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.
Finally, we recently orgaized an International Systems Biology Course and created a Systems Biology blog for that.
Platform
Publications
- G-orthomcl: grid-based OrthoMCL for the identification of orthologous genes X-meeting 2009
- ARPA: Automatic reconstruction of phylogenomic analysis X-meeting 2009
- Exploring PKS domains diversity present in environmental database using hmm profiles X-meeting 2009
- Preliminar study and mining of chitinases in environmental metagenome X-meetig 2009
- An integrated system for the genotyping of parasitic protozoan based on universal orthologous genes X-meeting 2009
- Faceweb: a platform to support the execution and monitoring of workflows on the web X-meeting 2009
- Detecting Distant Homologies on Protozoans metabolic pathways using scientific workflows. International Journal of Data Mining and Bioinformatics, 2009. [In press]
- Transcriptome analysis of Taenia solium cysticerci using Open Reading Frame ESTs (ORESTES). Parasit Vectors. 2009 Jul 31;2(1):35. [PubMed]
- EST sequencing of blood-fed and Leishmania-infected midgut of Lutzomyia longipalpis, the principal visceral leishmaniasis vector in the Americas. Mol Genet Genomics. 2009 Sep;282(3):307-17. [PubMed]
- OrthoSearch: a scientific workflow approach to detect distant homologies on protozoans - [ACM/SAC08 ACM/SAC08 ]
- ProtozoaDB: dynamic visualization and exploration of protozoan genomes. Nucleic Acids Res. 2008 Jan;36(Database issue):D547-52. [PubMed]
- Improving model construction of profile HMMs for remote homology detection through structural alignment. BMC Bioinformatics. 2007 Nov 9;8:435. [PubMed ]
- 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.
