Linking To Biological Databases

Pro-bioinformatic wiki features

Biowiki implements several !TWiki plugins useful in computational biology:

Quick permalinks to Pubmed citations using TWiki.EFetchPlugin
- e.g. Miklós &: MCMC genome rearrangement. Bioinformatics 2003;19 Suppl 2:ii130-7.
- more examples: Phylogenetic Alignment Reader, Paper Archive
Embedded latex via TWiki.MathModePlugin
- e.g. $t=\mathcal{O}\left(l^3 m^3\right)$
TWiki.InterWikis and TWiki.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 Generic Genome Browser
  - Worm:I/1000-3000, Fly:2L/30000-40000 (defined on TWiki.InterSeqs)
  - Also links to gene reports in flybase and wormbase (see TWiki.InterWikis)

Ideas for more stuff: