JUN 7 2010

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Grant Update

Responses from Advisors

- In general, several people said 'kick in the pants' sounds to submissive. And we should not say that we just did all the gene curation initiatives in response to reviews, but reviews pushed us to implement faster and milestones.

- in sum:

  1. Other genomes: synteny, genetic variation, phylogenetic trees, separate section 'protozoa orthologs'; closely related isolates, cis-acting sequences.
  2. Expression: temporal, spatial(?)
  3. Proteomics: PTM, Phospho-sites, temporal
  4. Community annotation, improved (maybe we need to have a user curation interface? Section on gene page with name of annotator?)
  5. Calipho project



  1. Expression: Search for genes with expression at certain times. Says he would prefer to have this n dictyBase than to go offsite to dictyExpress!
  2. Small extra grants for collaborative projects
  3. Thinks we should be more 'integrated' with other databases.


  1. More organization and incentives for community annotation.
  2. Proteomics data / PTMs, phosphoproteomics. (in gbrowse?)
  3. Better expression interface
  4. Genomes of other protozoa
  5. Calipho project (orphan gene functions)/Amos


  1. New genomes, genetic variation display. Have several wildtype strain genomes, not assembled, just mapped to AX4 genome. Mentions pseudogene annotations.


  1. Annotating genes in other Dictyostelids that are not in Dd?
  2. Likes integration of RNaseq data/ expression!
  3. Community annotation/authorship
  4. Clarify gene numbers, asks about pseudogenes.


  1. Synteny viewer
  2. Gantt chart needs to be simpler
  3. Be specific about new genomes and proteomics projects


  1. Clearer list of what is curated, metrics.
  2. Small group - bump up number of FTEs?
  3. Specify new software to meat milestones; clear description of priority lists in gene curation.
  4. What new technologies? Frame as the innovative strategy you're using to deal with issues of scale and new data types (like the SNPs)
  5. Letters of collaborators


  1. Need to explain points in specific aims more, e.g. expression, edit genome, etc.
  2. New genomes, tools for comparison. Will have a sequenced genome of all groups by end of year.
  3. Show trends in gene and gene family evolution / phylogenetic trees
  4. List of useful tools for bioinformatics (e.g. phylogenetic trees)

Robert Insall:

  1. Emphasize different user groups

Rob Kay:

  1. Integrate phophomics data, describes projects going on in lab.


  1. Host site for the community to post working models of circuits for various aspects of Dicty development.
  2. Sequences of closely related D.d. isolates, comparisons might shed light on cis-acting sequences.
  3. Thinks dictyBase as is could just stay like that without further funding. Can we make a strong point this cannot be done? Also suggests cutting the budget (has no idea what money is for).

Community Annotation test (Pascale)

  1. Several people responded. Info is not 'complete'. in evaluation stage (Petra)

Release updates

Next Release 2.19 (End of June 2010) Review/Update

1. Migrating reference tables to Chado Sidd [3 months] Plans and estimate

Current status
Writing software adaptor for handling reference in chado schema : [~ 2 more weeks from now]
Migrate data from SGD <-> Chado [~ 1 week ]
Fix code that depends on legacy code [~ 2 and half weeks]
Public pages
Search classes
Batch scripts

[Approx estimate ] July 9th

2. Ortholog display (Yulia) [2 months]

  • Data model for storing in chado [0.5 weeks] Done
  • Write middleware to handle data manipulation [2 weeks] In Process
  • Write script(s) for data insertion [1 week]
  • Write display part [1.5 weeks]
Including Bold text track in new GBrowse (would be great!) What do we display, actual alignment?

Next next release

1. Interpro domains for all dicty genes (Yulia)

Running interpro analysis using InterProScan web service instead of relying on interpro-uniprot-dictybase mapping)

2. GO migration [Sidd, 3 months]

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