NIAID Bioinformatics Resource Centers Valentina Di Francesco Bioinformatics Program Director Microbial Genomics Program, DMID

Overview and Goals 5 year initiative launched in the summer of 2004 (-> 2 years, 4 months) To provide the scientific community with a robust point of entry for access of genomic and related data in a user-friendly format. To facilitate the identification of potential targets for the development of vaccines, therapeutics and diagnostics The centers cover ALL the organisms listed in the NIAID Category A-C priority list, invertebrate vectors and pathogens causing emerging or re-emerging diseases that are relevant for biodefense

BRCs features  Database of genomics data types  Web, GUI, API interfaces to the DB  Computational annotation, human curation and data integration  Comparative genomics  Development and distribution of open source s/w for analysis and interpretation of genomics data  Multidisciplinary teams  Outreach to the organism experts and developers of diagnostics, vaccine and therapeutics Scientific Working Groups  Training and Workshops

The Institute for Genomic Research PI: Dr. Owen White - PATHEMAPATHEMA Bacillus anthracis, Clostridium botulinum, Burkholderia mallei, Burkholderia pseudomallei, Clostridium perfringens, Entamoeba histolytica University of Pennsylvania; University of Georgia PI: Dr. David Roos, U-Penn - ApiDBApiDB Apicomplexa species: Toxoplasma gondii, Cryptosporidium parvum, Plasmodium phylum University of Notre Dame (UND); European Bioinformatics Institute; Imperial College of London; Institute of Molecular Biology and Biotechnology; Harvard University; Purdue University; University of California Riverside PI: Dr. Frank Collins, UND - VectorBaseVectorBase Invertebrate vectors of human pathogens: Anopheles gambiae, Aedes aegypti, Culex pipiens, Ixodes scapularis SRA International; University of Wisconsin Madison PI: Dr. John Greene, SRA - ERIC Yersinia pestis, Diarrheagenic E. coli, Yersinia enterocolitica, Shigella, SalmonellaERIC Virginia Bioinformatics Institute (VBI); Loyola University Medical Center; Social and Scientific Systems; University of Maryland PI: Dr. Bruno Sobral, VBI - PATRICPATRIC Rickettsiae species, Brucella species, Coxiella burnetii, Calicivirus, Hepatitis A virus, Rabies virus, Lyssavirus, Coronavirus University of Alabama Birmingham (UAB); University of Victoria, Canada PI: Dr. Elliot Lefkowitz, UAB - VBRCVBRC Variola major virus, Arenavirus, Hanta virus, Rift Valley fever virus, Ebola virus, Marburg virus, Dengue virus California encephalitis group virus, Kyasanar forest disease virus, Omsk hemorrhagic fever virus, West Nile virus, Alphavirus, Hantaan virus, Puumala virus, Crimean-Congo hemorrhagic fever virus, Yellow fever virus, Tick-borne encephalitis, Nipah virus, Equine morbillivirus Northrop Grumman; University of Texas Southwestern Medical Center (UTSMC); Vecna Technologies; Amar International PI: Dr. Richard Scheuermann, UTSMC - BioHealthBase Francisella tularensis, Giardia lamblia, Microsporidia, Ricinus communis, Multi-drug resistant Mycobacterium tuberculosis, Influenza virus University of Chicago (UC); Fellowship for Interpretation of Genomes; University of Illinois Urbana-Champaign PI: Prof. Rick Stevens, UC - NMPDRNMPDR Staphylococcus aureus, pathogenic vibrios, Listeria monocytogenes, Campylobacter jejuni, Streptococcus pyogenes, Streptococcus pneumoniae

BRC-Central

BRCs services to the scientific community  Computational Annotation  Data curation (genes, pathways, literature)  Comparative genomics and intra-species variation  Phylogenic analysis  Integration with other datasets (genomics, gene expression, proteomics)  Training and workshops (ApiDB, NMPDR)

General Challenges for the BRCs  Demostrate BRCs added value to the scientific community Improvements to the Genbank/EMBL annotations Integration of a variety of genomic data types  Collaborations with developers of ‘products’ in the biodefense community Lists of therapeutic targets  Outreach to the community of organism experts and bench scientists SWG members can help  Customize genomics information to meet the needs of the community – there is a lack of specification and requirements