Needs Analysis Workshop/Report-out Day1

Evo Group report-out

• need to improve ontologies, e.g. for describing behavior
• need to improve tools for analyzing images
• covariance of entities, attributes
• broader queries of entities within particular constraints, such as structures
• need capacity to store media (e.g., images, movies)
• need environmental, ecological, and geographical data

Devo Group report-out

• identifying homologies among distantly related taxa
  • for example, do fishes have digits? E.g., if genes have similar effects on fins as on digit development.
• patterns of covariation
  • for example, cusps on mammalian teeth
  • could be used to identify "character modules" that are well-connected
  • connections within modules should be more stable than between
• for a branch hypothesized to be under positive selection (from e.g. a molecular analysis), identify candidate phenotypes that could have been selected for
  • map synapomorphies onto a phylogeny
  • identify phenotypes with highest rate of change on that lineage
  • needs phylogeny that is selectable and manipulable
• use the database to point out holes in the knowledge

Discussion

• enrichment analysis: given a list of genes, which phenotype terms are overrepresented among them
• capturing representing variation seems to be a general problem and challenge, but critically needed
  • variation in regulatory (or morphogenic) gene expression and corresponding phenotypic changes (Hox gene expression example)
  • polyphenism: variability of phenotype that can distinguish species but is also dependent on environmental factors or variable levels of gene expression
  • do we need to capture frequencies for polymorphisms to represent variability
  • there are morphological differences even between inbred strains, for example for JAX mouse strains in cranial morphology
• integrating with genomic resources:
  • linking out to genome databases seems mandatory
• alerting features
  • for example, saving queries as RSS feeds