RG: Software (Retired)

Reference Genome Software

Software for use with the Reference Genome project.

Status Tracker

There is a very early alpha of the status tracker here. Mostly a placeholder. The tool's front end is written with GWT and the backend will be with the new OBD API. All data passed between the two will have to be serializable.

API and Objects

• Meta: a general object for general queries.
  • #target_genes -> int
  • species -> list of Species

• Species
  • homologs -> list of Ortholog
  • !homologs -> list of Ortholog
  • #homologs -> int
  • #!homologs -> int
  • #comprehensive -> int
  • common_name -> string
  • ncbi_taxa_id -> int
  • etc...

• GenesProduct
  • symbol ->string
  • species -> Species
  • full_name ->string
  • etc...

• Target

• Ortholog

The Target and Ortholog objects may be a subclass of a YTD superclass. This superclass will need to be able to read and write to the database and be able to maintain temporary values in case of validation/sanity issues (or similar functionality). Maybe also a subclass of GeneProduct.

Parsers

Two parsers will also be necessary for the tool.

• A target parser that converts a tab-delimited file to a list of Target. The files format looks like:

foo bar bibble babble

• An ortholog parser that converts a tab-delimited file to a list of Ortholog. The files format looks like:

foo bar bibble babble

Summary and Graph Views

An alpha of the summary and graph views can currently be found here. This uses parts of a newer AmiGO framework written in perl.

This viewer has only been tested in Safari 3.x, FireFox 2.x, and Opera 9.x.

• Hovering over a node brings up details.
• The graph can be clicked and dragged.
• The mouse wheel zooms in and out.
• The zoom may also be controlled by ctrl-a and ctrl-z (if the browser does not use these for other functions).
• Checking a species causes them to highlight.