[Biodevelopers] Another question...

[Joe Landman]

What issues are people running into for their development work?  

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

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.

Joe