[Biodevelopers] Another question...

[Titus Brown]

-> What issues are people running into for their development work?  

None!  Well, not enough time...

-> Most of my work is done on Linux machines and clusters, so my issues are
-> related to the compilers (gcc et al), and related.

Everything pretty much works; I'm not using any oddball software for anything,
so *shrug* it all works.  Mainly I'm irritated that a new version of Python
comes out every week...

-> A question I have is, for those doing algorithm development, would a
-> very high level environment (e.g. Matlab-ish) make sense for
-> bioinformatics?  That is, it would be not so difficult to imagine
-> setting up a language where you could perform calculations like this:
-> 
->     [high_scoring_sequences, low_scoring_sequences] = NCBI_BLAST("sequence_file", [database1, database2]);
->     alignment=ClustalW(high_scoring_sequences[subset]);
->     .
->     .
->     .
-> 
-> 
-> I have been thinking about doing something like this for a long time. 
-> You can get near to this concept using BioPerl.

Who would be your target audience?  Other developers, or biology researchers?
In neuroscience Matlab seems to be enshrined as the language of choice, so
it might be a good way to give bioinformatics capabilities to biologists...

--t