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Genome Query 1.0

.1 (deadline: 17 March

(deadline: 1 June)

  • Info
    • SNPs
  • Show
    • Protein sequence
  • Find/Count
    • Common algorithms interface for KMP, SA, K-mers (Victor, Nadya)
    • Slow inexact search (wildcards M, R, N etc.) (Alexey A.)
    • Wildcards for inexact search (Alexey A.)
    • Protein search through wild-carded DNA search (Alexey A.)
  • What
  • Other
    • Better layout on browser window resize
    • More crosslinks in result's output (to INFO, SHOW, WHAT queries)
    • Javadoc comments to some classes (Everybody)

Genome Query 0.3 (deadline: 11 May, feature freeze: 10 May)

  • Search algorithms:
    • (tick) KMP
    • (tick) Suffix arrays (Victor)
    • (lightbulb) K-mers (Andrew)
    • Fast inexact search (wildcards M, R, N etc.)
    • (tick) WHAT command fast implementation
    • (tick) Real-time results
    • (tick) Inexact search (at least k mismatches)
    • (tick) search by shift before/after gene (Alexey A.)
  • Parser:
  • UI:
    • (tick) History of queries
    • (tick) FIND/COUNT result grouping based on locations in query (extLoc)
  • Annotation
    • (tick) repeats
  • Other:
    • Javadoc comments to all classes (Everybody)

Genome Query 0.2 (deadline: 20 April, feature freeze: 13 April)

  • Search algorithms:
    • (tick) K-mers for all chromosomes
    • (tick) WHAT command slow implementation
  • Annotations:
    • (tick) locuses
  • Parser:
    • (tick) WHAT command
  • Other:
    • Javadoc comments to some classes (Everybody)

Genome Query 0.1 (deadline: 23 March)

  • Search algorithms:
    • (tick) KMP
    • (tick) Suffix arrays for all chromosomes
  • Annotations are used to get more precised location:
    • (tick) search in genes
    • (tick) protein  protein id
    • (lightbulb) (tick) exons & introns (Kate)
  • UI:
    • (tick) on the fly error checking (Alexey K.)
    • (lightbulb) (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 (Vlad R.)(lightbulb) preprocessing,
    • (tick) sequence condensed structure (Vlad R.)
    • (tick) preprocessing script

Backlog

Search algorithms:

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

Annotations are used to get more precised location: (Kate) in progress

  • repeats
  • locuses

Parser

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

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

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