[Bioperl-l] contributing? sure!

Ewan Birney birney@ebi.ac.uk
Tue, 11 Jul 2000 08:56:52 +0100 (GMT)

On Tue, 11 Jul 2000, Lorenz Pollak wrote:

> Hi to all bioperl developers!
> First of all I have to say: great work!! I was so impressed when I found
> www.bioperl.org! (Two great things combined: perl & molecular biology)
> Now I would really love to contribute something to bioperl.


> I am studying medicine (fifth semester) and a few weeks ago I have
> attended a course of genetic engineering where I learned some
> basics of molecular biology techniques and discovered the whole
> bioinformatics scene on the internet! (getting to bioperl was just a
> matter of time)
> Regarding my perl skills: Besides my studies I'm working part-time in an
> IT company where my job is mainly coding some CGI scripts in perl.
> So let me know, what I could for you!

The open jobs range from the mundane to the tricky:

 o Chris needs help maintaining the web site, in particular the links

 o It would be great to write/have more "working programs" in the bioperl
distribution which actually used parts of bioperl in a serious manner.

 o There are a bunch of modules that need to be converted/written in

    - Ian Korf's BPLite modules
    - RepeatMasker module
    - Genscan module (? could donate from Ensembl)

 o There are a bunch of easish extensions for bioperl

    - GenBank format flat file indexer (should be trivial)
    - swissprot format flat file indexer 

 o We have no decent beginners documentation.

 o There are some much harder extensions/modules to be written

    - EMBOSS linking (system call or XS?)

 o There are bugs to be fixed - look at the bug tracker. However
   it is usually best to start off with a small project first
   before you get into serious bug squashing

 o There are projects that need deepening -

    - biocorba access
    - bioperl-db might be running (? Jason)

 o And of course, whatever you want to do ;)

> regards,
> Lorenz
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420