Difference between revisions of "Update Matrix WS206"
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|<i>C elegans</i> | |<i>C elegans</i> | ||
| ok | | ok | ||
− | | | + | | troubleshooting |
− | | | + | | ok |
| ok | | ok | ||
|- | |- | ||
|<i>C briggsae</i> | |<i>C briggsae</i> | ||
| ok | | ok | ||
− | | | + | | troubleshooting |
| N/A | | N/A | ||
| ok | | ok | ||
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|<i>C remanei</i> | |<i>C remanei</i> | ||
| troubleshooting | | troubleshooting | ||
− | | | + | | troubleshooting |
| N/A | | N/A | ||
| ok | | ok | ||
Line 169: | Line 169: | ||
| N/A | | N/A | ||
| ok | | ok | ||
+ | |||
+ | |||
+ | |||
+ | [[Category:Developer documentation]] |
Latest revision as of 18:20, 17 August 2010
Check | Note | Related Compile Step |
---|---|---|
Have directories been created for given release in /u/l/w/databases? | ok | Create Data Directories |
Has a wormbase_RELEASE directory been created in /u/l/w/acedb? | ok | Mirror and Unpack AceDB files |
Is the Dev site running with the correct release number? | ok | Mirror and Unpack AceDB files |
Is the wormbase pointer linked to the newly created acedb? | ok | Mirror and Unpack AceDB files |
Is the database running and providing the correct version number? | ok | Mirror and Unpack AceDB files |
Are the correct ontology files in /u/l/w/databases? | ok | Mirror Ontology from Sanger |
Were the additional ontology files generated? | ok | Compile Ontology Resources |
Is the Multi-Ontology Search Running? URL: http://dev.wormbase.org/db/ontology/search |
ok | Compile Ontology Resources |
Are the Ontology related summary pages working? | ok | Compile Ontology Resources |
Can you do a blast searches on the appropriate genomes? http://dev.wormbase.org/db/searches/blast_blat |
see table below | Create Blast DBs |
Can you do a blat search on the appropriate genomes? http://dev.wormbase.org/db/searches/blast_blat |
see table below | Create Blat DBs |
Does ePCR work? http://dev.wormbase.org/db/searches/epcr |
see table below | Create ePRC DBs |
Are the appropriate tracks visible on the appropriate genomes http://dev.wormbase.org/db/seq/sequence?name=AC7;class=Sequence |
ok | Load GFF DBs |
Is the EST aligner working? http://dev.wormbase.org/db/seq/aligner |
ok | 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 |
ok | Load GFF DBs |
Are the supplementary GFF tracks available http://dev.wormbase.org/db/seq/gbrowse/c_elegans/ |
ok | Load GFF DBs |
Are the GBrowsers for the various species working http://dev.wormbase.org/db/seq/gbrowse/ |
see table below | Load GFF DBs |
Are the Genetic Limit Tracks available http://dev.wormbase.org/db/seq/gbrowse/c_elegans/ |
ok | 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 |
ok | Build and Load GFF Patches |
Can you do a disease search? http://dev.wormbase.org/db/orthology/disease |
ok | Compile orthology resources |
Can you list diseases for a gene? http://dev.wormbase.org/db/orthology/disease?related=WBGene00006803 |
ok | Compile orthology resources |
Can you list interactions? http://dev.wormbase.org/db/gene/interaction?list=WBGene00001188 |
ok | Compile interaction resources |
Can you list the available position matrices? http://dev.wormbase.org/db/seq/position_matrix?list=all |
ok | Compile position matrices |
Can you run a CLUSTAL search? http://dev.wormbase.org/db/seq/show_mult_align |
ok | Update CLUSTAL database |
GENOME MATRIX | ||||
---|---|---|---|---|
species | Blast | Blat | ePCR | GBrowse |
C elegans | ok | troubleshooting | ok | ok |
C briggsae | ok | troubleshooting | N/A | ok |
C brenneri | ok | N/A | N/A | ok |
C remanei | troubleshooting | troubleshooting | N/A | ok |
C japonica | ok | N/A | N/A | ok |
M hapla | ok | N/A | N/A | up; needs evaluation |
M incognita | ok | N/A | N/A | up; needs evaluation |
B malayi | ok | N/A | N/A | up; needs some debugging |
P pacificus | ok | N/A | N/A | ok |