[Bioperl-l] Feedback from the course we ran

Ewan Birney birney@ebi.ac.uk
Tue, 26 Sep 2000 12:12:01 +0100 (GMT)

Hilmar asked me to post about the bioperl course we ran. This was a 2 day
course run by myself and James gilbert.

In general it went very smoothly. I ran a similar course a year ago on the
0.5 release series and very quickly people hit "bugs" or "issues" with
bioperl (ie, in their second script! things like case sensitivity for
translate functions etc). 

This time around it took us a day to hit the bugs, so their 6th or 7th
script, in areas like the Bio::Index stuff and other places. We fixed any
bugs we found on the 0.6 branch, so these should be fixed for 0.6.2


  (a) Documentation out of sync. It is annoying for developers, but for
people learning the package, out of sync documentation is just plain
*unhelpful*. This is an tough area for us as it is hard to get programmers
motivated about real documentation (that's what the code is for, right?)

     I think I might see if I can figure out how to *pay* for a full time
documentation person. Do people think this is a good route? Can I drum up
any support here?

  (b) BLAST parsing is not well integrated in. I am pretty sure that the
saviour to this is the BPLite code waiting for the main trunk 0.7 release

  (c) niceities to the SeqIO parsing. Is this '_span' system really good?

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