Genome Query 0.3 (deadline: 11 May, feature freeze: 4 May)

  • Search algorithms:
    • Fast inexact search (wildcards M, R, N etc.)
    • WHAT command fast implementation (Alexey A.)
  • Annotations:
  • Parser:
  • UI:
  • Other:
    • Javadoc comments to all classes (Everybody)

Genome Query 0.2 (deadline: 20 April)

  • Search algorithms:
    • (tick) K-mers for all chromosomes (Andrew)
    • (question) Inexact search (at least k mismatches) (Victor)
    • (question) Slow inexact search (wildcards M, R, N etc.) (Alexey A.)
    • (question) Real-time results (Vlad R.)
    • (question) WHAT command slow implementation (Alexey A.)
    • Protein search through wild-carded DNA search (Alexey A.)
  • Annotations:
    • repeats
    • (tick) locuses (Kate)
  • Parser:
    • (tick) WHAT command (Alexey A.)
    • Wildcards for inexact search (Alexey A.)
  • UI:
    • (question) Better layout on browser window resize
    • FIND/COUNT result grouping based on locations in query (extLoc)
    • More crosslinks in result's output (to INFO, SHOW, WHAT queries)
  • Other:
    • Javadoc comments to some classes (Everybody)

Genome Query 0.1 (deadline: 23 March)

  • Search algorithms:
    • (tick) KMP
    • (tick) Suffix arrays for all chromosomes (Victor)
  • Annotations are used to get more precised location:
    • (tick) search in genes
    • (tick) ┬áprotein id
    • (tick) exons & introns (Kate)
  • UI:
    • (tick) on the fly error checking (Alexey K.)
    • (tick) better layout for info/show/count/find results (Vlad O.)
    • (tick) improve help layout: see current right side help (Natalya K.)
    • (tick) show sample queries on startup page (Alexey K.)
  • Other:
    • (tick) ability to stop long running tasks (Alexey K., Vlad R.)
    • (tick) sequence condensed structure (Vlad R.)
    • (tick) preprocessing script

Backlog

Search algorithms:

  • (don't need) Compressed Suffix arrays (Andrew)
  • (lightbulb) BLAST (Vlad O.)

Parser

  • (tick) inexact search syntax (Alexey A.)
  • (tick) regular expressions (Alexey A.)
  • (question) parsing on client side
  • (question) syntax for search by shift before/after gene
  • find in protein-coding genes
  • find in exons, introns, genes, genome
  • alternatives for nucleotides

TODO:

  • Use issue tracker!
  • on the fly syntax check (question) client side with better error recovery (question)
  • task estimation time based on algorithm used
  • better instant input validation
  • think about result layout
  • HISTORY of queries















(red star) - Must have feature
(blue star) - Nice to have feature

(question) - Under Investigation
(lightbulb) - In Progress
(tick) - Feature Implemented