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Bioinformatics Resource Days
Barcelona, Spain. November 26-28, 2007
November 26-27
Vertex Building
Sala d'actes
Floor -1
November 28
Auditorium
This three-day workshop is aimed at scientists at all levels who want to increase their knowledge of the bioinformatics tools available for use in their research activities. The first two days will be dedicated to the "EBI Bioinformatics Roadshow", organized and led by instructors from the European Bioinformatics Institute of the European Molecular Biology Laboratory. The third day will be devoted to a hands-on look at the resources offered by the Spanish National Bioinformatics Institute(INB).
1. EBI Bioinformatics Roadshow
The Bioinformatics Roadshow aims to address the needs of European scientists for hands-on bioinformatics training. The roadshow combines presentations and hands-on practical sessions where users are lead through.
This particular Roadshow will explore some of the main resources and tools at the EBI along several levels of the life: from sequences to systems biology. In particular you will learn about, how to use and when to use:
- Genomics Resources: Ensembl, Integr8, Genome Review and Biomart
- Proteomics Resources: UniProt, InterPro, Intact, PRIDE, CheBi, International Protein Index
- Structural Biology: MSD, ProFunc and PDBsum
- Expression Data: ArrayExpress (Repository and Warehouse)
- Pathways: Reactome
Resources covered:
Ensembl – www.ensembl.org
A genomic sequence database providing a comprehensive and integrated source of annotation of mainly vertebrate genome sequences.
BioMart – www.biomart.org
A query-oriented data management system used for data-mining biological databases, for example, extracting genomic information from Ensembl.
Integr8 – wwww.ebi.ac.uk/integr8/
A web portal that provides access to integrated information about deciphered genomes and corresponding transcriptomic and proteomic data. Data are integrated from several resources including EMBL-Bank, Genome Reviews, Ensembl, UniProt Knowledgebase and International Protein Index (IPI).
Genome Reviews – www.ebi.ac.uk/GenomeReviews/
A database of completely deciphered genomes of archaea, bacteria, bacteriophages and selected eukaryotes.
MSD – wwww.ebi.ac.uk/msd
The EBI’s Macromolecular Structure Database (MSD) is Europe’s representative in the Worldwide Protein Data Bank. It contains structural data from crystallography, nuclear magnetic resonance spectroscopy and electron microscopy experiments, in addition to derived information linking structure to biochemical function, protein sequence and taxonomy.
ProFunc – www.ebi.ac.uk/thornton-srv/databases/profunc/index.html
ProFunc is a server that helps you to determine the biological function of a protein from its 3D structure.
PDBsum – www.ebi.ac.uk/thornton-srv/databases/pdbsum/
PDBsum is a structural database that contains schematic diagrams of every macromolecular structure in the Protein Data Bank (PDB).
InterPro – www.ebi.ac.uk/interpro/
InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences. The database can be queried with both protein and nucleic acid sequence data.
PRIDE – www.ebi.ac.uk/pride/
The Proteomics Identifications Database is a public data repository for proteomic identifications and associated mass spectra, linked to supporting publications.
International Protein Index – www.ebi.ac.uk/ipi/
IPI is an access mechanism to several source databases containing information on the proteomes of higher eukaryotic organisms.
ArrayExpress – www.ebi.ac.uk/arrayexpress
EMBL-EBI’s MIAME-compliant repository for gene expression data from microarray and transcriptomics experiments (MIAME - Minimum Information About a Microarray Experiment).
Reactome – www.reactome.org
Reactome is a collaborative project to develop a curated resource of key pathways and reactions in human biology. The information held in the database is cross-referenced with various EBI resources including Ensembl and UniProt.
2. Spanish National Bioinformatics Institute (INB)
Resources covered
INB web services and workflows (A. Valencia’s group):
- CARGO - http://cargo.bioinfo.cnio.es/
A web system for the analysis of Cancer and Related Gene lists, where information is dynamically extracted from distributed databases and web services using a technology similar to the one of the popular Google and Apple widgets.
- Taverna – http://taverna.sourceforge.net/
A tool that allows a biologist or bioinformatician with limited computing background and limited technical resources and support to construct highly complex analyses over public and private data and computational resources, all from a standard PC, UNIX box or Apple computer.
- INB web services – http://www.inab.org/en/resources.htm
A compilation of available resources for automation of common bioinformatics operations, offered via the INB.
Building and editing workflows for genome analysis annotation (A. Valencia’s + R. Guigo’s groups):
- GENID - http://www1.imim.es/software/geneid/
A program to predict genes in anonymous genomic sequences designed with a hierarchical structure.
- DAS – the Distributed Annotation System (DAS) defines a communication protocol used to exchange biological sequence annotations. It is motivated by the idea that such annotations should not be provided by single centralized databases, but should instead be spread over multiple sites. Data distribution, performed by DAS servers, is separated from visualization, which is done by DAS clients.
- GBrowse - displays a graphical representation of a section of a genome, and shows the positions of genes and other functional elements. It can be configured to show both qualitative data such as the splicing structure of a gene, and quantitative data such as microarray expression levels.
Analysis of DNA arrays (J. Dopazo's group):
- GEPAS - http://www.gepas.org
The Gene Expression Pattern Analysis Suite is an integrated web-based pipeline for the analysis of gene expression patterns, including tools for normalization, clustering, differential gene expression, predictors, array CGH and functional annotation. - Babelomics - http://www.babelomics.org
A complete suite of web tools for functional profiling of microarray experiments and other high-throughput data, which include different classes of relevant biological information such as functional (GO, KEGG, Biocarta, etc.), regulatory (TFBS, miRNAs, etc.) and protein interactions.
INB text mining suite (F. Leitner/Martin Krallinger):
- iHop – http://www.ihop-net.org/UniPub/iHOP/
The Information Hyperlinked over Proteins tool provides this network as a natural way of accessing millions of PubMed abstracts. By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource, bringing all advantages of the internet to scientific literature research.
- Biocreative metaserver - http://biocreative.sourceforge.net/
(inspired in DAS) Integrating predictions of multiple teams as online systems, allowing human and machine access (web-services).
Venue: The workshop will take place at the Universitat Politecnica de Catalunya.
Registration: Sala d'Actes (floor -1)
Courses: Rooms VS 208 and VS210
Edifici Vertex
Campus Nord de la UPC
Plaça Eusebi Güell, 6
Barcelona
Registration: Deadline for registration: October 19, 2007
Workshop participation limited to 80. Participants will be notified of their acceptance.
There is a nominal registration fee of 100 euros for this course (applicable to participants not from one of the organizing insitutes), which includes training, course materials, lunches and coffee breaks. Please only transfer the course fee once you have received confirmation that you have been accepted.
Cancellation policy: For cancellation after the deadline full course costs will be charged unless a replacement can be found.
Organised by the Institute for Research in Biomedicine (IRB Barcelona) and the Barcelona Supercomputing Center through the joint programme on computational biology, with the collaboration of the Banco Bilbao Vizcaya Argentaria Foundation.
For more information, please contact the Barcelona BioMed Secretariat at biomed
irbbarcelona.org
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