wFleaBase Daphnia Genome Database from Common Components

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wFleaBaseDaphnia Genome Database from Common
Components

• Daphnia Genomic Consortium
• Meeting, Sept. 2003

Don Gilbert, gilbertd_at_indiana.edu
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http//iubio.bio.indiana.edu/daphnia
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A Replicable Genome infOrmation System ( Argos )

• http//eugenes.org/argos flybase.net/flybase
  -ng
• common/
• java/ perl/ -- program libraries and packages
• servers/ -- major programs (BLAST,
  MySql/PostgreSQL, 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

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Argos features

• Common genome tool set
• 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
• Project needs specify tool set (compare EnsEMBL
  where all use one set)
• Own looknfeel web pages, contents, functions
• Security for protected and public sections
• Easy replication to any Unix computer
• 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

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Argos - advanced features

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

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Argos common parts

• Java common library, Ant builds, XML Tools,
• Web Services (Axis), Lucene for Google-like
  searches
• Perl common library of BioPerl, GBrowse, others
• Servers include
• Apache, Tomcat web servers
• MySQL, PostgreSQL databases
• BLAST (NCBI)
• Systems compiled for
• apple-powerpc-darwin, intel-linux,
  sun-sparc-solaris

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wFleaBase 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

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Search wFleaBase
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BLAST wFleaBase
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Edit wFleaBase
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Where to put Daphnia Genome?

• Database needs
• Automated annotation and curated updates
• Search and retrieve data subsets
• Choices
• EnsEMBL - working now, Gramene others use
• GMODChado - in development (FlyBase,WormBase,
  ChlamyGenome,TIGR, others will use)
• Others choices?

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Generic Model Organism Database Construction Set
www.gmod.org

• Genome Database (more than annotations)
• Genome visualization tools
• Genome annotation pipeline planned
• Literature curation and Gene Ontology tools
• Component system (pick and choose)
• Developing - more complete in 2004

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EnsEMBL Genome Database
www.ensembl.org

• Genome annotation database
• Genome visualization tools
• Genome annotation pipeline
• Comprehensive system (all or none)
• Production - useable now

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From Shawn Hoon, Fugu Informatics Group
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wFleaBase issues

• Basic web system ready for genome data?
• Start with EnsEMBL for management move to
  GMODChado 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.bio.indiana.edu/daphnia
/
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GBrowse Maps
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Apollo Annotator