Version 5 of BioTcl

Updated 2005-02-18 13:59:35 by lwv

Preliminary Framework for biology related stuff

DDG this is just a starter, I will add a snittype for BlastFiles 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 [L1 ].

Now let's start:

  • FastaFile snittype for parsing fasta files
  • 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