'''Preliminary Framework for biology related stuff''' [DDG] this is just some starters, I will add snittypes for GeneOntology, LocusLink-data as well. My suggestions is to use the following libraries: * [oomk] as a RDBMS for [Mk4tcl] which is inbuild into [tclkit], [oomk] provides joins, intersections, unions and so on for easy access to the data. A database system is neccessary to get data from large files. You need to index them via [tell] before retrieving the data via [seek] * [snit] as an object oriented framework, because it is tclonly, it is tcllike and it is needed by oomk * [md5pure] in order to webenable the packages it might be neccessary to convert some identifiers to url-harmless strings. md5-strings fullfill this criteria If focusing on those packages everything can be easily bundled into starkits and run on a variety of platforms [http://www.equi4.com/pub/tk/downloads.html]. Now let's start: Candidates for inclusion into a biotcl-package: * [FastaFile] snittype for parsing fasta files * [BlastFile] snittype for parsing Blast-output files * [LocusLinkFile] snittype for getting informations for LocusLink-IDs * [Progress] snittype for a console progressbar, required to get feedback during parsing of gigabytes of biological data Other relevant Software for biologists: * [GRS] graphic tool for genome segment visualization * [MASIA] bio sequence pattern searching * [tkDCSE] dedicated comparative sequence editor * [bioTk] widgets for computational biology and genomes * [Biowish] sequence editing, translations, etc. ---- [Category Science]