Update Matrix WS210
From WormBaseWiki
| 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 | 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/ | didn't see any | 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 | waiting for correct clustal file from MH | 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 |
