Biowebdb.org - News

Contents 1 BiowebDB in Brazil 2 Aims 3 Developments 4 Platform 5 In house software 6 Third party software 7 BiowebDB feeds 7.1 BiowebDB Feeds Implemented 7.2 Comparative genomics literature 8 Third party feeds 9 Comparative genomics literature feeds 10 Biotech news 11 Most relevant BiowebDB publications BiowebDB in Brazil 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 nearly 4000 visits a month, mostly from Brazil, USA and some parts of Europe.

BiowebDB at FIOCRUZ At FIOCRUZ, BiowebDB is the official "Comparative Genomics" multi-user platform of the Oswaldo Cruz Institute and coordinated by Dr. Alberto Dávila.

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

In house software Genomic Analyses Resources for Sequence Annotation (GARSA) : http://garsa.biowebdb.org System for Integrated Genomic Resources and Analysis (STINGRAY) : http://stingray.biowebdb.org ProtoGIM : http://protogim.biowebdb.org ProtozoaDB : http://protozoadb.biowebdb.org

Third party software Primer3 : http://primer3plus.biowebdb.org Weblogo : http://weblogo.biowebdb.org ReadSeq : http://readseq.biowebdb.org EMBOSS : http://emboss.biowebdb.org

BiowebDB feeds

News about BiowebDB

BiowebDB Feeds Implemented

All news about BiowebDB will be available by RSS from now --Davila 14:15, 16 June 2008 (UTC)

Comparative genomics literature

Feeds on comparative genomics papers available in the literature has been added to the frontpage --Davila 14:15, 16 June 2008 (UTC)

Third party feeds

Comparative genomics literature feeds LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites Use of machine learning algorithms to classify binary protein sequences as highly-designable or poorly-designable mtDNAmanager: a Web-based tool for the management and quality analysis of mitochondrial DNA control-region sequences Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database Specific alignment of structured RNA: stochastic grammars and sequence annealing The Protein Feature Ontology: a tool for the unification of protein feature annotations Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications Genome annotation in the presence of insertional RNA editing Direct mapping and alignment of protein sequences onto genomic sequence Improving subcellular localization prediction using text classification and the gene ontology F-Seq: a feature density estimator for high-throughput sequence tags GOfetcher: a database with complex searching facility for gene ontology varDB: a pathogen-specific sequence database of protein families involved in antigenic variation Genomic characterization of putative allergen genes in peach/almond and their synteny with apple ArrayPlex: distributed, interactive and programmatic access to genome sequence, annotation, ontology, and analytical toolsets From sequence to structure to networks Human SWI/SNF directs sequence-specific chromatin changes on promoter polynucleosomes Amino acid sequence variations in Nicotiana CRR4 orthologs determine the species-specific efficiency of RNA editing in plastids Testing the palindromic target site model for DNA transposon insertion using the Drosophila melanogaster P-element A novel DNA sequence periodicity decodes nucleosome positioning Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers Serial analysis of mutation spectra (SAMS): a new approach for the determination of mutation spectra of site-specific DNA damage and their sequence dependence Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major Accurate prediction of protein?protein interactions from sequence alignments using a Bayesian method Validating Annotations for Uncharacterized Proteins in Shewanella oneidensis IMGT, a system and an ontology that bridge biological and computational spheres in bioinformatics Recent developments in the MAFFT multiple sequence alignment program MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences ROC analysis: applications to the classification of biological sequences and 3D structures Significance of Gapped Sequence Alignments Analyzing Protein-Protein Spatial-Temporal Dependencies from Image Sequences Using Fuzzy Temporal Random Sets The SWAN biomedical discourse ontology An ontology-driven semantic mashup of gene and biological pathway information: Application to the domain of nicotine dependence Towards an ontology for sharing medical images and regions of interest in neuroimaging yOWL: An ontology-driven knowledge base for yeast biologists Dynamic sub-ontology evolution for traditional Chinese medicine web ontology

Biotech news Epigenomics AG and Abbott Molecular Inc. Expand Strategic In Vitro Diagnostics Partnership Woolly-mammoth Genome Sequenced DNA Chunks, Chimps And Humans: Marks Of Differences Between Human And Chimp Genomes Pacific BioSciences: Rapid DNA Test Could Reveal Patient Genome in Minutes Some Day

Most relevant BiowebDB publications

• ProtozoaDB: dynamic visualization and exploration of protozoan genome. Nucleic Acids Res. 2008 Jan;36(Database issue):D547-52. [PubMed]

• OrthoSearch: A Scientific Workflow Approach to Detect Distant Homologies on Protozoans. In: ACM Symposium on Applied Computing, 2008, Fortaleza. ACM SAC 2008, 2008. v. II. p. 1281-1285. [Bio-2, Page 10]

• Improving model construction of profile HMMs for remote homology detection through structural alignment Improving model construction of profile HMMs for remote homology detection through structural alignment. BMC Bioinformatics, v. 8, p. 435, 2007.

• In Services: Data Management for In Silico Workflows. In: 17th International Workshop on Database and Expert Systems Applications (DEXA 2006), 2006, Cracóvia - Polônia. DEXA Workshops, 2006. p. 206-210. [IEEEXplore]

• Managing Structural Genomic Workflows using Web Services. Data & knowledge engineering, Holanda, v. 53, n. 1, p. 45-74, 2005. [ACM] [Elsevier]

• GARSA: genomic analysis resources for sequence annotation. Bioinformatics. 2005 Dec 1;21(23):4302-3. Epub 2005 Oct 6. [PubMed] [HubMed]

• Trypanosoma rangeli Transcriptome Project: Generation and analysis of expressed sequence tags. Kinetoplastid Biol Dis. 2004; 3(1):1. [PubMed] [HubMed]

• A Distribution Design Methodology for Object DBMS. Distributed and Parallel Databases, Kluwer Academic Publishers, v. 16, n. 1, p. 45-90, 2004. [Springer]

• 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]

• Comparative genomics to uncover the secrets of tsetse and livestock-infective trypanosomes. Trends Parasitol. 2003, 19(10):436-9. [PubMed] [HubMed]

• Response to Hertz-Fowler and Berriman: Continuing tsetse and Trypanosoma genome sequencing projects, Trends in Parasitology, 2003 [Elsevier]

• Bioinformatics in developing countries: how many tools are needed? 7th Internet World Congress for Biomedical Sciences, INABIS 2002 [PDF]