Pro-bioinformatic wiki features

Biowiki implements several TWiki plugins useful in computational biology:

• Quick permalinks to Pubmed citations using EFetchPlugin
  • e.g. Miklos I.  MCMC genome rearrangement.  Bioinformatics. 2003 Oct;19 Suppl 2:ii130-7.
  • more examples: PhylogeneticAlignmentReader, PaperArchive
• Embedded latex via MathModePlugin
  • e.g.
• InterWikis and InterSeqs
  • Links to books via the ISBN, e.g. ISBN:0521629713
  • Links to sequence, structure and analysis databases
    • e.g. EMBL:CR767821 is the Ehrlichia ruminantium genome (repetitive)
    • and Rfam:RF00167 the delicious purine riboswitch
  • Easy to assemble a quick summary of a biological feature of interest
    • e.g. PDB:1ACY is a gp120 structure; Genbank:AF513249 and Swiss:P04578 are sequences, Pfam:PF00516 is the protein family and GO:0019031 the gene ontology term
  • Links to sequence addresses on bioinformatics servers like the GenericGenomeBrowser
    • Worm:I/1000-3000, Fly:2L/30000-40000 (defined on InterSeqs)
    • Also links to gene reports in flybase and wormbase (see InterWikis)

Ideas for more stuff:

• automatic rendering of trees, dotplots, alignments, RNA secondary structures