Update Matrix WS208

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/	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
H contortus	TBA	TBA	N/A	http://dev.wormbase.org/db/seq/gbrowse/h_contortus/#search ok