What is the Spanish Bioinformatics Institute?

The INB (Instituto Nacional de Bioinformática) is a community-driven technology platform of Genoma Espana founded in 2003 with the mission to consolidate Bioinformatics as a scientific discipline and to generate and apply solutions for the development and execution of projects related to genomics and proteomics, providing technical support in Bioinformatics to laboratories, institutions and companies throughout the Spanish territory.

Who is involved?

The INB is composed of 9 nodes including some of the top leading scientists in the field, located across the Spanish geography , and a wide range of fields. Some of the best known tools in the INB include: GENEID, CARGO, GEPAS, MODEL database and SNPator.

What services does INB provide?

INB’s basic services can be classified as follows:

1. Bioinformatics Services

An important part of the INB involves the automation of workflows, integrating in-house methods developed by INB researchers as well as workflow platforms developed elsewhere. A selection of workflows can be downloaded from the Institute’s website. Such workflows include, among others, gene search tools, protein function prediction, SNP mapping and SNP effect on gene products. For the annotation of gene products in particular, it has been used the DAS protocol (Distributed Annotation System), which is a communication system used for the exchange of annotation. DAS is based on the idea that annotations should not be given by centralised databases, but they should be extended by multiple sites. Data distribution, carried out by DAS servers, is separated from visualisation, which is performed by DAS clients.

2. Bioinformatics Tools

   • GENEID — a program to predict genes in anonymous genomic sequences designed with a hierarchical structure.
   • CARGO — 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 widgets.
   • GEPAS — 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.
   • MODEL database and the associated PCA suite -“ The largest repository of Molecular Dynamics trajectories featuring trajectory compression using Principal Component Analysis (PCA) techniques.
   • SNPator -“ A large set of tools and its associated database for the statistical analysis of genomic variation. This tool is the most common access point for the analysis of experimental results provided by the CeGen platform.

3. Access to the Barcelona Supercomputer Center (BSC)

   The INB offers through its Node 6 (MareNostrum) MN access to services that are highly demanding in terms of computational power. The use of MareNostrum requires BSC’s Access Committee approval. In
   order to be granted approval it is requested that potential users apply trough the BSC web. There are several aspects of the process where the INB may give support:

   • Project consulting. Analysis of supercomputational needs and its adaptation to the calculus infrastructure of INB-BSC.
   • Support to software adaptation for supercomputing, in collaboration with the Systems Department of the BSC.
   • Support using MareNostrum.
   • Support disseminating, hosting and maintaining results

4. Collaboration in Bioinformatics projects.

As part of the commitment of the INB to the development of the field in Spain, we are constantly seeking collaborations with high-throughput genomics and proteomics projects. Some of the projects we are currently involved in include (i) the identification of genes and molecules associated to tomato fruit quality and participation in the sequencing of euchromatic regions of chr 9; (ii) the analysis, annotation and integration of the olive tree genome sequence data and (iii) selection of SNPs for high-throughput genotyping studies.

5. Courses, seminars and Roadshows.

In addition to projects, we also provide educational opportunities (workshops, seminars, courses) on the technologies developed by the INB. As an example, we present here a bioinformatics workshop in Barcelona (26-28 Nov. 2007), which was carried out in collaboration with the European Bioinformatics Instutute . Here some of the most used genomics and proteomics resources provided by the EBI will be demonstrated. In addition, the INB will present some of its most used software, featuring GEPAS, CARGO, and GENEID.

Access Protocol to INB Services

We welcome proposals for each one of the services we offer. All proposals are channelled through the central node from which a scientific panel is coordinated involving revelant nodes. This scientific panel will rigurously assess each proposal.

For all proposals, comments and suggestions please contact us. We welcome your cooperation to help us give a better service to our community and look forward to hearing from you soon!