National Health System Support Services
INB: A National Bioinformatics Support Platform for 'Omic' R&D in Spain
About the INB
The INB is an institutional platform promoted by Genoma España (www.gen-es.org), whose overarching mission is to disseminate and provide bioinformatic support to laboratories, research institutions and companies throughout Spain.
Comprising 9 nodes, including a total of 33 staff and internationally renowned Spanish scientists in Bioinformatics (Figure 1), the INB offers a wide range of bioinformatic techniques in genomics and proteomics. The INB is directed by Alfonso Valencia at the CNIO.
Figure 1. Geographical distribution and specialties of each of the 9 INB nodes.
Technical Plataform
An essential area of INB activity involves the automation of workflows, integrating in-house methods developed by INB researchers as well as incorporating workflow platforms developed elsewhere. A variety of workflows can be downloaded from the Institute’s website (www.inab.org). including gene search tools, protein function prediction, SNP mapping and SNP effect on gene products. For the annotation of gene products in particular, the DAS protocol (Distributed Annotation System), a communication system used for the exchange of annotation, has been employed. The DAS is base on the idea that annotations should not be given through centralised databases rather, they should be extended by multiple sites. Data distribution carried out by DAS servers is separate from the visualisation performed by the DAS clients.
The Bioinformatics Analyses of Streptomyces Genome Project uses FUNcut and the DAS protocol for its functional annotations, and is funded by the Spanish Ministry of Science and Education, incorporating eight different groups (Osvaldo Grana, CNIO, Alfonso Valencia’s Group). The objective of this project is to study Streptomyces coelicolor (SCO) specific and global regulation pathways related to antibiotic production. SCO is the representative model of a series of organisms that live in the soil and are remarkable for production of chemical compounds, including anti-tumour compounds, immuno-suppressors and two thirds of natural antibiotics available. The chromosome is formed by 8,667,507pb - 7825 genes predicted. Annotations are available in DAS.
Figure 2. Schematic representation of a workflow developed by the INB for the annotation of proteins. These bioinformaticservices use BioMoby and the results of this workflow are entered into a database, available under a DAS server.
The Encyclopaedia of DNA Elements (ENCODE) Project aims to provide a more biologically informative representation of the human genome using high-throughput methods to identify and catalogue the functional elements encoded. In its pilot phase, 35 groups (including nodes 1 and 2 of the INB), provided more than 200 experimental and computational data sets that examined 30 Mb in unprecedented detailed - equivalent to %1 of the human genome.
Figure 3..Visual output for the three variants of the TH locus (AC132217.7) in the ENCODE project. On the basis of this output, the hypothesis that these two variants could give rise to the principal functional isoform was rejected.
COLLABORATION IN GENOMIC PROJECTS
The Sequencing of Solacenae Project (EPS-SOL) is another important initiative in which the INB aims to provide the necessary bioinformatic support. One main objective is to determine genetic factors affecting the fruit’s quality. Another aspect of EPS-SOL includes the exhaustive study of the effect of common viruses interacting with tomato. In addition, Spain participates in the sequencing project of chromosome 9. For further information visit: http://chirimoyo.ac.uma.es/espsol.
An additionally important project involves the development of a diagnostic Kit for inflammatory illnesses mediated by immune mechanisms (IMID-KIT). This project forms part of the Singular and Strategic Projects Framework of the Ministry of Science and Education. The Principal Investigator is Sara Marsal, the Vall d’Hebrón Hospital (Barcelona). This Project will last three years, significantly involve INB groups, such as the Barcelona Supercomputer Center, and PIs such as Arcadi Navarro (UPF), Alfonso Valencia (CNIO) and Joaquín Dopazo (CIPF). 12000 samples will be collected from patients with rheumatoid arthritis, ulcerous colitis, psoriasis, Crohn’s illness and hypernormal controls.
Access to the Barcelona Supercomputer Center Services (BSC)
Through INB Node 6 (MareNostrum) MN access to services that are highly demanding in terms of computational power is facilitated. The use of MareNostrum requires BSC’s Access Committee approval. In order to be granted approval potential users must apply online at: http://www.bsc.es/.
There are several aspects to the process where INB may offer support:
- Project consulting. Analysis of supercomputational requirements 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 dissemination and hosting and maintaining results.
Education/ Outreach
INB is also highly dedicated to organising courses, seminars and workshops on the techniques it has developed. These educational programs are organised as much as possible in collaboration with the EBI (European Bioinformatics Institute) to demonstrate genomic and proteomic tools such as GEPAS, CARGO and GENEID. We welcome proposals for collaboration in projects centred on and around the genomic proteomic fields, as well as requests and invitations to organise educational events anywhere in Spain. All proposals are rigorously assessed by a scientific panel.
Contact
Proposals may be sent directly to: contacto@inab.org
