Difference between revisions of "Update Matrix WS220"

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{| cellpadding="5" border="1"
 
|-
 
! Check
 
! Note
 
! Related Compile Step
 
|-
 
| Are the correct ontology files in /u/l/w/databases?
 
| <br>
 
| Mirror Ontology from Sanger
 
|-
 
| Were the additional ontology files generated?
 
| <br>
 
| Compile Ontology Resources
 
|-
 
| Is the Multi-Ontology Search Running? <br>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?<br>http://dev.wormbase.org/db/searches/blast_blat
 
| see matrix below
 
| Create Blast DBs
 
|-
 
|Can you do a blat search on the appropriate genomes?<br>http://dev.wormbase.org/db/searches/blast_blat
 
| see matrix below
 
|Create Blat DBs
 
|-
 
|Does ePCR work? <br> http://dev.wormbase.org/db/searches/epcr
 
|ok
 
|Create ePRC DBs
 
|-
 
|Are the appropriate tracks visible on the appropriate genomes <br>http://dev.wormbase.org/db/seq/sequence?name=AC7;class=Sequence
 
| ok
 
| Load GFF DBs
 
|-
 
|Is the EST aligner working? <br>http://dev.wormbase.org/db/seq/aligner
 
| ok
 
| Load GFF DBs
 
|-
 
|Is the Gene Details Page working? <br>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  <br> http://dev.wormbase.org/db/gb2/gbrowse/c_elegans/
 
| ok
 
| Load GFF DBs
 
|-
 
|Are the GBrowsers for the various species working <br> http://dev.wormbase.org/db/gb2/gbrowse/
 
| see matrix below
 
| Load GFF DBs
 
|-
 
|Are the Genetic Limit Tracks available <br> http://dev.wormbase.org/db/gb2/gbrowse/c_elegans/
 
| ok
 
| Build and Load GFF Patches
 
|-
 
| Are protein motifs available on the Protein page?<br> http://dev.wormbase.org/db/gb2/gbrowse/c_elegans/
 
| ok
 
| Build and Load GFF Patches
 
|-
 
|Can you do a disease search?<br>http://dev.wormbase.org/db/orthology/disease
 
| ok
 
| Compile orthology resources
 
|-
 
|Can you list diseases for a gene?<br>http://dev.wormbase.org/db/orthology/disease?related=WBGene00006803
 
| ok
 
| Compile orthology resources
 
|-
 
|Can you list interactions? <br>http://dev.wormbase.org/db/gene/interaction?list=WBGene00001188
 
| ok
 
| Compile interaction resources
 
|-
 
|Can you list the available position matrices?<br>http://dev.wormbase.org/db/seq/position_matrix?list=all
 
| ok
 
| Compile position matrices
 
|-
 
|Can you run a CLUSTAL search? <br> http://dev.wormbase.org/db/seq/show_mult_align
 
| ok
 
| Update CLUSTAL database
 
|-
 
|Is strain data available?
 
| ok
 
| run Strain update
 
|-
 
|Are all the files for FTP present?
 
| ok
 
| <br>
 
|-
 
 
 
{| cellpadding="5" border="1"
 
{| cellpadding="5" border="1"
  
Line 102: Line 11:
 
|-
 
|-
 
|<i>C elegans</i>
 
|<i>C elegans</i>
| ok
+
| genome:<br>gene:
 
| ok
 
| ok
 
|troubleshooting  
 
|troubleshooting  
| http://dev.wormbase.org/db/gb2/gbrowse/c_elegans/<br>ok
+
| http://dev.wormbase.org/db/gb2/gbrowse/c_elegans/<br>General Browser status:<br>Supplementary Tracks:<br>Protein Motifs:<br>Genetic Limits:
 
|-
 
|-
 
|<i>C briggsae</i>
 
|<i>C briggsae</i>
Line 154: Line 63:
 
| N/A
 
| N/A
 
| http://dev.wormbase.org/db/gb2/gbrowse/p_pacificus/#search<br>ok
 
| http://dev.wormbase.org/db/gb2/gbrowse/p_pacificus/#search<br>ok
 +
|-
 +
|<i>H contortus</i>
 +
| ok
 +
| ok
 +
| N/A
 +
| http://dev.wormbase.org/db/gb2/gbrowse/h_contortus/#search<br>ok
 +
|-
 +
|<i>C angaria</i>
 +
| ok
 +
| ok
 +
| N/A
 +
| http://dev.wormbase.org/db/gb2/gbrowse/c_angaria/#search<br>ok
 +
|-
 +
 +
 +
 +
 +
 +
{| cellpadding="5" border="1"
 +
|-
 +
! Check
 +
! Note
 +
! Related Compile Step
 +
|-
 +
| Are the phenotype tables rendering properly in the Gene Summary page? <br> http://dev.wormbase.org/db/gene/gene?name=WBGene00006763;class=Gene
 +
| ok
 +
| Compile Gene Resources
 +
|-
 +
| Is the Multi-Ontology Search Running? <br> http://dev.wormbase.org/db/ontology/search
 +
| ok
 +
| Compile Ontology Resources
 +
|-
 +
| Are the Ontology related summary pages working?<br>Check off search results
 +
|GO: <br>----------------------<br>Phenotype: <br>---------------------<br>Anatomy:
 +
| Compile Ontology Resources
 +
|-
 +
|Does ePCR work? <br> http://dev.wormbase.org/db/searches/epcr
 +
|ok
 +
|Create ePRC DBs
 +
|-
 +
|Are the appropriate tracks visible on the appropriate genomes <br>http://dev.wormbase.org/db/seq/sequence?name=AC7;class=Sequence
 +
| ok
 +
| Load GFF DBs
 +
|-
 +
|Is the EST aligner working? <br>http://dev.wormbase.org/db/seq/aligner
 +
| ok
 +
| Load GFF DBs
 +
|-
 +
|Is the Gene Details Page working? <br>http://dev.wormbase.org/db/gene/gene?name=amx-2;class=Gene;details=1;dna=B0019.1
 +
| ok
 +
| Load GFF DBs
 +
|-
 +
|Can you do a disease search?<br>http://dev.wormbase.org/db/orthology/disease
 +
| ok
 +
| Compile orthology resources
 +
|-
 +
|Can you list diseases for a gene?<br>http://dev.wormbase.org/db/orthology/disease?related=WBGene00006803
 +
| ok
 +
| Compile orthology resources
 +
|-
 +
|Can you list interactions? <br>http://dev.wormbase.org/db/gene/interaction?list=WBGene00001188
 +
| ok
 +
| Compile interaction resources
 +
|-
 +
|Can you list the available position matrices?<br>http://dev.wormbase.org/db/seq/position_matrix?list=all
 +
| ok
 +
| Compile position matrices
 +
|-
 +
|Can you run a CLUSTAL search? <br> http://dev.wormbase.org/db/seq/show_mult_align
 +
| ok
 +
| Update CLUSTAL database
 +
|-
 +
|Is strain data available?
 +
| ok
 +
| run Strain update
 +
|-
 +
|Are all the files for FTP present?
 +
| ok
 +
| <br>
 +
|-

Latest revision as of 16:43, 17 February 2011

GENOME MATRIX
species Blastn
http://dev.wormbase.org/db/searches/blast_blat
Blastp
Blat
GBrowse
C elegans genome:
gene:
ok troubleshooting http://dev.wormbase.org/db/gb2/gbrowse/c_elegans/
General Browser status:
Supplementary Tracks:
Protein Motifs:
Genetic Limits:
C briggsae ok ok troubleshooting http://dev.wormbase.org/db/gb2/gbrowse/c_briggsae/?name=chrI%3A80000..120000
page didn't render
C brenneri ok ok N/A http://dev.wormbase.org/db/gb2/gbrowse/c_brenneri/#search
ok
C remanei ok ok N/A http://dev.wormbase.org/db/gb2/gbrowse/c_remanei/?name=CRE02801
ok
C japonica ok N/A N/A http://dev.wormbase.org/db/gb2/gbrowse/c_japonica/?name=Cjap_Contig2%3A140000..180000
ok
M hapla ok N/A N/A http://dev.wormbase.org/db/gb2/gbrowse/m_hapla/?name=MhA1_Contig0
ok
M incognita ok N/A N/A http://dev.wormbase.org/db/gb2/gbrowse/m_incognita/#search
ok
B malayi ok N/A N/A http://dev.wormbase.org/db/gb2/gbrowse/b_malayi/?name=Bmal_supercontig12883
ok
P pacificus ok ok N/A http://dev.wormbase.org/db/gb2/gbrowse/p_pacificus/#search
ok
H contortus ok ok N/A http://dev.wormbase.org/db/gb2/gbrowse/h_contortus/#search
ok
C angaria ok ok N/A http://dev.wormbase.org/db/gb2/gbrowse/c_angaria/#search
ok
Check Note Related Compile Step
Are the phenotype tables rendering properly in the Gene Summary page?
http://dev.wormbase.org/db/gene/gene?name=WBGene00006763;class=Gene
ok Compile Gene Resources
Is the Multi-Ontology Search Running?
http://dev.wormbase.org/db/ontology/search
ok Compile Ontology Resources
Are the Ontology related summary pages working?
Check off search results
GO:
----------------------
Phenotype:
---------------------
Anatomy:
Compile Ontology Resources
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
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
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
Is strain data available? ok run Strain update
Are all the files for FTP present? ok