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Presentation of the National Institute for Bioinformatics (INB)

Presentation of the National Institute for Bioinformatics (INB). Pharmacogenomics and Pharmacogenetics: Current Challenges and Bioinformatics support. Barcelona, 11-12 July 2005. Instituto Nacional de Bioinformática National Institute for Bioinformatics (INB). Una plataforma de Genoma España

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Presentation of the National Institute for Bioinformatics (INB)

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  1. Presentation of the National Institute for Bioinformatics (INB) Pharmacogenomics and Pharmacogenetics: Current Challenges and Bioinformatics support Barcelona, 11-12 July 2005

  2. Instituto Nacional de BioinformáticaNational Institute for Bioinformatics(INB) Una plataforma de Genoma España A Genome Spain platform

  3. INB Mission “To generate and apply bioinformatics solutions to needs detected in development and implementation of genomics and proteomics focused projects” • To support Bioinformatics and Computational Biology development in Spain • To collaborate and provide scientific and technical support to national genomics and proteomics projects • To contribute to the creation and establishment of local Bioinformatics groups with research and services components through bioinformaticians training • To train bioinformaticians for genomics and proteomics research groups • To develop pure Bioinformatics projects related with the Institute activities • To support companies with activity in this sector in Spain • To internationalize all its activities

  4. INB Potential Partners • Bioinformaticians (particularly small groups) • Resources (software and hardware) • Expertise and training Genomics projects and platforms (the one bioinformatician problem) - Integrated analysis - Organized analysis paths - Access to experts Companies - Portfolio of projects and services - Enabling participation in projects - Access to expertise and training Biologist in general -Access to integrated services - Facilitated access to training activities International Consortiums - A reliable partners with a wide expertise range

  5. Recursos Computacionales 2(GHNC-PCM) Jose M. Carazo Natalia Jimenez Enrique de Andres Philippe Mazzerand Organigrama Recursos Computacionales 1(GNHC-UPC) Xavier Messeguer Roman Rosset Alexis Torrano David Garcia (*) Carlos Pons (*) Javier Vera (*) Jordi Campos (*) NODO CENTRAL Alfonso Valencia Federico MoranDavid Gonzalez Pisano Marta de la Riva Eduardo Leon (*) Acuerdo con el BSC GNV1Bioinformática y Genómica Roderic Guigo Arnaud Kerhornou Tayler Alioto Domenec Farré GNV2Bioinformática y Proteómica Alfonso Valencia Jose Manuel Rodriguez Jose M. Fernandez Iakes Ezkurdia GNV3Genómica Funcional Joaquin Dopazo David Montaner Jaime Huerta Joaquín Tárraga GNV4Bioinformática Estructural Modesto Orozco Leire Zamacolea Ivan Párraga Damian Blanco GNV5Bioinformática Integrada Oswaldo Trelles Sergio Ramirez Antonio J. Perez Ismael Navas, Mar Rojano Formación (GNHF) Ferrán Sanz (UPF) Fernando Martin (ISCIII) / Federico Moran (UCM) Nathalie Veronica Villahoz, Juan Antonio de los Cobos, Raquel Furió, Guillermo López (ISCIII), Teresa Díez (CNB / UCM)

  6. Parque Cientifico de Madrid 24 CPUs and 40Gb of shared memory

  7. BSC: The Consortium • Consortium includes • Spanish Government (MEC) • Catalonian Government (DURSI) • Technical University of Catalunya • To start operations on September, 2005 • Computational Biology Department Max. 20% capacity equivalent for the INB Access to expert resources Collaboration with the INB node in the BSC

  8. Training Node Ferrán Sanz - UPF Nodo Central -CNB Fernando Martín -ISCII

  9. ECCB05 European Conference in Computational Biology ECCB05 www.eccb05.org Sept 28 - 1 Oct 05 Fundacion BBVA Applied Biosystems BioMed Central Ltd Silicon Graphics Inc Merc and Co. Inc. USA Ministerio Educacion y Ciencia U. Complutense Madrid Fundacion Ramón Areces Biogen Idec Red nacional de Modelización

  10. Genomics projects Streptomyces (Martin) Aspergillus (Peñalva) Drosophila (Corominas) Pancreas (Real / Ferrer) Plataforms (Abril) Proteored (Albar/Mato/Carazo) SolES: Tomato Genomics (Granell) Associations Small companies in the topic Pharma/ Biotech INB: collaboration with projects, platform and associations

  11. runGeneID runFUNCut runPupaSNP runPMUTHotSpot Gene Finding Function Prediction SNP Mapping SNP to 3D Function Bioinformatics and Proteomics A. Valencia – CNB/CSIC Bioinformatics and F.Genomics J. Dopazo– CNIO Bioinformatics and Prot. Str. M. Orozco– PCB/UB Estructura Inicial de Recursos Users Genomic & Proteomic Platforms Genomic & Proteomic Projects Bioinformatics Pipeline Users and Developers Resources Access Programatic Access GUI/Web/Tools Access Computational Resources RunBlast INB BioMOBY Services Server RunFasta Integrated Bioinformatics O. Trelles – UMA RunClustalW Analysis MOBY Services MOBY Services Retrieval getfromUniProt Conversion getfromGenBank getInteractions fromAASeqtoFASTA fromStringtoSeq JM. Carazo – PCM Bioinformatics and Genomics R.Guigó – IMIM-CRG X.Messeguer – UPC/IBM fromXMLtoText DAS Annotations

  12. IBPrincipe Felipe / CEGEN Workflows for the analysis of SNPs(NV3) Problem 1: feed the monster. E.g. Illumina: 150.000 genotipes at a time Problem 3: query the database... Problem 2: store results... Computer-aided selection. PupaSNP and PupasView Conde et al. 2004, 2005, NAR Cancer SNPs DB server Experimental design (linkage, pathway, etc) ...and submit to analysis programs ...along with clinical data October 2004: 45.000 SNPs designed LD, Case-control, haplotypes, ODD ratios, etc.

  13. CNB-CSIC / U. Leon A. Homology Search Genome Annotation pipeline (application to the Streptomyces coelicolor genome JF Martin) - NV2 Query Protein Sequence Space BLAST ISS B. Sequence Space Mapping C. Automatic identification of groups. Clustering. D. Annotation Problem Protein Annotation Neighbor Groups Annotation by Osvaldo Graña

  14. Hoffmann Valencia Nat Genet 2004

  15. Relative entropy cut,del Sol, Valencia 2002 Mutational behaviour Pazos Valencia, 2001 Casari, Sander, Valencia Nature Str. Biol. 95 Pazos, Valencia 2003 Romero, Valencia submitted 05 Del Sol, Pazos, Valencia JMB 03 • The SQUARE server (Tress et al JMB 2004, Bioinformatics 2004) Server: TreeDet: a web server to explore the space of sequences. Rojas et al., 05www.pdg.cnb.uam.es/treedet

  16. Residues determinant of the dimerization of Chemokine receptors Two residues are able to control CCR5 chemokine receptor dimerization, both in vitro and in vivo blocking CCL5-induced responses in human cell lines and in primary T cells. Hernanz-Falcon, et al., Nat Immunol. 2004

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