Updated 2015-10-13 23:12:34 by RLE

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 [1].

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
  • GeneOntol snittype for quering Gene Ontology [2]
  • 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.