Monday, April 30, 2007

Genealogy Transitive Closure

This is just a reminder to myself to check out how the different open source genealogy software projects implement transitive closure type algorithms.

Sunday, April 29, 2007

CVS Account Activated

My CVS account for BioPerl/BioSQL was approved. I have logged on to the account and changed the password and signed up for the obf-developers mailing list.

After working with POD documentation yesterday, it seems like a pretty straightforward way to do inline documentation. I will probably switch a lot of my existing code of to POD.

Saturday, April 28, 2007

POD Documentation

Today I am playing around with including POD documentation in my PERL scripts. I am working loosely with the type of POD documentation that is used by the BioPerl project. Using POD should make it easier to extract documentation from the PERL code. It does not look as good in emacs as the internal documentation I usually make, but it will be easier to extract the relevant information from my PERL code.

Monday, April 23, 2007

CVS Accounts and Subversion.

I requested a CVS account from both BioSQL and BioPerl.

I checked out the bioperl-db from bioperl CVS to get familiar with this code.

I have been playing around with subversion as supplied by google at I have been using jperl as my test space. I will probably continue to use google for hosting the repository for the jperl code but will use open-bio CVS for my PhyloSoC project.

I don't like the wiki syntax that is available from google, so I will probably stick with the MediaWiki pages that are available through PhyloSoC and NESCent. The project homepage will therefore be hosted at the PhyloSoc wiki.

Friday, April 20, 2007

The Beginning

Started the blog for the google summer of code project "A Perl-based Command Line Interface to a Topological Query Application for BioSQL in Support of High Throughput Classification and Analysis of LTR Retrotransposons in Plant Genomes". I don't know if I will actually make use of this.

Today I worked on getting subversion working with Emacs on my work computer. I also worked a bit on the website .. checking out the available features etc.