1 / 13

MGI/GMOD Update 9/03

MGI/GMOD Update 9/03. Joel Richardson. seqdb_engine. A framework for building and maintaining customized blastable databases Used by MGI to build the MouseBLAST set of databases (19 external, 25 internal) Java class framework for filtering and routing sequence records

catherine-beasley
Download Presentation

MGI/GMOD Update 9/03

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. MGI/GMOD Update 9/03 Joel Richardson

  2. seqdb_engine • A framework for building and maintaining customized blastable databases • Used by MGI to build the MouseBLAST set of databases (19 external, 25 internal) • Java class framework for filtering and routing sequence records • Build processing based on make • Recent work: • handle change in GenBank release proceedures • rebundling for external use • Status: released

  3. mouse mRNA mouse mRNA ROD mouse mRNA filter route pressdb hum mRNA hum mRNA hum mRNA PRI mouse mRNAs mouse mRNA HTC hum mRNA human mRNAs mouse mRNA NC hum mRNA Example GenBank files intermediate files sequence files sequence. databases

  4. GEN: Gene Expression Notebook • A lab-notebook application for managing gene expression data • assays, reagents, results • electronic data submission to GXD • Implemented in Excel • Working on ports to Win 2000, Mac OS/X • Excel ain’t so cross-platform! • Status: released

  5. Ontology Browser/Annotation Viewer • Original proposal: reimplement MGI’s text-based browser in Java, then release • Better browsers already available • Recent prototyping work at MGI: • graphical displays (using AT&T GraphViz) • Python • similar to SGD’s TermFinder • New plan: release the prototype! • Status: soon (core libraries ready to go)

  6. Prototype GO Annotation Viewer

  7. Fgf4

  8. Test Set: 78 genes

  9. Pruned

  10. UML: digraph

  11. UML: trans

  12. UML: render

  13. UML: app

More Related