> > 0. Loci is data independent, netgenetics in bioinformatics-centric > > Right. Speaking a data independence. It looks as though SYNERGY uses an > internal format for their biodata, which we have decided against. An internal > format requires 2 conversions between incompatible components: > > GENBANK 1 Internal 2 Analysis > document ---> format ---> that doesn't > read GENBANK > > The 'converter locus' scheme that Loci uses, would do only 1 conversion via the > converter. Jeff, you've got this exactly backwards. We need an internal format, we decided it would be xml based, perhaps extended BSML. Converters should be written to any format to ours and from any format to ours, otherwise we get to write a converter for every pair of formats we support. Example, image we want to support 4 file formats: genbank - internal pdb - internal fasta - internal bsml - internal vs converters between the same 4 formats: genbank - pdb genbank - fasta genbank - bsml pdb - fasta pdb - bsml fasta - bsml this comparison gets worse as you add more file formats. This is why the netpbm tools all convert to pnm files. What we had decided is that we can defer defining our file formats until we actually have any loci that use them, and that we can have many small languages instead of a big language that tries to capture all possible data types. So we'll have an internal format for nucleotide sequences, one for amino acid sequences, one for multi sequence objects, one for sequence annotations, one for bibliographic references, ... -- Humberto Ortiz Zuazaga Bioinformatics Specialist Institute of Neurobiology hortiz at neurobio.upr.clu.edu