BiowebDB in Brazil
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| The BiowebDB consortium was created in 2003 and initially funded by CNPq in 2004. While it involves several Brazilian universities and research institutes, its multi-user "Comparative genomics" platform is physically hosted at the Oswaldo Cruz Institute, FIOCRUZ. Its portal and tools receive many visits a month, mostly from Brazil, USA and some parts of Europe.
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BiowebDB at FIOCRUZ
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| At FIOCRUZ, BiowebDB is the official "Comparative Genomics" multi-user platform of the Oswaldo Cruz Institute and coordinated by Dr. Alberto Dávila.
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Aims
Comparative approaches involving the integrative use of heterogeneous databases, analyses tools, distributed computing and (re)annotation system as well as sensitive similarity detection algorithms have been catalyzed by a variety of sequenced genomes. The BiowebDB consortium has initially established collaborations with GeneDB and TcruziDB. Aiming to build an integrated, user-friendly and flexible multi-user platform, capable to deal with different datasets and genome projects, BiowebDB's platform is being designed to provide interoperability among different analyses tools and more sensitive algorithms for distant homology detection. It centers on the use of ontology based metadata, XML, Web services, as well as a combination of Hidden Markov Models with AI technologies for algorithm improvement. The BiowebDB multi-user platform is being progressively implemented and is publicly available at http://www.biowebdb.org.
Developments
Since its creation the BiowebDB consortium aimed to establish collaborations with several groups to complement and spread its researches and activities. Some international events as the International Workshops on Genomics Databases [ IWGD ] and EMBO Courses [ EMBO ] has been organized during the last years. Also, the consortium has been instrumental in the creation of (a) the Graduate Program on Computational and Systems Biology at FIOCRUZ and (b) the Rio de Janeiro Network for Computational and Systems Biology : http://rbcs.biowebdb.org as well as supporting the Comparative genomics and proteomics of pathogenic trypanosomatids project funded by FINEP. More recently, several member institutes of BiowebDB joined a European-funded project for grid development [ EELA-2 ] in several areas, including Bioinformatics.
Platform
Publications
- Comparative genomics to uncover the secrets of tsetse and livestock-infective trypanosomes. Trends Parasitol. 2003, 19(10):436-9. [PubMed] [HubMed]
- Bioinformatics in developing countries: how many tools are needed? 7th Internet World Congress for Biomedical Sciences, INABIS 2002
- Response to Hertz-Fowler and Berriman: Continuing tsetse and Trypanosoma genome sequencing projects
- Trypanosoma rangeli Transcriptome Project: Generation and analysis of expressed sequence tags. Kinetoplastid Biol Dis. 2004; 3(1):1. [PubMed] [HubMed]
- Report of a consultation on prioritites and strategies for analysis and exploitation of the genomes of Trypanosoma vivax, T. congolense and tse-tse
- Tropical diseases, pathogens, and vectors biodiversity in developing countries: need for development of genomics and bioinformatics approaches. Ann N Y Acad Sci. 2004, 1026:41-6. [PubMed] [HubMed]
- Exploring the genome of Trypanosoma vivax through GSS and in silico comparative analysis. OMICS. 2005 Spring;9(1):116-28. [PubMed] [HubMed]
- GARSA: genomic analysis resources for sequence annotation. Bioinformatics. 2005 Dec 1;21(23):4302-3. Epub 2005 Oct 6. [PubMed] [HubMed]
- An Agent-oriented Notification System for Sequence (Re) Annotation in Genomic Databases. WTDBD. 2005. [WTDBD2005]
- Intermediate Data Management for In-Silico Workflows Using Web Services. WTDBD. 2005. [WTDBD2005]
- Managing Annotation Notification and Scientific Workflow Execution in Genomic Databases. IWGD. 2005. [IWGD2005]
Please see documentation on customizing the interface
and the User's Guide for usage and configuration help.
