SME Bioinformatics Forum, Barcelona

Date:

  Monday 8 October 2012

Contact: 

Holly Foster

Registration closed

Overview

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 coordinate biological 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).

Additional information

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

Travel Directions

The SME Bioinformatic Forum will be held at the PRBB Auditorium (capacity: 250).

Location:
Barcelona Biomedical Research Park, PRBB
C/ Doctor Aiguader, 88
08003 Barcelona

PRBB map

PRBB map 2

How to reach the building from Barcelona city
By Metro
L4 (yellow line):
- Direction La Pau
- Station Ciutadella/Vila Olímpica

By Tram
Trambesòs, line T4:
- Direction Ciutadella/Vila Olímpica
- Station Ciutadella/Vila Olímpica (last station)

PRBB map 3

How to reach the building from the airport:
The easiest way to get to the meeting venue is by taxi, as both the bus and the train take you to the city centre, which means that you will have to take the metro afterwards. The trip takes from 20-35 minutes depending on the traffic, and costs 30-35 Euros.

You can find all the information on public transportation from/to the airport with detailed explanations at:
http://www.barcelona‐tourist‐guide.com/en/airport/barcelona‐airport‐transport.html

By train
The RENFE train service runs approximately every 30 minutes to and from Barcelona airport to the city centre. Travel time is about 25 minutes.
Travelling from the airport to the city centre you can get off at Passeig de Gracia station that has connection to the metro. Take the yellow line (L4) to direction La Pau – get off at Ciutadella/Vila Olímpica station.

By Bus
Aerobus
Timetable: every 5‐10 minutes
Stops: Plaça Espanya or Plaça Catalunya, both with connection to the metro.
Price: 5,65€
(http://www.aerobusbcn.com/index.php/en.html)

 

Hotel recommendations

H10 Marina**** (Single 130e, double 150e)
Av. Bogatell, 64‐68
08005 Barcelona
Tel: +34 93 309 79 17
Fax: +34 93 300 33 10

Hotel ICARIA**** (117e)
Avda. Icaria 195,
08005 Barcelona
Tel: +34 93 221 82 00

Hotel Four Points by Sheraton Barcelona Diagonal*** (Single 100e)
Avda. Diagonal, 161‐163
08018 Barcelona
Tel. 93 486 88 00
Fax. 93 309 67 27

Confortel Barcelona**** (Single 110e, Double 120e)
C/ Ramón Turró, 196‐198 esq. C/Llacuna
08005 Barcelona
Tel. +34 932 43 88 00

 
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Programme

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