Joshua,

Thank you for you interest. Unfortunately we've just heard that
the  Open Bioinformatics Foundation (OBF) was not accepted
into the Google Summer of Code 2015 programme:

http://news.open-bio.org/news/2015/03/sadly-obf-not-accepted-for-gsoc-2015/

It may be possible to pursue your project idea with one of the
accepted organisations (perhaps the Python Software Foundation)
by including a mentor from Biopython. We've not yet approached
any of the other potential partner organisations yet though.

Good luck,

Peter



Peter


On Tue, Mar 3, 2015 at 2:58 AM, Joshua Klein <mobiusklein at gmail.com> wrote:
> Hello,
>
> I've been working on a python library for reading, writing, and manipulating
> glycan structures and glycomics data. One of my collaborators suggested I
> inquire here if this might be of interest to the Biopython team and if it
> was not too late to apply for a Google Summer of Code sponsorship.
>
> The library can currently do the following:
>
> Read and write GlycoCT Condensed format carbohydrate structures that are
> concrete (having no variable or undefined structures)
> Read GlycoCTXML format carbohydrate structures that are concrete
> Manipulate the tree structure, adding and removing monosaccharide and
> substituent nodes, as well as altering existing nodes.
> Calculate elemental compositions for glycan structures
> Create arbitrary chemical derivitizations (e.g. permethylation) of glycan
> structures
> Generate B, C, Y, and Z fragments from structures as observed when analyzing
> a structure with tandem mass spectrometry.
> Make API calls against GlycomeDB to download structures and annotations on
> the fly
> Perform sub-tree inclusion and maximum common substructure searches with
> fuzzy matching.
> Plot glycan structures using the Consortium for Functional Glycomics symbol
> nomenclature with matplotlib.
> Perform error tolerance name inference on monosaccharides
>
> I am currently working on adding support for A and X cross-ring fragment
> generation and adding other serialization formats such as IUPAC and
> GlycoMinds Linear Codes.
>
> Currently, all of the features are implemented purely in Python.
>
> What other information, if any, can I provide?
>
> Thank you,
> Joshua Klein
>
> _______________________________________________
> GSoC mailing list
> GSoC at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/gsoc

From p.j.a.cock at googlemail.com  Tue Mar  3 15:50:59 2015
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 3 Mar 2015 15:50:59 +0000
Subject: [Biopython-dev] Sadly OBF not accepted for GSoC 2015
Message-ID: <CAKVJ-_7du44Dx+A7tMa=KdmjSG4_ZQ40hm_=cY9tQTDujsh+xQ@mail.gmail.com>

This announcement was posted to the OBF blog here:
http://news.open-bio.org/news/2015/03/sadly-obf-not-accepted-for-gsoc-2015/

Dear all,

Last year?s Google Summer of Code 2014 was very productive for the OBF
with six students working on Bio* and related bioinformatics projects
[1]. We applied to be part of GSoC 2015, but unfortunately this year
were not accepted.

Google?s program is enormously popular, and over-subscribed, meaning
Google has had to rotate organisation membership. The OBF is grateful
to have been accepted in 2010, 2011, 2012 and 2014. This year any
participation will be down to individual projects to find a willing
umbrella group from the organisations accepted for GSoC 2015 [2]. For
example, a Biopython project was included under NESCent for GSoC 2013.

Other organizations with bioinformatics as keyword are Ruby Science
Foundation, Department of Biomedical Informatics, Stony Brook
University, OncoBlocks, University of Nebraska ? Helikar Lab. Other
organizations related to sciences are ASCEND , BRL-CAD, Debian Project
, HPCC Systems?,  International Neuroinformatics Coordinating
Facility, lmonade: scientific software distribution, OSGeo ? Open
Source Geospatial Foundation, The Concord Consortium, The
Visualization Toolkit. Languages: Python, Scala, Apache Foundation.
Last but not least : Global Alliance for Genomics & Health. [3]

On behalf of the OBF, we would like to thank our volunteer GSoC
Administrators, Raoul Bonnal and Francesco Strozzi, for organising our
application - and all our potential mentors across the Bio* projects
who put forward potential project suggestions.

Peter
OBF Secretary

[1] http://news.open-bio.org/news/2015/02/obf-gsoc-2014-wrapup/
[2] https://www.google-melange.com/gsoc/org/list/public/google/gsoc2015
[3] See links on
http://news.open-bio.org/news/2015/03/sadly-obf-not-accepted-for-gsoc-2015/


From mobiusklein at gmail.com  Tue Mar  3 17:05:00 2015
From: mobiusklein at gmail.com (Joshua Klein)
Date: Tue, 3 Mar 2015 12:05:00 -0500
Subject: [Biopython-dev] [GSoC] Project Proposal for Google Summer of
	Code
In-Reply-To: <CAKVJ-_48Gnpda8BVbPwqee894xRW2FqAvC635dGdRZyAAo0NXg@mail.gmail.com>
References: <CAFZWoGZjEpajLSH+gHA6n-drD2DLFVN=SmysQr8VC2YtbjqYsA@mail.gmail.com>
	<CAKVJ-_48Gnpda8BVbPwqee894xRW2FqAvC635dGdRZyAAo0NXg@mail.gmail.com>
Message-ID: <CAFZWoGapZJvso084jiGzDeG0g_dT_6p75fG24-TkUwA9nFJHvg@mail.gmail.com>

I am sorry to hear that the OBF did not make it in this year. We are still
interested in finding out if the Biopython team is interested in including
glycomics tools in the core library, or in some other looser association.
Real glycoinformatics is relatively inaccessible outside of two titanic
Java libraries, which doesn't jive with how a lot of modern bioinformatics
is done today.

Thank you,
Joshua Klein

On Tue, Mar 3, 2015 at 10:25 AM, Peter Cock <p.j.a.cock at googlemail.com>
wrote:

> Hi Joshua,
>
> Thank you for you interest. Unfortunately we've just heard that
> the  Open Bioinformatics Foundation (OBF) was not accepted
> into the Google Summer of Code 2015 programme:
>
> http://news.open-bio.org/news/2015/03/sadly-obf-not-accepted-for-gsoc-2015/
>
> It may be possible to pursue your project idea with one of the
> accepted organisations (perhaps the Python Software Foundation)
> by including a mentor from Biopython. We've not yet approached
> any of the other potential partner organisations yet though.
>
> Good luck,
>
> Peter
>
>
>
> Peter
>
>
> On Tue, Mar 3, 2015 at 2:58 AM, Joshua Klein <mobiusklein at gmail.com>
> wrote:
> > Hello,
> >
> > I've been working on a python library for reading, writing, and
> manipulating
> > glycan structures and glycomics data. One of my collaborators suggested I
> > inquire here if this might be of interest to the Biopython team and if it
> > was not too late to apply for a Google Summer of Code sponsorship.
> >
> > The library can currently do the following:
> >
> > Read and write GlycoCT Condensed format carbohydrate structures that are
> > concrete (having no variable or undefined structures)
> > Read GlycoCTXML format carbohydrate structures that are concrete
> > Manipulate the tree structure, adding and removing monosaccharide and
> > substituent nodes, as well as altering existing nodes.
> > Calculate elemental compositions for glycan structures
> > Create arbitrary chemical derivitizations (e.g. permethylation) of glycan
> > structures
> > Generate B, C, Y, and Z fragments from structures as observed when
> analyzing
> > a structure with tandem mass spectrometry.
> > Make API calls against GlycomeDB to download structures and annotations
> on
> > the fly
> > Perform sub-tree inclusion and maximum common substructure searches with
> > fuzzy matching.
> > Plot glycan structures using the Consortium for Functional Glycomics
> symbol
> > nomenclature with matplotlib.
> > Perform error tolerance name inference on monosaccharides
> >
> > I am currently working on adding support for A and X cross-ring fragment
> > generation and adding other serialization formats such as IUPAC and
> > GlycoMinds Linear Codes.
> >
> > Currently, all of the features are implemented purely in Python.
> >
> > What other information, if any, can I provide?
> >
> > Thank you,
> > Joshua Klein
> >
> > _______________________________________________
> > GSoC mailing list
> > GSoC at mailman.open-bio.org
> > http://mailman.open-bio.org/mailman/listinfo/gsoc
>
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From p.j.a.cock at googlemail.com  Tue Mar  3 18:25:17 2015
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 3 Mar 2015 18:25:17 +0000
Subject: [Biopython-dev] [GSoC] Project Proposal for Google Summer of
	Code
In-Reply-To: <CAFZWoGapZJvso084jiGzDeG0g_dT_6p75fG24-TkUwA9nFJHvg@mail.gmail.com>
References: <CAFZWoGZjEpajLSH+gHA6n-drD2DLFVN=SmysQr8VC2YtbjqYsA@mail.gmail.com>
	<CAKVJ-_48Gnpda8BVbPwqee894xRW2FqAvC635dGdRZyAAo0NXg@mail.gmail.com>
	<CAFZWoGapZJvso084jiGzDeG0g_dT_6p75fG24-TkUwA9nFJHvg@mail.gmail.com>
Message-ID: <CAKVJ-_5hrrPdrOAw3ZLoUA0WM0AfVwte=YDWkx60utnJ+DDr1w@mail.gmail.com>

Thanks Joshua,

Outside GSoC, adding glycoinformatics to Biopython sounds interesting.
As far as I know none of our existing contributors do much in this area,
so our feedback may be limited to Python style (PEP8 please) and
practicalities like unit tests and documentation.

We should probably also ask on the main Biopython mailing list - that
might reveal some potential users of the code?

Is your code public already? e.g. GitHub or Bitbucket?

Are there any pre-existing licences associated with your code? Can
you simply adopt the Biopython Licence? This like the MIT/BSD
licence in spirit (indeed we're considering moving to the 3-clause
BSD licence as that is more mainstream).

After a brief debate about appropriate namespace(s), I would suggest
you fork our repository and work on a branch...

Regards,

Peter

On Tue, Mar 3, 2015 at 5:05 PM, Joshua Klein <mobiusklein at gmail.com> wrote:
> I am sorry to hear that the OBF did not make it in this year. We are still
> interested in finding out if the Biopython team is interested in including
> glycomics tools in the core library, or in some other looser association.
> Real glycoinformatics is relatively inaccessible outside of two titanic Java
> libraries, which doesn't jive with how a lot of modern bioinformatics is
> done today.
>
> Thank you,
> Joshua Klein
>
> On Tue, Mar 3, 2015 at 10:25 AM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
>>
>> Hi Joshua,
>>
>> Thank you for you interest. Unfortunately we've just heard that
>> the  Open Bioinformatics Foundation (OBF) was not accepted
>> into the Google Summer of Code 2015 programme:
>>
>>
>> http://news.open-bio.org/news/2015/03/sadly-obf-not-accepted-for-gsoc-2015/
>>
>> It may be possible to pursue your project idea with one of the
>> accepted organisations (perhaps the Python Software Foundation)
>> by including a mentor from Biopython. We've not yet approached
>> any of the other potential partner organisations yet though.
>>
>> Good luck,
>>
>> Peter
>>
>>
>>
>> Peter
>>
>>
>> On Tue, Mar 3, 2015 at 2:58 AM, Joshua Klein <mobiusklein at gmail.com>
>> wrote:
>> > Hello,
>> >
>> > I've been working on a python library for reading, writing, and
>> > manipulating
>> > glycan structures and glycomics data. One of my collaborators suggested
>> > I
>> > inquire here if this might be of interest to the Biopython team and if
>> > it
>> > was not too late to apply for a Google Summer of Code sponsorship.
>> >
>> > The library can currently do the following:
>> >
>> > Read and write GlycoCT Condensed format carbohydrate structures that are
>> > concrete (having no variable or undefined structures)
>> > Read GlycoCTXML format carbohydrate structures that are concrete
>> > Manipulate the tree structure, adding and removing monosaccharide and
>> > substituent nodes, as well as altering existing nodes.
>> > Calculate elemental compositions for glycan structures
>> > Create arbitrary chemical derivitizations (e.g. permethylation) of
>> > glycan
>> > structures
>> > Generate B, C, Y, and Z fragments from structures as observed when
>> > analyzing
>> > a structure with tandem mass spectrometry.
>> > Make API calls against GlycomeDB to download structures and annotations
>> > on
>> > the fly
>> > Perform sub-tree inclusion and maximum common substructure searches with
>> > fuzzy matching.
>> > Plot glycan structures using the Consortium for Functional Glycomics
>> > symbol
>> > nomenclature with matplotlib.
>> > Perform error tolerance name inference on monosaccharides
>> >
>> > I am currently working on adding support for A and X cross-ring fragment
>> > generation and adding other serialization formats such as IUPAC and
>> > GlycoMinds Linear Codes.
>> >
>> > Currently, all of the features are implemented purely in Python.
>> >
>> > What other information, if any, can I provide?
>> >
>> > Thank you,
>> > Joshua Klein
>> >
>> > _______________________________________________
>> > GSoC mailing list
>> > GSoC at mailman.open-bio.org
>> > http://mailman.open-bio.org/mailman/listinfo/gsoc
>
>

From vincent at vincentdavis.net  Tue Mar  3 19:02:41 2015
From: vincent at vincentdavis.net (Vincent Davis)
Date: Tue, 3 Mar 2015 12:02:41 -0700
Subject: [Biopython-dev] Experimenting with migrating wiki to GitHub
	pages
In-Reply-To: <CAKVJ-_50F0OkGLZ3wMw-Y+iXg4uM1pLqsgdpMCEj4K4_Zur_Og@mail.gmail.com>
References: <CAKVJ-_50F0OkGLZ3wMw-Y+iXg4uM1pLqsgdpMCEj4K4_Zur_Og@mail.gmail.com>
Message-ID: <CALyJZZXnmLZurr6zKYoZX16j9Bj6-9Bx3U=e91XEHw7NHvOfaA@mail.gmail.com>

I think this I great! If I can help let me know.

On Monday, March 2, 2015, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> Dear all,
>
> Those of you who have contributed to the Biopython wiki
> in the past, and who have a GitHub account, might have
> spotted this new repository:
>
> https://github.com/peterjc/peterjc.github.io
>
> I am experimenting with migrating the MediaWiki content
> on biopython.org into MarkDown files (using pandoc, and
> saving each wiki revision as a git commit), for display as
> a webpage via GitHub Pages using Jekyll.
>
> https://github.com/peterjc/mediawiki_to_git_md
>
> The mapping from wiki user accounts to GitHub accounts
> was done by hand. Please email me directly if I made a
> mistake with your contributions. If I continue this effort I
> will be re-running the migration script in future.
>
> This conversion may not prove practical, and is not yet pretty
> or even functional, but potentially could one day ofter an
> alternative approach - and means we (the OBF) wouldn't
> need to maintain a server running MediaWiki and Apache.
>
> Note I'm not going to make any sudden changes to the
> current biopython.org site without any warning or discussion.
>
> Regards,
>
> Peter
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev at mailman.open-bio.org <javascript:;>
> http://mailman.open-bio.org/mailman/listinfo/biopython-dev
>


-- 
Sent from mobile app.
Vincent Davis
720-301-3003
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From p.j.a.cock at googlemail.com  Tue Mar  3 22:28:42 2015
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 3 Mar 2015 22:28:42 +0000
Subject: [Biopython-dev] Experimenting with migrating wiki to GitHub
	pages
In-Reply-To: <CALyJZZXnmLZurr6zKYoZX16j9Bj6-9Bx3U=e91XEHw7NHvOfaA@mail.gmail.com>
References: <CAKVJ-_50F0OkGLZ3wMw-Y+iXg4uM1pLqsgdpMCEj4K4_Zur_Og@mail.gmail.com>
	<CALyJZZXnmLZurr6zKYoZX16j9Bj6-9Bx3U=e91XEHw7NHvOfaA@mail.gmail.com>
Message-ID: <CAKVJ-_6VDeoEKX0NHGRmgrTnXvuLuX9z8n5rmwAvpiyP46pf6Q@mail.gmail.com>

On Tue, Mar 3, 2015 at 7:02 PM, Vincent Davis <vincent at vincentdavis.net> wrote:
> I think this I great! If I can help let me know.
>

Thanks!

I made some good progress tonight, first off to get tables to work
just required asking pandoc to produce GitHub Flavour Markdown:
https://github.com/peterjc/mediawiki_to_git_md/commit/4a0271a3a86d9b0fa8fcc4c2feb9aa54e77034d6

Getting the python snippets to display nicely on GitHub both in
mediawiki format at markdown was surprisingly simple:
https://github.com/peterjc/mediawiki_to_git_md/commit/0a94c8fc9206cfb1cb2c366dc6a69a4f07feb098

The good news is this means most of the pages now look pretty
when browsing my latest test branch on GitHub :)

There are still plenty of things which might be desirable, first
amongst them is getting the URLs to work (ideally preserving
the old wiki page URL patterns to make server migration
easier).

Peter

From mobiusklein at gmail.com  Wed Mar  4 03:57:38 2015
From: mobiusklein at gmail.com (Joshua Klein)
Date: Tue, 3 Mar 2015 22:57:38 -0500
Subject: [Biopython-dev] [GSoC] Project Proposal for Google Summer of
	Code
In-Reply-To: <CAKVJ-_5hrrPdrOAw3ZLoUA0WM0AfVwte=YDWkx60utnJ+DDr1w@mail.gmail.com>
References: <CAFZWoGZjEpajLSH+gHA6n-drD2DLFVN=SmysQr8VC2YtbjqYsA@mail.gmail.com>
	<CAKVJ-_48Gnpda8BVbPwqee894xRW2FqAvC635dGdRZyAAo0NXg@mail.gmail.com>
	<CAFZWoGapZJvso084jiGzDeG0g_dT_6p75fG24-TkUwA9nFJHvg@mail.gmail.com>
	<CAKVJ-_5hrrPdrOAw3ZLoUA0WM0AfVwte=YDWkx60utnJ+DDr1w@mail.gmail.com>
Message-ID: <CAFZWoGaQ7Ns-1rHQDEVS_J6Ada3BtK=0b=vLgMQrbup6uS8j+Q@mail.gmail.com>

The codebase can be found at https://github.com/mobiusklein/pygly2 where I
am actively committing new code. I had borrowed a large portion of an
implementation of one facet of the library from another project released
under the Apache 2.0 license, which is more restrictive than the BSD
license. I've contacted the author with regard to how he would like us to
treat that component.

Assuming all these things pass smoothly, namespaces may be a complicated
matter now that I have read through more of the Bio codebase. At the risk
of sounding too general, the vast majority of the common namespaces in Bio
are related to operations on many different data formats that happen to
result in Seq or SeqRecord objects. This leads to lots of infrastructure
and class design being built up around ways of converting many different
resources into those types of objects. It would be sensible to keep the
structures I'm building in a separate namespace as they talk about
distinctly different data structures that don't share any class hierarchy.

I should post to the general user mailing list to find out about general
interest before trying to make the value judgement on whether integration
is a worthwhile investment. That's biopython at mailman.open-bio.org, correct?

Thank you,
Joshua Klein

On Tue, Mar 3, 2015 at 1:25 PM, Peter Cock <p.j.a.cock at googlemail.com>
wrote:

> Thanks Joshua,
>
> Outside GSoC, adding glycoinformatics to Biopython sounds interesting.
> As far as I know none of our existing contributors do much in this area,
> so our feedback may be limited to Python style (PEP8 please) and
> practicalities like unit tests and documentation.
>
> We should probably also ask on the main Biopython mailing list - that
> might reveal some potential users of the code?
>
> Is your code public already? e.g. GitHub or Bitbucket?
>
> Are there any pre-existing licences associated with your code? Can
> you simply adopt the Biopython Licence? This like the MIT/BSD
> licence in spirit (indeed we're considering moving to the 3-clause
> BSD licence as that is more mainstream).
>
> After a brief debate about appropriate namespace(s), I would suggest
> you fork our repository and work on a branch...
>
> Regards,
>
> Peter
>
> On Tue, Mar 3, 2015 at 5:05 PM, Joshua Klein <mobiusklein at gmail.com>
> wrote:
> > I am sorry to hear that the OBF did not make it in this year. We are
> still
> > interested in finding out if the Biopython team is interested in
> including
> > glycomics tools in the core library, or in some other looser association.
> > Real glycoinformatics is relatively inaccessible outside of two titanic
> Java
> > libraries, which doesn't jive with how a lot of modern bioinformatics is
> > done today.
> >
> > Thank you,
> > Joshua Klein
> >
> > On Tue, Mar 3, 2015 at 10:25 AM, Peter Cock <p.j.a.cock at googlemail.com>
> > wrote:
> >>
> >> Hi Joshua,
> >>
> >> Thank you for you interest. Unfortunately we've just heard that
> >> the  Open Bioinformatics Foundation (OBF) was not accepted
> >> into the Google Summer of Code 2015 programme:
> >>
> >>
> >>
> http://news.open-bio.org/news/2015/03/sadly-obf-not-accepted-for-gsoc-2015/
> >>
> >> It may be possible to pursue your project idea with one of the
> >> accepted organisations (perhaps the Python Software Foundation)
> >> by including a mentor from Biopython. We've not yet approached
> >> any of the other potential partner organisations yet though.
> >>
> >> Good luck,
> >>
> >> Peter
> >>
> >>
> >>
> >> Peter
> >>
> >>
> >> On Tue, Mar 3, 2015 at 2:58 AM, Joshua Klein <mobiusklein at gmail.com>
> >> wrote:
> >> > Hello,
> >> >
> >> > I've been working on a python library for reading, writing, and
> >> > manipulating
> >> > glycan structures and glycomics data. One of my collaborators
> suggested
> >> > I
> >> > inquire here if this might be of interest to the Biopython team and if
> >> > it
> >> > was not too late to apply for a Google Summer of Code sponsorship.
> >> >
> >> > The library can currently do the following:
> >> >
> >> > Read and write GlycoCT Condensed format carbohydrate structures that
> are
> >> > concrete (having no variable or undefined structures)
> >> > Read GlycoCTXML format carbohydrate structures that are concrete
> >> > Manipulate the tree structure, adding and removing monosaccharide and
> >> > substituent nodes, as well as altering existing nodes.
> >> > Calculate elemental compositions for glycan structures
> >> > Create arbitrary chemical derivitizations (e.g. permethylation) of
> >> > glycan
> >> > structures
> >> > Generate B, C, Y, and Z fragments from structures as observed when
> >> > analyzing
> >> > a structure with tandem mass spectrometry.
> >> > Make API calls against GlycomeDB to download structures and
> annotations
> >> > on
> >> > the fly
> >> > Perform sub-tree inclusion and maximum common substructure searches
> with
> >> > fuzzy matching.
> >> > Plot glycan structures using the Consortium for Functional Glycomics
> >> > symbol
> >> > nomenclature with matplotlib.
> >> > Perform error tolerance name inference on monosaccharides
> >> >
> >> > I am currently working on adding support for A and X cross-ring
> fragment
> >> > generation and adding other serialization formats such as IUPAC and
> >> > GlycoMinds Linear Codes.
> >> >
> >> > Currently, all of the features are implemented purely in Python.
> >> >
> >> > What other information, if any, can I provide?
> >> >
> >> > Thank you,
> >> > Joshua Klein
> >> >
> >> > _______________________________________________
> >> > GSoC mailing list
> >> > GSoC at mailman.open-bio.org
> >> > http://mailman.open-bio.org/mailman/listinfo/gsoc
> >
> >
>
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From p.j.a.cock at googlemail.com  Wed Mar  4 09:22:52 2015
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 4 Mar 2015 09:22:52 +0000
Subject: [Biopython-dev] [GSoC] Project Proposal for Google Summer of
	Code
In-Reply-To: <CAFZWoGaQ7Ns-1rHQDEVS_J6Ada3BtK=0b=vLgMQrbup6uS8j+Q@mail.gmail.com>
References: <CAFZWoGZjEpajLSH+gHA6n-drD2DLFVN=SmysQr8VC2YtbjqYsA@mail.gmail.com>
	<CAKVJ-_48Gnpda8BVbPwqee894xRW2FqAvC635dGdRZyAAo0NXg@mail.gmail.com>
	<CAFZWoGapZJvso084jiGzDeG0g_dT_6p75fG24-TkUwA9nFJHvg@mail.gmail.com>
	<CAKVJ-_5hrrPdrOAw3ZLoUA0WM0AfVwte=YDWkx60utnJ+DDr1w@mail.gmail.com>
	<CAFZWoGaQ7Ns-1rHQDEVS_J6Ada3BtK=0b=vLgMQrbup6uS8j+Q@mail.gmail.com>
Message-ID: <CAKVJ-_6xPT9FaZiALjhC1=raR3pRmxTomM3wHkACGeDEOZqtxA@mail.gmail.com>

On Wed, Mar 4, 2015 at 3:57 AM, Joshua Klein <mobiusklein at gmail.com> wrote:
> The codebase can be found at https://github.com/mobiusklein/pygly2 where I
> am actively committing new code. I had borrowed a large portion of an
> implementation of one facet of the library from another project released
> under the Apache 2.0 license, which is more restrictive than the BSD
> license. I've contacted the author with regard to how he would like us to
> treat that component.

OK.

> Assuming all these things pass smoothly, namespaces may be a complicated
> matter now that I have read through more of the Bio codebase. At the risk of
> sounding too general, the vast majority of the common namespaces in Bio are
> related to operations on many different data formats that happen to result
> in Seq or SeqRecord objects. This leads to lots of infrastructure and class
> design being built up around ways of converting many different resources
> into those types of objects. It would be sensible to keep the structures I'm
> building in a separate namespace as they talk about distinctly different
> data structures that don't share any class hierarchy.

Certainly, e.g. Bio.Cluster is self contained and has nothing to do with
Seq/SeqRecord.

> I should post to the general user mailing list to find out about general
> interest before trying to make the value judgement on whether integration is
> a worthwhile investment. That's biopython at mailman.open-bio.org, correct?

Yes, although there are aliases that work too. See:
http://mailman.open-bio.org/mailman/listinfo/biopython

Thanks,

Peter

From j.p.g.l.m.rodrigues at gmail.com  Wed Mar  4 16:22:29 2015
From: j.p.g.l.m.rodrigues at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues?=)
Date: Wed, 04 Mar 2015 16:22:29 +0000
Subject: [Biopython-dev] Experimenting with migrating wiki to GitHub
	pages
References: <CAKVJ-_50F0OkGLZ3wMw-Y+iXg4uM1pLqsgdpMCEj4K4_Zur_Og@mail.gmail.com>
	<CALyJZZXnmLZurr6zKYoZX16j9Bj6-9Bx3U=e91XEHw7NHvOfaA@mail.gmail.com>
	<CAKVJ-_6VDeoEKX0NHGRmgrTnXvuLuX9z8n5rmwAvpiyP46pf6Q@mail.gmail.com>
Message-ID: <CAB=-b2a38bJ-FnGJK=jc6K59E5EHmMDF=96J1X1iev24Jum9+g@mail.gmail.com>

Hi Peter, all,

I've used Jekyll + Github to create our lab webpage
<http://www.bonvinlab.org>. Turns out to be an amazingly simple solution
and very collaborative as well. Nice thought of moving the wiki to such a
system.

A quick question: why not make a page from "scratch" ? Using a template and
converting the HTML to markdown seems pretty simple, it's just a matter of
agreeing on a layout.

Maybe I'm missing the point and you're doing this already..

Cheers,

Jo?o
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From p.j.a.cock at googlemail.com  Wed Mar  4 16:46:02 2015
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 4 Mar 2015 16:46:02 +0000
Subject: [Biopython-dev] Experimenting with migrating wiki to GitHub
	pages
In-Reply-To: <CAB=-b2a38bJ-FnGJK=jc6K59E5EHmMDF=96J1X1iev24Jum9+g@mail.gmail.com>
References: <CAKVJ-_50F0OkGLZ3wMw-Y+iXg4uM1pLqsgdpMCEj4K4_Zur_Og@mail.gmail.com>
	<CALyJZZXnmLZurr6zKYoZX16j9Bj6-9Bx3U=e91XEHw7NHvOfaA@mail.gmail.com>
	<CAKVJ-_6VDeoEKX0NHGRmgrTnXvuLuX9z8n5rmwAvpiyP46pf6Q@mail.gmail.com>
	<CAB=-b2a38bJ-FnGJK=jc6K59E5EHmMDF=96J1X1iev24Jum9+g@mail.gmail.com>
Message-ID: <CAKVJ-_5LZvOj8reiMn9Mgg_rk5JzM62=dEcTRPX-HWqhqAxwpQ@mail.gmail.com>

On Wed, Mar 4, 2015 at 4:22 PM, Jo?o Rodrigues
<j.p.g.l.m.rodrigues at gmail.com> wrote:
> Hi Peter, all,
>
> I've used Jekyll + Github to create our lab webpage. Turns out to be an
> amazingly simple solution and very collaborative as well. Nice thought of
> moving the wiki to such a system.
>
> A quick question: why not make a page from "scratch" ? Using a template and
> converting the HTML to markdown seems pretty simple, it's just a matter of
> agreeing on a layout.
>
> Maybe I'm missing the point and you're doing this already..
>
> Cheers,
>
> Jo?o

I've got the basic wiki content converted in markdown and showing nicely
(while preserving the wiki revisions and most of the contributors). Adding
a theme for a pretty layout is a finishing touch. First, all the links and files
need doing - definitely possible.

A key question is will it be as easy for people to edit as the wiki is/was?

Peter


From j.p.g.l.m.rodrigues at gmail.com  Wed Mar  4 16:48:27 2015
From: j.p.g.l.m.rodrigues at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues?=)
Date: Wed, 04 Mar 2015 16:48:27 +0000
Subject: [Biopython-dev] Experimenting with migrating wiki to GitHub
	pages
References: <CAKVJ-_50F0OkGLZ3wMw-Y+iXg4uM1pLqsgdpMCEj4K4_Zur_Og@mail.gmail.com>
	<CALyJZZXnmLZurr6zKYoZX16j9Bj6-9Bx3U=e91XEHw7NHvOfaA@mail.gmail.com>
	<CAKVJ-_6VDeoEKX0NHGRmgrTnXvuLuX9z8n5rmwAvpiyP46pf6Q@mail.gmail.com>
	<CAB=-b2a38bJ-FnGJK=jc6K59E5EHmMDF=96J1X1iev24Jum9+g@mail.gmail.com>
	<CAKVJ-_5LZvOj8reiMn9Mgg_rk5JzM62=dEcTRPX-HWqhqAxwpQ@mail.gmail.com>
Message-ID: <CAB=-b2arjHs708e+_S8XKS2cdwoxeRJQOikNsoPve-0ui7NT5w@mail.gmail.com>

We've been using our site as a "blog". It's extremely easy. Each commit is
a change to the website, e.g. a new page, new content, changing an image,
etc. Hosting on GitHub also makes it easy for everybody to make changes:
fork, change, pull request.

Peter Cock <p.j.a.cock at googlemail.com> escreveu no dia qua, 4/03/2015 ?s
17:46:

> On Wed, Mar 4, 2015 at 4:22 PM, Jo?o Rodrigues
> <j.p.g.l.m.rodrigues at gmail.com> wrote:
> > Hi Peter, all,
> >
> > I've used Jekyll + Github to create our lab webpage. Turns out to be an
> > amazingly simple solution and very collaborative as well. Nice thought of
> > moving the wiki to such a system.
> >
> > A quick question: why not make a page from "scratch" ? Using a template
> and
> > converting the HTML to markdown seems pretty simple, it's just a matter
> of
> > agreeing on a layout.
> >
> > Maybe I'm missing the point and you're doing this already..
> >
> > Cheers,
> >
> > Jo?o
>
> I've got the basic wiki content converted in markdown and showing nicely
> (while preserving the wiki revisions and most of the contributors). Adding
> a theme for a pretty layout is a finishing touch. First, all the links and
> files
> need doing - definitely possible.
>
> A key question is will it be as easy for people to edit as the wiki is/was?
>
> Peter
>
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From vincent at vincentdavis.net  Wed Mar  4 17:15:23 2015
From: vincent at vincentdavis.net (Vincent Davis)
Date: Wed, 4 Mar 2015 10:15:23 -0700
Subject: [Biopython-dev] mediawiki api.php
Message-ID: <CALyJZZX=BWqM=Wzz6zgo8jCrA7DrZSFkYR_YaMng67b9BiKVLA@mail.gmail.com>

Mediawiki seems to have an api. One of the things you can get is a list of
images.
for example on the mediwiki.org site, data for 5 in a xml format
http://en.wikipedia.org/w//api.php?format=xml&action=query&list=allimages&ailimit=5

I get nothing when I try this here.
http://biopython.org/wiki/api.php?format=xml&action=query&list=allimages&ailimit=5

more documentation on the images api
https://www.mediawiki.org/wiki/API:Allimages
and all api's
https://www.mediawiki.org/wiki/API:Main_page


Vincent Davis
720-301-3003
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From p.j.a.cock at googlemail.com  Wed Mar  4 20:22:37 2015
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 4 Mar 2015 20:22:37 +0000
Subject: [Biopython-dev] Experimenting with migrating wiki to GitHub
	pages
In-Reply-To: <CAB=-b2arjHs708e+_S8XKS2cdwoxeRJQOikNsoPve-0ui7NT5w@mail.gmail.com>
References: <CAKVJ-_50F0OkGLZ3wMw-Y+iXg4uM1pLqsgdpMCEj4K4_Zur_Og@mail.gmail.com>
	<CALyJZZXnmLZurr6zKYoZX16j9Bj6-9Bx3U=e91XEHw7NHvOfaA@mail.gmail.com>
	<CAKVJ-_6VDeoEKX0NHGRmgrTnXvuLuX9z8n5rmwAvpiyP46pf6Q@mail.gmail.com>
	<CAB=-b2a38bJ-FnGJK=jc6K59E5EHmMDF=96J1X1iev24Jum9+g@mail.gmail.com>
	<CAKVJ-_5LZvOj8reiMn9Mgg_rk5JzM62=dEcTRPX-HWqhqAxwpQ@mail.gmail.com>
	<CAB=-b2arjHs708e+_S8XKS2cdwoxeRJQOikNsoPve-0ui7NT5w@mail.gmail.com>
Message-ID: <CAKVJ-_5-ovm40f98KNcsE_yEHpeoaYv8f1fEm7O-fBCTr16CRw@mail.gmail.com>

On Wed, Mar 4, 2015 at 4:48 PM, Jo?o Rodrigues
<j.p.g.l.m.rodrigues at gmail.com> wrote:
> We've been using our site as a "blog". It's extremely easy. Each commit is a
> change to the website, e.g. a new page, new content, changing an image, etc.
> Hosting on GitHub also makes it easy for everybody to make changes: fork,
> change, pull request.

I'm glad to hear positive experiences about using GitHub Pages for
a group blog :)

I'm also thing about using this approach instead of WordPress
for the OBF blog, http://news.open-bio.org/ - ideally having first
extracted all the old posts with any images.

Peter


From p.j.a.cock at googlemail.com  Thu Mar  5 19:16:35 2015
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 5 Mar 2015 19:16:35 +0000
Subject: [Biopython-dev] Fwd: [Bosc-announce] BOSC 2015 Call for Abstracts
In-Reply-To: <26FBF6E4-4CDB-4BB9-A1F3-E72E4FB8C7DA@gmail.com>
References: <26FBF6E4-4CDB-4BB9-A1F3-E72E4FB8C7DA@gmail.com>
Message-ID: <CAKVJ-_6uzD5YyrLrxpKtkrFTW=wweQSa0_VxTfL9bL8-kY60+w@mail.gmail.com>

Shameless advert as BOSC co-chair: please come to give a talk
or poster at BOSC in Dublin this summer (and maybe stay on for
the full ISMB 2015 conference too?)

Peter

---------- Forwarded message ----------
From: Nomi Harris <nlharris at gmail.com>
Date: Thu, Mar 5, 2015 at 6:50 PM
Subject: [Bosc-announce] BOSC 2015 Call for Abstracts
To: bosc-announce at mailman.open-bio.org, members at open-bio.org, GMOD
Announcements List <gmod-announce at lists.sourceforge.net>
Cc: BOSC 2014 <bosc at open-bio.org>


Call for Abstracts for the 16th Annual Bioinformatics Open Source
Conference (BOSC 2015)
A Special Interest Group (SIG) of ISMB/ECCB 2015

Dates: 10-11 July, 2015
Location: Dublin, Ireland
Web site: http://www.open-bio.org/wiki/BOSC_2015
Email: bosc at open-bio.org
BOSC announcements mailing list:
http://lists.open-bio.org/mailman/listinfo/bosc-announce

Important Dates:
March 24, 2015: Registration opens for ISMB and BOSC
(https://www.iscb.org/ismb2015-registration)
April 3, 2015: Deadline for submitting BOSC abstracts
May 3, 2015: Notification of accepted talk abstracts emailed to authors
July 8-9, 2015: Codefest 2015, Dublin
(http://www.open-bio.org/wiki/Codefest_2015)
July 10-11, 2015: BOSC 2015, Dublin (http://www.open-bio.org/wiki/BOSC_2015)
July 10-14, 2015: ISMB/ECCB 2015, Dublin

The Bioinformatics Open Source Conference (BOSC) covers the wide range
of open source bioinformatics software being developed, and
encompasses the growing movement of Open Science, with its focus on
transparency, reproducibility, and data provenance. We welcome
submissions relating to all aspects of bioinformatics and open science
software, including new computational methods, reusable software
components, visualization, interoperability, and other approaches that
help to advance research in the biomolecular sciences. We particularly
wish to invite those who have not participated in previous BOSCs to
join us this year!

Two full days of talks, posters, panel discussions, and informal
discussion groups will enable BOSC attendees to interact with other
developers and share ideas and code, as well as learning about some of
the latest developments in the field of open source bioinformatics.
BOSC is sponsored by the Open Bioinformatics Foundation, a non-profit,
volunteer-run group dedicated to promoting the practice and philosophy
of Open Source software development and Open Science within the
biological research community.

We invite you to submit one-page abstracts for talks and posters. As
mentioned, any topics relevant to open source bioinformatics and open
science are welcome. Here are some potential session topics (but
please don't feel limited to these!):
   Open Science and Reproducible Research
   Standards and Interoperability
   Data Science
   Visualization
   Translational Bioinformatics
   Bioinformatics Open Source Libraries and Projects

If your company or organization is interested in being a sponsor for
BOSC 2015, please contact us! Sponsors in 2014 included Google, Eagle
Genomics, GigaScience, and Curoverse--we thank them for their support.

BOSC 2015 Organizing Committee:
Nomi Harris and Peter Cock (co-chairs), Raoul Jean Pierre Bonnal, Brad
Chapman, Robert Davey, Christopher Fields, Sarah Hird, Karsten Hokamp,
Hilmar Lapp.
http://www.open-bio.org/wiki/BOSC_2015
_______________________________________________
Bosc-announce mailing list
Bosc-announce at mailman.open-bio.org
http://mailman.open-bio.org/mailman/listinfo/bosc-announce

From p.j.a.cock at googlemail.com  Thu Mar  5 19:18:33 2015
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 5 Mar 2015 19:18:33 +0000
Subject: [Biopython-dev] Biopython Project Update 2015;
	was BOSC 2015 Call for Abstracts
Message-ID: <CAKVJ-_5yGzQMkoeZwVeymPpPaM2wEZe5GGTZ09+Rf1tvnQq3Gg@mail.gmail.com>

Who is thinking about attending BOSC 2015 and might like to
present the traditional "Biopython Project Update" short talk
this year?

Thanks,

Peter

On Thu, Mar 5, 2015 at 7:16 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> Shameless advert as BOSC co-chair: please come to give a talk
> or poster at BOSC in Dublin this summer (and maybe stay on for
> the full ISMB 2015 conference too?)
>
> Peter
>
> ---------- Forwarded message ----------
> From: Nomi Harris <nlharris at gmail.com>
> Date: Thu, Mar 5, 2015 at 6:50 PM
> Subject: [Bosc-announce] BOSC 2015 Call for Abstracts
> To: bosc-announce at mailman.open-bio.org, members at open-bio.org, GMOD
> Announcements List <gmod-announce at lists.sourceforge.net>
> Cc: BOSC 2014 <bosc at open-bio.org>
>
>
> Call for Abstracts for the 16th Annual Bioinformatics Open Source
> Conference (BOSC 2015)
> A Special Interest Group (SIG) of ISMB/ECCB 2015
>
> Dates: 10-11 July, 2015
> Location: Dublin, Ireland
> Web site: http://www.open-bio.org/wiki/BOSC_2015
> Email: bosc at open-bio.org
> BOSC announcements mailing list:
> http://lists.open-bio.org/mailman/listinfo/bosc-announce
>
> Important Dates:
> March 24, 2015: Registration opens for ISMB and BOSC
> (https://www.iscb.org/ismb2015-registration)
> April 3, 2015: Deadline for submitting BOSC abstracts
> May 3, 2015: Notification of accepted talk abstracts emailed to authors
> July 8-9, 2015: Codefest 2015, Dublin
> (http://www.open-bio.org/wiki/Codefest_2015)
> July 10-11, 2015: BOSC 2015, Dublin (http://www.open-bio.org/wiki/BOSC_2015)
> July 10-14, 2015: ISMB/ECCB 2015, Dublin
>
> The Bioinformatics Open Source Conference (BOSC) covers the wide range
> of open source bioinformatics software being developed, and
> encompasses the growing movement of Open Science, with its focus on
> transparency, reproducibility, and data provenance. We welcome
> submissions relating to all aspects of bioinformatics and open science
> software, including new computational methods, reusable software
> components, visualization, interoperability, and other approaches that
> help to advance research in the biomolecular sciences. We particularly
> wish to invite those who have not participated in previous BOSCs to
> join us this year!
>
> Two full days of talks, posters, panel discussions, and informal
> discussion groups will enable BOSC attendees to interact with other
> developers and share ideas and code, as well as learning about some of
> the latest developments in the field of open source bioinformatics.
> BOSC is sponsored by the Open Bioinformatics Foundation, a non-profit,
> volunteer-run group dedicated to promoting the practice and philosophy
> of Open Source software development and Open Science within the
> biological research community.
>
> We invite you to submit one-page abstracts for talks and posters. As
> mentioned, any topics relevant to open source bioinformatics and open
> science are welcome. Here are some potential session topics (but
> please don't feel limited to these!):
>    Open Science and Reproducible Research
>    Standards and Interoperability
>    Data Science
>    Visualization
>    Translational Bioinformatics
>    Bioinformatics Open Source Libraries and Projects
>
> If your company or organization is interested in being a sponsor for
> BOSC 2015, please contact us! Sponsors in 2014 included Google, Eagle
> Genomics, GigaScience, and Curoverse--we thank them for their support.
>
> BOSC 2015 Organizing Committee:
> Nomi Harris and Peter Cock (co-chairs), Raoul Jean Pierre Bonnal, Brad
> Chapman, Robert Davey, Christopher Fields, Sarah Hird, Karsten Hokamp,
> Hilmar Lapp.
> http://www.open-bio.org/wiki/BOSC_2015
> _______________________________________________
> Bosc-announce mailing list
> Bosc-announce at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/bosc-announce

From alexeymorozov1991 at gmail.com  Tue Mar 10 07:59:33 2015
From: alexeymorozov1991 at gmail.com (Alexey Morozov)
Date: Tue, 10 Mar 2015 15:59:33 +0800
Subject: [Biopython-dev] Binary blast DB reader
Message-ID: <CAK=7cMNggLeWRiw8ow763KDD6Am39Edva0-W6WtDbzjghMzgMg@mail.gmail.com>

Dear colleagues,
I have a pretty crude pure Python3 module that reads binary BLAST databases
(https://github.com/SynedraAcus/BinaryBlast). Is there any chance it'll
make to main distribuition as SeqIO subclass if I add iterator behaviour
and fix dirty hacks?

-- 
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.
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From p.j.a.cock at googlemail.com  Tue Mar 10 09:17:21 2015
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 10 Mar 2015 09:17:21 +0000
Subject: [Biopython-dev] Binary blast DB reader
In-Reply-To: <CAK=7cMNggLeWRiw8ow763KDD6Am39Edva0-W6WtDbzjghMzgMg@mail.gmail.com>
References: <CAK=7cMNggLeWRiw8ow763KDD6Am39Edva0-W6WtDbzjghMzgMg@mail.gmail.com>
Message-ID: <CAKVJ-_47h3NgGhH1mX+r8H_0-0rWF-t=gokiA0xH7h54MGkn3Q@mail.gmail.com>

Hi Alexey,

I think this would be a very interesting addition to Bio.SeqIO,
initially a simple iterator for parsing the records one by one
(like a binary FASTA file), but with more work if we can decode
the BLAST lookup files efficient random access via the
Bio.SeqIO.index interface would be great.

Your code currently only looks at protein databases - have
you tried nucleotide BLAST databases yet? I would expect
the basic structure to be quite similar...

Also for many uses parsing *.pal (and *.nal) alias files would
be important (e.g. accessing sequencing from the nr/nt
databases).

Once you have some functional tests, generalising Python 3
code to also run on Python 2.6 and 2.7 is not too hard - and
we would need to do that for inclusion in Biopython. See
the code in SffIO.py for another example which deals with
a binary sequence file format:

https://github.com/biopython/biopython/blob/master/Bio/SeqIO/SffIO.py

Peter



On Tue, Mar 10, 2015 at 7:59 AM, Alexey Morozov
<alexeymorozov1991 at gmail.com> wrote:
> Dear colleagues,
> I have a pretty crude pure Python3 module that reads binary BLAST databases
> (https://github.com/SynedraAcus/BinaryBlast). Is there any chance it'll make
> to main distribuition as SeqIO subclass if I add iterator behaviour and fix
> dirty hacks?
>
> --
> Alexey Morozov,
> LIN SB RAS, bioinformatics group.
> Irkutsk, Russia.
>
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython-dev

From alexeymorozov1991 at gmail.com  Wed Mar 11 03:54:26 2015
From: alexeymorozov1991 at gmail.com (Alexey Morozov)
Date: Wed, 11 Mar 2015 11:54:26 +0800
Subject: [Biopython-dev] Binary blast DB reader
In-Reply-To: <CAKVJ-_47h3NgGhH1mX+r8H_0-0rWF-t=gokiA0xH7h54MGkn3Q@mail.gmail.com>
References: <CAK=7cMNggLeWRiw8ow763KDD6Am39Edva0-W6WtDbzjghMzgMg@mail.gmail.com>
	<CAKVJ-_47h3NgGhH1mX+r8H_0-0rWF-t=gokiA0xH7h54MGkn3Q@mail.gmail.com>
Message-ID: <CAK=7cMOBCW_SrVp4=+dCRteWM7mW6voSZbJVhL7BJz452iBEXw@mail.gmail.com>

Yes, DNA support, alias files and so on will be added. I'm not sure about
indexing, though. That may be a nice option to have, but definitely not
default.

2015-03-10 17:17 GMT+08:00 Peter Cock <p.j.a.cock at googlemail.com>:

> Hi Alexey,
>
> I think this would be a very interesting addition to Bio.SeqIO,
> initially a simple iterator for parsing the records one by one
> (like a binary FASTA file), but with more work if we can decode
> the BLAST lookup files efficient random access via the
> Bio.SeqIO.index interface would be great.
>
> Your code currently only looks at protein databases - have
> you tried nucleotide BLAST databases yet? I would expect
> the basic structure to be quite similar...
>
> Also for many uses parsing *.pal (and *.nal) alias files would
> be important (e.g. accessing sequencing from the nr/nt
> databases).
>
> Once you have some functional tests, generalising Python 3
> code to also run on Python 2.6 and 2.7 is not too hard - and
> we would need to do that for inclusion in Biopython. See
> the code in SffIO.py for another example which deals with
> a binary sequence file format:
>
> https://github.com/biopython/biopython/blob/master/Bio/SeqIO/SffIO.py
>
> Peter
>
>
>
> On Tue, Mar 10, 2015 at 7:59 AM, Alexey Morozov
> <alexeymorozov1991 at gmail.com> wrote:
> > Dear colleagues,
> > I have a pretty crude pure Python3 module that reads binary BLAST
> databases
> > (https://github.com/SynedraAcus/BinaryBlast). Is there any chance it'll
> make
> > to main distribuition as SeqIO subclass if I add iterator behaviour and
> fix
> > dirty hacks?
> >
> > --
> > Alexey Morozov,
> > LIN SB RAS, bioinformatics group.
> > Irkutsk, Russia.
> >
> > _______________________________________________
> > Biopython-dev mailing list
> > Biopython-dev at mailman.open-bio.org
> > http://mailman.open-bio.org/mailman/listinfo/biopython-dev
>



-- 
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.
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From ben.bob at gmail.com  Wed Mar 11 12:45:05 2015
From: ben.bob at gmail.com (Bo Peng)
Date: Wed, 11 Mar 2015 07:45:05 -0500
Subject: [Biopython-dev] A workflow management module for BioPython.
Message-ID: <CAGX8AEnLQ=Jqxo2jJWdLvDUUswR4LBO7QF2w2eR6qN6Z=82cMA@mail.gmail.com>

Dear BioPython developers,

There has been dozens of workflow management systems but most of them
require users to learn a new system and even a new language. Because of the
strong need to convert shell commands to pipelines with advanced execution
features, we have developed a light-weight bioinformatics pipeline system
with emphasis on readability and sharing. The system uses .ini format for
pipeline specification (in comparison to XML format used by many other
systems such as galaxy) and specifies the core of pipelines (actions and
file flow) in a highly condensed and readable way. This makes it easier for
users to share pipelines with collaborators, adapt them to local running
environment, and update them for newer versions of tools and annotation
sources. The system uses a number of Python features in its pipeline
specification system (e.g. use of python expressions and lambda functions)
and uses Python for user-defined actions.

This tool has been developed and used by the variant tools community for a
while (tentatively named VPT,
http://varianttools.sourceforge.net/Pipeline/HomePage, with features
described in a powerpoint presentation on its home page). As a general
pipeline management tool that has been applied to many other areas such as
RNA seq data analysis, VPT does not really belong to variant tools so we
are thinking of moving it out of variant tools. Because BioPython does not
currently provide such a module, I am writing to see if there is any
interest in merging VPT to BioPython. It would most likely be a complete
re-design and re-implementation after incorporating your ideas but we are
willing to contribute the code to BioPython if you consider it as a
valuable addition to BioPython. In addition to the existing features, I am
thinking of actions that make use of BioPython's ability to query
databases, and functions to convert VPT pipelines to other systems such as
Galaxy and Taverna.

Thank you very much for your attention and please feel free to let me know
if you have any question or suggestion. If you are wondering about my
qualification, I am the author of a Python-based population genetics
simulation program simuPOP and had a long history of contributing to open
source projects such as the LyX project (former core developer).

Bo
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From alexeymorozov1991 at gmail.com  Fri Mar 13 11:06:01 2015
From: alexeymorozov1991 at gmail.com (Alexey Morozov)
Date: Fri, 13 Mar 2015 19:06:01 +0800
Subject: [Biopython-dev] Binary blast DB reader
In-Reply-To: <CAK=7cMOBCW_SrVp4=+dCRteWM7mW6voSZbJVhL7BJz452iBEXw@mail.gmail.com>
References: <CAK=7cMNggLeWRiw8ow763KDD6Am39Edva0-W6WtDbzjghMzgMg@mail.gmail.com>
	<CAKVJ-_47h3NgGhH1mX+r8H_0-0rWF-t=gokiA0xH7h54MGkn3Q@mail.gmail.com>
	<CAK=7cMOBCW_SrVp4=+dCRteWM7mW6voSZbJVhL7BJz452iBEXw@mail.gmail.com>
Message-ID: <CAK=7cMO32+AhKVC9P6rtPuLcoitmPaSa3Bv0Z1YTW-eT=Kg6Hw@mail.gmail.com>

I got the iterator support and random access working. Alias support can
also be worked around by using each of nr.*.pin bases as a separate DB. So
before I go to more complex stuff like proper Aliases and support for DNA,
I have a few integration-related questions:
1) How adding code to Biopython work anyway? Do I send a pull request to
main Biopython repo?
2) What handle you think SeqIO-compatible module should take, if any? BLAST
database is at least 3 files (if there are no aliases and no additional
indexes)
3) Is there any need to even bother with SeqIO.write()? Writing one
sequence is a major hassle and no one is gonna generate these bases
directly from Python when there is Bio.Applications

2015-03-11 11:54 GMT+08:00 Alexey Morozov <alexeymorozov1991 at gmail.com>:

> Yes, DNA support, alias files and so on will be added. I'm not sure about
> indexing, though. That may be a nice option to have, but definitely not
> default.
>
> 2015-03-10 17:17 GMT+08:00 Peter Cock <p.j.a.cock at googlemail.com>:
>
>> Hi Alexey,
>>
>> I think this would be a very interesting addition to Bio.SeqIO,
>> initially a simple iterator for parsing the records one by one
>> (like a binary FASTA file), but with more work if we can decode
>> the BLAST lookup files efficient random access via the
>> Bio.SeqIO.index interface would be great.
>>
>> Your code currently only looks at protein databases - have
>> you tried nucleotide BLAST databases yet? I would expect
>> the basic structure to be quite similar...
>>
>> Also for many uses parsing *.pal (and *.nal) alias files would
>> be important (e.g. accessing sequencing from the nr/nt
>> databases).
>>
>> Once you have some functional tests, generalising Python 3
>> code to also run on Python 2.6 and 2.7 is not too hard - and
>> we would need to do that for inclusion in Biopython. See
>> the code in SffIO.py for another example which deals with
>> a binary sequence file format:
>>
>> https://github.com/biopython/biopython/blob/master/Bio/SeqIO/SffIO.py
>>
>> Peter
>>
>>
>>
>> On Tue, Mar 10, 2015 at 7:59 AM, Alexey Morozov
>> <alexeymorozov1991 at gmail.com> wrote:
>> > Dear colleagues,
>> > I have a pretty crude pure Python3 module that reads binary BLAST
>> databases
>> > (https://github.com/SynedraAcus/BinaryBlast). Is there any chance
>> it'll make
>> > to main distribuition as SeqIO subclass if I add iterator behaviour and
>> fix
>> > dirty hacks?
>> >
>> > --
>> > Alexey Morozov,
>> > LIN SB RAS, bioinformatics group.
>> > Irkutsk, Russia.
>> >
>> > _______________________________________________
>> > Biopython-dev mailing list
>> > Biopython-dev at mailman.open-bio.org
>> > http://mailman.open-bio.org/mailman/listinfo/biopython-dev
>>
>
>
>
> --
> Alexey Morozov,
> LIN SB RAS, bioinformatics group.
> Irkutsk, Russia.
>



-- 
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.
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From p.j.a.cock at googlemail.com  Fri Mar 13 11:29:35 2015
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 13 Mar 2015 11:29:35 +0000
Subject: [Biopython-dev] Binary blast DB reader
In-Reply-To: <CAK=7cMO32+AhKVC9P6rtPuLcoitmPaSa3Bv0Z1YTW-eT=Kg6Hw@mail.gmail.com>
References: <CAK=7cMNggLeWRiw8ow763KDD6Am39Edva0-W6WtDbzjghMzgMg@mail.gmail.com>
	<CAKVJ-_47h3NgGhH1mX+r8H_0-0rWF-t=gokiA0xH7h54MGkn3Q@mail.gmail.com>
	<CAK=7cMOBCW_SrVp4=+dCRteWM7mW6voSZbJVhL7BJz452iBEXw@mail.gmail.com>
	<CAK=7cMO32+AhKVC9P6rtPuLcoitmPaSa3Bv0Z1YTW-eT=Kg6Hw@mail.gmail.com>
Message-ID: <CAKVJ-_73N5QfnR3+6DTPPAe4xrJSJLBr1wS+g3AwkoHeakp8qw@mail.gmail.com>

On Fri, Mar 13, 2015 at 11:06 AM, Alexey Morozov
<alexeymorozov1991 at gmail.com> wrote:
> I got the iterator support and random access working. Alias support can also
> be worked around by using each of nr.*.pin bases as a separate DB. So before
> I go to more complex stuff like proper Aliases and support for DNA, I have a
> few integration-related questions:

Great.

> 1) How adding code to Biopython work anyway? Do I send a pull request to
> main Biopython repo?

Yes please.

> 2) What handle you think SeqIO-compatible module should take, if any?
> BLAST database is at least 3 files (if there are no aliases and no additional
> indexes)

Unlike the rest of Bio.SeqIO, a single handle does not make sense here.

>From a user perspective I suggest we require the user give us the
BLAST database name as used with the BLAST command line tools.
i.e. The stem of the filename without the .p?? or .n?? extension.

The high level SeqIO API accepts either a filename or a handle. We have
special case code to determine which mode to open handles with (text or
binary), see variable _BinaryFormats in Bio/SeqIO/__init__.py - we'd
need something similar for BLAST database where we'd check the
argument is a string and not a handle.

> 3) Is there any need to even bother with SeqIO.write()?

I see no strong reason to attempt to write out a BLAST database from
within SeqIO (note the same issues apply regarding setting the filename).

> Writing one sequence is a major hassle and no one is gonna generate
> these bases directly from Python when there is Bio.Applications

Writing a single sequence BLAST database would be near useless,
but ought to be just part of the general case of writing a BLAST
database with many sequences.

Recommending the user call makeblastdb seems much more sensible.

Regards,

Peter

From christian at brueffer.de  Tue Mar 17 11:34:24 2015
From: christian at brueffer.de (Christian Brueffer)
Date: Tue, 17 Mar 2015 12:34:24 +0100
Subject: [Biopython-dev] Reproducible Biopython VM images
Message-ID: <55081140.2000609@brueffer.de>

Hi everyone,

for development, testing, and release engineering, it would be nice to 
have a comprehensive VM image that has all dependencies, and tools we 
have wrappers for already installed.  Even better if it's easy to 
re-create by anyone!

I've started working on this based on Vagrant 
(https://www.vagrantup.com/).  My current (minimal) work is in the "vm" 
branch at https://github.com/cbrueffer/biopython ; it consists the two 
added files Vagrantfile and vmbootstrap.sh.

A VM can be created by first installing Vagrant and a supported VM 
software (e.g., Virtualbox). Then:

git clone -b vm https://git at github.com/cbrueffer/biopython.git
cd biopython
vagrant up  # downloads the base OS image and executes vmbootstrap.sh
vagrant ssh  # SSH access to the VM

The vmbootstrap.sh script currently installs an (incomplete) set of 
dependencies, installs the checked out Biopython version and runs the 
tests in offline mode.  Some tests still fail due to the aforementioned 
(currently) unmet dependencies.

The directory from which "vagrant up" was called (in this case the 
repository root) is available as /vagrant from within the VM.

Feedback welcome!

Cheers,

Chris

From p.j.a.cock at googlemail.com  Tue Mar 17 12:01:51 2015
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 17 Mar 2015 12:01:51 +0000
Subject: [Biopython-dev] Reproducible Biopython VM images
In-Reply-To: <55081140.2000609@brueffer.de>
References: <55081140.2000609@brueffer.de>
Message-ID: <CAKVJ-_7epCGW=ObrX40CNaZOD4gqUeTtKaMvBZ8Lk8CUMNrFwQ@mail.gmail.com>

Hi Christian,

This seems interesting, although perhaps better in a separate repository
to the Biopython source code, which targets the current Biopython release?

Tiago might have looked at something similar when he was setting up
additional buildbot slaves for testing...

See also https://github.com/bioboxes/ - possibly of relevance?

Peter

On Tue, Mar 17, 2015 at 11:34 AM, Christian Brueffer
<christian at brueffer.de> wrote:
> Hi everyone,
>
> for development, testing, and release engineering, it would be nice to have
> a comprehensive VM image that has all dependencies, and tools we have
> wrappers for already installed.  Even better if it's easy to re-create by
> anyone!
>
> I've started working on this based on Vagrant (https://www.vagrantup.com/).
> My current (minimal) work is in the "vm" branch at
> https://github.com/cbrueffer/biopython ; it consists the two added files
> Vagrantfile and vmbootstrap.sh.
>
> A VM can be created by first installing Vagrant and a supported VM software
> (e.g., Virtualbox). Then:
>
> git clone -b vm https://git at github.com/cbrueffer/biopython.git
> cd biopython
> vagrant up  # downloads the base OS image and executes vmbootstrap.sh
> vagrant ssh  # SSH access to the VM
>
> The vmbootstrap.sh script currently installs an (incomplete) set of
> dependencies, installs the checked out Biopython version and runs the tests
> in offline mode.  Some tests still fail due to the aforementioned
> (currently) unmet dependencies.
>
> The directory from which "vagrant up" was called (in this case the
> repository root) is available as /vagrant from within the VM.
>
> Feedback welcome!
>
> Cheers,
>
> Chris
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython-dev

From christian at brueffer.de  Tue Mar 17 12:54:29 2015
From: christian at brueffer.de (Christian Brueffer)
Date: Tue, 17 Mar 2015 13:54:29 +0100
Subject: [Biopython-dev] Reproducible Biopython VM images
In-Reply-To: <CAKVJ-_7epCGW=ObrX40CNaZOD4gqUeTtKaMvBZ8Lk8CUMNrFwQ@mail.gmail.com>
References: <55081140.2000609@brueffer.de>
	<CAKVJ-_7epCGW=ObrX40CNaZOD4gqUeTtKaMvBZ8Lk8CUMNrFwQ@mail.gmail.com>
Message-ID: <55082405.4070402@brueffer.de>

Hi Peter,

as far as I understand efforts like BioBoxes, they are geared towards 
shipping released versions of tools.  Vagrant-based VMs are primarily 
meant for developer use, as they enable quick throw-away VM use.

That's also the reason having support for his in the main repository 
would be most beneficial; it allows one to check out the repository, run 
one command and have a fresh VM with a complete set of tests and the 
dependencies to run them.  This sets the bar for contributions very low.

Having something things in a separate repository would also work, 
probably best with instructions like this:

cd biopython
wget url-to-Vagrantfile
wget url-to-bootstrap-file
vagrant up

Tiago, I'd be very interested to hear about your work in this area :-)

Chris


On 2015-03-17 13:01, Peter Cock wrote:
> Hi Christian,
>
> This seems interesting, although perhaps better in a separate repository
> to the Biopython source code, which targets the current Biopython release?
>
> Tiago might have looked at something similar when he was setting up
> additional buildbot slaves for testing...
>
> See also https://github.com/bioboxes/ - possibly of relevance?
>
> Peter
>
> On Tue, Mar 17, 2015 at 11:34 AM, Christian Brueffer
> <christian at brueffer.de> wrote:
>> Hi everyone,
>>
>> for development, testing, and release engineering, it would be nice to have
>> a comprehensive VM image that has all dependencies, and tools we have
>> wrappers for already installed.  Even better if it's easy to re-create by
>> anyone!
>>
>> I've started working on this based on Vagrant (https://www.vagrantup.com/).
>> My current (minimal) work is in the "vm" branch at
>> https://github.com/cbrueffer/biopython ; it consists the two added files
>> Vagrantfile and vmbootstrap.sh.
>>
>> A VM can be created by first installing Vagrant and a supported VM software
>> (e.g., Virtualbox). Then:
>>
>> git clone -b vm https://git at github.com/cbrueffer/biopython.git
>> cd biopython
>> vagrant up  # downloads the base OS image and executes vmbootstrap.sh
>> vagrant ssh  # SSH access to the VM
>>
>> The vmbootstrap.sh script currently installs an (incomplete) set of
>> dependencies, installs the checked out Biopython version and runs the tests
>> in offline mode.  Some tests still fail due to the aforementioned
>> (currently) unmet dependencies.
>>
>> The directory from which "vagrant up" was called (in this case the
>> repository root) is available as /vagrant from within the VM.
>>
>> Feedback welcome!
>>
>> Cheers,
>>
>> Chris
>> _______________________________________________
>> Biopython-dev mailing list
>> Biopython-dev at mailman.open-bio.org
>> http://mailman.open-bio.org/mailman/listinfo/biopython-dev

From tra at popgen.net  Tue Mar 17 15:01:40 2015
From: tra at popgen.net (Tiago Antao)
Date: Tue, 17 Mar 2015 15:01:40 +0000
Subject: [Biopython-dev] Reproducible Biopython VM images
In-Reply-To: <55082405.4070402@brueffer.de>
References: <55081140.2000609@brueffer.de>
	<CAKVJ-_7epCGW=ObrX40CNaZOD4gqUeTtKaMvBZ8Lk8CUMNrFwQ@mail.gmail.com>
	<55082405.4070402@brueffer.de>
Message-ID: <20150317150140.45d42be4@lnx>

Hi,

I have been working quite a bit with docker. I have quite a few
containers available:

https://github.com/tiagoantao/my-containers/tree/master/biopython
Here you can find:
buildbot containers:
Biopython2-Test
Biopython3-Test

Currently operational on buildbot

Probably more interesting:
tutorials:
Biopython2-Tutorial
Biopython3-Tutorial
A work in progress with part of the tutorial converted to ipython
notebooks. They should work fine (but the tutorials are incomplete)

There is also
Biopython2
Biopython3

Which give you a installed Biopython on a docker container (which you
can login into and start using from the command line)

If you want to discuss this, I would be very happy.
I ended up going for docker and not vagrant...

Tiago

On Tue, 17 Mar 2015 13:54:29 +0100
Christian Brueffer <christian at brueffer.de> wrote:

> Hi Peter,
> 
> as far as I understand efforts like BioBoxes, they are geared towards 
> shipping released versions of tools.  Vagrant-based VMs are primarily 
> meant for developer use, as they enable quick throw-away VM use.
> 
> That's also the reason having support for his in the main repository 
> would be most beneficial; it allows one to check out the repository,
> run one command and have a fresh VM with a complete set of tests and
> the dependencies to run them.  This sets the bar for contributions
> very low.
> 
> Having something things in a separate repository would also work, 
> probably best with instructions like this:
> 
> cd biopython
> wget url-to-Vagrantfile
> wget url-to-bootstrap-file
> vagrant up
> 
> Tiago, I'd be very interested to hear about your work in this area :-)
> 
> Chris
> 
> 
> On 2015-03-17 13:01, Peter Cock wrote:
> > Hi Christian,
> >
> > This seems interesting, although perhaps better in a separate
> > repository to the Biopython source code, which targets the current
> > Biopython release?
> >
> > Tiago might have looked at something similar when he was setting up
> > additional buildbot slaves for testing...
> >
> > See also https://github.com/bioboxes/ - possibly of relevance?
> >
> > Peter
> >
> > On Tue, Mar 17, 2015 at 11:34 AM, Christian Brueffer
> > <christian at brueffer.de> wrote:
> >> Hi everyone,
> >>
> >> for development, testing, and release engineering, it would be
> >> nice to have a comprehensive VM image that has all dependencies,
> >> and tools we have wrappers for already installed.  Even better if
> >> it's easy to re-create by anyone!
> >>
> >> I've started working on this based on Vagrant
> >> (https://www.vagrantup.com/). My current (minimal) work is in the
> >> "vm" branch at https://github.com/cbrueffer/biopython ; it
> >> consists the two added files Vagrantfile and vmbootstrap.sh.
> >>
> >> A VM can be created by first installing Vagrant and a supported VM
> >> software (e.g., Virtualbox). Then:
> >>
> >> git clone -b vm https://git at github.com/cbrueffer/biopython.git
> >> cd biopython
> >> vagrant up  # downloads the base OS image and executes
> >> vmbootstrap.sh vagrant ssh  # SSH access to the VM
> >>
> >> The vmbootstrap.sh script currently installs an (incomplete) set of
> >> dependencies, installs the checked out Biopython version and runs
> >> the tests in offline mode.  Some tests still fail due to the
> >> aforementioned (currently) unmet dependencies.
> >>
> >> The directory from which "vagrant up" was called (in this case the
> >> repository root) is available as /vagrant from within the VM.
> >>
> >> Feedback welcome!
> >>
> >> Cheers,
> >>
> >> Chris
> >> _______________________________________________
> >> Biopython-dev mailing list
> >> Biopython-dev at mailman.open-bio.org
> >> http://mailman.open-bio.org/mailman/listinfo/biopython-dev
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython-dev


From christian at brueffer.de  Tue Mar 24 09:46:48 2015
From: christian at brueffer.de (Christian Brueffer)
Date: Tue, 24 Mar 2015 10:46:48 +0100
Subject: [Biopython-dev] Reproducible Biopython VM images
In-Reply-To: <20150317150140.45d42be4@lnx>
References: <55081140.2000609@brueffer.de>	<CAKVJ-_7epCGW=ObrX40CNaZOD4gqUeTtKaMvBZ8Lk8CUMNrFwQ@mail.gmail.com>	<55082405.4070402@brueffer.de>
	<20150317150140.45d42be4@lnx>
Message-ID: <55113288.3090200@brueffer.de>

Hi Tiago,

nice work!  Looks like my Vagrant stuff in redundant indeed and I can 
abandon it.

Any chance we can make this a bit more visible?  A paragraph in the 
README would be a good start; I can whip something up if we agree this 
is a good idea.

Cheers,

Chris


On 2015-03-17 16:01, Tiago Antao wrote:
> Hi,
>
> I have been working quite a bit with docker. I have quite a few
> containers available:
>
> https://github.com/tiagoantao/my-containers/tree/master/biopython
> Here you can find:
> buildbot containers:
> Biopython2-Test
> Biopython3-Test
>
> Currently operational on buildbot
>
> Probably more interesting:
> tutorials:
> Biopython2-Tutorial
> Biopython3-Tutorial
> A work in progress with part of the tutorial converted to ipython
> notebooks. They should work fine (but the tutorials are incomplete)
>
> There is also
> Biopython2
> Biopython3
>
> Which give you a installed Biopython on a docker container (which you
> can login into and start using from the command line)
>
> If you want to discuss this, I would be very happy.
> I ended up going for docker and not vagrant...
>
> Tiago
>
> On Tue, 17 Mar 2015 13:54:29 +0100
> Christian Brueffer <christian at brueffer.de> wrote:
>
>> Hi Peter,
>>
>> as far as I understand efforts like BioBoxes, they are geared towards
>> shipping released versions of tools.  Vagrant-based VMs are primarily
>> meant for developer use, as they enable quick throw-away VM use.
>>
>> That's also the reason having support for his in the main repository
>> would be most beneficial; it allows one to check out the repository,
>> run one command and have a fresh VM with a complete set of tests and
>> the dependencies to run them.  This sets the bar for contributions
>> very low.
>>
>> Having something things in a separate repository would also work,
>> probably best with instructions like this:
>>
>> cd biopython
>> wget url-to-Vagrantfile
>> wget url-to-bootstrap-file
>> vagrant up
>>
>> Tiago, I'd be very interested to hear about your work in this area :-)
>>
>> Chris
>>
>>
>> On 2015-03-17 13:01, Peter Cock wrote:
>>> Hi Christian,
>>>
>>> This seems interesting, although perhaps better in a separate
>>> repository to the Biopython source code, which targets the current
>>> Biopython release?
>>>
>>> Tiago might have looked at something similar when he was setting up
>>> additional buildbot slaves for testing...
>>>
>>> See also https://github.com/bioboxes/ - possibly of relevance?
>>>
>>> Peter
>>>
>>> On Tue, Mar 17, 2015 at 11:34 AM, Christian Brueffer
>>> <christian at brueffer.de> wrote:
>>>> Hi everyone,
>>>>
>>>> for development, testing, and release engineering, it would be
>>>> nice to have a comprehensive VM image that has all dependencies,
>>>> and tools we have wrappers for already installed.  Even better if
>>>> it's easy to re-create by anyone!
>>>>
>>>> I've started working on this based on Vagrant
>>>> (https://www.vagrantup.com/). My current (minimal) work is in the
>>>> "vm" branch at https://github.com/cbrueffer/biopython ; it
>>>> consists the two added files Vagrantfile and vmbootstrap.sh.
>>>>
>>>> A VM can be created by first installing Vagrant and a supported VM
>>>> software (e.g., Virtualbox). Then:
>>>>
>>>> git clone -b vm https://git at github.com/cbrueffer/biopython.git
>>>> cd biopython
>>>> vagrant up  # downloads the base OS image and executes
>>>> vmbootstrap.sh vagrant ssh  # SSH access to the VM
>>>>
>>>> The vmbootstrap.sh script currently installs an (incomplete) set of
>>>> dependencies, installs the checked out Biopython version and runs
>>>> the tests in offline mode.  Some tests still fail due to the
>>>> aforementioned (currently) unmet dependencies.
>>>>
>>>> The directory from which "vagrant up" was called (in this case the
>>>> repository root) is available as /vagrant from within the VM.
>>>>
>>>> Feedback welcome!
>>>>
>>>> Cheers,
>>>>
>>>> Chris
>>>> _______________________________________________
>>>> Biopython-dev mailing list
>>>> Biopython-dev at mailman.open-bio.org
>>>> http://mailman.open-bio.org/mailman/listinfo/biopython-dev
>> _______________________________________________
>> Biopython-dev mailing list
>> Biopython-dev at mailman.open-bio.org
>> http://mailman.open-bio.org/mailman/listinfo/biopython-dev
>

From p.j.a.cock at googlemail.com  Tue Mar 24 11:54:54 2015
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 24 Mar 2015 11:54:54 +0000
Subject: [Biopython-dev] Reproducible Biopython VM images
In-Reply-To: <55113288.3090200@brueffer.de>
References: <55081140.2000609@brueffer.de>
	<CAKVJ-_7epCGW=ObrX40CNaZOD4gqUeTtKaMvBZ8Lk8CUMNrFwQ@mail.gmail.com>
	<55082405.4070402@brueffer.de> <20150317150140.45d42be4@lnx>
	<55113288.3090200@brueffer.de>
Message-ID: <CAKVJ-_7=OASG8--CuWuNi3zqR+si5VQZO=nJAqCxXX6K=SF=PQ@mail.gmail.com>

On Tue, Mar 24, 2015 at 9:46 AM, Christian Brueffer
<christian at brueffer.de> wrote:
> Hi Tiago,
>
> nice work!  Looks like my Vagrant stuff in redundant indeed and I can
> abandon it.
>
> Any chance we can make this a bit more visible?  A paragraph in the README
> would be a good start; I can whip something up if we agree this is a good
> idea.
>
> Cheers,
>
> Chris

Related to this, if there is general interest we could have another
repository on GitHub for docker containers (much like we have
a small repository for Biopython's Galaxy packaging).

Peter

From dalloliogm at gmail.com  Tue Mar 24 14:00:27 2015
From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio)
Date: Tue, 24 Mar 2015 14:00:27 +0000
Subject: [Biopython-dev] Reproducible Biopython VM images
In-Reply-To: <CAKVJ-_7=OASG8--CuWuNi3zqR+si5VQZO=nJAqCxXX6K=SF=PQ@mail.gmail.com>
References: <55081140.2000609@brueffer.de>
	<CAKVJ-_7epCGW=ObrX40CNaZOD4gqUeTtKaMvBZ8Lk8CUMNrFwQ@mail.gmail.com>
	<55082405.4070402@brueffer.de> <20150317150140.45d42be4@lnx>
	<55113288.3090200@brueffer.de>
	<CAKVJ-_7=OASG8--CuWuNi3zqR+si5VQZO=nJAqCxXX6K=SF=PQ@mail.gmail.com>
Message-ID: <CANv73HTL1xpjk=QXmSgh6FJrmhSoaVwMvgjaVTx=fYGHsHqvyw@mail.gmail.com>

Hello,
this is a very interesting discussion. For docker containers there is
already a Bio-Docker repository on github:
- http://biodocker.github.io/
- https://github.com/BioDocker

It also contains a BioPython image, although Tiago's containers are more
complete and include many tutorials.

Best,
Gio

G

On Tue, Mar 24, 2015 at 11:54 AM, Peter Cock <p.j.a.cock at googlemail.com>
wrote:

> On Tue, Mar 24, 2015 at 9:46 AM, Christian Brueffer
> <christian at brueffer.de> wrote:
> > Hi Tiago,
> >
> > nice work!  Looks like my Vagrant stuff in redundant indeed and I can
> > abandon it.
> >
> > Any chance we can make this a bit more visible?  A paragraph in the
> README
> > would be a good start; I can whip something up if we agree this is a good
> > idea.
> >
> > Cheers,
> >
> > Chris
>
> Related to this, if there is general interest we could have another
> repository on GitHub for docker containers (much like we have
> a small repository for Biopython's Galaxy packaging).
>
> Peter
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython-dev
>



-- 
Giovanni Marco Dall'Olio, PhD
Division of Cancer Studies,
King's College of London (UK)

My blog on bioinformatics: http://bioinfoblog.it
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From tra at popgen.net  Tue Mar 24 15:06:17 2015
From: tra at popgen.net (Tiago Antao)
Date: Tue, 24 Mar 2015 15:06:17 +0000
Subject: [Biopython-dev] Reproducible Biopython VM images
In-Reply-To: <55113288.3090200@brueffer.de>
References: <55081140.2000609@brueffer.de>
	<CAKVJ-_7epCGW=ObrX40CNaZOD4gqUeTtKaMvBZ8Lk8CUMNrFwQ@mail.gmail.com>
	<55082405.4070402@brueffer.de> <20150317150140.45d42be4@lnx>
	<55113288.3090200@brueffer.de>
Message-ID: <20150324150617.5be0c9ac@lnx>

Hi Christian and all,


Glad that you like it.

If people want to use this, I am fine with the idea.
As I said, I currently have 3 containers (times 2 for the Python
versions)

The test one is, I think just for us doing integration testing
(buildbot). I would not publicize it much (only on the dev pages).

The basic one, I think is fine. It allows direct ssh into a Biopython
environment complete with almost all binaries.

The tutorial one is also fine, though I still have to finalize the
porting of the Tutorial to notebooks (in truth, I think the Tutorial
should be adapted to the notebook environment).

I think there should be a fourth container which is basically the basic
with a IPython Notebook interface on top. This is trivial to produce
and could take care of it.

Again, I am fine with whatever you all decide what to do. For instance
Peter's suggestion is cool, probably with some change to the docs so
that people know that this exists...

Tiago

From p.j.a.cock at googlemail.com  Tue Mar 24 15:08:58 2015
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 24 Mar 2015 15:08:58 +0000
Subject: [Biopython-dev] Reproducible Biopython VM images
In-Reply-To: <CANv73HTL1xpjk=QXmSgh6FJrmhSoaVwMvgjaVTx=fYGHsHqvyw@mail.gmail.com>
References: <55081140.2000609@brueffer.de>
	<CAKVJ-_7epCGW=ObrX40CNaZOD4gqUeTtKaMvBZ8Lk8CUMNrFwQ@mail.gmail.com>
	<55082405.4070402@brueffer.de> <20150317150140.45d42be4@lnx>
	<55113288.3090200@brueffer.de>
	<CAKVJ-_7=OASG8--CuWuNi3zqR+si5VQZO=nJAqCxXX6K=SF=PQ@mail.gmail.com>
	<CANv73HTL1xpjk=QXmSgh6FJrmhSoaVwMvgjaVTx=fYGHsHqvyw@mail.gmail.com>
Message-ID: <CAKVJ-_4Tgu=c1eMRUHamUmPDzkxUcs8weQifrKT2mGHrBE=mDw@mail.gmail.com>

On Tue, Mar 24, 2015 at 2:00 PM, Giovanni Marco Dall'Olio
<dalloliogm at gmail.com> wrote:
> Hello,
> this is a very interesting discussion. For docker containers there is
> already a Bio-Docker repository on github:
> - http://biodocker.github.io/
> - https://github.com/BioDocker
>
> It also contains a BioPython image, although Tiago's containers are more
> complete and include many tutorials.
>
> Best,
> Gio
>
> G

There does not seem to have been any activity on BioDocker
since July 2014, however this might be combining with BioBoxes
which I mentioned earlier, see:

https://github.com/bioboxes/rfc/issues/70

Peter

From p.j.a.cock at googlemail.com  Fri Mar 27 13:07:34 2015
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 27 Mar 2015 13:07:34 +0000
Subject: [Biopython-dev] Biopython Project Update 2015;
	was BOSC 2015 Call for Abstracts
In-Reply-To: <CAKVJ-_5yGzQMkoeZwVeymPpPaM2wEZe5GGTZ09+Rf1tvnQq3Gg@mail.gmail.com>
References: <CAKVJ-_5yGzQMkoeZwVeymPpPaM2wEZe5GGTZ09+Rf1tvnQq3Gg@mail.gmail.com>
Message-ID: <CAKVJ-_5OQQaOhbEWjm8NM33B7X9WVY=H728uGr9Qz5o4=h_ATA@mail.gmail.com>

Hello again,

Still no volunteers to represent Biopython at BOSC in Dublin?
I would prefer someone else to do this - ideally one of our
newer/younger contributors?

Is anyone already planning to attend ISMB/ECCB 2015?
We can ask for a BOSC fee waiver if that makes a difference.

We've still got a week before the abstracts are due - as a
project update talk alone, this would normally be a short talk.
However, you could propose combining this with content on
how you'd used Biopython in your research, or something?

If there are no volunteers, then I guess I'll present again...

Regards,

Peter

On Thu, Mar 5, 2015 at 7:18 PM, Peter Cock <p.j.a.cock at googlemail.com>
wrote:

> Who is thinking about attending BOSC 2015 and might like to
> present the traditional "Biopython Project Update" short talk
> this year?
>
> Thanks,
>
> Peter
>
> On Thu, Mar 5, 2015 at 7:16 PM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
> > Shameless advert as BOSC co-chair: please come to give a talk
> > or poster at BOSC in Dublin this summer (and maybe stay on for
> > the full ISMB 2015 conference too?)
> >
> > Peter
> >
> > ---------- Forwarded message ----------
> > From: Nomi Harris <nlharris at gmail.com>
> > Date: Thu, Mar 5, 2015 at 6:50 PM
> > Subject: [Bosc-announce] BOSC 2015 Call for Abstracts
> > To: bosc-announce at mailman.open-bio.org, members at open-bio.org, GMOD
> > Announcements List <gmod-announce at lists.sourceforge.net>
> > Cc: BOSC 2014 <bosc at open-bio.org>
> >
> >
> > Call for Abstracts for the 16th Annual Bioinformatics Open Source
> > Conference (BOSC 2015)
> > A Special Interest Group (SIG) of ISMB/ECCB 2015
> >
> > Dates: 10-11 July, 2015
> > Location: Dublin, Ireland
> > Web site: http://www.open-bio.org/wiki/BOSC_2015
> > Email: bosc at open-bio.org
> > BOSC announcements mailing list:
> > http://lists.open-bio.org/mailman/listinfo/bosc-announce
> >
> > Important Dates:
> > March 24, 2015: Registration opens for ISMB and BOSC
> > (https://www.iscb.org/ismbeccb2015-registration)
> > April 3, 2015: Deadline for submitting BOSC abstracts
> > May 3, 2015: Notification of accepted talk abstracts emailed to authors
> > July 8-9, 2015: Codefest 2015, Dublin
> > (http://www.open-bio.org/wiki/Codefest_2015)
> > July 10-11, 2015: BOSC 2015, Dublin (
> http://www.open-bio.org/wiki/BOSC_2015)
> > July 10-14, 2015: ISMB/ECCB 2015, Dublin
> >
> > The Bioinformatics Open Source Conference (BOSC) covers the wide range
> > of open source bioinformatics software being developed, and
> > encompasses the growing movement of Open Science, with its focus on
> > transparency, reproducibility, and data provenance. We welcome
> > submissions relating to all aspects of bioinformatics and open science
> > software, including new computational methods, reusable software
> > components, visualization, interoperability, and other approaches that
> > help to advance research in the biomolecular sciences. We particularly
> > wish to invite those who have not participated in previous BOSCs to
> > join us this year!
> >
> > Two full days of talks, posters, panel discussions, and informal
> > discussion groups will enable BOSC attendees to interact with other
> > developers and share ideas and code, as well as learning about some of
> > the latest developments in the field of open source bioinformatics.
> > BOSC is sponsored by the Open Bioinformatics Foundation, a non-profit,
> > volunteer-run group dedicated to promoting the practice and philosophy
> > of Open Source software development and Open Science within the
> > biological research community.
> >
> > We invite you to submit one-page abstracts for talks and posters. As
> > mentioned, any topics relevant to open source bioinformatics and open
> > science are welcome. Here are some potential session topics (but
> > please don't feel limited to these!):
> >    Open Science and Reproducible Research
> >    Standards and Interoperability
> >    Data Science
> >    Visualization
> >    Translational Bioinformatics
> >    Bioinformatics Open Source Libraries and Projects
> >
> > If your company or organization is interested in being a sponsor for
> > BOSC 2015, please contact us! Sponsors in 2014 included Google, Eagle
> > Genomics, GigaScience, and Curoverse--we thank them for their support.
> >
> > BOSC 2015 Organizing Committee:
> > Nomi Harris and Peter Cock (co-chairs), Raoul Jean Pierre Bonnal, Brad
> > Chapman, Robert Davey, Christopher Fields, Sarah Hird, Karsten Hokamp,
> > Hilmar Lapp.
> > http://www.open-bio.org/wiki/BOSC_2015
> > _______________________________________________
> > Bosc-announce mailing list
> > Bosc-announce at mailman.open-bio.org
> > http://mailman.open-bio.org/mailman/listinfo/bosc-announce
>
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From j.p.g.l.m.rodrigues at gmail.com  Fri Mar 27 13:12:24 2015
From: j.p.g.l.m.rodrigues at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues?=)
Date: Fri, 27 Mar 2015 13:12:24 +0000
Subject: [Biopython-dev] Biopython Project Update 2015;
 was BOSC 2015 Call for Abstracts
In-Reply-To: <CAKVJ-_5OQQaOhbEWjm8NM33B7X9WVY=H728uGr9Qz5o4=h_ATA@mail.gmail.com>
References: <CAKVJ-_5yGzQMkoeZwVeymPpPaM2wEZe5GGTZ09+Rf1tvnQq3Gg@mail.gmail.com>
	<CAKVJ-_5OQQaOhbEWjm8NM33B7X9WVY=H728uGr9Qz5o4=h_ATA@mail.gmail.com>
Message-ID: <CAB=-b2bsQtCDKSdY98x6o7nRpC+Lnz3syBqeZ5058PxVVsnUhA@mail.gmail.com>

Hi Peter,

I'm considering going to the BOSC this year (not to ISMB/ECCB), still
weighing my options. If I would go, I wouldn't mind presenting, maybe
indeed including a bit of how we use Biopython here in the lab. How long is
a short talk? I would consider going for the Codefest and BOSC. Who else is
planning to go?

Cheers,

Jo?o

Peter Cock <p.j.a.cock at googlemail.com> escreveu no dia sex, 27/03/2015 ?s
14:07:

> Hello again,
>
> Still no volunteers to represent Biopython at BOSC in Dublin?
> I would prefer someone else to do this - ideally one of our
> newer/younger contributors?
>
> Is anyone already planning to attend ISMB/ECCB 2015?
> We can ask for a BOSC fee waiver if that makes a difference.
>
> We've still got a week before the abstracts are due - as a
> project update talk alone, this would normally be a short talk.
> However, you could propose combining this with content on
> how you'd used Biopython in your research, or something?
>
> If there are no volunteers, then I guess I'll present again...
>
> Regards,
>
> Peter
>
> On Thu, Mar 5, 2015 at 7:18 PM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
>
>> Who is thinking about attending BOSC 2015 and might like to
>> present the traditional "Biopython Project Update" short talk
>> this year?
>>
>> Thanks,
>>
>> Peter
>>
>> On Thu, Mar 5, 2015 at 7:16 PM, Peter Cock <p.j.a.cock at googlemail.com>
>> wrote:
>> > Shameless advert as BOSC co-chair: please come to give a talk
>> > or poster at BOSC in Dublin this summer (and maybe stay on for
>> > the full ISMB 2015 conference too?)
>> >
>> > Peter
>> >
>> > ---------- Forwarded message ----------
>> > From: Nomi Harris <nlharris at gmail.com>
>> > Date: Thu, Mar 5, 2015 at 6:50 PM
>> > Subject: [Bosc-announce] BOSC 2015 Call for Abstracts
>> > To: bosc-announce at mailman.open-bio.org, members at open-bio.org, GMOD
>> > Announcements List <gmod-announce at lists.sourceforge.net>
>> > Cc: BOSC 2014 <bosc at open-bio.org>
>> >
>> >
>> > Call for Abstracts for the 16th Annual Bioinformatics Open Source
>> > Conference (BOSC 2015)
>> > A Special Interest Group (SIG) of ISMB/ECCB 2015
>> >
>> > Dates: 10-11 July, 2015
>> > Location: Dublin, Ireland
>> > Web site: http://www.open-bio.org/wiki/BOSC_2015
>> > Email: bosc at open-bio.org
>> > BOSC announcements mailing list:
>> > http://lists.open-bio.org/mailman/listinfo/bosc-announce
>> >
>> > Important Dates:
>> > March 24, 2015: Registration opens for ISMB and BOSC
>>
> > (https://www.iscb.org/ismbeccb2015-registration)
>
>
>> > April 3, 2015: Deadline for submitting BOSC abstracts
>> > May 3, 2015: Notification of accepted talk abstracts emailed to authors
>> > July 8-9, 2015: Codefest 2015, Dublin
>> > (http://www.open-bio.org/wiki/Codefest_2015)
>> > July 10-11, 2015: BOSC 2015, Dublin (
>> http://www.open-bio.org/wiki/BOSC_2015)
>> > July 10-14, 2015: ISMB/ECCB 2015, Dublin
>> >
>> > The Bioinformatics Open Source Conference (BOSC) covers the wide range
>> > of open source bioinformatics software being developed, and
>> > encompasses the growing movement of Open Science, with its focus on
>> > transparency, reproducibility, and data provenance. We welcome
>> > submissions relating to all aspects of bioinformatics and open science
>> > software, including new computational methods, reusable software
>> > components, visualization, interoperability, and other approaches that
>> > help to advance research in the biomolecular sciences. We particularly
>> > wish to invite those who have not participated in previous BOSCs to
>> > join us this year!
>> >
>> > Two full days of talks, posters, panel discussions, and informal
>> > discussion groups will enable BOSC attendees to interact with other
>> > developers and share ideas and code, as well as learning about some of
>> > the latest developments in the field of open source bioinformatics.
>> > BOSC is sponsored by the Open Bioinformatics Foundation, a non-profit,
>> > volunteer-run group dedicated to promoting the practice and philosophy
>> > of Open Source software development and Open Science within the
>> > biological research community.
>> >
>> > We invite you to submit one-page abstracts for talks and posters. As
>> > mentioned, any topics relevant to open source bioinformatics and open
>> > science are welcome. Here are some potential session topics (but
>> > please don't feel limited to these!):
>> >    Open Science and Reproducible Research
>> >    Standards and Interoperability
>> >    Data Science
>> >    Visualization
>> >    Translational Bioinformatics
>> >    Bioinformatics Open Source Libraries and Projects
>> >
>> > If your company or organization is interested in being a sponsor for
>> > BOSC 2015, please contact us! Sponsors in 2014 included Google, Eagle
>> > Genomics, GigaScience, and Curoverse--we thank them for their support.
>> >
>> > BOSC 2015 Organizing Committee:
>> > Nomi Harris and Peter Cock (co-chairs), Raoul Jean Pierre Bonnal, Brad
>> > Chapman, Robert Davey, Christopher Fields, Sarah Hird, Karsten Hokamp,
>> > Hilmar Lapp.
>> > http://www.open-bio.org/wiki/BOSC_2015
>> > _______________________________________________
>> > Bosc-announce mailing list
>> > Bosc-announce at mailman.open-bio.org
>> > http://mailman.open-bio.org/mailman/listinfo/bosc-announce
>>
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython-dev
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From p.j.a.cock at googlemail.com  Fri Mar 27 13:32:13 2015
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 27 Mar 2015 13:32:13 +0000
Subject: [Biopython-dev] Biopython Project Update 2015;
 was BOSC 2015 Call for Abstracts
In-Reply-To: <CAB=-b2bsQtCDKSdY98x6o7nRpC+Lnz3syBqeZ5058PxVVsnUhA@mail.gmail.com>
References: <CAKVJ-_5yGzQMkoeZwVeymPpPaM2wEZe5GGTZ09+Rf1tvnQq3Gg@mail.gmail.com>
	<CAKVJ-_5OQQaOhbEWjm8NM33B7X9WVY=H728uGr9Qz5o4=h_ATA@mail.gmail.com>
	<CAB=-b2bsQtCDKSdY98x6o7nRpC+Lnz3syBqeZ5058PxVVsnUhA@mail.gmail.com>
Message-ID: <CAKVJ-_7V7QcGMKw=MJU5o-HSLnZARWr6Lkz7urN59fwAMY2+wQ@mail.gmail.com>

Hi Joao,

Last year all the main talks were 15 minutes plus 3 for questions
(i.e. 18 minute slots - shorter than ideal but good for scheduling
into the time blocks), except the project updates which got 10 mins
plus two for questions (12 minute slots), and lightning talks (5 mins
only, no questions). Exactly what we end up with for BOSC 2015
will depend in part on the number of good abstracts, but something
similar.

Having you present the Biopython Project Update would be good.

My plan is to attend the Galaxy conference in Norwich (GCC2015)
back-to-back with BOSC in Dublin (no funds to stay for ISMB/ECCB
as well, and frankly three meetings in a row would be exhausting).

Unfortunately GCC2015 will clash with the BOSC CodeFest, but
otherwise I would want to attend the CodeFest, which can be both
productive and good fun.

I yet don't know of any other Biopython people going to Dublin.

Bow: Do you remember if we put the abstract LaTeX files into
GitHub somewhere last year?

Peter


On Fri, Mar 27, 2015 at 1:12 PM, Jo?o Rodrigues <
j.p.g.l.m.rodrigues at gmail.com> wrote:

> Hi Peter,
>
> I'm considering going to the BOSC this year (not to ISMB/ECCB),
>
still weighing my options. If I would go, I wouldn't mind presenting,
>
maybe indeed including a bit of how we use Biopython here in the
>
lab. How long is a short talk? I would consider going for the
>
Codefest and BOSC. Who else is planning to go?
>
> Cheers,
>
> Jo?o
>
>
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From j.p.g.l.m.rodrigues at gmail.com  Fri Mar 27 13:50:31 2015
From: j.p.g.l.m.rodrigues at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues?=)
Date: Fri, 27 Mar 2015 13:50:31 +0000
Subject: [Biopython-dev] Biopython Project Update 2015;
 was BOSC 2015 Call for Abstracts
In-Reply-To: <CAKVJ-_7V7QcGMKw=MJU5o-HSLnZARWr6Lkz7urN59fwAMY2+wQ@mail.gmail.com>
References: <CAKVJ-_5yGzQMkoeZwVeymPpPaM2wEZe5GGTZ09+Rf1tvnQq3Gg@mail.gmail.com>
	<CAKVJ-_5OQQaOhbEWjm8NM33B7X9WVY=H728uGr9Qz5o4=h_ATA@mail.gmail.com>
	<CAB=-b2bsQtCDKSdY98x6o7nRpC+Lnz3syBqeZ5058PxVVsnUhA@mail.gmail.com>
	<CAKVJ-_7V7QcGMKw=MJU5o-HSLnZARWr6Lkz7urN59fwAMY2+wQ@mail.gmail.com>
Message-ID: <CAB=-b2YyfoKyZ3k1T=CM7vNMJb46YtXJOxYZQq+gQMNKDV3ZsA@mail.gmail.com>

https://github.com/bow/talks ? What would be the main updates of this year?

I'll talk with my supervisor here and I'll let you know. In any case, it
would be a fun experience, I've been wanting to join for a while but could
never find time (or funds) to do so. IT would be great if others were there
though!

Cheers,

Jo?o

Peter Cock <p.j.a.cock at googlemail.com> escreveu no dia sex, 27/03/2015 ?s
14:32:

> Hi Joao,
>
> Last year all the main talks were 15 minutes plus 3 for questions
> (i.e. 18 minute slots - shorter than ideal but good for scheduling
> into the time blocks), except the project updates which got 10 mins
> plus two for questions (12 minute slots), and lightning talks (5 mins
> only, no questions). Exactly what we end up with for BOSC 2015
> will depend in part on the number of good abstracts, but something
> similar.
>
> Having you present the Biopython Project Update would be good.
>
> My plan is to attend the Galaxy conference in Norwich (GCC2015)
> back-to-back with BOSC in Dublin (no funds to stay for ISMB/ECCB
> as well, and frankly three meetings in a row would be exhausting).
>
> Unfortunately GCC2015 will clash with the BOSC CodeFest, but
> otherwise I would want to attend the CodeFest, which can be both
> productive and good fun.
>
> I yet don't know of any other Biopython people going to Dublin.
>
> Bow: Do you remember if we put the abstract LaTeX files into
> GitHub somewhere last year?
>
> Peter
>
>
> On Fri, Mar 27, 2015 at 1:12 PM, Jo?o Rodrigues <
> j.p.g.l.m.rodrigues at gmail.com> wrote:
>
>> Hi Peter,
>>
>> I'm considering going to the BOSC this year (not to ISMB/ECCB),
>>
> still weighing my options. If I would go, I wouldn't mind presenting,
>>
> maybe indeed including a bit of how we use Biopython here in the
>>
> lab. How long is a short talk? I would consider going for the
>>
> Codefest and BOSC. Who else is planning to go?
>>
>> Cheers,
>>
>> Jo?o
>>
>>
>
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From christian at brueffer.de  Fri Mar 27 14:23:07 2015
From: christian at brueffer.de (Christian Brueffer)
Date: Fri, 27 Mar 2015 15:23:07 +0100
Subject: [Biopython-dev] Reproducible Biopython VM images
In-Reply-To: <CAKVJ-_7=OASG8--CuWuNi3zqR+si5VQZO=nJAqCxXX6K=SF=PQ@mail.gmail.com>
References: <55081140.2000609@brueffer.de>	<CAKVJ-_7epCGW=ObrX40CNaZOD4gqUeTtKaMvBZ8Lk8CUMNrFwQ@mail.gmail.com>	<55082405.4070402@brueffer.de>	<20150317150140.45d42be4@lnx>	<55113288.3090200@brueffer.de>
	<CAKVJ-_7=OASG8--CuWuNi3zqR+si5VQZO=nJAqCxXX6K=SF=PQ@mail.gmail.com>
Message-ID: <551567CB.2020301@brueffer.de>

On 2015-03-24 12:54, Peter Cock wrote:
> On Tue, Mar 24, 2015 at 9:46 AM, Christian Brueffer
> <christian at brueffer.de> wrote:
>> Hi Tiago,
>>
>> nice work!  Looks like my Vagrant stuff in redundant indeed and I can
>> abandon it.
>>
>> Any chance we can make this a bit more visible?  A paragraph in the README
>> would be a good start; I can whip something up if we agree this is a good
>> idea.
>>
>> Cheers,
>>
>> Chris
>
> Related to this, if there is general interest we could have another
> repository on GitHub for docker containers (much like we have
> a small repository for Biopython's Galaxy packaging).
>

I think that would be helpful.

Chris

From p.j.a.cock at googlemail.com  Fri Mar 27 14:58:09 2015
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 27 Mar 2015 14:58:09 +0000
Subject: [Biopython-dev] Biopython Project Update 2015;
 was BOSC 2015 Call for Abstracts
In-Reply-To: <CAB=-b2YyfoKyZ3k1T=CM7vNMJb46YtXJOxYZQq+gQMNKDV3ZsA@mail.gmail.com>
References: <CAKVJ-_5yGzQMkoeZwVeymPpPaM2wEZe5GGTZ09+Rf1tvnQq3Gg@mail.gmail.com>
	<CAKVJ-_5OQQaOhbEWjm8NM33B7X9WVY=H728uGr9Qz5o4=h_ATA@mail.gmail.com>
	<CAB=-b2bsQtCDKSdY98x6o7nRpC+Lnz3syBqeZ5058PxVVsnUhA@mail.gmail.com>
	<CAKVJ-_7V7QcGMKw=MJU5o-HSLnZARWr6Lkz7urN59fwAMY2+wQ@mail.gmail.com>
	<CAB=-b2YyfoKyZ3k1T=CM7vNMJb46YtXJOxYZQq+gQMNKDV3ZsA@mail.gmail.com>
Message-ID: <CAKVJ-_7m=EKji8OBbqe2+5G+zukmqGvOP0jsiXLTGTD1EJTDOQ@mail.gmail.com>

On Fri, Mar 27, 2015 at 1:50 PM, Jo?o Rodrigues
<j.p.g.l.m.rodrigues at gmail.com> wrote:
> https://github.com/bow/talks ?

Yes, that was it - we can use this as a template for this year's abstract:

https://github.com/bow/talks/tree/master/2014_bosc/abstract

> What would be the main updates of this year?
>

I normally start by re-reading the NEWS file for all the releases,
in this case just Biopython 1.65 (December 2014), which brings
up another issue - its about time for the Biopython 1.66 release.

> I'll talk with my supervisor here and I'll let you know. In any case, it
> would be a fun experience, I've been wanting to join for a while but could
> never find time (or funds) to do so. IT would be great if others were there
> though!
>
> Cheers,
>
> Jo?o

Great - and I agree, conferences are one of the few chances
to met online collaborators in person, and that makes things
more fun.

Peter


From christian at brueffer.de  Fri Mar 27 15:32:35 2015
From: christian at brueffer.de (Christian Brueffer)
Date: Fri, 27 Mar 2015 16:32:35 +0100
Subject: [Biopython-dev] Biopython Project Update 2015;
 was BOSC 2015 Call for Abstracts
In-Reply-To: <CAB=-b2YyfoKyZ3k1T=CM7vNMJb46YtXJOxYZQq+gQMNKDV3ZsA@mail.gmail.com>
References: <CAKVJ-_5yGzQMkoeZwVeymPpPaM2wEZe5GGTZ09+Rf1tvnQq3Gg@mail.gmail.com>	<CAKVJ-_5OQQaOhbEWjm8NM33B7X9WVY=H728uGr9Qz5o4=h_ATA@mail.gmail.com>	<CAB=-b2bsQtCDKSdY98x6o7nRpC+Lnz3syBqeZ5058PxVVsnUhA@mail.gmail.com>	<CAKVJ-_7V7QcGMKw=MJU5o-HSLnZARWr6Lkz7urN59fwAMY2+wQ@mail.gmail.com>
	<CAB=-b2YyfoKyZ3k1T=CM7vNMJb46YtXJOxYZQq+gQMNKDV3ZsA@mail.gmail.com>
Message-ID: <55157813.7040107@brueffer.de>

Hi Jo?o,

if you can't make it, I could jump in for the update.

Cheers,

Chris


On 2015-03-27 14:50, Jo?o Rodrigues wrote:
> https://github.com/bow/talks ? What would be the main updates of this year?
>
> I'll talk with my supervisor here and I'll let you know. In any case, it
> would be a fun experience, I've been wanting to join for a while but
> could never find time (or funds) to do so. IT would be great if others
> were there though!
>
> Cheers,
>
> Jo?o
>
> Peter Cock <p.j.a.cock at googlemail.com
> <mailto:p.j.a.cock at googlemail.com>> escreveu no dia sex, 27/03/2015 ?s
> 14:32:
>
>     Hi Joao,
>
>     Last year all the main talks were 15 minutes plus 3 for questions
>     (i.e. 18 minute slots - shorter than ideal but good for scheduling
>     into the time blocks), except the project updates which got 10 mins
>     plus two for questions (12 minute slots), and lightning talks (5 mins
>     only, no questions). Exactly what we end up with for BOSC 2015
>     will depend in part on the number of good abstracts, but something
>     similar.
>
>     Having you present the Biopython Project Update would be good.
>
>     My plan is to attend the Galaxy conference in Norwich (GCC2015)
>     back-to-back with BOSC in Dublin (no funds to stay for ISMB/ECCB
>     as well, and frankly three meetings in a row would be exhausting).
>
>     Unfortunately GCC2015 will clash with the BOSC CodeFest, but
>     otherwise I would want to attend the CodeFest, which can be both
>     productive and good fun.
>
>     I yet don't know of any other Biopython people going to Dublin.
>
>     Bow: Do you remember if we put the abstract LaTeX files into
>     GitHub somewhere last year?
>
>     Peter
>
>
>     On Fri, Mar 27, 2015 at 1:12 PM, Jo?o Rodrigues
>     <j.p.g.l.m.rodrigues at gmail.com
>     <mailto:j.p.g.l.m.rodrigues at gmail.com>> wrote:
>
>         Hi Peter,
>
>         I'm considering going to the BOSC this year (not to ISMB/ECCB),
>
>         still weighing my options. If I would go, I wouldn't mind
>         presenting,
>
>         maybe indeed including a bit of how we use Biopython here in the
>
>         lab. How long is a short talk? I would consider going for the
>
>         Codefest and BOSC. Who else is planning to go?
>
>         Cheers,
>
>         Jo?o
>
>
>
>
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython-dev
>

From j.p.g.l.m.rodrigues at gmail.com  Fri Mar 27 17:05:21 2015
From: j.p.g.l.m.rodrigues at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues?=)
Date: Fri, 27 Mar 2015 17:05:21 +0000
Subject: [Biopython-dev] Biopython Project Update 2015;
 was BOSC 2015 Call for Abstracts
In-Reply-To: <55157813.7040107@brueffer.de>
References: <CAKVJ-_5yGzQMkoeZwVeymPpPaM2wEZe5GGTZ09+Rf1tvnQq3Gg@mail.gmail.com>
	<CAKVJ-_5OQQaOhbEWjm8NM33B7X9WVY=H728uGr9Qz5o4=h_ATA@mail.gmail.com>
	<CAB=-b2bsQtCDKSdY98x6o7nRpC+Lnz3syBqeZ5058PxVVsnUhA@mail.gmail.com>
	<CAKVJ-_7V7QcGMKw=MJU5o-HSLnZARWr6Lkz7urN59fwAMY2+wQ@mail.gmail.com>
	<CAB=-b2YyfoKyZ3k1T=CM7vNMJb46YtXJOxYZQq+gQMNKDV3ZsA@mail.gmail.com>
	<55157813.7040107@brueffer.de>
Message-ID: <CAB=-b2aPJM18Ua9k7P5dLx7Sd5ApSZ-GTSWWWtmoVr=MUvP99A@mail.gmail.com>

Hi Christian, and all,

I am looking into registration and flights, so I'm good to go. Had already
mentioned it to Peter privately.

I found Bow's abstract from last year and forked it, should update it to
include new developments. Also, I thought it would be nice to mention the
Docker containers Tiago & Christian developed. What do you think?

Cheers,

Jo?o
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From christian at brueffer.de  Fri Mar 27 17:08:13 2015
From: christian at brueffer.de (Christian Brueffer)
Date: Fri, 27 Mar 2015 18:08:13 +0100
Subject: [Biopython-dev] Biopython Project Update 2015;
 was BOSC 2015 Call for Abstracts
In-Reply-To: <CAB=-b2aPJM18Ua9k7P5dLx7Sd5ApSZ-GTSWWWtmoVr=MUvP99A@mail.gmail.com>
References: <CAKVJ-_5yGzQMkoeZwVeymPpPaM2wEZe5GGTZ09+Rf1tvnQq3Gg@mail.gmail.com>
	<CAKVJ-_5OQQaOhbEWjm8NM33B7X9WVY=H728uGr9Qz5o4=h_ATA@mail.gmail.com>
	<CAB=-b2bsQtCDKSdY98x6o7nRpC+Lnz3syBqeZ5058PxVVsnUhA@mail.gmail.com>
	<CAKVJ-_7V7QcGMKw=MJU5o-HSLnZARWr6Lkz7urN59fwAMY2+wQ@mail.gmail.com>
	<CAB=-b2YyfoKyZ3k1T=CM7vNMJb46YtXJOxYZQq+gQMNKDV3ZsA@mail.gmail.com>
	<55157813.7040107@brueffer.de>
	<CAB=-b2aPJM18Ua9k7P5dLx7Sd5ApSZ-GTSWWWtmoVr=MUvP99A@mail.gmail.com>
Message-ID: <55158E7D.2070608@brueffer.de>

Perfect!

I think mentioning the containers is worth it, especially now that 
Docker is all the rage!  However, the credit for that goes to Tiago 
alone, I didn't have anything to do with it :-)

Cheers,

Chris


On 2015-03-27 18:05, Jo?o Rodrigues wrote:
> Hi Christian, and all,
>
> I am looking into registration and flights, so I'm good to go. Had
> already mentioned it to Peter privately.
>
> I found Bow's abstract from last year and forked it, should update it to
> include new developments. Also, I thought it would be nice to mention
> the Docker containers Tiago & Christian developed. What do you think?
>
> Cheers,
>
> Jo?o

From p.j.a.cock at googlemail.com  Fri Mar 27 21:44:50 2015
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 27 Mar 2015 21:44:50 +0000
Subject: [Biopython-dev] Biopython Project Update 2015;
 was BOSC 2015 Call for Abstracts
In-Reply-To: <55158E7D.2070608@brueffer.de>
References: <CAKVJ-_5yGzQMkoeZwVeymPpPaM2wEZe5GGTZ09+Rf1tvnQq3Gg@mail.gmail.com>
	<CAKVJ-_5OQQaOhbEWjm8NM33B7X9WVY=H728uGr9Qz5o4=h_ATA@mail.gmail.com>
	<CAB=-b2bsQtCDKSdY98x6o7nRpC+Lnz3syBqeZ5058PxVVsnUhA@mail.gmail.com>
	<CAKVJ-_7V7QcGMKw=MJU5o-HSLnZARWr6Lkz7urN59fwAMY2+wQ@mail.gmail.com>
	<CAB=-b2YyfoKyZ3k1T=CM7vNMJb46YtXJOxYZQq+gQMNKDV3ZsA@mail.gmail.com>
	<55157813.7040107@brueffer.de>
	<CAB=-b2aPJM18Ua9k7P5dLx7Sd5ApSZ-GTSWWWtmoVr=MUvP99A@mail.gmail.com>
	<55158E7D.2070608@brueffer.de>
Message-ID: <CAKVJ-_4TnqRbz6zOauOxHUdQG+v_WVJoj_7JXwn4OzDhZ3oOrg@mail.gmail.com>

Very good idea :)

Let's settle on a repository name on that other thread...

Peter

On Fri, Mar 27, 2015 at 5:08 PM, Christian Brueffer
<christian at brueffer.de> wrote:
> Perfect!
>
> I think mentioning the containers is worth it, especially now that Docker is
> all the rage!  However, the credit for that goes to Tiago alone, I didn't
> have anything to do with it :-)
>
> Cheers,
>
> Chris
>
>
>
> On 2015-03-27 18:05, Jo?o Rodrigues wrote:
>>
>> Hi Christian, and all,
>>
>> I am looking into registration and flights, so I'm good to go. Had
>> already mentioned it to Peter privately.
>>
>> I found Bow's abstract from last year and forked it, should update it to
>> include new developments. Also, I thought it would be nice to mention
>> the Docker containers Tiago & Christian developed. What do you think?
>>
>> Cheers,
>>
>> Jo?o
>
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython-dev


From w.arindrarto at gmail.com  Fri Mar 27 22:36:23 2015
From: w.arindrarto at gmail.com (Wibowo Arindrarto)
Date: Fri, 27 Mar 2015 23:36:23 +0100
Subject: [Biopython-dev] Biopython Project Update 2015;
 was BOSC 2015 Call for Abstracts
In-Reply-To: <CAKVJ-_4TnqRbz6zOauOxHUdQG+v_WVJoj_7JXwn4OzDhZ3oOrg@mail.gmail.com>
References: <CAKVJ-_5yGzQMkoeZwVeymPpPaM2wEZe5GGTZ09+Rf1tvnQq3Gg@mail.gmail.com>
	<CAKVJ-_5OQQaOhbEWjm8NM33B7X9WVY=H728uGr9Qz5o4=h_ATA@mail.gmail.com>
	<CAB=-b2bsQtCDKSdY98x6o7nRpC+Lnz3syBqeZ5058PxVVsnUhA@mail.gmail.com>
	<CAKVJ-_7V7QcGMKw=MJU5o-HSLnZARWr6Lkz7urN59fwAMY2+wQ@mail.gmail.com>
	<CAB=-b2YyfoKyZ3k1T=CM7vNMJb46YtXJOxYZQq+gQMNKDV3ZsA@mail.gmail.com>
	<55157813.7040107@brueffer.de>
	<CAB=-b2aPJM18Ua9k7P5dLx7Sd5ApSZ-GTSWWWtmoVr=MUvP99A@mail.gmail.com>
	<55158E7D.2070608@brueffer.de>
	<CAKVJ-_4TnqRbz6zOauOxHUdQG+v_WVJoj_7JXwn4OzDhZ3oOrg@mail.gmail.com>
Message-ID: <CADEGkF6HNB8r7rDVo2QV6vzJAkWp55=UCLLXb7=3YeoCxJnqVA@mail.gmail.com>

Hi everyone,

Sorry for being late ~ things have been very hectic the past few weeks
(and will still be for the few coming weeks).

Regarding BOSC, I would love to come again this year. I have
some few outstanding issues that I want to work on for Biopython
anyway ~ would be great if I can just sit and work. Not 100% sure yet
about this yet (I still need to arrange my visa, etc.), so we'll see.

Thanks for volunteering by the way, Joao! Good to see that you've
found the repo, too. Everything from last year (abstract +
presentation) is in that repo, in text form. Let me know if I can
help you with anything, still.

Cheers,
Bow


On Fri, Mar 27, 2015 at 10:44 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> Very good idea :)
>
> Let's settle on a repository name on that other thread...
>
> Peter
>
> On Fri, Mar 27, 2015 at 5:08 PM, Christian Brueffer
> <christian at brueffer.de> wrote:
>> Perfect!
>>
>> I think mentioning the containers is worth it, especially now that Docker is
>> all the rage!  However, the credit for that goes to Tiago alone, I didn't
>> have anything to do with it :-)
>>
>> Cheers,
>>
>> Chris
>>
>>
>>
>> On 2015-03-27 18:05, Jo?o Rodrigues wrote:
>>>
>>> Hi Christian, and all,
>>>
>>> I am looking into registration and flights, so I'm good to go. Had
>>> already mentioned it to Peter privately.
>>>
>>> I found Bow's abstract from last year and forked it, should update it to
>>> include new developments. Also, I thought it would be nice to mention
>>> the Docker containers Tiago & Christian developed. What do you think?
>>>
>>> Cheers,
>>>
>>> Jo?o
>>
>> _______________________________________________
>> Biopython-dev mailing list
>> Biopython-dev at mailman.open-bio.org
>> http://mailman.open-bio.org/mailman/listinfo/biopython-dev
>
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython-dev


From tra at popgen.net  Sun Mar 29 17:47:05 2015
From: tra at popgen.net (Tiago Antao)
Date: Sun, 29 Mar 2015 18:47:05 +0100
Subject: [Biopython-dev] Reproducible Biopython VM images
In-Reply-To: <551567CB.2020301@brueffer.de>
References: <55081140.2000609@brueffer.de>
	<CAKVJ-_7epCGW=ObrX40CNaZOD4gqUeTtKaMvBZ8Lk8CUMNrFwQ@mail.gmail.com>
	<55082405.4070402@brueffer.de> <20150317150140.45d42be4@lnx>
	<55113288.3090200@brueffer.de>
	<CAKVJ-_7=OASG8--CuWuNi3zqR+si5VQZO=nJAqCxXX6K=SF=PQ@mail.gmail.com>
	<551567CB.2020301@brueffer.de>
Message-ID: <20150329184705.26cf5615@grandao>

Hi,

I have done another container with an empty IPython Notebook interface.
I will send details about this as soon as github web interface is back
up (which it not the case now).

Currently my containers are based on Ubuntu saucy (Python 2) and trusty
(Python 3). I was thinking in upgrading everything to Vivid (which will
be out next month but works fine - I am typing this on it). The
advantage would be that we would get IPython Notebook 3 (Jupyter).
This takes just a few minutes to do, but I was wanting to ask if
someone sees a problem with this?

Tiago

From tra at popgen.net  Sun Mar 29 17:48:42 2015
From: tra at popgen.net (Tiago Antao)
Date: Sun, 29 Mar 2015 18:48:42 +0100
Subject: [Biopython-dev] Biopython Project Update 2015;
 was BOSC 2015 Call for Abstracts
In-Reply-To: <CAKVJ-_4TnqRbz6zOauOxHUdQG+v_WVJoj_7JXwn4OzDhZ3oOrg@mail.gmail.com>
References: <CAKVJ-_5yGzQMkoeZwVeymPpPaM2wEZe5GGTZ09+Rf1tvnQq3Gg@mail.gmail.com>
	<CAKVJ-_5OQQaOhbEWjm8NM33B7X9WVY=H728uGr9Qz5o4=h_ATA@mail.gmail.com>
	<CAB=-b2bsQtCDKSdY98x6o7nRpC+Lnz3syBqeZ5058PxVVsnUhA@mail.gmail.com>
	<CAKVJ-_7V7QcGMKw=MJU5o-HSLnZARWr6Lkz7urN59fwAMY2+wQ@mail.gmail.com>
	<CAB=-b2YyfoKyZ3k1T=CM7vNMJb46YtXJOxYZQq+gQMNKDV3ZsA@mail.gmail.com>
	<55157813.7040107@brueffer.de>
	<CAB=-b2aPJM18Ua9k7P5dLx7Sd5ApSZ-GTSWWWtmoVr=MUvP99A@mail.gmail.com>
	<55158E7D.2070608@brueffer.de>
	<CAKVJ-_4TnqRbz6zOauOxHUdQG+v_WVJoj_7JXwn4OzDhZ3oOrg@mail.gmail.com>
Message-ID: <20150329184842.63a0c81a@grandao>

On Fri, 27 Mar 2015 21:44:50 +0000
Peter Cock <p.j.a.cock at googlemail.com> wrote:

> Let's settle on a repository name on that other thread...

Whatever you all decide is fine by me. I am putting together some
documentation that I will make available as soon as github's web
interface is back up.

Tiago

From tra at popgen.net  Sun Mar 29 18:37:05 2015
From: tra at popgen.net (Tiago Antao)
Date: Sun, 29 Mar 2015 19:37:05 +0100
Subject: [Biopython-dev] Biopython Project Update 2015;
 was BOSC 2015 Call for Abstracts
In-Reply-To: <CAKVJ-_7V7QcGMKw=MJU5o-HSLnZARWr6Lkz7urN59fwAMY2+wQ@mail.gmail.com>
References: <CAKVJ-_5yGzQMkoeZwVeymPpPaM2wEZe5GGTZ09+Rf1tvnQq3Gg@mail.gmail.com>
	<CAKVJ-_5OQQaOhbEWjm8NM33B7X9WVY=H728uGr9Qz5o4=h_ATA@mail.gmail.com>
	<CAB=-b2bsQtCDKSdY98x6o7nRpC+Lnz3syBqeZ5058PxVVsnUhA@mail.gmail.com>
	<CAKVJ-_7V7QcGMKw=MJU5o-HSLnZARWr6Lkz7urN59fwAMY2+wQ@mail.gmail.com>
Message-ID: <20150329193705.173304c3@grandao>

On Fri, 27 Mar 2015 13:32:13 +0000
Peter Cock <p.j.a.cock at googlemail.com> wrote:

> Unfortunately GCC2015 will clash with the BOSC CodeFest, but
> otherwise I would want to attend the CodeFest, which can be both
> productive and good fun.


Being in Liverpool it is actually quite easy for me to get to both. I
was actually more interested in the codefests than anything else.
Bummer for the overlap. I think I am going to GCC for sure (again, at
least the codefest) and then, depending on the size of the contingent
of Biopython folks at BOSC, I might either stay at the Galaxy
conference or go to the BOSC codefest.

I have no interest in presenting, but I am available in case of
desperation and nobody else is available (which does not seem to be the
case anyway).

Tiago

From p.j.a.cock at googlemail.com  Sun Mar 29 20:42:56 2015
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Sun, 29 Mar 2015 21:42:56 +0100
Subject: [Biopython-dev] Biopython Project Update 2015;
 was BOSC 2015 Call for Abstracts
In-Reply-To: <20150329193705.173304c3@grandao>
References: <CAKVJ-_5yGzQMkoeZwVeymPpPaM2wEZe5GGTZ09+Rf1tvnQq3Gg@mail.gmail.com>
	<CAKVJ-_5OQQaOhbEWjm8NM33B7X9WVY=H728uGr9Qz5o4=h_ATA@mail.gmail.com>
	<CAB=-b2bsQtCDKSdY98x6o7nRpC+Lnz3syBqeZ5058PxVVsnUhA@mail.gmail.com>
	<CAKVJ-_7V7QcGMKw=MJU5o-HSLnZARWr6Lkz7urN59fwAMY2+wQ@mail.gmail.com>
	<20150329193705.173304c3@grandao>
Message-ID: <CAKVJ-_41momHO3BkbrnKNVdVKmFQ39mcyr4SiHrm-um=qmeN9w@mail.gmail.com>

On Sun, Mar 29, 2015 at 7:37 PM, Tiago Antao <tra at popgen.net> wrote:
> On Fri, 27 Mar 2015 13:32:13 +0000
> Peter Cock <p.j.a.cock at googlemail.com> wrote:
>
>> Unfortunately GCC2015 will clash with the BOSC CodeFest, but
>> otherwise I would want to attend the CodeFest, which can be both
>> productive and good fun.
>
>
> Being in Liverpool it is actually quite easy for me to get to both. I
> was actually more interested in the codefests than anything else.
> Bummer for the overlap. I think I am going to GCC for sure (again, at
> least the codefest) and then, depending on the size of the contingent
> of Biopython folks at BOSC, I might either stay at the Galaxy
> conference or go to the BOSC codefest.
>
> I have no interest in presenting, but I am available in case of
> desperation and nobody else is available (which does not seem to be the
> case anyway).
>
> Tiago

Thanks Tiago - it looks like we have a full roster of reserve speakers,
and that you and I ought to be able to meet up in Norwich (GCC2015)
or Dublin (BOSC2015). :)

Peter

From p.j.a.cock at googlemail.com  Sun Mar 29 20:46:21 2015
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Sun, 29 Mar 2015 21:46:21 +0100
Subject: [Biopython-dev] Biopython Project Update 2015;
 was BOSC 2015 Call for Abstracts
In-Reply-To: <55157813.7040107@brueffer.de>
References: <CAKVJ-_5yGzQMkoeZwVeymPpPaM2wEZe5GGTZ09+Rf1tvnQq3Gg@mail.gmail.com>
	<CAKVJ-_5OQQaOhbEWjm8NM33B7X9WVY=H728uGr9Qz5o4=h_ATA@mail.gmail.com>
	<CAB=-b2bsQtCDKSdY98x6o7nRpC+Lnz3syBqeZ5058PxVVsnUhA@mail.gmail.com>
	<CAKVJ-_7V7QcGMKw=MJU5o-HSLnZARWr6Lkz7urN59fwAMY2+wQ@mail.gmail.com>
	<CAB=-b2YyfoKyZ3k1T=CM7vNMJb46YtXJOxYZQq+gQMNKDV3ZsA@mail.gmail.com>
	<55157813.7040107@brueffer.de>
Message-ID: <CAKVJ-_4JE0jHTHOz6KXbcsGb6_ThfyZ+yCCBjZJpiGE6HhaeJg@mail.gmail.com>

On Fri, Mar 27, 2015 at 3:32 PM, Christian Brueffer
<christian at brueffer.de> wrote:
> Hi Jo?o,
>
> if you can't make it, I could jump in for the update.
>
> Cheers,
>
> Chris

Thanks :)

If you have any of your own work you'd like to talk about,
please do think about submitting a BOSC abstract (and/or
one of the other ISMB/ECCB opportunities like our sister
SIG meetings).

Peter


From tra at popgen.net  Mon Mar 30 00:26:51 2015
From: tra at popgen.net (Tiago Antao)
Date: Mon, 30 Mar 2015 01:26:51 +0100
Subject: [Biopython-dev] Reproducible Biopython VM images
In-Reply-To: <551567CB.2020301@brueffer.de>
References: <55081140.2000609@brueffer.de>
	<CAKVJ-_7epCGW=ObrX40CNaZOD4gqUeTtKaMvBZ8Lk8CUMNrFwQ@mail.gmail.com>
	<55082405.4070402@brueffer.de> <20150317150140.45d42be4@lnx>
	<55113288.3090200@brueffer.de>
	<CAKVJ-_7=OASG8--CuWuNi3zqR+si5VQZO=nJAqCxXX6K=SF=PQ@mail.gmail.com>
	<551567CB.2020301@brueffer.de>
Message-ID: <20150330012651.0c68d958@grandao>

Hi,

After retesting, the containers were quite old. I am producing new
versions with up to date software. As soon as they are ready I will
email here.

On Fri, 27 Mar 2015 15:23:07 +0100
Christian Brueffer <christian at brueffer.de> wrote:

> On 2015-03-24 12:54, Peter Cock wrote:
> > On Tue, Mar 24, 2015 at 9:46 AM, Christian Brueffer
> > <christian at brueffer.de> wrote:
> >> Hi Tiago,
> >>
> >> nice work!  Looks like my Vagrant stuff in redundant indeed and I
> >> can abandon it.
> >>
> >> Any chance we can make this a bit more visible?  A paragraph in
> >> the README would be a good start; I can whip something up if we
> >> agree this is a good idea.
> >>
> >> Cheers,
> >>
> >> Chris
> >
> > Related to this, if there is general interest we could have another
> > repository on GitHub for docker containers (much like we have
> > a small repository for Biopython's Galaxy packaging).
> >
> 
> I think that would be helpful.
> 
> Chris


From tra at popgen.net  Mon Mar 30 09:50:14 2015
From: tra at popgen.net (Tiago Antao)
Date: Mon, 30 Mar 2015 10:50:14 +0100
Subject: [Biopython-dev] Tutorial Notebooks
Message-ID: <20150330105014.161d8928@lnx>

Hi,

I updated the tutorial notebooks to version 4 format. This means that
you will need Project Jupyter (IPython 3.0) to run them. This does not
mean Python 3 is a requirement: IPython 3.0 has nothing to do with
Python versioning.

The (incomplete) notebooks are here:
https://github.com/tiagoantao/biopython-notebook

And can be viewed here:
http://nbviewer.ipython.org/github/tiagoantao/biopython-notebook/blob/master/notebooks/01%20-%20Introduction.ipynb

I hope to complete the porting of the Tutorial somewhere in the
future...

Tiago

From p.j.a.cock at googlemail.com  Mon Mar 30 10:24:43 2015
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 30 Mar 2015 11:24:43 +0100
Subject: [Biopython-dev] Reproducible Biopython VM images
In-Reply-To: <551567CB.2020301@brueffer.de>
References: <55081140.2000609@brueffer.de>
	<CAKVJ-_7epCGW=ObrX40CNaZOD4gqUeTtKaMvBZ8Lk8CUMNrFwQ@mail.gmail.com>
	<55082405.4070402@brueffer.de> <20150317150140.45d42be4@lnx>
	<55113288.3090200@brueffer.de>
	<CAKVJ-_7=OASG8--CuWuNi3zqR+si5VQZO=nJAqCxXX6K=SF=PQ@mail.gmail.com>
	<551567CB.2020301@brueffer.de>
Message-ID: <CAKVJ-_4JK9n4t6SRhmC5QfzDx8wR=3YEnM9we6wS7bh2gzpaxQ@mail.gmail.com>

On Fri, Mar 27, 2015 at 2:23 PM, Christian Brueffer
<christian at brueffer.de> wrote:
> On 2015-03-24 12:54, Peter Cock wrote:
>>
>> On Tue, Mar 24, 2015 at 9:46 AM, Christian Brueffer
>> <christian at brueffer.de> wrote:
>>>
>>> Hi Tiago,
>>>
>>> nice work!  Looks like my Vagrant stuff in redundant indeed and I can
>>> abandon it.
>>>
>>> Any chance we can make this a bit more visible?  A paragraph in the
>>> README
>>> would be a good start; I can whip something up if we agree this is a good
>>> idea.
>>>
>>> Cheers,
>>>
>>> Chris
>>
>>
>> Related to this, if there is general interest we could have another
>> repository on GitHub for docker containers (much like we have
>> a small repository for Biopython's Galaxy packaging).
>>
>
> I think that would be helpful.
>
> Chris

We seem to be in agreement then - what should we call this new
repository under Biopython's GitHub account? e.g. biopython-docker

Peter

From p.j.a.cock at googlemail.com  Mon Mar 30 10:55:32 2015
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 30 Mar 2015 11:55:32 +0100
Subject: [Biopython-dev] Reproducible Biopython VM images
In-Reply-To: <CAKVJ-_4JK9n4t6SRhmC5QfzDx8wR=3YEnM9we6wS7bh2gzpaxQ@mail.gmail.com>
References: <55081140.2000609@brueffer.de>
	<CAKVJ-_7epCGW=ObrX40CNaZOD4gqUeTtKaMvBZ8Lk8CUMNrFwQ@mail.gmail.com>
	<55082405.4070402@brueffer.de> <20150317150140.45d42be4@lnx>
	<55113288.3090200@brueffer.de>
	<CAKVJ-_7=OASG8--CuWuNi3zqR+si5VQZO=nJAqCxXX6K=SF=PQ@mail.gmail.com>
	<551567CB.2020301@brueffer.de>
	<CAKVJ-_4JK9n4t6SRhmC5QfzDx8wR=3YEnM9we6wS7bh2gzpaxQ@mail.gmail.com>
Message-ID: <CAKVJ-_4J+9-Jti3JNKM6PmMA6Od+R-rqtEnv=cJEsez66v2KTA@mail.gmail.com>

On Mon, Mar 30, 2015 at 11:24 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>
> We seem to be in agreement then - what should we call this new
> repository under Biopython's GitHub account? e.g. biopython-docker
>
> Peter

I just created this empty repository (with an underscore rather
than a minus sign/hyphen to match our existing use pattern),
with a new "team" on GitHub with write access:

https://github.com/biopython/biopython_docker

Tiago - can I leave this with you to setup the initial README
file, .gitignore, etc?

For the licence, I suggest (given past discussion for the main
project) this be dual licensed under the historic Biopython
Licence Agreement AND the more standard 3-clause BSD
licence?

https://github.com/biopython/biopython/blob/master/LICENSE
http://opensource.org/licenses/BSD-3-Clause

This reminds me we ought to press ahead with moving
Biopython itself to dual and eventually 3-clause BSD only...

Peter

From tra at popgen.net  Mon Mar 30 11:09:01 2015
From: tra at popgen.net (Tiago Antao)
Date: Mon, 30 Mar 2015 12:09:01 +0100
Subject: [Biopython-dev] Reproducible Biopython VM images
In-Reply-To: <CAKVJ-_4J+9-Jti3JNKM6PmMA6Od+R-rqtEnv=cJEsez66v2KTA@mail.gmail.com>
References: <55081140.2000609@brueffer.de>
	<CAKVJ-_7epCGW=ObrX40CNaZOD4gqUeTtKaMvBZ8Lk8CUMNrFwQ@mail.gmail.com>
	<55082405.4070402@brueffer.de> <20150317150140.45d42be4@lnx>
	<55113288.3090200@brueffer.de>
	<CAKVJ-_7=OASG8--CuWuNi3zqR+si5VQZO=nJAqCxXX6K=SF=PQ@mail.gmail.com>
	<551567CB.2020301@brueffer.de>
	<CAKVJ-_4JK9n4t6SRhmC5QfzDx8wR=3YEnM9we6wS7bh2gzpaxQ@mail.gmail.com>
	<CAKVJ-_4J+9-Jti3JNKM6PmMA6Od+R-rqtEnv=cJEsez66v2KTA@mail.gmail.com>
Message-ID: <20150330120901.6e9c4213@lnx>

Hi,

On Mon, 30 Mar 2015 11:55:32 +0100
Peter Cock <p.j.a.cock at googlemail.com> wrote:

> I just created this empty repository (with an underscore rather
> than a minus sign/hyphen to match our existing use pattern),
> with a new "team" on GitHub with write access:
> 
> https://github.com/biopython/biopython_docker
> 
> Tiago - can I leave this with you to setup the initial README
> file, .gitignore, etc?

I will, but before that there are a few things that need to be
discussed. I just want everyone to be made aware of what is in my
current docker files, and plans for the future. There will be a
separate email on this very soon.


> For the licence, I suggest (given past discussion for the main
> project) this be dual licensed under the historic Biopython
> Licence Agreement AND the more standard 3-clause BSD
> licence?

I am fine with this.

Tiago

From p.j.a.cock at googlemail.com  Mon Mar 30 11:12:23 2015
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 30 Mar 2015 12:12:23 +0100
Subject: [Biopython-dev] Reproducible Biopython VM images
In-Reply-To: <20150330120901.6e9c4213@lnx>
References: <55081140.2000609@brueffer.de>
	<CAKVJ-_7epCGW=ObrX40CNaZOD4gqUeTtKaMvBZ8Lk8CUMNrFwQ@mail.gmail.com>
	<55082405.4070402@brueffer.de> <20150317150140.45d42be4@lnx>
	<55113288.3090200@brueffer.de>
	<CAKVJ-_7=OASG8--CuWuNi3zqR+si5VQZO=nJAqCxXX6K=SF=PQ@mail.gmail.com>
	<551567CB.2020301@brueffer.de>
	<CAKVJ-_4JK9n4t6SRhmC5QfzDx8wR=3YEnM9we6wS7bh2gzpaxQ@mail.gmail.com>
	<CAKVJ-_4J+9-Jti3JNKM6PmMA6Od+R-rqtEnv=cJEsez66v2KTA@mail.gmail.com>
	<20150330120901.6e9c4213@lnx>
Message-ID: <CAKVJ-_7U0wz9xAFZ34mscJnPBhrEb3Wh+jMpq0+HKxMgOV5txA@mail.gmail.com>

On Mon, Mar 30, 2015 at 12:09 PM, Tiago Antao <tra at popgen.net> wrote:
> Hi,
>
> On Mon, 30 Mar 2015 11:55:32 +0100
> Peter Cock <p.j.a.cock at googlemail.com> wrote:
>
>> I just created this empty repository (with an underscore rather
>> than a minus sign/hyphen to match our existing use pattern),
>> with a new "team" on GitHub with write access:
>>
>> https://github.com/biopython/biopython_docker
>>
>> Tiago - can I leave this with you to setup the initial README
>> file, .gitignore, etc?
>
> I will, but before that there are a few things that need to be
> discussed. I just want everyone to be made aware of what is in my
> current docker files, and plans for the future. There will be a
> separate email on this very soon.
>
>
>> For the licence, I suggest (given past discussion for the main
>> project) this be dual licensed under the historic Biopython
>> Licence Agreement AND the more standard 3-clause BSD
>> licence?
>
> I am fine with this.
>
> Tiago

Great (and if anyone has a stronger naming proposal, we
can easily rename this at this early point).

Peter

From tra at popgen.net  Mon Mar 30 11:20:40 2015
From: tra at popgen.net (Tiago Antao)
Date: Mon, 30 Mar 2015 12:20:40 +0100
Subject: [Biopython-dev] Docker containers
Message-ID: <20150330122040.175bbeac@lnx>

Dear all,

Before I port my containers to the project there are a few things that
you should be made aware of:

1. There are 4 containers x 2 versions (Python 2 and 3): empty (shell),
notebook, notebook with tutorial and buildbot. The buildbot one is
currently under maintenance, but I would expect all the others to work.

2. I am maintaining all these containers with a simple template system
on my repository (https://github.com/tiagoantao/my-containers). It is
clumsy, but does the work. I will probably port the script also to the
new main repo.

3. The containers themselves were my first attempt at doing docker
containers, so they are a bit naive. But they do work. A future plan
would be to use anaconda (well, miniconda) as a basis. Also force the
versions of all packages.

4. You can find instructions here:
http://fe.popgen.net/2015/03/docker-containers-for-biopython/ .

Comments and criticism appreciated.

When everyone is happy, I will put everything under the biopython repo.

Tiago

From p.j.a.cock at googlemail.com  Mon Mar 30 12:30:43 2015
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 30 Mar 2015 13:30:43 +0100
Subject: [Biopython-dev] Docker containers
In-Reply-To: <20150330122040.175bbeac@lnx>
References: <20150330122040.175bbeac@lnx>
Message-ID: <CAKVJ-_7Ua0=um+PXmfYCja1bBiroiuBSCFxpMDB7sDUbZ2xeFQ@mail.gmail.com>

On Mon, Mar 30, 2015 at 12:20 PM, Tiago Antao <tra at popgen.net> wrote:
> Dear all,
>
> Before I port my containers to the project there are a few things that
> you should be made aware of:
>
> 1. There are 4 containers x 2 versions (Python 2 and 3): empty (shell),
> notebook, notebook with tutorial and buildbot. The buildbot one is
> currently under maintenance, but I would expect all the others to work.
>
> 2. I am maintaining all these containers with a simple template system
> on my repository (https://github.com/tiagoantao/my-containers). It is
> clumsy, but does the work. I will probably port the script also to the
> new main repo.
>
> 3. The containers themselves were my first attempt at doing docker
> containers, so they are a bit naive. But they do work. A future plan
> would be to use anaconda (well, miniconda) as a basis. Also force the
> versions of all packages.
>
> 4. You can find instructions here:
> http://fe.popgen.net/2015/03/docker-containers-for-biopython/ .
>
> Comments and criticism appreciated.
>
> When everyone is happy, I will put everything under the biopython repo.
>
> Tiago

i.e. This new (currently empty) repository:
https://github.com/biopython/biopython_docker

See also discussion on these threads:
http://lists.open-bio.org/pipermail/biopython-dev/2015-March/020847.html
http://lists.open-bio.org/pipermail/biopython-dev/2015-March/020864.html

Peter

From j.p.g.l.m.rodrigues at gmail.com  Mon Mar 30 17:53:36 2015
From: j.p.g.l.m.rodrigues at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues?=)
Date: Mon, 30 Mar 2015 17:53:36 +0000
Subject: [Biopython-dev] Biopython Project Update 2015;
 was BOSC 2015 Call for Abstracts
In-Reply-To: <CAKVJ-_4JE0jHTHOz6KXbcsGb6_ThfyZ+yCCBjZJpiGE6HhaeJg@mail.gmail.com>
References: <CAKVJ-_5yGzQMkoeZwVeymPpPaM2wEZe5GGTZ09+Rf1tvnQq3Gg@mail.gmail.com>
	<CAKVJ-_5OQQaOhbEWjm8NM33B7X9WVY=H728uGr9Qz5o4=h_ATA@mail.gmail.com>
	<CAB=-b2bsQtCDKSdY98x6o7nRpC+Lnz3syBqeZ5058PxVVsnUhA@mail.gmail.com>
	<CAKVJ-_7V7QcGMKw=MJU5o-HSLnZARWr6Lkz7urN59fwAMY2+wQ@mail.gmail.com>
	<CAB=-b2YyfoKyZ3k1T=CM7vNMJb46YtXJOxYZQq+gQMNKDV3ZsA@mail.gmail.com>
	<55157813.7040107@brueffer.de>
	<CAKVJ-_4JE0jHTHOz6KXbcsGb6_ThfyZ+yCCBjZJpiGE6HhaeJg@mail.gmail.com>
Message-ID: <CAB=-b2Z2JJqOJ_XCckyQfQqpw0MFzf6fh8LH5DuLirBAR4P7Lg@mail.gmail.com>

Hi all,

A tentative draft for the BOSC abstract.
<https://github.com/JoaoRodrigues/talks/tree/master/2015_BOSC/abstract>

Please feel free to change things. I never worked with LaTeX before so I
might have damaged the beautiful formatting Bow had..

Cheers,

Jo?o
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From christian at brueffer.de  Mon Mar 30 18:09:13 2015
From: christian at brueffer.de (Christian Brueffer)
Date: Mon, 30 Mar 2015 20:09:13 +0200
Subject: [Biopython-dev] Biopython Project Update 2015;
 was BOSC 2015 Call for Abstracts
In-Reply-To: <CAB=-b2Z2JJqOJ_XCckyQfQqpw0MFzf6fh8LH5DuLirBAR4P7Lg@mail.gmail.com>
References: <CAKVJ-_5yGzQMkoeZwVeymPpPaM2wEZe5GGTZ09+Rf1tvnQq3Gg@mail.gmail.com>
	<CAKVJ-_5OQQaOhbEWjm8NM33B7X9WVY=H728uGr9Qz5o4=h_ATA@mail.gmail.com>
	<CAB=-b2bsQtCDKSdY98x6o7nRpC+Lnz3syBqeZ5058PxVVsnUhA@mail.gmail.com>
	<CAKVJ-_7V7QcGMKw=MJU5o-HSLnZARWr6Lkz7urN59fwAMY2+wQ@mail.gmail.com>
	<CAB=-b2YyfoKyZ3k1T=CM7vNMJb46YtXJOxYZQq+gQMNKDV3ZsA@mail.gmail.com>
	<55157813.7040107@brueffer.de>
	<CAKVJ-_4JE0jHTHOz6KXbcsGb6_ThfyZ+yCCBjZJpiGE6HhaeJg@mail.gmail.com>
	<CAB=-b2Z2JJqOJ_XCckyQfQqpw0MFzf6fh8LH5DuLirBAR4P7Lg@mail.gmail.com>
Message-ID: <55199149.6020007@brueffer.de>

On 2015-03-30 19:53, Jo?o Rodrigues wrote:
> Hi all,
>
> A tentative draft for the BOSC abstract.
> <https://github.com/JoaoRodrigues/talks/tree/master/2015_BOSC/abstract>
>
> Please feel free to change things. I never worked with LaTeX before so I
> might have damaged the beautiful formatting Bow had..
>

Reads nicely!  Some improvements in 
https://github.com/JoaoRodrigues/talks/pull/1

Cheers,

Chris

From christian at brueffer.de  Mon Mar 30 18:14:09 2015
From: christian at brueffer.de (Christian Brueffer)
Date: Mon, 30 Mar 2015 20:14:09 +0200
Subject: [Biopython-dev] Reproducible Biopython VM images
In-Reply-To: <CAKVJ-_4JK9n4t6SRhmC5QfzDx8wR=3YEnM9we6wS7bh2gzpaxQ@mail.gmail.com>
References: <55081140.2000609@brueffer.de>	<CAKVJ-_7epCGW=ObrX40CNaZOD4gqUeTtKaMvBZ8Lk8CUMNrFwQ@mail.gmail.com>	<55082405.4070402@brueffer.de>	<20150317150140.45d42be4@lnx>	<55113288.3090200@brueffer.de>	<CAKVJ-_7=OASG8--CuWuNi3zqR+si5VQZO=nJAqCxXX6K=SF=PQ@mail.gmail.com>	<551567CB.2020301@brueffer.de>
	<CAKVJ-_4JK9n4t6SRhmC5QfzDx8wR=3YEnM9we6wS7bh2gzpaxQ@mail.gmail.com>
Message-ID: <55199271.80708@brueffer.de>

On 2015-03-30 12:24, Peter Cock wrote:
> On Fri, Mar 27, 2015 at 2:23 PM, Christian Brueffer
> <christian at brueffer.de> wrote:
>> On 2015-03-24 12:54, Peter Cock wrote:
>>>
>>> On Tue, Mar 24, 2015 at 9:46 AM, Christian Brueffer
>>> <christian at brueffer.de> wrote:
>>>>
>>>> Hi Tiago,
>>>>
>>>> nice work!  Looks like my Vagrant stuff in redundant indeed and I can
>>>> abandon it.
>>>>
>>>> Any chance we can make this a bit more visible?  A paragraph in the
>>>> README
>>>> would be a good start; I can whip something up if we agree this is a good
>>>> idea.
>>>>
>>>> Cheers,
>>>>
>>>> Chris
>>>
>>>
>>> Related to this, if there is general interest we could have another
>>> repository on GitHub for docker containers (much like we have
>>> a small repository for Biopython's Galaxy packaging).
>>>
>>
>> I think that would be helpful.
>>
>> Chris
>
> We seem to be in agreement then - what should we call this new
> repository under Biopython's GitHub account? e.g. biopython-docker
>

I wonder whether a more generic name would be better.  Once the "next 
best thing" comes along and makes Docker obsolete, we have a stale 
repository :-)

How about biopython-containers? (a bit more bulky I admit, but aren't 
all containers? :-) )

Chris

From christian at brueffer.de  Mon Mar 30 18:16:57 2015
From: christian at brueffer.de (Christian Brueffer)
Date: Mon, 30 Mar 2015 20:16:57 +0200
Subject: [Biopython-dev] Biopython Project Update 2015;
 was BOSC 2015 Call for Abstracts
In-Reply-To: <CAKVJ-_4JE0jHTHOz6KXbcsGb6_ThfyZ+yCCBjZJpiGE6HhaeJg@mail.gmail.com>
References: <CAKVJ-_5yGzQMkoeZwVeymPpPaM2wEZe5GGTZ09+Rf1tvnQq3Gg@mail.gmail.com>	<CAKVJ-_5OQQaOhbEWjm8NM33B7X9WVY=H728uGr9Qz5o4=h_ATA@mail.gmail.com>	<CAB=-b2bsQtCDKSdY98x6o7nRpC+Lnz3syBqeZ5058PxVVsnUhA@mail.gmail.com>	<CAKVJ-_7V7QcGMKw=MJU5o-HSLnZARWr6Lkz7urN59fwAMY2+wQ@mail.gmail.com>	<CAB=-b2YyfoKyZ3k1T=CM7vNMJb46YtXJOxYZQq+gQMNKDV3ZsA@mail.gmail.com>	<55157813.7040107@brueffer.de>
	<CAKVJ-_4JE0jHTHOz6KXbcsGb6_ThfyZ+yCCBjZJpiGE6HhaeJg@mail.gmail.com>
Message-ID: <55199319.9000406@brueffer.de>

On 2015-03-29 22:46, Peter Cock wrote:
> On Fri, Mar 27, 2015 at 3:32 PM, Christian Brueffer
> <christian at brueffer.de> wrote:
>> Hi Jo?o,
>>
>> if you can't make it, I could jump in for the update.
>>
>> Cheers,
>>
>> Chris
>
> Thanks :)
>
> If you have any of your own work you'd like to talk about,
> please do think about submitting a BOSC abstract (and/or
> one of the other ISMB/ECCB opportunities like our sister
> SIG meetings).
>

It's on my list for next year; my projects haven't progressed enough for 
this year.

Thanks for the hint though!

Chris

From p.j.a.cock at googlemail.com  Mon Mar 30 21:29:24 2015
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 30 Mar 2015 22:29:24 +0100
Subject: [Biopython-dev] Reproducible Biopython VM images
In-Reply-To: <55199271.80708@brueffer.de>
References: <55081140.2000609@brueffer.de>
	<CAKVJ-_7epCGW=ObrX40CNaZOD4gqUeTtKaMvBZ8Lk8CUMNrFwQ@mail.gmail.com>
	<55082405.4070402@brueffer.de> <20150317150140.45d42be4@lnx>
	<55113288.3090200@brueffer.de>
	<CAKVJ-_7=OASG8--CuWuNi3zqR+si5VQZO=nJAqCxXX6K=SF=PQ@mail.gmail.com>
	<551567CB.2020301@brueffer.de>
	<CAKVJ-_4JK9n4t6SRhmC5QfzDx8wR=3YEnM9we6wS7bh2gzpaxQ@mail.gmail.com>
	<55199271.80708@brueffer.de>
Message-ID: <CAKVJ-_7qkx3soc9LEKt_620ktV+J92=tjgbmQ15VgpwnhMtMiw@mail.gmail.com>

On Mon, Mar 30, 2015 at 7:14 PM, Christian Brueffer
<christian at brueffer.de> wrote:
> On 2015-03-30 12:24, Peter Cock wrote:
>>
>> We seem to be in agreement then - what should we call this new
>> repository under Biopython's GitHub account? e.g. biopython-docker
>
> I wonder whether a more generic name would be better.  Once the "next best
> thing" comes along and makes Docker obsolete, we have a stale repository :-)

That seems fine if/when Docket becomes obsolete - we'd move our
efforts to a new repository biopython_thenextbestthing instead ;)

> How about biopython-containers? (a bit more bulky I admit, but aren't all
> containers? :-) )
>
> Chris

The open ended naming makes sense if we would envision
translating Docker recipes into "the next best thing" recipes.

Peter

P.S. Does anyone with artistic talent want to draw a cartoon blue whale
(Docker logo) being squeezed by a pair of yellow (Biopython) pythons?
Note sure it would work, but could also try the snake-helix as a whale's
spout ...