The backend MovableType software powering this site was upgraded and the backend storage was switched from berkelyDB to SQL. These preparations are being done to ease the transition of http://news.open-bio.org to a new server. The primary purpose of this news entry is to confirm that the posting system still works after the upgrade!
BioKnoppix
BioKnoppix is a new live CD linux, based on KNOPPIX, with EMBOSS 2.8.0, jemboss, artemis, clustalx, Cn3D, ImageJ, BioPython, Rasmol, Bioperl, Bioconductor. It being made available by The University of Puerto Rico High Performance Computing facility (HPCf) and the Puerto Rico Biomedical Research Infrastructure Network (BRIN-PR). Great stuff!
Server downtime announcement
Hi Everyone,
Apologies for the mass cross-posting but this email is about server and IP changes that will affect all of our projects and servers.
Simply put – Wyeth, the company that provides us with our hosting and wonderful T3 connection to the internet is cutting their internet connection circuits over from one ISP to a different Tier 1 internet backbone.
[Read More]BioPython 1.2.0 released
Available now at http://biopython.org/download/
Changes include: added Andrew Dalke’s EUtils library added Michiel de Hoon’s gene expression analysis package updates to setup code, now smarter about dependencies updates to test suite, now smarter about code that is imported Michael Hoffman’s fixes to DocSQL syntax fixes in triemodule.c to compile on SGI, Python 2.1 compatible updates in NCBIStandalone, short query error Sebastian Bassi submitted code to calculate LCC complexity Greg Kettler’s NCBIStandalone fix for long query lengths slew of miscellaneous fixes from George Paci miscellaneous cleanups and updates from Andreas Kuntzagk Peter Bienstman’s fixes to Genbank code – now parses whole database Kayte Lindner’s LocusLink package miscellaneous speedups and code cleanup in ParserSupport by Brad Chapman miscellaneous BLAST fixes and updates Iddo added new code to parse BLAST table output format Karl Diedrich’s patch to read T_Coffee files Larry Heisler’s fix for primer3 output Bio.
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BOSC'2003 Pictures are online
Our “Bioinformatics Open Source Conference” was held in Brisbane, Australia in conjunction with the larger ISMB'2003 meeting. It was quite successful — 96 attendees, wireless internet, BOF rooms and 30+ presentations over 2 days.
Pictures are online here: http://gallery.open-bio.org/
Foundation views wrongly characterized in Genome Technology
In the March 2003 issue of Genome Technology, “Opposite Strand” contributor Gerald Barnett’s insightful article on “free choice for open source” is blighted by a gross misattribution. He writes that Open Bioinformatics Foundation has proposed that “all federally funded bioinformatics software should be released as open source.” In fact, the O|B|F has explicitly rejected this extreme and inflexible view, as specified in our January 2002 statement on public funding & open source, which states:
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New mailing list Bioped-l
A new mailing list has been created for discussion of software system for genotypes, pedigrees, and linkage data at /mailman/listinfo/bioped-l
This is intended to build off the initial work done in Perl for bioperl-pedigree but is applicable to all who want to contribute to the design or implementation in any language. Database persistence and pedigree rendering are initial areas that will be addressed.
NCICB reviews two LSID Resolution proposals
Members of the caCORE team at the NCICB have been discussing if and how best to use LSIDs. Attached is an analysis of the two LSID Resolution proposals. The document also includes brief descriptions of two use cases that seem appropriate to us. We would be very interested in any responses to this analysis.
The document is also available at: ftp://ftp1.nci.nih.gov/pub/cacore/caBIO/lsid/lsid_memo.doc
Joshua Phillips SAIC Advanced Information Technology Center, Annapolis, MD NCI Center for Bioinformatics, Gaithersburg, MD Phone: (301) 402-7087
2003 Singapore Hackathon
About 30 open source informatics developers are hacking away in Singapore now working on various efforts. The main website is at http://hackathon.open-bio.org and contains links to the Blog site and the picture gallery.
Chris breaks dev.open-bio.org
Urgent notice –> Primary CVS server has been relocated to pub.open-bio.org
“dev.open-bio.org” – our primary developer server is down in Boston with a corrupt password file. Chris blames the Solaris audit subsystem for not liking root commands issued via SSH connections :)
We have moved the CVS repositories to a Linux box called “pub.open-bio.org”. Developer accounts have been created but with different passwords. Email the OBF Sysadmin team at root-l@open-bio.org to get your new password.
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