Difference between revisions of "Update Matrix WS207"
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|- | |- | ||
|Does ePCR work? <br> http://dev.wormbase.org/db/searches/epcr | |Does ePCR work? <br> http://dev.wormbase.org/db/searches/epcr | ||
− | | Search by position | + | | Search by position from example works |
|Create ePRC DBs | |Create ePRC DBs | ||
|- | |- | ||
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|- | |- | ||
|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/ | ||
− | | | + | | ok |
| Load GFF DBs | | Load GFF DBs | ||
|- | |- | ||
Line 122: | Line 122: | ||
| ok | | ok | ||
| ok | | ok | ||
− | |troubleshooting | + | |troubleshooting |
− | | ok | + | | http://dev.wormbase.org/db/seq/gbrowse/c_elegans/<br>ok |
|- | |- | ||
|<i>C briggsae</i> | |<i>C briggsae</i> | ||
Line 129: | Line 129: | ||
| ok | | ok | ||
| troubleshooting | | troubleshooting | ||
− | | ok | + | | http://dev.wormbase.org/db/seq/gbrowse/c_briggsae/?name=chrI%3A80000..120000<br>ok |
|- | |- | ||
|<i>C brenneri</i> | |<i>C brenneri</i> | ||
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| ok | | ok | ||
| N/A | | N/A | ||
− | | ok | + | | http://dev.wormbase.org/db/seq/gbrowse/c_brenneri/#search<br>ok |
|- | |- | ||
|<i>C remanei</i> | |<i>C remanei</i> | ||
− | | troubleshooting | + | | troubleshooting<br>nixed option in the meantime |
− | | troubleshooting | + | | troubleshooting<br>nixed option in the meantime |
− | | troubleshooting | + | | troubleshooting<br>nixed option in the meantime |
− | | ok | + | | http://dev.wormbase.org/db/seq/gbrowse/c_remanei/?name=CRE02801<br>ok |
|- | |- | ||
|<i>C japonica</i> | |<i>C japonica</i> | ||
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| N/A | | N/A | ||
| N/A | | N/A | ||
− | | ok | + | | http://dev.wormbase.org/db/seq/gbrowse/c_japonica/?name=Cjap_Contig2%3A140000..180000<br>ok |
|- | |- | ||
|<i>M hapla</i> | |<i>M hapla</i> | ||
Line 153: | Line 153: | ||
| N/A | | N/A | ||
| N/A | | N/A | ||
− | | | + | | http://dev.wormbase.org/db/seq/gbrowse/m_hapla/?name=MhA1_Contig0<br>ok |
|- | |- | ||
|<i>M incognita</i> | |<i>M incognita</i> | ||
Line 159: | Line 159: | ||
| N/A | | N/A | ||
| N/A | | N/A | ||
− | | | + | |http://dev.wormbase.org/db/seq/gbrowse/m_incognita/#search<br>ok |
|- | |- | ||
|<i>B malayi</i> | |<i>B malayi</i> | ||
Line 165: | Line 165: | ||
| N/A | | N/A | ||
| N/A | | N/A | ||
− | | up | + | | debugging: names of the Gene Models not coming up in browser as well as details page |
|- | |- | ||
|<i>P pacificus</i> | |<i>P pacificus</i> | ||
Line 171: | Line 171: | ||
| ok | | ok | ||
| N/A | | N/A | ||
− | | ok | + | | http://dev.wormbase.org/db/seq/gbrowse/p_pacificus/#search<br>ok |
+ | |- | ||
+ | |<i>H contortus</i> | ||
+ | | TBA | ||
+ | | TBA | ||
+ | | N/A | ||
+ | | http://dev.wormbase.org/db/seq/gbrowse/h_contortus/#search<br>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? | Create Data Directories | |
Has a wormbase_RELEASE directory been created in /u/l/w/acedb? | Mirror and Unpack AceDB files | |
Is the Dev site running with the correct release number? | Mirror and Unpack AceDB files | |
Is the wormbase pointer linked to the newly created acedb? | Mirror and Unpack AceDB files | |
Is the database running and providing the correct version number? | Mirror and Unpack AceDB files | |
Are the correct ontology files in /u/l/w/databases? | Mirror Ontology from Sanger | |
Were the additional ontology files generated? | Compile Ontology Resources | |
Is the Multi-Ontology Search Running? URL: http://dev.wormbase.org/db/ontology/search |
Compile Ontology Resources | |
Are the Ontology related summary pages working? | Compile Ontology Resources | |
Can you do a blast searches on the appropriate genomes? http://dev.wormbase.org/db/searches/blast_blat |
see matrix below | Create Blast DBs |
Can you do a blat search on the appropriate genomes? http://dev.wormbase.org/db/searches/blast_blat |
see matrix below | Create Blat DBs |
Does ePCR work? http://dev.wormbase.org/db/searches/epcr |
Search by position from example works | 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 matrix 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 |