Difference between revisions of "Update Matrix WS205"

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| <br> yes
 
| <br> yes
 
| Load GFF DBs
 
| Load GFF DBs
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 +
 +
[[Category:Developer documentation]]
 
|-
 
|-
 
|Are the supplementary GFF tracks available  <br> http://dev.wormbase.org/db/seq/gbrowse/c_elegans/
 
|Are the supplementary GFF tracks available  <br> http://dev.wormbase.org/db/seq/gbrowse/c_elegans/

Latest revision as of 18:14, 17 August 2010

Check Note Related Compile Step
Have directories been created for given release in /u/l/w/databases?
yes
Create Data Directories
Has a wormbase_RELEASE directory been created in /u/l/w/acedb?
yes
Mirror and Unpack AceDB files
Is the Dev site running with the correct release number?
yes
Mirror and Unpack AceDB files
Is the wormbase pointer linked to the newly created acedb?
yes
Mirror and Unpack AceDB files
Is the database running and providing the correct version number?
yes
Mirror and Unpack AceDB files
Are the correct ontology files in /u/l/w/databases?
yes
Mirror Ontology from Sanger
Were the additional ontology files generated?
yes
Compile Ontology Resources
Is the Multi-Ontology Search Running?
URL: http://dev.wormbase.org/db/ontology/search

yes
Compile Ontology Resources
Are the Ontology related summary pages working?
yes
Compile Ontology Resources
Can you do a blast searches on the appropriate genomes?
http://dev.wormbase.org/db/searches/blast_blat

yes
Create Blast DBs
Can you do a blat search on the appropriate genomes?
http://dev.wormbase.org/db/searches/blast_blat

yes
Create Blat DBs
Does ePCR work?
http://dev.wormbase.org/db/searches/epcr

yes
Create ePRC DBs
Are the appropriate tracks visible on the appropriate genomes
http://dev.wormbase.org/db/seq/sequence?name=AC7;class=Sequence

yes
Load GFF DBs
Is the EST aligner working?
http://dev.wormbase.org/db/seq/aligner

yes
Load GFF DBs
Is the Gene Details Page working?
http://dev.wormbase.org/db/gene/gene?name=amx-2;class=Gene;details=1;dna=B0019.1

yes
Load GFF DBs
Are the supplementary GFF tracks available
http://dev.wormbase.org/db/seq/gbrowse/c_elegans/

not all, update to GFF conf scheduled for WS206
Load GFF DBs
Are the GBrowsers for the various species working
http://dev.wormbase.org/db/seq/gbrowse/

yes, except mh and mi -- data loaded, updating conf files
Load GFF DBs
Are the Genetic Limit Tracks available
http://dev.wormbase.org/db/seq/gbrowse/c_elegans/

yes
Build and Load GFF Patches
Are protein motifs available on the Protein page?
http://dev.wormbase.org/db/seq/protein?name=T21C12.1;class=Protein

yes
Build and Load GFF Patches
Can you do a disease search?
http://dev.wormbase.org/db/orthology/disease

yes
Compile orthology resources
Can you list diseases for a gene?
http://dev.wormbase.org/db/orthology/disease?related=WBGene00006803

yes
Compile orthology resources
Can you list interactions?
http://dev.wormbase.org/db/gene/interaction?list=WBGene00001188

yes
Compile interaction resources
Can you list the available position matrices?
http://dev.wormbase.org/db/seq/position_matrix?list=all

yes
Compile position matrices
Can you run a CLUSTAL search?
http://dev.wormbase.org/db/seq/show_mult_align

yes
Update CLUSTAL database