Difference between revisions of "Update Matrix WS211"
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|Are the Genetic Limit Tracks available <br> http://dev.wormbase.org/db/seq/gbrowse/c_elegans/ | |Are the Genetic Limit Tracks available <br> http://dev.wormbase.org/db/seq/gbrowse/c_elegans/ | ||
− | | | + | | ok |
| Build and Load GFF Patches | | Build and Load GFF Patches | ||
|- | |- | ||
Line 100: | Line 100: | ||
|- | |- | ||
|Can you run a CLUSTAL search? <br> http://dev.wormbase.org/db/seq/show_mult_align | |Can you run a CLUSTAL search? <br> http://dev.wormbase.org/db/seq/show_mult_align | ||
− | | | + | | ok |
| Update CLUSTAL database | | Update CLUSTAL database | ||
|- | |- | ||
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|- | |- | ||
|<i>C elegans</i> | |<i>C elegans</i> | ||
− | | | + | | ok |
− | | | + | | ok |
|troubleshooting | |troubleshooting | ||
| http://dev.wormbase.org/db/seq/gbrowse/c_elegans/<br>ok | | http://dev.wormbase.org/db/seq/gbrowse/c_elegans/<br>ok | ||
|- | |- | ||
|<i>C briggsae</i> | |<i>C briggsae</i> | ||
− | | | + | | ok |
− | | | + | | ok |
| troubleshooting | | troubleshooting | ||
| http://dev.wormbase.org/db/seq/gbrowse/c_briggsae/?name=chrI%3A80000..120000<br>ok | | http://dev.wormbase.org/db/seq/gbrowse/c_briggsae/?name=chrI%3A80000..120000<br>ok | ||
|- | |- | ||
|<i>C brenneri</i> | |<i>C brenneri</i> | ||
− | | | + | | ok |
− | | | + | | ok |
| N/A | | N/A | ||
| http://dev.wormbase.org/db/seq/gbrowse/c_brenneri/#search<br>ok | | http://dev.wormbase.org/db/seq/gbrowse/c_brenneri/#search<br>ok | ||
|- | |- | ||
|<i>C remanei</i> | |<i>C remanei</i> | ||
− | | | + | | ok |
− | | | + | | ok |
| N/A | | N/A | ||
| http://dev.wormbase.org/db/seq/gbrowse/c_remanei/?name=CRE02801<br>ok | | http://dev.wormbase.org/db/seq/gbrowse/c_remanei/?name=CRE02801<br>ok | ||
|- | |- | ||
|<i>C japonica</i> | |<i>C japonica</i> | ||
− | | | + | | ok |
| N/A | | N/A | ||
| N/A | | N/A | ||
Line 150: | Line 150: | ||
|- | |- | ||
|<i>M hapla</i> | |<i>M hapla</i> | ||
− | | | + | | ok |
| N/A | | N/A | ||
| N/A | | N/A | ||
Line 156: | Line 156: | ||
|- | |- | ||
|<i>M incognita</i> | |<i>M incognita</i> | ||
− | | | + | | ok |
| N/A | | N/A | ||
| N/A | | N/A | ||
Line 162: | Line 162: | ||
|- | |- | ||
|<i>B malayi</i> | |<i>B malayi</i> | ||
− | | | + | | ok |
| N/A | | N/A | ||
| N/A | | N/A | ||
Line 168: | Line 168: | ||
|- | |- | ||
|<i>P pacificus</i> | |<i>P pacificus</i> | ||
− | | | + | | ok |
− | | | + | | ok |
| N/A | | N/A | ||
| http://dev.wormbase.org/db/seq/gbrowse/p_pacificus/#search<br>ok | | http://dev.wormbase.org/db/seq/gbrowse/p_pacificus/#search<br>ok | ||
+ | |||
+ | |||
+ | |||
+ | [[Category:Developer documentation]] |
Latest revision as of 18:21, 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 |
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 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 |
ok | 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 |
aligner acting up -- can't find entry | 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 |
GENOME MATRIX | ||||
---|---|---|---|---|
species | Blastn http://dev.wormbase.org/db/searches/blast_blat |
Blastp |
Blat |
GBrowse |
C elegans | ok | ok | troubleshooting | http://dev.wormbase.org/db/seq/gbrowse/c_elegans/ ok |
C briggsae | ok | ok | troubleshooting | http://dev.wormbase.org/db/seq/gbrowse/c_briggsae/?name=chrI%3A80000..120000 ok |
C brenneri | ok | ok | N/A | http://dev.wormbase.org/db/seq/gbrowse/c_brenneri/#search ok |
C remanei | ok | ok | N/A | http://dev.wormbase.org/db/seq/gbrowse/c_remanei/?name=CRE02801 ok |
C japonica | ok | N/A | N/A | http://dev.wormbase.org/db/seq/gbrowse/c_japonica/?name=Cjap_Contig2%3A140000..180000 ok |
M hapla | ok | N/A | N/A | http://dev.wormbase.org/db/seq/gbrowse/m_hapla/?name=MhA1_Contig0 ok |
M incognita | ok | N/A | N/A | http://dev.wormbase.org/db/seq/gbrowse/m_incognita/#search ok |
B malayi | ok | N/A | N/A | http://dev.wormbase.org/db/seq/gbrowse/b_malayi/?name=Bmal_supercontig12883 ok |
P pacificus | ok | ok | N/A | http://dev.wormbase.org/db/seq/gbrowse/p_pacificus/#search ok |