Difference between revisions of "Update Matrix WS213"

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|<i>C brenneri</i>
 
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Revision as of 18:55, 16 April 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
page didn't render
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