Talk:Catalog

Revision as of 14:23, 22 January 2009 by Bcanton (Talk | contribs)

Software tools

Just the start of a list -

  • Tool for marking parts to be included or not included in the distribution
    • This might simply just be an excel spreadsheet initially of every part, how often it is used, QC info, summed size of all part pages etc.
  • Being able to enter parameter values into a new table
  • Copy and rename functionality for column sets
  • Automated parameter generation
    • See Talk:Protein coding sequences and Talk:Protein tags and modifiers for more details; Note that these computer generated values ought to be able to be overwritten by a human.
    • Auto-translation to amino acid sequence for protein tags and modifiers
    • Auto-detection of direction of protein coding sequences based on sequence
    • Auto-detection as to whether a protein coding sequence has a start and stop codon and therefore is complete, N-terminal half, C-terminal half or a domain; as part of this the start and stop codons could be automatically annotated in the feature list
  • An RBS strength calculator should be available on RBS and coding sequence pages.
  • Sites for transcriptional regulators should be automatically identified for all promoters (and maybe other parts), add any identified sites as features to the promoters.
  • Auto-detection of the swissprot and kegg database references for protein coding regions
  • Secondary structure predictor that can show a graphic of the predicted secondary structure for a part.
    • This should be done for all protein generators and terminators
  • A method for importing promoters (and other parts) from ecocyc (and other similar databases).