- Are you going to ISMB/BOSC 2007?
- If you’ll be at BOSC or ISMB - please see this page and sign your name if you would like to try and meet up.
- Hey what?s happening?
- So Mailing list summaries have stopped because we need someone else to help post these summaries. Not a light job unfortunately. If you are interested, please post to the mailing list or contact Jason, Sendu, or Chris for more details. This is one way you can help BioPerl without contributing code if you [...]
- HOWTO automate tree drawing
- I updated the Trees HowTo with some code demonstrating how to automatically generate postscript trees from newick or nexus tree files. This uses the Bio::Tree::Draw::Cladogram module that will draw Phylograms or Cladograms. With a few unix tools (eps2png and epstopdf [part of TeX]) you can generate png and pdf files automatically making this an [...]
- mediawiki updated
- Updated mediawiki to 1.10 Did a bulk creation of a number of modules wiki pages for modules that had been previously created but not added to the wiki. Added them with default module templates. © Jason Stajich for BioPerl, 2007. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more [...]
- Bioperl 1.5.2 Release
- I’m proud to announce the final release of Bioperl 1.5.2. Full details are available at http://www.bioperl.org/wiki/Release_1.5.2 © Sendu Bala for BioPerl, 2006. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse the archive of posts filed under Code.
- RC5 for 1.5.2
- Sendu has posted 1.5.2 RC5. There may be a few more kinks to work out, so try this release and report if there are problems with the tests. © Jason Stajich for BioPerl, 2006. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse [...]
- RC 1.5.3
- Sendu has announced that Release Candidate 3 is available for download and testing. This may be the last RC before the 1.5.2 release so give it a whirl and speak up with any problems or concerns. © Jason Stajich for BioPerl, 2006. | Permalink | No comment Add to del.icio.us Search blogs linking this post [...]
- Mediawiki updated
- Bioperl wiki is now running Mediawiki 1.8.2. nothing too different under the hood at this point, the mediawiki people probably have more to say in the release-notes. © Jason Stajich for BioPerl, 2006. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse the archive of [...]
- Next BioPerl Release
- We are currently planning a timetable for the next few Bioperl releases, including the next developer release (v1.5.2), the next stable release (1.6) and beyond. Users are welcome to add requests (within reason!), donate code, etc. Lots of changes in store! The release schedule can be found here. In order to add comments, [...]
- Updated PDoc software
- Raphaël Leplae has updated the Pdoc software to have an improved stylesheet and fix several bugs including problems rendering Bio::DB::Fasta. Thanks a lot Raphaël and Patrick Meidl for getting the bugs reported and fixed for this nice POD to HTML converter. You can see the Pdoc for Bioperl packages in action at the doc.bioperl.org site. [...]
- mediawiki 1.6.7
- Upgraded MW install for some bugfixes and security fixes. © Jason Stajich for BioPerl, 2006. | Permalink | One comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse the archive of posts filed under Website.
- bioperl-network added to Pdoc
- Bioperl Network package documentation added to the Pdoc site and is automaticly updated daily. © Jason Stajich for BioPerl, 2006. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse the archive of posts filed under Website.
- Mediawiki upgraded
- Upgraded BioPerl mediawiki to 1.6.6. © Jason Stajich for BioPerl, 2006. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse the archive of posts filed under Website.
- Modware: a BioPerl based API for Chado
- We are announcing a new Sourceforge Project called Modware. It is an object-oriented API written in Perl that creates BioPerl object representations of biological features stored in a Chado database. It basically creates a Bio::Seq object for chromosomes in Chado and creates Bio::SeqFeature::Gene objects for protein coding transcripts stored in Chado. Things like contigs [...]
- Deobfuscator interface now available
- I’m glad to announce the availability of the Deobfuscator interface at the BioPerl website. You can use it at the following URL: http://bioperl.org/cgi-bin/deob_interface.cgi Many thanks to Laura Kavanaugh and David Messina for this great contribution to the BioPerl project! © Mauricio Herrera Cuadra for BioPerl, 2006. | Permalink | No comment Add to del.icio.us Search blogs linking this [...]
- ListSummaries for April 26-May 9
- ListSummaries for April 26-May 9 are up at the usual place: http://www.bioperl.org/wiki/Mailing_list_summaries Direct link: http://www.bioperl.org/wiki/ListSummary:April_26-May_9%2C2006 It?s a bit of a hurried one so don?t be surprised to find a few spelling errors here and there. I?m getting ready for a conference in a couple weeks so I may be off the radar a bit here and there. [...]
- BioPerl-run in FreeBSD
- It’s my great pleasure to announce the availability of the BioPerl-run packages (stable & developer releases) for the FreeBSD operating system. For instructions on how to install BioPerl ports in FreeBSD, please take a look into the Getting Bioperl section of the BioPerl Wiki. © Mauricio Herrera Cuadra for BioPerl, 2006. | Permalink | No [...]
- RSS feeds
- I’ve added a page about RSS feeds in BioPerl. These include links to CVS commits as a RSS feed. This a bit of a hack using cvs2rss and cvs2cl and I have hardcoded it to show the last 30 commits only. In addition RSS news is now embedded on the main BioPerl [...]
- Bioperl ListSummaries for April 12-25
- The newest summary of the BioPerl mailing lists has been posted to the wiki: April 12-25 Post gripes, harrassments, and faint praises at the regular places. © Chris Fields for BioPerl, 2006. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse the archive of posts filed [...]
- BioPerl Mailing List Summaries
- The first of a biweekly summary of BioPerl mailing list summaries has been posted to the wiki: April 1-11 These will likely be archived on the wiki but may be moved to a more suitable location in the future (maybe to this blog?). © Chris Fields for BioPerl, 2006. | Permalink | 2 comments Add to del.icio.us Search [...]
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- Julian Lombardi will present keynote at BOSC 2008
- The BOSC 2008 Organizing Committee is pleased to announce that Julian Lombardi will be giving the keynote address this year. Dr. Lombardi is one of the original architects of the open-source, peer-to-peer OpenCroquet platform for creating and deploying deeply collaborative...
- Biopython release 1.45
- We are pleased to announce the release of Biopython 1.45. This release includes numerous code improvements and fixes, including in Bio.Seq, Bio.SeqIO, Bio.Entrez, Bio.PopGen, Bio.SwissProt, Bio.Cluster, Bio.SCOP, Bio.InterPro, Bio.GenBank, Bio.ExPASy, BioSQL, and the Biopython documentation. Too many to list them...
- BioSQL v1.0.0 released
- After a long wait and several earlier attempts, version 1.0.0 (code-named Tokyo, see below) of BioSQL has finally been released. The release can be downloaded at http://biosql.org/DIST/ as .tar.gz, .tar.bz, and Zip (which also has Windows-style end-of-line characters) archives. The...
- BOSC 2008 is on
- Our application to hold BOSC as a two-day SIG (Special Interest Group) meeting in conjunction with ISMB has been accepted for this year. BOSC will take place July 18 and 19 in Toronto, Canada....
- Biopython release 1.44
- We are pleased to announce the release of Biopython 1.44. This release includes lots of code improvements and fixes in the Blast interface and parsers, sequence input/output, the SwissProt parser, the clustering routines, as well as a brand new module...
- Biopython release 1.43
- We are pleased to announce the release of Biopython 1.43. This release includes a brand-new set of parsers in Bio.SeqIO by Peter Cock for reading biological sequence files in various formats, an updated Blast XML parser in Bio.Blast.NCBIXML, a new...
- Bioperl 1.5.2 Release
- I'm proud to announce the final release of Bioperl 1.5.2. Full details are available at http://www.bioperl.org/wiki/Release_1.5.2...
- Biopython release 1.42
- Dear biopythoneers, We are pleased to announce the release of Biopython 1.42. This release includes a brand-new Genbank parser in Bio.GenBank by Peter Cock, numerous updates to Bio.Nexus by Frank Kauff and to Bio.Geo by Peter, lots of bug fixes...
- CVS server move
- The CVS repository is migrating from 'pub' to a new host called 'dev' and requires us to re-issue accounts. This will be a good opportunity to verify email addresses and remove unused accounts. You should have received an email from...
- Gallery updated
- The BOSC 2002 pictures have been migrated to the O|B|F gallery site hackathon2002....
- new Bioperl website
- I am pleased to announce the release of a new website for BioPerl. The site is based on the mediawiki software that was developed for the wikipedia project. We intend the site to be a place for community input on documentation and design for the BioPerl project. There is also a fair amount of documentation started surrounding bioinformatics tools and techniques applicable to using BioPerl and some of the authors who created these resources.
- BIOPYTHON 1.41 RELEASED
- We are pleased to announce the release of Biopython 1.41. Many improvements were made in Biopython during the eight months since the previous release, and the new release contains lots of bugfixes, improvements, new functionalities, and better documentation. To pick...
- Bioperl 1.5.1
- I am pleased to announce the 1.5.1 developer release of Bioperl.
- Bioperl 1.5.1 RC4
- Release Candidate 4 for bioperl 1.5.1 (Developer release) core, run, and ext packages is available. Several bug fixes went in last week so I've made what I hope to be the last release candidate before 1.5.1 goes out. More Info:...
- O|B|F Board of Directors Meeting
- The 2005 Board of Directors meeting for the Open Bioinformatics Foundation was held on Thursday, June 24th 2005 in Detroit, MI USA at the site of the BOSC2005 meeting. This was a major meeting and represents the first attempt to...
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