The Bioinformatics Core Facility aims to provide researchers at CRG, PRBB, and other external institutions with services of consultation, data analysis and management, software development, and access to computing resources. As further important commitment, the core will periodically organize courses and workshops in order to train biologists on the implementation of the main bioinformatics tools in their research.
The Unit is open to all researchers at the PRBB and also to external users anywhere in the world.
For further information please contact Guglielmo Roma (phone: +34933160181).
FACILITY OVERVIEW
Starting in September 2009, the Bioinformatics Unit currently comprises six members. The team contributes to research projects by providing support and expertise in programming and advanced data analysis, focusing primarily on high-throughput genomics technologies including microarrays, genotyping, and next-generation sequencing.
SERVICES
The main goal of the unit is to set up a collaborative environment within CRG/PRBB and contribute to research projects providing support to scientists on several bioinformatics aspects.
Basic services:
- Consultation on bioinformatics methods and resources
Assistance with the computational aspects of research by providing support and consultation in relation to data management, statistical data analysis, and interpretation of experimental data, focusing primarily on high-throughput genomics technologies.
- Software evaluation, implementation, and training
Support on the evaluation and implementation of new bioinformatics software (gathering of users requirements, scheduling, implementation, validation, documentation, training, and end-users support).
- Customization of bioinformatics resources
Local implementation of genome-related software (e.g. genomics browsers like Ensembl, UCSC, and GBrowse) and most common bioinformatics tools (Galaxy, EMBOSS, among others).
Advanced services:
- High-throughput data analysis of genomics, transcriptomics, and proteomics datasets;
- Downstream analysis for the interpretation of gene lists, including gene set enrichment and over-representation of biological functions using Gene Ontology terms;
- Identification of functional genomics elements, such as genes and regulatory sequences, through comparative genomics approaches;
- Construction of ad-hoc databases and web interfaces to allow systematically storage, management, analysis, and search of biologically relevant information;
- Development of bioinformatics scripts and more advanced pipelines to automate sequence analyses and genome annotation tasks
The unit will be also focused on the education of biologists in the analysis and interpretation of their experimental data through the provision of custom advice and training in bioinformatics as well as in the acquisition of basic programming skills.
Publications from the unit
= 2010 =
Hermoso A, Bertero M, Speroni S, Alloza M, Roma G. Lab Service Wiki: a wiki-based data management solution for laboratories production services. SemWiki2010 - Conference Proceedings. 2010 May.
Sanseverino W*, Roma G*, De Simone M, Faino L, Melito S, Stupka E, Frusciante L, Ercolano MR. “PRGdb: a bioinformatics platform for plant resistance gene analysis.” Nucleic Acids Res. 2010 Jan;38(Database issue):D814-21. (* joint first authors)
Romito A, Lonardo E, Roma G, Minchiotti G, Ballabio A and Cobellis G, “Lack of Sik1 in Mouse Embryonic Stem Cells Impairs Cardiomyogenesis by Down-Regulating the Cyclin-Dependent Kinase Inhibitor p57kip2.” PLoS One. 2010 Feb 3;5(2):e9029.
