SME Bioinformatics Forum, Barcelona
The full list of sponsors and sponsoring projects are:
We would also like to acknowledge support from the European Council of Bioregions, www.cebr.net and UK Trade & Investment www.ukti.gov.uk for disseminating information about this event to member organisations.
All tools and services provided by EMBL-EBI are available free of charge. For more information about EMBL-EBI, see our website: www.ebi.ac.uk. For more information about support for SMEs, see: www.ebi.ac.uk/industry/SME/
The EMBL-European Bioinformatics Institute is the outstation of EMBL with the primary responsibility of providing bioinformatics services to European researchers. Our mission is:
- To provide freely available data and bioinformatics services to all facets of the scientific community in ways that promote scientific progress
- To contribute to the advancement of biology through basic investigator-driven research in bioinformatics
- To provide advanced bioinformatics training to scientists at all levels, from PhD students to independent investigators
- To help disseminatecutting-edge technologies to industry
- To coordinatebiological data provision across Europe
As part of our support for industry, we have established an annual series of information workshops based in various locations across Europe. These workshops are designed to allow SMEs to hear about molecular and genomic databases and services that are provided freely by EMBL-EBI and our collaborators, to understand the international data sharing agreements underlying these data resources and the road map for future developments.
Biocat is the cluster organization that coordinates biotechnology and medical technologies in Catalonia, the main bioregion of Spain. It promotes relationships and synergies among the BioRegion of Catalonia stakeholders, that include more than 481 companies (biotech, pharma and services), 449 research groups on life sciences, 80 related research centers, 19 science and technology parks focused in biomedicine, 12 universities offering studies in life sciences and 15 big research hospitals. Catalonia also has 9 high level scientific and technological big infrastructures created during the last years.
The BioRegion of Catalonia has become one of the great biotechnology hubs in Spain and an outstanding cluster in Southern Europe. As a group, Catalan biotech companies have an estimated turnover of €15,600 million per year, which accounts for 29.4% of the national total in the sector. By number of companies, Catalonia is ranked second in Spain, with 20.5% of the total, only behind Madrid, and first with regard to the creation of new companies, with 23% of the total in 2010. Furthermore, capitalization of Catalan companies in the sector has tripled in the past two years and reached €2,357 million in 2010, mostly from private sources.
The Spanish National Bioinformatics Institute (‘Instituto Nacional de Bioinformática’ in Spanish, or short INB) is an institutional platform founded in 2003 by the mayor bioinformatics research groups in Spain with financing from Genome Spain (‘Genoma España’ ). It is now part of the Carlos III Health Institute (‘Instituto de Salud Carlos III‘ or ISCIII) and its overarching mission is to disseminate and provide bioinformatics support to laboratories, research institutions and companies throughout Spain. The INB serves in the coordination, integration and development of Spanish bioinformatics resources in projects in the areas of genomics, proteomics and translational medicine. It has contributed to the creation of a consistent computational infrastructure in the area of bioinformatics, participated in national and international genome projects, and trained bioinformatics users and developers.
The Research Programme on Biomedical Informatics (GRIB) is a joint research group of IMIM-Hospital del Mar Research Institute and Universitat Pompeu Fabra (UPF). The GRIB carries out fundamental research and technological developments on the application of advanced information technologies and computational methods in the health and life sciences. GRIB brings together a multidisciplinary team of more than seventy scientists.
The workshop will introduce bioinformatics tools and data resources and will present the opportunities for SMEs to use and integrate these resources in order to derive business benefit from the existing and developing infrastructure.
The topics of the workshop have been specifically selected on the basis of previous interactions with SMEs, priorities specified by SMEs as part of a recent user survey and discussions with a regional focus group. The data resources and services include:
- Genomic resources: the Ensembl genome browser and the European Nucleotide Archive (ENA)
- Proteomics resources: UniProt and InterPro
- Chemical resources: the ChEMBL database, ChEBI and MetaboLights
- Functional genomics: ArrayExpress and the Gene Expression Atlas
- Molecular interactions: the Protein Data Bank (PDB) and ligand information
- The Enzyme Portal
- Integration services and EBI Search
- Web services
There will also be an opportunity to hear from several companies based in the region and for some hands-on tutorials. The registration costs for the workshop have been highly subsidised through the sponsorship of EMBL-EBI (a non-profit intergovernmental organisation).
| Time | Item | Speaker |
|---|---|---|
| Monday 8 October 2012 | ||
| PRBB Auditorium, Barcelona Biomedical Research Park | ||
| 12:00 | Registration and refreshments | |
| 13:10 |
Welcome from BioCat and GRIB | Montserrat Vendrell (BioCat) & Ferran Sanz (GRIB) |
| 13:30 | SME workshop overview | Dominic Clark, Industry Programme Manager (EMBL-EBI) |
| 13:40 | Overview of EMBL-EBI’s data resources and services | Katrina Pavelin, Scientific Engagement Officer (EMBL-EBI) |
| 14:00 | Overview of EMBL-EBI’s Web Services with worked examples | Andrew Cowley, Bioinformatics Trainer (EMBL-EBI) |
| 14:30 | Genomics: Ensembl and the ENA. High level overview and use cases | Denise Carvalho-Silva, Ensembl User Support Officer (EMBL-EBI) |
| 15:15 | Coffee break |
|
| 15:45 | Functional genomics: High level overview and use cases | Emma Hastings, ArrayExpress Curator (EMBL-EBI) |
| 16:15 | Proteins: UniProt and proteomics services (including Reactome) | Sandra Orchard, Proteomics Services Team Coordinator (EMBL-EBI) |
| 16:45 | The PSIMEX Project: Proteomics Standards Initiative and International Molecular Exchange | Sandra Orchard, Proteomics Services Team Coordinator (EMBL-EBI) |
| 17:00 | Chemical resources (structure, bioactivity and metabolomics): ChEMBL, ChEBI, MetaboLights and the Enzyme Portal | Pablo Conesa Mingo Software Engineer (EMBL-EBI) Anne Hersey, ChEMBL Coordinator (EMBL-EBI) |
| 18:00 | Bringing Structure to Biology: small molecules and PDBe | Gary Battle PDBe Outreach Coordinator (EMBL-EBI) |
| 18:30 | Tapas reception |
|
| 20:00 | Close of day | |
| Tuesday 9 October 2012 | ||
| PRBB Auditorium, Barcelona Biomedical Research Park | ||
| 08:30 | Welcome coffee | |
| 09:00 | Introduction to the second day | Alfonso Valencia (CNIO) and Ferran Sanz (GRIB) |
| Presentations by Spanish regional service providers | ||
| 09:15 | Flexportal | Josep Lluis Gelpí (GN4- IRB) |
| 09:40 | APPRIS | Christian Blaschke (GN2-CNIO) |
| 10:05 | GRAPE | David Gonzalez (GN1-CRG) |
| 10:30 | Babelomics | Ignacio Medina (GN3-CIPF) |
| 10:55 | IntOGen | Núria Lopez (GN9-IMIM/UPF) |
| 11:20 | PharmaTrek | Jordi Mestres (GN9-IMIM/UPF) |
| 11:45 | DISGENET | Laura Furlong (GN9-IMIM/UPF) |
| 12:10 | Challenges and needs for Systems Biology in Pharma industry | Lourdes Cucurull-Sanchez (GSK) |
| 12:40 | Closing comments | Ferran Sanz (GRIB) and Dominic Clark (EMBL-EBI) |
| 13:00 | Buffet lunch |
|
| Three parallel hands-on tutorials (bring your own laptop!) | ||
| 14:00 | Protein services (UniProt, Flexportal & APPRIS) | Sandra Orchard (EMBL-EBI), Josep Lluis Gelpí (GN4- IRB) & Christian Blaschke (GN2-CNIO) |
| 14:00 | Functional Genomics services (ArrayExpress/Atlas, GRAPE & Babelomics) | Emma Hastings (EMBL-EBI), David Gonzalez (GN1-CRG) & Ignacio Medina (GN3-CIPF) |
| 14:00 | Pharma informatics (ChEMBL, IntOGen, PharmaTrek & DISGENET) | Anne Hersey (EMBL-EBI), Núria Lopez (GN9-IMIM/UPF), Jordi Mestres (GN9-IMIM/UPF), & Laura Furlong (GN9-IMIM/UPF) |
| 16:30 | Final Departures | |
Registration for this workshop is now closed.
Please note that for all attendees a £50 registration fee is required, this will need to be paid by credit/debit card at the time of registering.
Contacts
Local Organisers
Martina Gasull Masip
Research Programme on Biomedical Informatics - GRIB (IMIM-UPF) Parc de Recerca Biomèdica de Barcelona Doctor Aiguader, 88
08003 Barcelona (Spain)
Tel: +34/ 933 160 535
E-mail: mgasull2@imim.es
EMBL-EBI contacts
Dr. Dominic Clark
Industry Programme Manager
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge
CB10 1SD
United Kingdom
Tel: +44 1223 492575
Fax: +44 1223 494468
E-mail: clark@ebi.ac.uk
Holly Foster
Events Supervisor
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge
CB10 1SD
United Kingdom
Tel: +44 (0) 1223 492650
Fax: +44 (0) 1223 492621
Email: holly@ebi.ac.uk
![]() |
||||











