Date: February 24, 2003 Author: Lincoln Stein Version: early
This report concerns the messaging layer of the Moby project, that point at which semantic information is exchanged between the data consumer (i.e. the biologist) and the data provider (i.e. the model organism system administrator).
[Read More]Mark has updated his “Biojava in Anger” website to add three more tutorials. One on OrderNDistributions another on WeightMatrices and one on Profile HMMs.
The website URL is http://bioconf.otago.ac.nz/biojava/
Generic and gene-specific coordinate system mappers are ready for use. These modules can ease the pain of mapping sequence features from one sequence coordinate to other ones, e.g. from cds to genomic and chromosomal.
See the announcement at http://bioperl.org/pipermail/bioperl-l/2003-February/011110.html
[Read More]Ewan talks about how one becomes a bioperl developer and how those invitations to hackathons get sorted out…
http://bioperl.org/pipermail/bioperl-l/2003-February/011226.html
[Excerpt] …Bioperl hackers who have been at Singapore have been discussing the next generation of sequence feature handling. As any developer - and indeed user - who has used bioperl might have noticed, our sequence feature model is quite complex - this is because we have a number of drivers, in particular…
The full message was posted to the bioperl-l mailing list and can be read online at http://bioperl.org/pipermail/bioperl-l/2003-February/011225.html
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.
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.
[Read More]Mark reports:
Just noticed a little snippit about biojava in the latest issue of the scientist http://www.the-scientist.com/yr2003/jan/labcon_030127.html (free registration required to view the article)
Jason reports:
Bioperl 1.2 was mentioned in ‘The Scientist’ (free registration required to read this link) http://www.the-scientist.com/yr2003/jan/labcon_030113.html
Thomas Down reports:
We’ve had a number of requests recently for a more recent snapshot of the biojava-live code, so I’ve just put together a biojava-1.3pre1 release. Get source, binaries, and javadocs from: http://www.biojava.org/download/
This isn’t absolutely set in stone yet, but should give a reasonable indication of what the forthcoming 1.3 series is going to look like. All testing and comments welcome!
One thing to note about the *binary* release: I’ve compiled this using Sun JDK 1.4.1. There may be compatibility problems with Java 1.3 runtime envionments in some cases, so if you’re using Java 1.3 and think you’ve found a bug, please try downloading the source and recompiling. I’ve released jdk1.4 binaries this time as an experiment. If there are violent objections, we can always do back to jdk1.3.1 for compiling binary releases, or perhaps provide both. Please let me know if you have any thoughts on this, or if it causes you trouble.
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