From peter at maubp.freeserve.co.uk Tue Dec 1 15:00:43 2009 From: peter at maubp.freeserve.co.uk (Peter) Date: Tue, 1 Dec 2009 20:00:43 +0000 Subject: [Open-bio-l] Fwd: [Utilities-announce] NCBI E-Utility Policy Change In-Reply-To: <7B6F170840CA6C4DA63EE0C8A7BB43EC09CA7387@NIHCESMLBX15.nih.gov> References: <7B6F170840CA6C4DA63EE0C8A7BB43EC09CA7387@NIHCESMLBX15.nih.gov> Message-ID: <320fb6e00912011200j6121d6c5w779bedf3a3c54189@mail.gmail.com> Hi all, I know Biopython and BioPerl are aware of this change, but in case the other Bio* projects are not please see below. Sign up here: http://www.ncbi.nlm.nih.gov/Sitemap/Summary/email_lists.html Peter @ Biopython ---------- Forwarded message ---------- From: Date: Tue, Dec 1, 2009 at 6:59 PM Subject: [Utilities-announce] NCBI E-Utility Policy Change To: utilities-announce at ncbi.nlm.nih.gov As part of an ongoing effort to ensure efficient access to the Entrez Utilities (E-utilities) by all users, NCBI has decided to change the usage policy for the E-utilities effective June 1, 2010. Effective on June 1, 2010, all E-utility requests, either using standard URLs or SOAP, must contain non-null values for both the &tool and &email parameters. Any E-utility request made after June 1, 2010 that does not contain values for both parameters will return an error explaining that these parameters must be included in E-utility requests. The value of the &tool parameter should be a URI-safe string that is the name of the software package, script or web page producing the E-utility request. The value of the &email parameter should be a valid e-mail address for the appropriate contact person or group responsible for maintaining the tool producing the E-utility request. NCBI uses these parameters to contact users whose use of the E-utilities violates the standard usage policies described at http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html#UserSystemRequirements. These usage policies are designed to prevent excessive requests from a small group of users from reducing or eliminating the wider community's access to the E-utilities. NCBI will attempt to contact a user at the e-mail address provided in the &email parameter prior to blocking access to the E-utilities. NCBI realizes that this policy change will require many of our users to change their code. Based on past experience, we anticipate that most of our users should be able to make the necessary changes before the June 1, 2010 deadline. If you have any concerns about making these changes by that date, or if you have any questions about these policies, please contact eutilities at ncbi.nlm.nih.gov. Thank you for your understanding and cooperation in helping us continue to deliver a reliable and efficient web service. _______________________________________________ Utilities-announce mailing list http://www.ncbi.nlm.nih.gov/mailman/listinfo/utilities-announce From dan.bolser at gmail.com Thu Dec 3 08:12:08 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 3 Dec 2009 13:12:08 +0000 Subject: [Open-bio-l] Best practices for quality trimming? Message-ID: <2c8757af0912030512t12470ac9y179fb4f54bb8539d@mail.gmail.com> What is there a Standard Operating Procedure (SOP) for quality trimming reads? i.e. which tool, what settings and for what purpose? It seems that, when using a window, the median quality of the window should be used as the threshold for deciding where to 'end clip' sequences. Is there a database of the assemblers, for example, that do or don't take quality information into account when assembling? I'm working on a software database for NGS tools here: http://seqwiki.com (It's still quite beta, and at some point it may move to http://bifx.org/wiki) Cheers, Dan. From biopython at maubp.freeserve.co.uk Thu Dec 3 09:29:29 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 3 Dec 2009 14:29:29 +0000 Subject: [Open-bio-l] Best practices for quality trimming? In-Reply-To: <2c8757af0912030512t12470ac9y179fb4f54bb8539d@mail.gmail.com> References: <2c8757af0912030512t12470ac9y179fb4f54bb8539d@mail.gmail.com> Message-ID: <320fb6e00912030629kdfac492r691c78fa73f6a7bd@mail.gmail.com> On Thu, Dec 3, 2009 at 1:12 PM, Dan Bolser wrote: > What is there a Standard Operating Procedure (SOP) for quality > trimming reads? i.e. which tool, what settings and for what purpose? > > It seems that, when using a window, the median quality of the window > should be used as the threshold for deciding where to 'end clip' > sequences. > > Is there a database of the assemblers, for example, that do or don't > take quality information into account when assembling? Hi Dan, It was nice to say hello again in Edinburgh this week: http://www.sbforum.org/earchive.php?e_id=79 As the group discussed, this is tricky - especially as it will depend greatly on what you are going to do with the reads next (e.g. assembly or mapping onto a reference) and which tools. For velvet trimming seems to help (especially in terms of reducing the memory demands). If we can settle on a reasonable set of procedures, it would be great to have implementations in EMBOSS (i.e. this could be the "quaffle" tool Peter Rice has suggested) plus BioPerl, Biopython etc. The later would be especially useful as base points for people to modify the algorithm to try new ideas. See also: http://lists.open-bio.org/pipermail/emboss/2009-December/003788.html > I'm working on a software database for NGS tools here: > > http://seqwiki.com > > (It's still quite beta, and at some point it may move to http://bifx.org/wiki) Currently it points at http://seqanswers.com/wiki/SEQanswers which is perhaps a good idea given the good reputation of seqanswers. Peter C. From MEC at stowers.org Thu Dec 3 10:00:23 2009 From: MEC at stowers.org (Cook, Malcolm) Date: Thu, 3 Dec 2009 09:00:23 -0600 Subject: [Open-bio-l] Best practices for quality trimming? In-Reply-To: <320fb6e00912030629kdfac492r691c78fa73f6a7bd@mail.gmail.com> References: <2c8757af0912030512t12470ac9y179fb4f54bb8539d@mail.gmail.com> <320fb6e00912030629kdfac492r691c78fa73f6a7bd@mail.gmail.com> Message-ID: Surprisingly I've seen no mention on SeqAnswers of fastx-toolkit ("a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing") http://hannonlab.cshl.edu/fastx_toolkit/commandline.html We have had good experience with it for quality trimming, quality reporting, adaptor removal and duplicate "collapsing" of Illumina read.... and it has an integration with galaxy.... Any EMBOSS integration might seek to provide similar capabilities.... Malcolm Cook Bioinformatics Stowers Institute for Medical Research - Kansas City, Missouri > -----Original Message----- > From: open-bio-l-bounces at lists.open-bio.org > [mailto:open-bio-l-bounces at lists.open-bio.org] On Behalf Of Peter > Sent: Thursday, December 03, 2009 8:29 AM > To: Dan Bolser > Cc: open-bio-l at lists.open-bio.org > Subject: Re: [Open-bio-l] Best practices for quality trimming? > > On Thu, Dec 3, 2009 at 1:12 PM, Dan Bolser > wrote: > > What is there a Standard Operating Procedure (SOP) for quality > > trimming reads? i.e. which tool, what settings and for what purpose? > > > > It seems that, when using a window, the median quality of > the window > > should be used as the threshold for deciding where to 'end clip' > > sequences. > > > > Is there a database of the assemblers, for example, that do > or don't > > take quality information into account when assembling? > > Hi Dan, > > It was nice to say hello again in Edinburgh this week: > http://www.sbforum.org/earchive.php?e_id=79 > > As the group discussed, this is tricky - especially as it > will depend greatly on what you are going to do with the > reads next (e.g. > assembly or mapping onto a reference) and which tools. For > velvet trimming seems to help (especially in terms of > reducing the memory demands). > > If we can settle on a reasonable set of procedures, it would > be great to have implementations in EMBOSS (i.e. this could > be the "quaffle" tool Peter Rice has suggested) plus BioPerl, > Biopython etc. The later would be especially useful as base > points for people to modify the algorithm to try new ideas. > > See also: > http://lists.open-bio.org/pipermail/emboss/2009-December/003788.html > > > I'm working on a software database for NGS tools here: > > > > http://seqwiki.com > > > > (It's still quite beta, and at some point it may move to > > http://bifx.org/wiki) > > Currently it points at http://seqanswers.com/wiki/SEQanswers > which is perhaps a good idea given the good reputation of seqanswers. > > Peter C. > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l > From dan.bolser at gmail.com Thu Dec 3 11:57:21 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 3 Dec 2009 16:57:21 +0000 Subject: [Open-bio-l] Best practices for quality trimming? In-Reply-To: References: <2c8757af0912030512t12470ac9y179fb4f54bb8539d@mail.gmail.com> <320fb6e00912030629kdfac492r691c78fa73f6a7bd@mail.gmail.com> Message-ID: <2c8757af0912030857n7d495c29na2e1a8a17650979d@mail.gmail.com> 2009/12/3 Cook, Malcolm : > Surprisingly I've seen no mention on SeqAnswers of fastx-toolkit ("a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing") > > http://hannonlab.cshl.edu/fastx_toolkit/commandline.html > > We have had good experience with it for quality trimming, quality reporting, adaptor removal and duplicate "collapsing" of Illumina read.... and it has an integration with galaxy.... The great thing about SeqWiki is that it's a wiki, which means that when things are found to be missing, they can be added. Unfortunately, by far the coolest page of SeqWiki only works when you are logged in (its a mysterious bug related to the interaction of vBulletin logins and MW logins). However, if you have logged in to SeqAnswers, or if you don't mind registering, you may like to try this page: http://seqanswers.com/wiki/Special:BrowseData Dan. From biopython at maubp.freeserve.co.uk Tue Dec 15 07:07:48 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Tue, 15 Dec 2009 12:07:48 +0000 Subject: [Open-bio-l] Updating http://www.open-bio.org/wiki/SourceCode Message-ID: <320fb6e00912150407o48fd981fn16dedaf0581e5fef@mail.gmail.com> Hello all, We just had a puzzling mailing list query about the Biopython CVS repository, which turned out to be partly due to some very dated information here: http://www.open-bio.org/wiki/SourceCode I've made a few minor improvements, but feel the whole page could be simplified. Am I right in thinking it is just EMBOSS still using CVS (all the other projects are now on SVN or github, or obsolete)? If so, since EMBOSS has nice CVS documentation on their own webpages, could we remove most of the CVS text from the OBF wiki: http://emboss.sourceforge.net/developers/cvs.html Thanks, Peter (@Biopython) From andy.jenkinson at ebi.ac.uk Tue Dec 15 07:42:47 2009 From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson) Date: Tue, 15 Dec 2009 12:42:47 +0000 Subject: [Open-bio-l] Updating http://www.open-bio.org/wiki/SourceCode In-Reply-To: <320fb6e00912150407o48fd981fn16dedaf0581e5fef@mail.gmail.com> References: <320fb6e00912150407o48fd981fn16dedaf0581e5fef@mail.gmail.com> Message-ID: To be honest I'm not sure which (if any) of the BioDAS project's components are using CVS. IIRC something was but I don't have access so have never looked into it. Perhaps someone else can confirm? On 15 Dec 2009, at 12:07, Peter wrote: > Hello all, > > We just had a puzzling mailing list query about the Biopython CVS > repository, which turned out to be partly due to some very dated > information here: http://www.open-bio.org/wiki/SourceCode > > I've made a few minor improvements, but feel the whole page > could be simplified. > > Am I right in thinking it is just EMBOSS still using CVS (all the > other projects are now on SVN or github, or obsolete)? If so, since > EMBOSS has nice CVS documentation on their own webpages, > could we remove most of the CVS text from the OBF wiki: > http://emboss.sourceforge.net/developers/cvs.html > > Thanks, > > Peter > (@Biopython) > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l From biopython at maubp.freeserve.co.uk Tue Dec 15 08:11:55 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Tue, 15 Dec 2009 13:11:55 +0000 Subject: [Open-bio-l] Updating http://www.open-bio.org/wiki/SourceCode In-Reply-To: References: <320fb6e00912150407o48fd981fn16dedaf0581e5fef@mail.gmail.com> Message-ID: <320fb6e00912150511u928e0a3s2187a11a634bda0a@mail.gmail.com> On Tue, Dec 15, 2009 at 12:42 PM, Andy Jenkinson wrote: > To be honest I'm not sure which (if any) of the BioDAS project's > components are using CVS. IIRC something was but I don't have > access so have never looked into it. Perhaps someone else can confirm? This wiki page suggests that BioDAS is also still using CVS: http://www.biodas.org/wiki/DAS/2#CVS_Access Peter From pmr at ebi.ac.uk Tue Dec 15 11:32:38 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 15 Dec 2009 16:32:38 +0000 Subject: [Open-bio-l] [emboss-dev] Updating http://www.open-bio.org/wiki/SourceCode In-Reply-To: <320fb6e00912150407o48fd981fn16dedaf0581e5fef@mail.gmail.com> References: <320fb6e00912150407o48fd981fn16dedaf0581e5fef@mail.gmail.com> Message-ID: <4B27BA26.3050004@ebi.ac.uk> On 15/12/09 12:07, Peter wrote: > Hello all, > > We just had a puzzling mailing list query about the Biopython CVS > repository, which turned out to be partly due to some very dated > information here: http://www.open-bio.org/wiki/SourceCode > > I've made a few minor improvements, but feel the whole page > could be simplified. > > Am I right in thinking it is just EMBOSS still using CVS (all the > other projects are now on SVN or github, or obsolete)? If so, since > EMBOSS has nice CVS documentation on their own webpages, > could we remove most of the CVS text from the OBF wiki: > http://emboss.sourceforge.net/developers/cvs.html No problem for EMBOSS. regards, Peter Rice From andy.jenkinson at ebi.ac.uk Tue Dec 15 11:58:07 2009 From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson) Date: Tue, 15 Dec 2009 16:58:07 +0000 Subject: [Open-bio-l] Updating http://www.open-bio.org/wiki/SourceCode In-Reply-To: <320fb6e00912150511u928e0a3s2187a11a634bda0a@mail.gmail.com> References: <320fb6e00912150407o48fd981fn16dedaf0581e5fef@mail.gmail.com> <320fb6e00912150511u928e0a3s2187a11a634bda0a@mail.gmail.com> Message-ID: On 15 Dec 2009, at 13:11, Peter wrote: > On Tue, Dec 15, 2009 at 12:42 PM, Andy Jenkinson > wrote: >> To be honest I'm not sure which (if any) of the BioDAS project's >> components are using CVS. IIRC something was but I don't have >> access so have never looked into it. Perhaps someone else can confirm? > > This wiki page suggests that BioDAS is also still using CVS: > http://www.biodas.org/wiki/DAS/2#CVS_Access > > Peter Then I guess we should be OK. From biopython at maubp.freeserve.co.uk Tue Dec 15 19:02:20 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Wed, 16 Dec 2009 00:02:20 +0000 Subject: [Open-bio-l] Open-Bio Main Wiki Page Message-ID: <320fb6e00912151602g5515a2cftfce5c3ef004c07ed@mail.gmail.com> Hi all, I'll like to update the main page to embed the OBF news feed on the right hand side, rather than having a short manually updated "news" section at the top of the page. i.e. Make this: http://www.open-bio.org/wiki/Main_Page Look more like this: http://biopython.org/wiki/Main_Page And thoughts? It would also be nice to include BioRuby and EMBOSS on the front page somewhere. Peter From hlapp at drycafe.net Tue Dec 15 22:34:23 2009 From: hlapp at drycafe.net (Hilmar Lapp) Date: Tue, 15 Dec 2009 22:34:23 -0500 Subject: [Open-bio-l] Open-Bio Main Wiki Page Message-ID: <3132F739-78AA-4209-8421-598278C0F973@drycafe.net> Sounds great to me. Have you seen the GMOD wiki? It also has feeds embedded in the front page, just as another example. -hilmar Sent from away On Dec 15, 2009, at 7:02 PM, Peter wrote: > Hi all, > > I'll like to update the main page to embed the OBF news > feed on the right hand side, rather than having a short > manually updated "news" section at the top of the page. > > i.e. Make this: > http://www.open-bio.org/wiki/Main_Page > > Look more like this: > http://biopython.org/wiki/Main_Page > > And thoughts? > > It would also be nice to include BioRuby and EMBOSS on the front > page somewhere. > > Peter > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l > From biopython at maubp.freeserve.co.uk Wed Dec 16 09:44:42 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Wed, 16 Dec 2009 14:44:42 +0000 Subject: [Open-bio-l] Open-Bio Main Wiki Page In-Reply-To: <3132F739-78AA-4209-8421-598278C0F973@drycafe.net> References: <3132F739-78AA-4209-8421-598278C0F973@drycafe.net> Message-ID: <320fb6e00912160644m35ddf831kf727801ccc3af87c@mail.gmail.com> On Wed, Dec 16, 2009 at 3:34 AM, Hilmar Lapp wrote: > Sounds great to me. Have you seen the GMOD wiki? It also has feeds embedded > in the front page, just as another example. > > -hilmar The GMOD one is pretty slick. Someone with suitable permissions on the open-bio wiki will need to make any changes, since the main page is (quite sensibly) protected. Peter From cjfields at illinois.edu Wed Dec 16 10:15:54 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 16 Dec 2009 09:15:54 -0600 Subject: [Open-bio-l] Open-Bio Main Wiki Page In-Reply-To: <320fb6e00912160644m35ddf831kf727801ccc3af87c@mail.gmail.com> References: <3132F739-78AA-4209-8421-598278C0F973@drycafe.net> <320fb6e00912160644m35ddf831kf727801ccc3af87c@mail.gmail.com> Message-ID: <09F1CD93-6049-4A7C-9AAB-C51527BFE102@illinois.edu> On Dec 16, 2009, at 8:44 AM, Peter wrote: > On Wed, Dec 16, 2009 at 3:34 AM, Hilmar Lapp wrote: >> Sounds great to me. Have you seen the GMOD wiki? It also has feeds embedded >> in the front page, just as another example. >> >> -hilmar > > The GMOD one is pretty slick. Yes, I like that one as well, had been thinking about using something like it for the bioperl page. > Someone with suitable permissions on the open-bio > wiki will need to make any changes, since the main > page is (quite sensibly) protected. > > Peter What is your user id on that wiki? I think I can grant you sysop privs. If not, I can definitely edit that page for you, just let me know what you want. chris From clements at nescent.org Wed Dec 16 18:14:35 2009 From: clements at nescent.org (Dave Clements) Date: Wed, 16 Dec 2009 15:14:35 -0800 Subject: [Open-bio-l] Open-Bio Main Wiki Page In-Reply-To: <09F1CD93-6049-4A7C-9AAB-C51527BFE102@illinois.edu> References: <3132F739-78AA-4209-8421-598278C0F973@drycafe.net> <320fb6e00912160644m35ddf831kf727801ccc3af87c@mail.gmail.com> <09F1CD93-6049-4A7C-9AAB-C51527BFE102@illinois.edu> Message-ID: Hi Peter, Chris, The GMOD home page (http://gmod.org) news item list is created from the GMOD News RSS Feed. The home page renders the feed using the FeedImport extension ( http://www.mediawiki.org/wiki/Extension:FeedImport). The RSS feed is generated from the GMOD News page ( http://gmod.org/wiki/GMOD_News) using the WikiArticleFeeds extension ( http://www.mediawiki.org/wiki/Extension:WikiArticleFeeds). My memory is that FeedImport was a tough install due to its dependency on Magpie and Snoopy. I just updated the WikiArticleFeeds extension and that was easy. Be warned that something in the process is sensitive to bad MediaWiki markup. That is, if you, for example, don't close a tag in your news item text, your list of news items may be garbage until you fix it and the feed refreshes. I also have a sneaking suspicion that rendering the news feed on the home page might be slowing down load times noticeably. :-( Hope this helps, Dave C. On Wed, Dec 16, 2009 at 7:15 AM, Chris Fields wrote: > On Dec 16, 2009, at 8:44 AM, Peter wrote: > > > On Wed, Dec 16, 2009 at 3:34 AM, Hilmar Lapp wrote: > >> Sounds great to me. Have you seen the GMOD wiki? It also has feeds > embedded > >> in the front page, just as another example. > >> > >> -hilmar > > > > The GMOD one is pretty slick. > > Yes, I like that one as well, had been thinking about using something like > it for the bioperl page. > > > Someone with suitable permissions on the open-bio > > wiki will need to make any changes, since the main > > page is (quite sensibly) protected. > > > > Peter > > What is your user id on that wiki? I think I can grant you sysop privs. > If not, I can definitely edit that page for you, just let me know what you > want. > > chris > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l > -- http://gmod.org/wiki/January_2010_GMOD_Meeting http://gmod.org/wiki/GMOD_News From biopython at maubp.freeserve.co.uk Wed Dec 16 18:53:34 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Wed, 16 Dec 2009 23:53:34 +0000 Subject: [Open-bio-l] Open-Bio Main Wiki Page In-Reply-To: References: <3132F739-78AA-4209-8421-598278C0F973@drycafe.net> <320fb6e00912160644m35ddf831kf727801ccc3af87c@mail.gmail.com> <09F1CD93-6049-4A7C-9AAB-C51527BFE102@illinois.edu> Message-ID: <320fb6e00912161553v57a5c087q3e9c04645a830ac8@mail.gmail.com> On Wed, Dec 16, 2009 at 11:14 PM, Dave Clements wrote: > Hi Peter, Chris, > > The GMOD home page (http://gmod.org) news item list is created from > the GMOD News RSS Feed. > > The home page renders the feed using the FeedImport extension ( > http://www.mediawiki.org/wiki/Extension:FeedImport). > > The RSS feed is generated from the GMOD News page ( > http://gmod.org/wiki/GMOD_News) using the WikiArticleFeeds extension ( > http://www.mediawiki.org/wiki/Extension:WikiArticleFeeds). > > My memory is that FeedImport was a tough install due to its dependency on > Magpie and Snoopy. ?I just updated the WikiArticleFeeds extension and that > was easy. > > Be warned that something in the process is sensitive to bad MediaWiki > markup. ?That is, if you, for example, don't close a tag in your news item > text, your list of news items may be garbage until you fix it and the feed > refreshes. > > I also have a sneaking suspicion that rendering the news feed on the home > page might be slowing down load times noticeably. ?:-( > > Hope this helps, Thanks for the info Dave - its enough to know its beyond my current knowledge of MediaWiki! Perhaps Chris or someone else want to try the extra plugin option... In the meantime (having been given access by Chris - thanks), I have just copied the simple RSS embedding as already in use on the Biopython page. How does it look now - hopefully a worthwhile improvement in itself? http://www.open-bio.org/wiki/Main_Page I would also suggest we consider making the "News" page just redirect to the news server... Peter From p.j.a.cock at googlemail.com Fri Dec 18 10:30:28 2009 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 18 Dec 2009 15:30:28 +0000 Subject: [Open-bio-l] Sanger FASTQ format and the Solexa/Illumina variants Message-ID: <320fb6e00912180730n1d951969ga2c5c461d97f581a@mail.gmail.com> Hi all, I?m delighted to announce an open access publication in Nucleic Acids Research describing the FASTQ file format based on the conventions agreed by the OBF projects (largely on this mailing list): The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Peter J. A. Cock (Biopython), Christopher J. Fields (BioPerl), Naohisa Goto (BioRuby), Michael L. Heuer (BioJava) and Peter M. Rice (EMBOSS). Nucleic Acids Research, doi:10.1093/nar/gkp1137 This open access publication will hopefully serve as a reference describing the original standard Sanger FASTQ, and the two variants from Solexa/Illumina, and how to inter-convert between them. Peter P.S. This was also posted on the OBF news server: http://news.open-bio.org/news/2009/12/nar-fastq-format/ From hlapp at drycafe.net Fri Dec 18 11:25:03 2009 From: hlapp at drycafe.net (Hilmar Lapp) Date: Fri, 18 Dec 2009 11:25:03 -0500 Subject: [Open-bio-l] Sanger FASTQ format and the Solexa/Illumina variants In-Reply-To: <320fb6e00912180730n1d951969ga2c5c461d97f581a@mail.gmail.com> References: <320fb6e00912180730n1d951969ga2c5c461d97f581a@mail.gmail.com> Message-ID: Congratulations! I'm delighted and truly pleased to see this come out of our community of member projects. Kudos to the team for taking this work all the way through to writing it up formally for publication & archival for everyone's benefit. -hilmar On Dec 18, 2009, at 10:30 AM, Peter Cock wrote: > Hi all, > > I?m delighted to announce an open access publication in Nucleic Acids > Research describing the FASTQ file format based on the conventions > agreed by the OBF projects (largely on this mailing list): > > The Sanger FASTQ file format for sequences with quality scores, > and the Solexa/Illumina FASTQ variants. > Peter J. A. Cock (Biopython), Christopher J. Fields (BioPerl), > Naohisa Goto (BioRuby), Michael L. Heuer (BioJava) > and Peter M. Rice (EMBOSS). > Nucleic Acids Research, doi:10.1093/nar/gkp1137 > > This open access publication will hopefully serve as a reference > describing the original standard Sanger FASTQ, and the two variants > from Solexa/Illumina, and how to inter-convert between them. > > Peter > > P.S. This was also posted on the OBF news server: > http://news.open-bio.org/news/2009/12/nar-fastq-format/ > > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From lpritc at scri.ac.uk Fri Dec 18 13:54:53 2009 From: lpritc at scri.ac.uk (Leighton Pritchard) Date: Fri, 18 Dec 2009 18:54:53 +0000 Subject: [Open-bio-l] Sanger FASTQ format and the Solexa/Illumina variants In-Reply-To: Message-ID: I second Hilmar - congratulations to all the authors! I think it's a very important contribution that summarises the history and current usage of FASTQ, and provides constructive suggestions for how to go forward with what will be a central file format for many areas of biology. L. On 18/12/2009 16:25, "Hilmar Lapp" wrote: > Congratulations! I'm delighted and truly pleased to see this come out > of our community of member projects. Kudos to the team for taking this > work all the way through to writing it up formally for publication & > archival for everyone's benefit. > > -hilmar > > On Dec 18, 2009, at 10:30 AM, Peter Cock wrote: > >> Hi all, >> >> I?m delighted to announce an open access publication in Nucleic Acids >> Research describing the FASTQ file format based on the conventions >> agreed by the OBF projects (largely on this mailing list): >> >> The Sanger FASTQ file format for sequences with quality scores, >> and the Solexa/Illumina FASTQ variants. >> Peter J. A. Cock (Biopython), Christopher J. Fields (BioPerl), >> Naohisa Goto (BioRuby), Michael L. Heuer (BioJava) >> and Peter M. Rice (EMBOSS). >> Nucleic Acids Research, doi:10.1093/nar/gkp1137 >> >> This open access publication will hopefully serve as a reference >> describing the original standard Sanger FASTQ, and the two variants >> from Solexa/Illumina, and how to inter-convert between them. >> >> Peter >> >> P.S. This was also posted on the OBF news server: >> http://news.open-bio.org/news/2009/12/nar-fastq-format/ >> >> _______________________________________________ >> Open-Bio-l mailing list >> Open-Bio-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/open-bio-l -- Dr Leighton Pritchard MRSC D131, Plant Pathology Programme, SCRI Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA e:lpritc at scri.ac.uk w:http://www.scri.ac.uk/staff/leightonpritchard gpg/pgp: 0xFEFC205C tel:+44(0)1382 562731 x2405 ______________________________________________________ SCRI, Invergowrie, Dundee, DD2 5DA. The Scottish Crop Research Institute is a charitable company limited by guarantee. Registered in Scotland No: SC 29367. Recognised by the Inland Revenue as a Scottish Charity No: SC 006662. DISCLAIMER: This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries. This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed. It may not be disclosed or used by any other than that addressee. If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify postmaster at scri.ac.uk quoting the name of the sender and delete the email from your system. Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any). ______________________________________________________ From chapmanb at 50mail.com Mon Dec 21 16:32:02 2009 From: chapmanb at 50mail.com (Brad Chapman) Date: Mon, 21 Dec 2009 16:32:02 -0500 Subject: [Open-bio-l] [Bosc] BOSC 2010 Request for Input In-Reply-To: <6.1.2.0.2.20091218113046.03f84bc8@incoming.lmu.edu> References: <6.1.2.0.2.20091218113046.03f84bc8@incoming.lmu.edu> Message-ID: <20091221213202.GD35116@sobchak.mgh.harvard.edu> Kam and Open Bio folks; It's great to see planning for BOSC 2010 going on already. Lots of exciting ideas. > --Mini-hackathon either before, during, or after the 2-day BOSC. The > subject of the hackathon would need to be organized by the individual > project leaders/teams. Some suggestions would be adding/extending support > for next-gen sequencing; organizing bugs/tasks so that new beginners can > start contributing to the project easily and working on some of those > bugs/tasks; organizing some type of contest like the Genome Annotation > Assessment Project (GASP) where solutions from different projects compete > on arriving at some type of goal. Would you be willing to organize/lead > this type of session? I can help organize a hackathon at Mass General Hospital, which is located fairly to close to Hynes Convention Center, where the conference is on. I booked conferences rooms for dates surrounding BOSC (July 6-8th and 11th) that will accommodate up to 30 developers from various projects. This could be a fairly informal get together for developers who can spare time before or after BOSC. If we could get a show of hands from people who might be interested, this would help gauge the size and scope. As you suggest above, we can hone in on specifics for the work based on the interests of attendees. > --Organizing/creating a LiveCD or Debian download of Bio* projects with > documentation to support outreach to the larger bioinformatics > community. Would you be willing to organize/lead this type of session? A cloud version of this goal is up and coming here: http://www.cloudbiolinux.com/ I cc'ed in the mailing list for folks there who aren't on the open bio mail servers and might be interested. Brad From maj at fortinbras.us Mon Dec 21 16:38:49 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 21 Dec 2009 16:38:49 -0500 Subject: [Open-bio-l] [Cloud BioLinux Community] [Bosc] BOSC 2010 Request for Input In-Reply-To: <20091221213202.GD35116@sobchak.mgh.harvard.edu> References: <6.1.2.0.2.20091218113046.03f84bc8@incoming.lmu.edu> <20091221213202.GD35116@sobchak.mgh.harvard.edu> Message-ID: <98EFA3B9190E49B491EFB4F9D59FC819@NewLife> count me in, somewhere! MAJ ----- Original Message ----- From: "Brad Chapman" To: Cc: ; Sent: Monday, December 21, 2009 4:32 PM Subject: Re: [Cloud BioLinux Community] [Bosc] BOSC 2010 Request for Input > Kam and Open Bio folks; > It's great to see planning for BOSC 2010 going on already. Lots of > exciting ideas. > >> --Mini-hackathon either before, during, or after the 2-day BOSC. The >> subject of the hackathon would need to be organized by the individual >> project leaders/teams. Some suggestions would be adding/extending support >> for next-gen sequencing; organizing bugs/tasks so that new beginners can >> start contributing to the project easily and working on some of those >> bugs/tasks; organizing some type of contest like the Genome Annotation >> Assessment Project (GASP) where solutions from different projects compete >> on arriving at some type of goal. Would you be willing to organize/lead >> this type of session? > > I can help organize a hackathon at Mass General Hospital, which is > located fairly to close to Hynes Convention Center, where the conference > is on. I booked conferences rooms for dates surrounding BOSC (July > 6-8th and 11th) that will accommodate up to 30 developers from various > projects. > > This could be a fairly informal get together for developers who can > spare time before or after BOSC. If we could get a show of hands > from people who might be interested, this would help gauge the size > and scope. As you suggest above, we can hone in on specifics for the > work based on the interests of attendees. > >> --Organizing/creating a LiveCD or Debian download of Bio* projects with >> documentation to support outreach to the larger bioinformatics >> community. Would you be willing to organize/lead this type of session? > > A cloud version of this goal is up and coming here: > > http://www.cloudbiolinux.com/ > > I cc'ed in the mailing list for folks there who aren't on the open > bio mail servers and might be interested. > > Brad > _______________________________________________ > Community mailing list > Community at cloudbiolinux.com > http://lists.cloudbiolinux.com/mailman/listinfo/community > > From hlapp at drycafe.net Mon Dec 21 18:39:33 2009 From: hlapp at drycafe.net (Hilmar Lapp) Date: Mon, 21 Dec 2009 18:39:33 -0500 Subject: [Open-bio-l] [Bosc] BOSC 2010 Request for Input In-Reply-To: <20091221213202.GD35116@sobchak.mgh.harvard.edu> References: <6.1.2.0.2.20091218113046.03f84bc8@incoming.lmu.edu> <20091221213202.GD35116@sobchak.mgh.harvard.edu> Message-ID: <57BC6503-C655-431C-88BB-0F63E1004BD6@drycafe.net> On Dec 21, 2009, at 4:32 PM, Brad Chapman wrote: > I can help organize a hackathon at Mass General Hospital, which is > located fairly to close to Hynes Convention Center, where the > conference > is on. I booked conferences rooms for dates surrounding BOSC (July > 6-8th and 11th) that will accommodate up to 30 developers from various > projects. Awesome!! Thanks so much Brad for stepping up so quickly and putting your foot down too! > If we could get a show of hands from people who might be interested, > this would help gauge the size and scope. :) -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From cjfields at illinois.edu Mon Dec 21 19:36:02 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 21 Dec 2009 18:36:02 -0600 Subject: [Open-bio-l] [Bosc] BOSC 2010 Request for Input In-Reply-To: <57BC6503-C655-431C-88BB-0F63E1004BD6@drycafe.net> References: <6.1.2.0.2.20091218113046.03f84bc8@incoming.lmu.edu> <20091221213202.GD35116@sobchak.mgh.harvard.edu> <57BC6503-C655-431C-88BB-0F63E1004BD6@drycafe.net> Message-ID: <11C4F67A-300B-420D-B68E-B175DAD283C1@illinois.edu> On Dec 21, 2009, at 5:39 PM, Hilmar Lapp wrote: > On Dec 21, 2009, at 4:32 PM, Brad Chapman wrote: > >> I can help organize a hackathon at Mass General Hospital, which is >> located fairly to close to Hynes Convention Center, where the conference >> is on. I booked conferences rooms for dates surrounding BOSC (July >> 6-8th and 11th) that will accommodate up to 30 developers from various >> projects. > > Awesome!! Thanks so much Brad for stepping up so quickly and putting your foot down too! > >> If we could get a show of hands from people who might be interested, this would help gauge the size and scope. > > > :) > > -hilmar Same here! Just need to sort out the dates, but I should be able to make that. chris From ohofmann at hsph.harvard.edu Mon Dec 21 18:33:50 2009 From: ohofmann at hsph.harvard.edu (Oliver Hofmann) Date: Mon, 21 Dec 2009 23:33:50 -0000 Subject: [Open-bio-l] [Cloud BioLinux Community] [Bosc] BOSC 2010 Request for Input In-Reply-To: <20091221213202.GD35116@sobchak.mgh.harvard.edu> References: <6.1.2.0.2.20091218113046.03f84bc8@incoming.lmu.edu> <20091221213202.GD35116@sobchak.mgh.harvard.edu> Message-ID: <4B3005DF.9030001@hsph.harvard.edu> Oooh, good timing. Happy to help with the organization, we'd have several researchers and developers in the Longwood area who are interested in this (DFCI, HMS and HSPH). Keep in mind MGED is _also_ somewhere around that time, and it might be difficult to motivate people for yet another extra day. Best, Oliver On 12/21/2009 4:32 PM, Brad Chapman wrote: > Kam and Open Bio folks; > It's great to see planning for BOSC 2010 going on already. Lots of > exciting ideas. > >> --Mini-hackathon either before, during, or after the 2-day BOSC. The >> subject of the hackathon would need to be organized by the individual >> project leaders/teams. Some suggestions would be adding/extending support >> for next-gen sequencing; organizing bugs/tasks so that new beginners can >> start contributing to the project easily and working on some of those >> bugs/tasks; organizing some type of contest like the Genome Annotation >> Assessment Project (GASP) where solutions from different projects compete >> on arriving at some type of goal. Would you be willing to organize/lead >> this type of session? > > I can help organize a hackathon at Mass General Hospital, which is > located fairly to close to Hynes Convention Center, where the conference > is on. I booked conferences rooms for dates surrounding BOSC (July > 6-8th and 11th) that will accommodate up to 30 developers from various > projects. > > This could be a fairly informal get together for developers who can > spare time before or after BOSC. If we could get a show of hands > from people who might be interested, this would help gauge the size > and scope. As you suggest above, we can hone in on specifics for the > work based on the interests of attendees. > >> --Organizing/creating a LiveCD or Debian download of Bio* projects with >> documentation to support outreach to the larger bioinformatics >> community. Would you be willing to organize/lead this type of session? > > A cloud version of this goal is up and coming here: > > http://www.cloudbiolinux.com/ > > I cc'ed in the mailing list for folks there who aren't on the open > bio mail servers and might be interested. > > Brad > _______________________________________________ > Community mailing list > Community at cloudbiolinux.com > http://lists.cloudbiolinux.com/mailman/listinfo/community -- Research Associate Department of Biostatistics Associate Director Bioinformatics Core Harvard School of Public Health Skype: ohofmann Phone: +1 (617) 365 0984 From peter at maubp.freeserve.co.uk Tue Dec 1 20:00:43 2009 From: peter at maubp.freeserve.co.uk (Peter) Date: Tue, 1 Dec 2009 20:00:43 +0000 Subject: [Open-bio-l] Fwd: [Utilities-announce] NCBI E-Utility Policy Change In-Reply-To: <7B6F170840CA6C4DA63EE0C8A7BB43EC09CA7387@NIHCESMLBX15.nih.gov> References: <7B6F170840CA6C4DA63EE0C8A7BB43EC09CA7387@NIHCESMLBX15.nih.gov> Message-ID: <320fb6e00912011200j6121d6c5w779bedf3a3c54189@mail.gmail.com> Hi all, I know Biopython and BioPerl are aware of this change, but in case the other Bio* projects are not please see below. Sign up here: http://www.ncbi.nlm.nih.gov/Sitemap/Summary/email_lists.html Peter @ Biopython ---------- Forwarded message ---------- From: Date: Tue, Dec 1, 2009 at 6:59 PM Subject: [Utilities-announce] NCBI E-Utility Policy Change To: utilities-announce at ncbi.nlm.nih.gov As part of an ongoing effort to ensure efficient access to the Entrez Utilities (E-utilities) by all users, NCBI has decided to change the usage policy for the E-utilities effective June 1, 2010. Effective on June 1, 2010, all E-utility requests, either using standard URLs or SOAP, must contain non-null values for both the &tool and &email parameters. Any E-utility request made after June 1, 2010 that does not contain values for both parameters will return an error explaining that these parameters must be included in E-utility requests. The value of the &tool parameter should be a URI-safe string that is the name of the software package, script or web page producing the E-utility request. The value of the &email parameter should be a valid e-mail address for the appropriate contact person or group responsible for maintaining the tool producing the E-utility request. NCBI uses these parameters to contact users whose use of the E-utilities violates the standard usage policies described at http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html#UserSystemRequirements. These usage policies are designed to prevent excessive requests from a small group of users from reducing or eliminating the wider community's access to the E-utilities. NCBI will attempt to contact a user at the e-mail address provided in the &email parameter prior to blocking access to the E-utilities. NCBI realizes that this policy change will require many of our users to change their code. Based on past experience, we anticipate that most of our users should be able to make the necessary changes before the June 1, 2010 deadline. If you have any concerns about making these changes by that date, or if you have any questions about these policies, please contact eutilities at ncbi.nlm.nih.gov. Thank you for your understanding and cooperation in helping us continue to deliver a reliable and efficient web service. _______________________________________________ Utilities-announce mailing list http://www.ncbi.nlm.nih.gov/mailman/listinfo/utilities-announce From dan.bolser at gmail.com Thu Dec 3 13:12:08 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 3 Dec 2009 13:12:08 +0000 Subject: [Open-bio-l] Best practices for quality trimming? Message-ID: <2c8757af0912030512t12470ac9y179fb4f54bb8539d@mail.gmail.com> What is there a Standard Operating Procedure (SOP) for quality trimming reads? i.e. which tool, what settings and for what purpose? It seems that, when using a window, the median quality of the window should be used as the threshold for deciding where to 'end clip' sequences. Is there a database of the assemblers, for example, that do or don't take quality information into account when assembling? I'm working on a software database for NGS tools here: http://seqwiki.com (It's still quite beta, and at some point it may move to http://bifx.org/wiki) Cheers, Dan. From biopython at maubp.freeserve.co.uk Thu Dec 3 14:29:29 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 3 Dec 2009 14:29:29 +0000 Subject: [Open-bio-l] Best practices for quality trimming? In-Reply-To: <2c8757af0912030512t12470ac9y179fb4f54bb8539d@mail.gmail.com> References: <2c8757af0912030512t12470ac9y179fb4f54bb8539d@mail.gmail.com> Message-ID: <320fb6e00912030629kdfac492r691c78fa73f6a7bd@mail.gmail.com> On Thu, Dec 3, 2009 at 1:12 PM, Dan Bolser wrote: > What is there a Standard Operating Procedure (SOP) for quality > trimming reads? i.e. which tool, what settings and for what purpose? > > It seems that, when using a window, the median quality of the window > should be used as the threshold for deciding where to 'end clip' > sequences. > > Is there a database of the assemblers, for example, that do or don't > take quality information into account when assembling? Hi Dan, It was nice to say hello again in Edinburgh this week: http://www.sbforum.org/earchive.php?e_id=79 As the group discussed, this is tricky - especially as it will depend greatly on what you are going to do with the reads next (e.g. assembly or mapping onto a reference) and which tools. For velvet trimming seems to help (especially in terms of reducing the memory demands). If we can settle on a reasonable set of procedures, it would be great to have implementations in EMBOSS (i.e. this could be the "quaffle" tool Peter Rice has suggested) plus BioPerl, Biopython etc. The later would be especially useful as base points for people to modify the algorithm to try new ideas. See also: http://lists.open-bio.org/pipermail/emboss/2009-December/003788.html > I'm working on a software database for NGS tools here: > > http://seqwiki.com > > (It's still quite beta, and at some point it may move to http://bifx.org/wiki) Currently it points at http://seqanswers.com/wiki/SEQanswers which is perhaps a good idea given the good reputation of seqanswers. Peter C. From MEC at stowers.org Thu Dec 3 15:00:23 2009 From: MEC at stowers.org (Cook, Malcolm) Date: Thu, 3 Dec 2009 09:00:23 -0600 Subject: [Open-bio-l] Best practices for quality trimming? In-Reply-To: <320fb6e00912030629kdfac492r691c78fa73f6a7bd@mail.gmail.com> References: <2c8757af0912030512t12470ac9y179fb4f54bb8539d@mail.gmail.com> <320fb6e00912030629kdfac492r691c78fa73f6a7bd@mail.gmail.com> Message-ID: Surprisingly I've seen no mention on SeqAnswers of fastx-toolkit ("a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing") http://hannonlab.cshl.edu/fastx_toolkit/commandline.html We have had good experience with it for quality trimming, quality reporting, adaptor removal and duplicate "collapsing" of Illumina read.... and it has an integration with galaxy.... Any EMBOSS integration might seek to provide similar capabilities.... Malcolm Cook Bioinformatics Stowers Institute for Medical Research - Kansas City, Missouri > -----Original Message----- > From: open-bio-l-bounces at lists.open-bio.org > [mailto:open-bio-l-bounces at lists.open-bio.org] On Behalf Of Peter > Sent: Thursday, December 03, 2009 8:29 AM > To: Dan Bolser > Cc: open-bio-l at lists.open-bio.org > Subject: Re: [Open-bio-l] Best practices for quality trimming? > > On Thu, Dec 3, 2009 at 1:12 PM, Dan Bolser > wrote: > > What is there a Standard Operating Procedure (SOP) for quality > > trimming reads? i.e. which tool, what settings and for what purpose? > > > > It seems that, when using a window, the median quality of > the window > > should be used as the threshold for deciding where to 'end clip' > > sequences. > > > > Is there a database of the assemblers, for example, that do > or don't > > take quality information into account when assembling? > > Hi Dan, > > It was nice to say hello again in Edinburgh this week: > http://www.sbforum.org/earchive.php?e_id=79 > > As the group discussed, this is tricky - especially as it > will depend greatly on what you are going to do with the > reads next (e.g. > assembly or mapping onto a reference) and which tools. For > velvet trimming seems to help (especially in terms of > reducing the memory demands). > > If we can settle on a reasonable set of procedures, it would > be great to have implementations in EMBOSS (i.e. this could > be the "quaffle" tool Peter Rice has suggested) plus BioPerl, > Biopython etc. The later would be especially useful as base > points for people to modify the algorithm to try new ideas. > > See also: > http://lists.open-bio.org/pipermail/emboss/2009-December/003788.html > > > I'm working on a software database for NGS tools here: > > > > http://seqwiki.com > > > > (It's still quite beta, and at some point it may move to > > http://bifx.org/wiki) > > Currently it points at http://seqanswers.com/wiki/SEQanswers > which is perhaps a good idea given the good reputation of seqanswers. > > Peter C. > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l > From dan.bolser at gmail.com Thu Dec 3 16:57:21 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 3 Dec 2009 16:57:21 +0000 Subject: [Open-bio-l] Best practices for quality trimming? In-Reply-To: References: <2c8757af0912030512t12470ac9y179fb4f54bb8539d@mail.gmail.com> <320fb6e00912030629kdfac492r691c78fa73f6a7bd@mail.gmail.com> Message-ID: <2c8757af0912030857n7d495c29na2e1a8a17650979d@mail.gmail.com> 2009/12/3 Cook, Malcolm : > Surprisingly I've seen no mention on SeqAnswers of fastx-toolkit ("a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing") > > http://hannonlab.cshl.edu/fastx_toolkit/commandline.html > > We have had good experience with it for quality trimming, quality reporting, adaptor removal and duplicate "collapsing" of Illumina read.... and it has an integration with galaxy.... The great thing about SeqWiki is that it's a wiki, which means that when things are found to be missing, they can be added. Unfortunately, by far the coolest page of SeqWiki only works when you are logged in (its a mysterious bug related to the interaction of vBulletin logins and MW logins). However, if you have logged in to SeqAnswers, or if you don't mind registering, you may like to try this page: http://seqanswers.com/wiki/Special:BrowseData Dan. From biopython at maubp.freeserve.co.uk Tue Dec 15 12:07:48 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Tue, 15 Dec 2009 12:07:48 +0000 Subject: [Open-bio-l] Updating http://www.open-bio.org/wiki/SourceCode Message-ID: <320fb6e00912150407o48fd981fn16dedaf0581e5fef@mail.gmail.com> Hello all, We just had a puzzling mailing list query about the Biopython CVS repository, which turned out to be partly due to some very dated information here: http://www.open-bio.org/wiki/SourceCode I've made a few minor improvements, but feel the whole page could be simplified. Am I right in thinking it is just EMBOSS still using CVS (all the other projects are now on SVN or github, or obsolete)? If so, since EMBOSS has nice CVS documentation on their own webpages, could we remove most of the CVS text from the OBF wiki: http://emboss.sourceforge.net/developers/cvs.html Thanks, Peter (@Biopython) From andy.jenkinson at ebi.ac.uk Tue Dec 15 12:42:47 2009 From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson) Date: Tue, 15 Dec 2009 12:42:47 +0000 Subject: [Open-bio-l] Updating http://www.open-bio.org/wiki/SourceCode In-Reply-To: <320fb6e00912150407o48fd981fn16dedaf0581e5fef@mail.gmail.com> References: <320fb6e00912150407o48fd981fn16dedaf0581e5fef@mail.gmail.com> Message-ID: To be honest I'm not sure which (if any) of the BioDAS project's components are using CVS. IIRC something was but I don't have access so have never looked into it. Perhaps someone else can confirm? On 15 Dec 2009, at 12:07, Peter wrote: > Hello all, > > We just had a puzzling mailing list query about the Biopython CVS > repository, which turned out to be partly due to some very dated > information here: http://www.open-bio.org/wiki/SourceCode > > I've made a few minor improvements, but feel the whole page > could be simplified. > > Am I right in thinking it is just EMBOSS still using CVS (all the > other projects are now on SVN or github, or obsolete)? If so, since > EMBOSS has nice CVS documentation on their own webpages, > could we remove most of the CVS text from the OBF wiki: > http://emboss.sourceforge.net/developers/cvs.html > > Thanks, > > Peter > (@Biopython) > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l From biopython at maubp.freeserve.co.uk Tue Dec 15 13:11:55 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Tue, 15 Dec 2009 13:11:55 +0000 Subject: [Open-bio-l] Updating http://www.open-bio.org/wiki/SourceCode In-Reply-To: References: <320fb6e00912150407o48fd981fn16dedaf0581e5fef@mail.gmail.com> Message-ID: <320fb6e00912150511u928e0a3s2187a11a634bda0a@mail.gmail.com> On Tue, Dec 15, 2009 at 12:42 PM, Andy Jenkinson wrote: > To be honest I'm not sure which (if any) of the BioDAS project's > components are using CVS. IIRC something was but I don't have > access so have never looked into it. Perhaps someone else can confirm? This wiki page suggests that BioDAS is also still using CVS: http://www.biodas.org/wiki/DAS/2#CVS_Access Peter From pmr at ebi.ac.uk Tue Dec 15 16:32:38 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 15 Dec 2009 16:32:38 +0000 Subject: [Open-bio-l] [emboss-dev] Updating http://www.open-bio.org/wiki/SourceCode In-Reply-To: <320fb6e00912150407o48fd981fn16dedaf0581e5fef@mail.gmail.com> References: <320fb6e00912150407o48fd981fn16dedaf0581e5fef@mail.gmail.com> Message-ID: <4B27BA26.3050004@ebi.ac.uk> On 15/12/09 12:07, Peter wrote: > Hello all, > > We just had a puzzling mailing list query about the Biopython CVS > repository, which turned out to be partly due to some very dated > information here: http://www.open-bio.org/wiki/SourceCode > > I've made a few minor improvements, but feel the whole page > could be simplified. > > Am I right in thinking it is just EMBOSS still using CVS (all the > other projects are now on SVN or github, or obsolete)? If so, since > EMBOSS has nice CVS documentation on their own webpages, > could we remove most of the CVS text from the OBF wiki: > http://emboss.sourceforge.net/developers/cvs.html No problem for EMBOSS. regards, Peter Rice From andy.jenkinson at ebi.ac.uk Tue Dec 15 16:58:07 2009 From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson) Date: Tue, 15 Dec 2009 16:58:07 +0000 Subject: [Open-bio-l] Updating http://www.open-bio.org/wiki/SourceCode In-Reply-To: <320fb6e00912150511u928e0a3s2187a11a634bda0a@mail.gmail.com> References: <320fb6e00912150407o48fd981fn16dedaf0581e5fef@mail.gmail.com> <320fb6e00912150511u928e0a3s2187a11a634bda0a@mail.gmail.com> Message-ID: On 15 Dec 2009, at 13:11, Peter wrote: > On Tue, Dec 15, 2009 at 12:42 PM, Andy Jenkinson > wrote: >> To be honest I'm not sure which (if any) of the BioDAS project's >> components are using CVS. IIRC something was but I don't have >> access so have never looked into it. Perhaps someone else can confirm? > > This wiki page suggests that BioDAS is also still using CVS: > http://www.biodas.org/wiki/DAS/2#CVS_Access > > Peter Then I guess we should be OK. From biopython at maubp.freeserve.co.uk Wed Dec 16 00:02:20 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Wed, 16 Dec 2009 00:02:20 +0000 Subject: [Open-bio-l] Open-Bio Main Wiki Page Message-ID: <320fb6e00912151602g5515a2cftfce5c3ef004c07ed@mail.gmail.com> Hi all, I'll like to update the main page to embed the OBF news feed on the right hand side, rather than having a short manually updated "news" section at the top of the page. i.e. Make this: http://www.open-bio.org/wiki/Main_Page Look more like this: http://biopython.org/wiki/Main_Page And thoughts? It would also be nice to include BioRuby and EMBOSS on the front page somewhere. Peter From hlapp at drycafe.net Wed Dec 16 03:34:23 2009 From: hlapp at drycafe.net (Hilmar Lapp) Date: Tue, 15 Dec 2009 22:34:23 -0500 Subject: [Open-bio-l] Open-Bio Main Wiki Page Message-ID: <3132F739-78AA-4209-8421-598278C0F973@drycafe.net> Sounds great to me. Have you seen the GMOD wiki? It also has feeds embedded in the front page, just as another example. -hilmar Sent from away On Dec 15, 2009, at 7:02 PM, Peter wrote: > Hi all, > > I'll like to update the main page to embed the OBF news > feed on the right hand side, rather than having a short > manually updated "news" section at the top of the page. > > i.e. Make this: > http://www.open-bio.org/wiki/Main_Page > > Look more like this: > http://biopython.org/wiki/Main_Page > > And thoughts? > > It would also be nice to include BioRuby and EMBOSS on the front > page somewhere. > > Peter > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l > From biopython at maubp.freeserve.co.uk Wed Dec 16 14:44:42 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Wed, 16 Dec 2009 14:44:42 +0000 Subject: [Open-bio-l] Open-Bio Main Wiki Page In-Reply-To: <3132F739-78AA-4209-8421-598278C0F973@drycafe.net> References: <3132F739-78AA-4209-8421-598278C0F973@drycafe.net> Message-ID: <320fb6e00912160644m35ddf831kf727801ccc3af87c@mail.gmail.com> On Wed, Dec 16, 2009 at 3:34 AM, Hilmar Lapp wrote: > Sounds great to me. Have you seen the GMOD wiki? It also has feeds embedded > in the front page, just as another example. > > -hilmar The GMOD one is pretty slick. Someone with suitable permissions on the open-bio wiki will need to make any changes, since the main page is (quite sensibly) protected. Peter From cjfields at illinois.edu Wed Dec 16 15:15:54 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 16 Dec 2009 09:15:54 -0600 Subject: [Open-bio-l] Open-Bio Main Wiki Page In-Reply-To: <320fb6e00912160644m35ddf831kf727801ccc3af87c@mail.gmail.com> References: <3132F739-78AA-4209-8421-598278C0F973@drycafe.net> <320fb6e00912160644m35ddf831kf727801ccc3af87c@mail.gmail.com> Message-ID: <09F1CD93-6049-4A7C-9AAB-C51527BFE102@illinois.edu> On Dec 16, 2009, at 8:44 AM, Peter wrote: > On Wed, Dec 16, 2009 at 3:34 AM, Hilmar Lapp wrote: >> Sounds great to me. Have you seen the GMOD wiki? It also has feeds embedded >> in the front page, just as another example. >> >> -hilmar > > The GMOD one is pretty slick. Yes, I like that one as well, had been thinking about using something like it for the bioperl page. > Someone with suitable permissions on the open-bio > wiki will need to make any changes, since the main > page is (quite sensibly) protected. > > Peter What is your user id on that wiki? I think I can grant you sysop privs. If not, I can definitely edit that page for you, just let me know what you want. chris From clements at nescent.org Wed Dec 16 23:14:35 2009 From: clements at nescent.org (Dave Clements) Date: Wed, 16 Dec 2009 15:14:35 -0800 Subject: [Open-bio-l] Open-Bio Main Wiki Page In-Reply-To: <09F1CD93-6049-4A7C-9AAB-C51527BFE102@illinois.edu> References: <3132F739-78AA-4209-8421-598278C0F973@drycafe.net> <320fb6e00912160644m35ddf831kf727801ccc3af87c@mail.gmail.com> <09F1CD93-6049-4A7C-9AAB-C51527BFE102@illinois.edu> Message-ID: Hi Peter, Chris, The GMOD home page (http://gmod.org) news item list is created from the GMOD News RSS Feed. The home page renders the feed using the FeedImport extension ( http://www.mediawiki.org/wiki/Extension:FeedImport). The RSS feed is generated from the GMOD News page ( http://gmod.org/wiki/GMOD_News) using the WikiArticleFeeds extension ( http://www.mediawiki.org/wiki/Extension:WikiArticleFeeds). My memory is that FeedImport was a tough install due to its dependency on Magpie and Snoopy. I just updated the WikiArticleFeeds extension and that was easy. Be warned that something in the process is sensitive to bad MediaWiki markup. That is, if you, for example, don't close a tag in your news item text, your list of news items may be garbage until you fix it and the feed refreshes. I also have a sneaking suspicion that rendering the news feed on the home page might be slowing down load times noticeably. :-( Hope this helps, Dave C. On Wed, Dec 16, 2009 at 7:15 AM, Chris Fields wrote: > On Dec 16, 2009, at 8:44 AM, Peter wrote: > > > On Wed, Dec 16, 2009 at 3:34 AM, Hilmar Lapp wrote: > >> Sounds great to me. Have you seen the GMOD wiki? It also has feeds > embedded > >> in the front page, just as another example. > >> > >> -hilmar > > > > The GMOD one is pretty slick. > > Yes, I like that one as well, had been thinking about using something like > it for the bioperl page. > > > Someone with suitable permissions on the open-bio > > wiki will need to make any changes, since the main > > page is (quite sensibly) protected. > > > > Peter > > What is your user id on that wiki? I think I can grant you sysop privs. > If not, I can definitely edit that page for you, just let me know what you > want. > > chris > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l > -- http://gmod.org/wiki/January_2010_GMOD_Meeting http://gmod.org/wiki/GMOD_News From biopython at maubp.freeserve.co.uk Wed Dec 16 23:53:34 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Wed, 16 Dec 2009 23:53:34 +0000 Subject: [Open-bio-l] Open-Bio Main Wiki Page In-Reply-To: References: <3132F739-78AA-4209-8421-598278C0F973@drycafe.net> <320fb6e00912160644m35ddf831kf727801ccc3af87c@mail.gmail.com> <09F1CD93-6049-4A7C-9AAB-C51527BFE102@illinois.edu> Message-ID: <320fb6e00912161553v57a5c087q3e9c04645a830ac8@mail.gmail.com> On Wed, Dec 16, 2009 at 11:14 PM, Dave Clements wrote: > Hi Peter, Chris, > > The GMOD home page (http://gmod.org) news item list is created from > the GMOD News RSS Feed. > > The home page renders the feed using the FeedImport extension ( > http://www.mediawiki.org/wiki/Extension:FeedImport). > > The RSS feed is generated from the GMOD News page ( > http://gmod.org/wiki/GMOD_News) using the WikiArticleFeeds extension ( > http://www.mediawiki.org/wiki/Extension:WikiArticleFeeds). > > My memory is that FeedImport was a tough install due to its dependency on > Magpie and Snoopy. ?I just updated the WikiArticleFeeds extension and that > was easy. > > Be warned that something in the process is sensitive to bad MediaWiki > markup. ?That is, if you, for example, don't close a tag in your news item > text, your list of news items may be garbage until you fix it and the feed > refreshes. > > I also have a sneaking suspicion that rendering the news feed on the home > page might be slowing down load times noticeably. ?:-( > > Hope this helps, Thanks for the info Dave - its enough to know its beyond my current knowledge of MediaWiki! Perhaps Chris or someone else want to try the extra plugin option... In the meantime (having been given access by Chris - thanks), I have just copied the simple RSS embedding as already in use on the Biopython page. How does it look now - hopefully a worthwhile improvement in itself? http://www.open-bio.org/wiki/Main_Page I would also suggest we consider making the "News" page just redirect to the news server... Peter From p.j.a.cock at googlemail.com Fri Dec 18 15:30:28 2009 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 18 Dec 2009 15:30:28 +0000 Subject: [Open-bio-l] Sanger FASTQ format and the Solexa/Illumina variants Message-ID: <320fb6e00912180730n1d951969ga2c5c461d97f581a@mail.gmail.com> Hi all, I?m delighted to announce an open access publication in Nucleic Acids Research describing the FASTQ file format based on the conventions agreed by the OBF projects (largely on this mailing list): The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Peter J. A. Cock (Biopython), Christopher J. Fields (BioPerl), Naohisa Goto (BioRuby), Michael L. Heuer (BioJava) and Peter M. Rice (EMBOSS). Nucleic Acids Research, doi:10.1093/nar/gkp1137 This open access publication will hopefully serve as a reference describing the original standard Sanger FASTQ, and the two variants from Solexa/Illumina, and how to inter-convert between them. Peter P.S. This was also posted on the OBF news server: http://news.open-bio.org/news/2009/12/nar-fastq-format/ From hlapp at drycafe.net Fri Dec 18 16:25:03 2009 From: hlapp at drycafe.net (Hilmar Lapp) Date: Fri, 18 Dec 2009 11:25:03 -0500 Subject: [Open-bio-l] Sanger FASTQ format and the Solexa/Illumina variants In-Reply-To: <320fb6e00912180730n1d951969ga2c5c461d97f581a@mail.gmail.com> References: <320fb6e00912180730n1d951969ga2c5c461d97f581a@mail.gmail.com> Message-ID: Congratulations! I'm delighted and truly pleased to see this come out of our community of member projects. Kudos to the team for taking this work all the way through to writing it up formally for publication & archival for everyone's benefit. -hilmar On Dec 18, 2009, at 10:30 AM, Peter Cock wrote: > Hi all, > > I?m delighted to announce an open access publication in Nucleic Acids > Research describing the FASTQ file format based on the conventions > agreed by the OBF projects (largely on this mailing list): > > The Sanger FASTQ file format for sequences with quality scores, > and the Solexa/Illumina FASTQ variants. > Peter J. A. Cock (Biopython), Christopher J. Fields (BioPerl), > Naohisa Goto (BioRuby), Michael L. Heuer (BioJava) > and Peter M. Rice (EMBOSS). > Nucleic Acids Research, doi:10.1093/nar/gkp1137 > > This open access publication will hopefully serve as a reference > describing the original standard Sanger FASTQ, and the two variants > from Solexa/Illumina, and how to inter-convert between them. > > Peter > > P.S. This was also posted on the OBF news server: > http://news.open-bio.org/news/2009/12/nar-fastq-format/ > > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From lpritc at scri.ac.uk Fri Dec 18 18:54:53 2009 From: lpritc at scri.ac.uk (Leighton Pritchard) Date: Fri, 18 Dec 2009 18:54:53 +0000 Subject: [Open-bio-l] Sanger FASTQ format and the Solexa/Illumina variants In-Reply-To: Message-ID: I second Hilmar - congratulations to all the authors! I think it's a very important contribution that summarises the history and current usage of FASTQ, and provides constructive suggestions for how to go forward with what will be a central file format for many areas of biology. L. On 18/12/2009 16:25, "Hilmar Lapp" wrote: > Congratulations! I'm delighted and truly pleased to see this come out > of our community of member projects. Kudos to the team for taking this > work all the way through to writing it up formally for publication & > archival for everyone's benefit. > > -hilmar > > On Dec 18, 2009, at 10:30 AM, Peter Cock wrote: > >> Hi all, >> >> I?m delighted to announce an open access publication in Nucleic Acids >> Research describing the FASTQ file format based on the conventions >> agreed by the OBF projects (largely on this mailing list): >> >> The Sanger FASTQ file format for sequences with quality scores, >> and the Solexa/Illumina FASTQ variants. >> Peter J. A. Cock (Biopython), Christopher J. Fields (BioPerl), >> Naohisa Goto (BioRuby), Michael L. Heuer (BioJava) >> and Peter M. Rice (EMBOSS). >> Nucleic Acids Research, doi:10.1093/nar/gkp1137 >> >> This open access publication will hopefully serve as a reference >> describing the original standard Sanger FASTQ, and the two variants >> from Solexa/Illumina, and how to inter-convert between them. >> >> Peter >> >> P.S. This was also posted on the OBF news server: >> http://news.open-bio.org/news/2009/12/nar-fastq-format/ >> >> _______________________________________________ >> Open-Bio-l mailing list >> Open-Bio-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/open-bio-l -- Dr Leighton Pritchard MRSC D131, Plant Pathology Programme, SCRI Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA e:lpritc at scri.ac.uk w:http://www.scri.ac.uk/staff/leightonpritchard gpg/pgp: 0xFEFC205C tel:+44(0)1382 562731 x2405 ______________________________________________________ SCRI, Invergowrie, Dundee, DD2 5DA. The Scottish Crop Research Institute is a charitable company limited by guarantee. Registered in Scotland No: SC 29367. Recognised by the Inland Revenue as a Scottish Charity No: SC 006662. DISCLAIMER: This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries. This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed. It may not be disclosed or used by any other than that addressee. If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify postmaster at scri.ac.uk quoting the name of the sender and delete the email from your system. Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any). ______________________________________________________ From chapmanb at 50mail.com Mon Dec 21 21:32:02 2009 From: chapmanb at 50mail.com (Brad Chapman) Date: Mon, 21 Dec 2009 16:32:02 -0500 Subject: [Open-bio-l] [Bosc] BOSC 2010 Request for Input In-Reply-To: <6.1.2.0.2.20091218113046.03f84bc8@incoming.lmu.edu> References: <6.1.2.0.2.20091218113046.03f84bc8@incoming.lmu.edu> Message-ID: <20091221213202.GD35116@sobchak.mgh.harvard.edu> Kam and Open Bio folks; It's great to see planning for BOSC 2010 going on already. Lots of exciting ideas. > --Mini-hackathon either before, during, or after the 2-day BOSC. The > subject of the hackathon would need to be organized by the individual > project leaders/teams. Some suggestions would be adding/extending support > for next-gen sequencing; organizing bugs/tasks so that new beginners can > start contributing to the project easily and working on some of those > bugs/tasks; organizing some type of contest like the Genome Annotation > Assessment Project (GASP) where solutions from different projects compete > on arriving at some type of goal. Would you be willing to organize/lead > this type of session? I can help organize a hackathon at Mass General Hospital, which is located fairly to close to Hynes Convention Center, where the conference is on. I booked conferences rooms for dates surrounding BOSC (July 6-8th and 11th) that will accommodate up to 30 developers from various projects. This could be a fairly informal get together for developers who can spare time before or after BOSC. If we could get a show of hands from people who might be interested, this would help gauge the size and scope. As you suggest above, we can hone in on specifics for the work based on the interests of attendees. > --Organizing/creating a LiveCD or Debian download of Bio* projects with > documentation to support outreach to the larger bioinformatics > community. Would you be willing to organize/lead this type of session? A cloud version of this goal is up and coming here: http://www.cloudbiolinux.com/ I cc'ed in the mailing list for folks there who aren't on the open bio mail servers and might be interested. Brad From maj at fortinbras.us Mon Dec 21 21:38:49 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 21 Dec 2009 16:38:49 -0500 Subject: [Open-bio-l] [Cloud BioLinux Community] [Bosc] BOSC 2010 Request for Input In-Reply-To: <20091221213202.GD35116@sobchak.mgh.harvard.edu> References: <6.1.2.0.2.20091218113046.03f84bc8@incoming.lmu.edu> <20091221213202.GD35116@sobchak.mgh.harvard.edu> Message-ID: <98EFA3B9190E49B491EFB4F9D59FC819@NewLife> count me in, somewhere! MAJ ----- Original Message ----- From: "Brad Chapman" To: Cc: ; Sent: Monday, December 21, 2009 4:32 PM Subject: Re: [Cloud BioLinux Community] [Bosc] BOSC 2010 Request for Input > Kam and Open Bio folks; > It's great to see planning for BOSC 2010 going on already. Lots of > exciting ideas. > >> --Mini-hackathon either before, during, or after the 2-day BOSC. The >> subject of the hackathon would need to be organized by the individual >> project leaders/teams. Some suggestions would be adding/extending support >> for next-gen sequencing; organizing bugs/tasks so that new beginners can >> start contributing to the project easily and working on some of those >> bugs/tasks; organizing some type of contest like the Genome Annotation >> Assessment Project (GASP) where solutions from different projects compete >> on arriving at some type of goal. Would you be willing to organize/lead >> this type of session? > > I can help organize a hackathon at Mass General Hospital, which is > located fairly to close to Hynes Convention Center, where the conference > is on. I booked conferences rooms for dates surrounding BOSC (July > 6-8th and 11th) that will accommodate up to 30 developers from various > projects. > > This could be a fairly informal get together for developers who can > spare time before or after BOSC. If we could get a show of hands > from people who might be interested, this would help gauge the size > and scope. As you suggest above, we can hone in on specifics for the > work based on the interests of attendees. > >> --Organizing/creating a LiveCD or Debian download of Bio* projects with >> documentation to support outreach to the larger bioinformatics >> community. Would you be willing to organize/lead this type of session? > > A cloud version of this goal is up and coming here: > > http://www.cloudbiolinux.com/ > > I cc'ed in the mailing list for folks there who aren't on the open > bio mail servers and might be interested. > > Brad > _______________________________________________ > Community mailing list > Community at cloudbiolinux.com > http://lists.cloudbiolinux.com/mailman/listinfo/community > > From hlapp at drycafe.net Mon Dec 21 23:39:33 2009 From: hlapp at drycafe.net (Hilmar Lapp) Date: Mon, 21 Dec 2009 18:39:33 -0500 Subject: [Open-bio-l] [Bosc] BOSC 2010 Request for Input In-Reply-To: <20091221213202.GD35116@sobchak.mgh.harvard.edu> References: <6.1.2.0.2.20091218113046.03f84bc8@incoming.lmu.edu> <20091221213202.GD35116@sobchak.mgh.harvard.edu> Message-ID: <57BC6503-C655-431C-88BB-0F63E1004BD6@drycafe.net> On Dec 21, 2009, at 4:32 PM, Brad Chapman wrote: > I can help organize a hackathon at Mass General Hospital, which is > located fairly to close to Hynes Convention Center, where the > conference > is on. I booked conferences rooms for dates surrounding BOSC (July > 6-8th and 11th) that will accommodate up to 30 developers from various > projects. Awesome!! Thanks so much Brad for stepping up so quickly and putting your foot down too! > If we could get a show of hands from people who might be interested, > this would help gauge the size and scope. :) -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From cjfields at illinois.edu Tue Dec 22 00:36:02 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 21 Dec 2009 18:36:02 -0600 Subject: [Open-bio-l] [Bosc] BOSC 2010 Request for Input In-Reply-To: <57BC6503-C655-431C-88BB-0F63E1004BD6@drycafe.net> References: <6.1.2.0.2.20091218113046.03f84bc8@incoming.lmu.edu> <20091221213202.GD35116@sobchak.mgh.harvard.edu> <57BC6503-C655-431C-88BB-0F63E1004BD6@drycafe.net> Message-ID: <11C4F67A-300B-420D-B68E-B175DAD283C1@illinois.edu> On Dec 21, 2009, at 5:39 PM, Hilmar Lapp wrote: > On Dec 21, 2009, at 4:32 PM, Brad Chapman wrote: > >> I can help organize a hackathon at Mass General Hospital, which is >> located fairly to close to Hynes Convention Center, where the conference >> is on. I booked conferences rooms for dates surrounding BOSC (July >> 6-8th and 11th) that will accommodate up to 30 developers from various >> projects. > > Awesome!! Thanks so much Brad for stepping up so quickly and putting your foot down too! > >> If we could get a show of hands from people who might be interested, this would help gauge the size and scope. > > > :) > > -hilmar Same here! Just need to sort out the dates, but I should be able to make that. chris From ohofmann at hsph.harvard.edu Mon Dec 21 23:33:50 2009 From: ohofmann at hsph.harvard.edu (Oliver Hofmann) Date: Mon, 21 Dec 2009 23:33:50 -0000 Subject: [Open-bio-l] [Cloud BioLinux Community] [Bosc] BOSC 2010 Request for Input In-Reply-To: <20091221213202.GD35116@sobchak.mgh.harvard.edu> References: <6.1.2.0.2.20091218113046.03f84bc8@incoming.lmu.edu> <20091221213202.GD35116@sobchak.mgh.harvard.edu> Message-ID: <4B3005DF.9030001@hsph.harvard.edu> Oooh, good timing. Happy to help with the organization, we'd have several researchers and developers in the Longwood area who are interested in this (DFCI, HMS and HSPH). Keep in mind MGED is _also_ somewhere around that time, and it might be difficult to motivate people for yet another extra day. Best, Oliver On 12/21/2009 4:32 PM, Brad Chapman wrote: > Kam and Open Bio folks; > It's great to see planning for BOSC 2010 going on already. Lots of > exciting ideas. > >> --Mini-hackathon either before, during, or after the 2-day BOSC. The >> subject of the hackathon would need to be organized by the individual >> project leaders/teams. Some suggestions would be adding/extending support >> for next-gen sequencing; organizing bugs/tasks so that new beginners can >> start contributing to the project easily and working on some of those >> bugs/tasks; organizing some type of contest like the Genome Annotation >> Assessment Project (GASP) where solutions from different projects compete >> on arriving at some type of goal. Would you be willing to organize/lead >> this type of session? > > I can help organize a hackathon at Mass General Hospital, which is > located fairly to close to Hynes Convention Center, where the conference > is on. I booked conferences rooms for dates surrounding BOSC (July > 6-8th and 11th) that will accommodate up to 30 developers from various > projects. > > This could be a fairly informal get together for developers who can > spare time before or after BOSC. If we could get a show of hands > from people who might be interested, this would help gauge the size > and scope. As you suggest above, we can hone in on specifics for the > work based on the interests of attendees. > >> --Organizing/creating a LiveCD or Debian download of Bio* projects with >> documentation to support outreach to the larger bioinformatics >> community. Would you be willing to organize/lead this type of session? > > A cloud version of this goal is up and coming here: > > http://www.cloudbiolinux.com/ > > I cc'ed in the mailing list for folks there who aren't on the open > bio mail servers and might be interested. > > Brad > _______________________________________________ > Community mailing list > Community at cloudbiolinux.com > http://lists.cloudbiolinux.com/mailman/listinfo/community -- Research Associate Department of Biostatistics Associate Director Bioinformatics Core Harvard School of Public Health Skype: ohofmann Phone: +1 (617) 365 0984