Download - MGI/GMOD Update 9/03
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MGI/GMOD Update 9/03
Joel Richardson
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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
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Example
mousemRNAs
humanmRNAs
hum mRNAhum
mRNA
mouse mRNAmouse mRNA
PRI
HTC
NC
mouse mRNAhum
mRNA
ROD
mouse mRNAhum
mRNAmouse mRNAhum
mRNA
filter route pressdb
GenBankfiles
intermediatefiles
sequencefiles
sequence.databases
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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
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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)
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Prototype GO Annotation Viewer
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Fgf4
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Test Set: 78 genes
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Pruned
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UML: digraph
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UML: trans
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UML: render
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UML: app