EMBRACE Workshop Appled Gene Ontology ITB – CNR Bari, Italy 7. – 9. November 2007 Domenica D’Elia, Giulia De Sario, Andreas Gisel, Cecilia Saccone, Angelica.

Slides:

Advertisements

Similar presentations

Pre-SIG meeting " Genome Annotation" A BioSapiens initiative Goal of the workshop were - to create an open forum to discuss current problems on function.

Advertisements

GENOMICS MEETS GRID INTRODUCTION CHRIS THOMPSON. BACKGROUND SR £120M NATIONAL PROGRAMME ON e- SCIENCE £8M BBSRC PROGRAMME ON BIOINFORMATICS AND.

HCS806 “Methods in Horticulture and Crop Science” Introduction to methods in Bioinformatics for plant science. David Francis (Coordinator) Ian Holford.

EMBRACE Gene Ontology Workshop, 7 th – 9 th November 2007 Bari High throughput functional annotation and analysis with the Blast2GO suite Ana Conesa Bioinformatics.

The European Molecular Biology Laboratory (EMBL) is supported by sixteen countries. Consists of the main Laboratory in Heidelberg (Germany), Outstations.

The design, construction and use of software tools to generate, store, annotate, access and analyse data and information relating to Molecular Biology.

Global Alignment and Collaboration Jo

Bioinformatics and the Engineering Library ASEE 2008 Amy Stout.

Bioinformatics for biomedicine Summary and conclusions. Further analysis of a favorite gene Lecture 8, Per Kraulis

Overview of Biomedical Informatics Rakesh Nagarajan.

Protein databases Morten Nielsen. Background- Nucleotide databases GenBank, National Center for Biotechnology Information.

Archives and Information Retrieval

Protein Databases EBI – European Bioinformatics Institute

The Cell, Central Dogma and Human Genome Project.

NICLS: Development of Biomedical Computing and Information Technology Infrastructure Presented by Simon Sherman August 15, 2005.

Scientific Data Mining: Emerging Developments and Challenges F. Seillier-Moiseiwitsch Bioinformatics Research Center Department of Mathematics and Statistics.

Protein databases Henrik Nielsen. Background- Nucleotide databases GenBank, National Center for Biotechnology Information.

Bioinformatics. Analysis of proteomic data. Dr Richard J Edwards 28 August 2009; CALMARO workshop. ©Gary Larson (In not much detail)

Class European Resources Protein Focused. Protein Databases EBI – European Bioinformatics Institute

ExPASy - Expert Protein Analysis System The bioinformatics resource portal and other resources An Overview.

An Introduction to Bioinformatics Molecular Biology Databases.

Login: BITseminar Pass: BITseminar2011 Login: BITseminar Pass: BITseminar2011.

Bioinformatics Grid Application for Life Science. COMMUNICATION NETWORK DEVELOPMENT SPECIFIC SUPPORT ACTION BIOINFOGRID Luciano Milanesi CNR-ITB.

 The institute started in 1989 as a UNDP funded project called the National Agricultural Genetic Engineering Laboratory (NAGEL).  The Agricultural.

Ch10. Intermolecular Interactions and Biological Pathways

Bioinformatics.

Institute of Systems Biology (INBIOSIS)/ School of Biosciences & Biotechnology (Faculty of Science & Technology), Bioinformatics Development in Malaysia.

Databases in Bioinformatics and Systems Biology Carsten O. Daub Omics Science Center RIKEN, Japan May 2008.

Introduction to databases Tuomas Hätinen. Topics File Formats Databases -Primary structure: UniProt -Tertiary structure: PDB Database integration system.

Network Services for Biologists in the Genome Era The Work of the European Bioinformatics Institute.

© What do bioinformaticians do?

EMBRACE Web Services Taavi Hupponen CSC – Center for Scientific Computing, Finland BOSC 2007.

EBI as a research infrastructure Graham Cameron, EBI.

Biological Databases and Tools Sandra Sinisi / Kathryn Steiger November 25, 2002.

INFSO-RI Enabling Grids for E-sciencE V. Breton, 30/08/05, seminar at SERONO Grid added value to fight malaria Vincent Breton EGEE.

Grup.bio.unipd.it CRIBI Genomics group Erika Feltrin PhD student in Biotechnology 6 months at EBI.

Gene Ontology TM (GO) Consortium Jennifer I Clark EMBL Outstation - European Bioinformatics Institute (EBI), Hinxton, Cambridge CB10 1SD, UK Objectives:

Biological Databases Biology outside the lab. Why do we need Bioinfomatics? Over the past few decades, major advances in the field of molecular biology,

EMBL-EBI EMBL-EBI EMBL-EBI What is the EBI's particular niche? Provides Core Biomolecular Resources in Europe –Nucleotide; genome, protein sequences,

Ontologies GO Workshop 3-6 August Ontologies  What are ontologies?  Why use ontologies?  Open Biological Ontologies (OBO), National Center for.

EMBRACE An example of Grid Integration (I): The EMBRACE project Jean SALZEMANN CNRS/IN2P3.

Bioinformatics Core Facility Guglielmo Roma January 2011.

INFSO-RI Enabling Grids for E-sciencE Status of the Biomedical Applications in EELA Project (E-Infrastructures Shared Between Europe.

Protein Information Resource Protein Information Resource, 3300 Whitehaven St., Georgetown University, Washington, DC Contact

Renaissance Computing Institute: An Overview Lavanya Ramakrishnan, John McGee, Alan Blatecky, Daniel A. Reed Renaissance Computing Institute.

Alvis Brazma, Johan Rung, Ugis Sarkans, Thomas Schlitt, Jaak Vilo European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge,

Building WormBase database(s). SAB 2008 Wellcome Trust Sanger Insitute Cold Spring Harbor Laboratory California Institute of Technology ● RNAi ● Microarray.

ACGT: Open Grid Services for Improving Medical Knowledge Discovery Stelios G. Sfakianakis, FORTH.

 Our mission Deploying and unifying the NMR e-Infrastructure in System Biology is to make bio-NMR available to the scientific community in.

2009 IADR, MIAMI, FL, USA Hands-on Experience for using the Human Oral Microbiome Database (HOMD) 2009 IADR Workshop, Miami, FL, USA Tsute (George) Chen.

Introduction to the Gene Ontology GO Workshop 3-6 August 2010.

Algorithms for Biological Sequence Analysis Kun-Mao Chao ( 趙坤茂 ) Department of Computer Science and Information Engineering National Taiwan University,

XML-Based Grid Data System for Bioinformatics Development Noppadon Khiripet, Ph.D Wasinee Rungsarityotin, MS Chularat Tanprasert, Ph.D Royol Chitradon.

Biomedical and Bioscience Gateway to National Cyberinfrastructure John McGee Renaissance Computing Institute

GeWorkbench Overview Support Team Molecular Analysis Tools Knowledge Center Columbia University and The Broad Institute of MIT and Harvard.

ArrayExpress - a Public Repository for Microarray Based Gene Expression Data European Bioinformatics Institute - EMBL outstation and German Cancer Research.

Dasty2 DAS workshop th March Rafael Jimenez.

An Introduction to NCBI & BLAST National Center for Biotechnology Information Richard Johnston Pasadena City College.

High Risk 1. Ensure productive use of GRID computing through participation of biologists to shape the development of the GRID. 2. Develop user-friendly.

EMBL- EBI Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK The BioInvestigation Index – Standards and Infrastructure for Omics Data Philippe.

Milanesi Luciano Catania, Italy 13/03/2007 Bioinformatics challenges in European projects in Grid. Milanesi Luciano National Research Council Institute.

Bioinformatics Grid Application for Life Science. COMMUNICATION NETWORK DEVELOPMENT SPECIFIC SUPPORT ACTION BIOINFOGRID Andreas Gisel & Luciano Milanesi.

Lecture 1.01 Developing the Tools Montreal 2004 Course Introduction John J. Salama.

J. Douglas Armstrong Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh. Bioinformatics at Edinburgh.

Tutorial on GRID computing

Archives and Information Retrieval

생물정보학 Bioinformatics.

Insight into GO and GOA Angelica Tulipano , INFN Bari CNR

Plans for LHC computing in Spain

SUBMITTED BY: DEEPTI SHARMA BIOLOGICAL DATABASE AND SEQUENCE ANALYSIS.

Presentation transcript:

EMBRACE Workshop Appled Gene Ontology ITB – CNR Bari, Italy 7. – 9. November 2007 Domenica D’Elia, Giulia De Sario, Andreas Gisel, Cecilia Saccone, Angelica Tulipano

Institute of Biomedical Technologies (ITB) – Bari, CNR The main research projects of ITB are focused on: SPECIALIZED DATABASES ALGORITHMS AND SOFTWARE FOR GENOME ANALYSIS MOLECULAR BIODIVERSITY AND DNA BARCODE COMPARATIVE GENOMICS AND EVOLUTION OF GENE FAMILIES GRID RESEARCH IDENTIFICATION OF P53 GENE FAMILY DIRECT TARGET GENES BY IN SILICO AND MICROARRAY APPROACHES

EMBRACE European Model for Bioinformatics Research and Community Education Work packages Content Integration Integration of the major databases such as EMBL, SwissProt, TrEMBL, PDB, ArrayExpress, GO, GOA and specific DBs developed by members Tool Integration Integration of bioinformatics tools such as BLAST, MultiBLAST, EMBOSS, and specific tools provided from the community Technology assessment and adoption Assessing the middleware solutions available and the IT trends such as Grid Computing Test-problems In close collaboration with experimental laboratories to test and prove the Network Outreach The aim is to enable bioinformatics research through better interoperability of servers, database, and services. Network of Excellence

Wednesday 7. November 2007 Introduction Cecilia Saccone ITB-CNR, Bari, Italy Ontology: An Introduction Claudia d'Amato Department of Informatics, University of Bari, Italy Gene Ontology Midori Harris EBI, Hinxton, GB GOA: Looking after GO annotations Emily Dimmer EBI, Hinxton, GB (UniProt GOA project) Insight into GO and GOA Andreas Gisel ITB-CNR Bari, Italy GO Browsers: AmiGO Erika Feltrin CRIBI, University of Padova, Italy Thursday 8. November 2007 Gene Analogue Finder Angelica Tulipano / Giulia De Sario INFN Bari, Italy / ITB-CNR Bari, Italy GO Annotation tools: GoPubMed Andreas Doms Biotech TU Dresden, Germany GO Microarray tools: GOToolBox David Martin Genome bioinformatics lab, Center for Genomic Regulation, Barcelona, Spain Friday 9. November 2007 GO Other tools: Blast2GO Ana Conesa Bioinformatics Department,Centro de Investigacion Principe Felipe, Valencia, Spain Collaborative tagging for GO Domenico Gendarmi Department of Informatics, University of Bari, Italy Final Discussion Final programme