Скачать презентацию w Flea Base Daphnia Genome Database from Common Скачать презентацию w Flea Base Daphnia Genome Database from Common

b6e4910eb35f4f421578fb10f423a51a.ppt

  • Количество слайдов: 17

w. Flea. Base Daphnia Genome Database from Common Components Daphnia Genomic Consortium Meeting, Sept. w. Flea. Base Daphnia Genome Database from Common Components Daphnia Genomic Consortium Meeting, Sept. 2003 Don Gilbert, [email protected] edu

http: //iubio. indiana. edu/daphnia http: //iubio. indiana. edu/daphnia

A Replicable Genome inf. Ormation System ( Argos ) http: //eugenes. org/argos | flybase. A Replicable Genome inf. Ormation System ( Argos ) http: //eugenes. org/argos | flybase. net/flybase-ng common/ java/ ; perl/ -- program libraries and packages servers/ -- major programs (BLAST, My. Sql/Postgre. SQL, others) systems/ -- OS executables of programs daphnia/. . implemented organism genome systems eugenes/ flybase/ docs/ & install/ -- Argos instructions and usage template/ -- structure for new projects ROOT/ -- common directory of installed projects

Argos features Common genome tool set ü ü Share benefits of “best of breed” Argos features Common genome tool set ü ü Share benefits of “best of breed” genome tools Common parts are tested & maintained by others Minimal IT expertise (no compiles or system management) Choice of tools (existing or new genome DB use parts desired) Flexible project packages ü Project needs specify tool set (compare Ens. EMBL where all use one set) ü Own look’n’feel web pages, contents, functions ü Security for protected and public sections Easy replication to any Unix computer ü ü ‘Live’ database system replication using rsync Keep remote servers up-to-date every day Local cluster/grid for high-volume traffic Works on common workstations, laptops

Argos - advanced features Data mining ü Fulfill need to search & retrieve 1000 Argos - advanced features Data mining ü Fulfill need to search & retrieve 1000 s of genes ü Web Services, Grid Services and LDAP for large data sets ü Simple, computable, industry standards for query by criteria and retrieval of volumes of data ü Bypass time-consuming web pages made for people ü Use with personal, lab databases to keep genome links up-to-date

Argos common parts Java common library, Ant builds, XML Tools, Web Services (Axis), Lucene Argos common parts Java common library, Ant builds, XML Tools, Web Services (Axis), Lucene for “Google”-like searches Perl common library of Bio. Perl, GBrowse, others Servers include Apache, Tomcat web servers My. SQL, Postgre. SQL databases BLAST (NCBI) Systems compiled for apple-powerpc-darwin, intel-linux, sun-sparc-solaris

w. Flea. Base structure Cgi-bin -- Web programs(Perl) Common -- Link to common, shared w. Flea. Base structure Cgi-bin -- Web programs(Perl) Common -- Link to common, shared tools Conf -- Site configurations for web, data Data -- Bulk data & FTP site folder Dbs -- Project databases: blast, lucene, mysql Indices -- Database indices Lib -- Program libraries Web -- Web structure and documents Genomics, Sequences, Maps, Literature, Stocks, Docs, other includes Public and Protected (project member only) parts Webapps -- Web programs (Java) includes Search system, Secure web and editing

Search w. Flea. Base Search w. Flea. Base

BLAST w. Flea. Base BLAST w. Flea. Base

Edit w. Flea. Base Edit w. Flea. Base

Where to put Daphnia Genome? Database needs n n Automated annotation and curated updates Where to put Daphnia Genome? Database needs n n Automated annotation and curated updates Search and retrieve data subsets Choices n n n Ens. EMBL - working now, Gramene & others use GMOD: Chado - in development (Fly. Base, Worm. Base, Chlamy. Genome, TIGR, others will use) Others choices?

Generic Model Organism Database Construction Set www. gmod. org n Genome+ Database (more than Generic Model Organism Database Construction Set www. gmod. org n Genome+ Database (more than annotations) n Genome visualization tools n Genome annotation pipeline planned n Literature curation and Gene Ontology tools n Component system (pick and choose) n Developing - more complete in 2004

Ens. EMBL Genome Database www. ensembl. org n Genome annotation database n Genome visualization Ens. EMBL Genome Database www. ensembl. org n Genome annotation database n Genome visualization tools n Genome annotation pipeline n Comprehensive system (all or none) n Production - useable now

From Shawn Hoon, Fugu Informatics Group From Shawn Hoon, Fugu Informatics Group

w. Flea. Base issues • Basic web system ready for genome data? • Start w. Flea. Base issues • Basic web system ready for genome data? • Start with Ens. EMBL for management; move to GMOD: Chado if better choice? • Add GMOD GBrowse; Apollo Editor with genome • Add “Self-service” database features for? • Easy management by scientists • Genome data; stocks; research literature • Add evolutionary, ecological, environmental data Prototype at http: //iubio. indiana. edu/daphnia/

GBrowse Maps GBrowse Maps

Apollo Annotator Apollo Annotator