CAMDA becomes itinerant CAMDA 07 Valencia Spain CAMDA

CAMDA becomes itinerant. . . CAMDA 07 Valencia Spain

CAMDA 07 CIPF, Valencia, Spain East coast of Spain, mediterranean warm wheather.

Valencia • Modern city with near 1 M inhabitants. • Agroalimentary industry (oranges, rice), R&D and biomedicine • Rich gastronomy (paella) • Old traditions: fire festival (fallas)

The city of the arts and the science The CIPF is located in Valencia downtown, in a wonderful environment surrounded by museums, exhibition centers, an opera theater and the biggest aquarium in Europe

Recently inaugurated (March 2005)

Scientific programs of the CIPF Genomics and pharmacoproteomics Regenerative medicine Cell therapy for: –Diabetes –Parkinson, Ictus –Cardiovascular –Spinal cord lesions –Skin regeneration –Osteoarthritis y reumathoid arthritis

The bioinformatics department at Centro de Investigación Príncipe Felipe (Valencia, Spain). . . Joaquín Dopazo Eva Alloza Leonardo Arbiza Fátima Al-Shahrour. . . and the INB, Instituto Nacional de Jordi Burguet Bioinformática (Functional Genomics Node) Lucía Conde Hernán Dopazo Toni Gabaldon Jaime Huerta Ignacio Medina Pablo Minguez David Montaner Joaquín Tárraga Juan Manuel Vaquerizas

Algorithms are used if they are available in programs. GEPAS, a package for DNA array data analysis Free web-based platform. Computer independent. Heavy calculations are made on the server side. New versions are immediately available. Covers 70 -80% of the normal calculation necessities in microarray data analysis. The GEPAS team (three people full time plus up to 15 people involved) External Avdvisors’ committee (J. Quackenbush, S. Dudoit, Y. Moreau) More than 150. 000 experiments analysed in 2005, more than 500 per day User’s profile: USA, UK, Germany, France Japan, . . . http: //www. gepas. org ; http: //gepas. bioinfo. cipf. es

http: //www. gepas. org Twocolour arrays Multi classes T-Rex DNMAD Two classes Preprocessor Tnasas Survival Correlation KNN DLDA SVM Expresso Affymetrix arrays Random forest Fati. Scan Fati. GO+ ISACGH Hierarchical GSEA Babelomics CAAT Raw data Blocks of genes Marmite TMT SOM K-means GEPAS Herrero et al. , 2003, 2004; Vaquerizas et al. , 2005 NAR; Montaner et al. , 2006 NAR; Al-Shahrour et al. , 2005, 2006 NAR; 2005 Bioinformatics SOTA Fati. GO Two sets of genes Normalization Clustering Differential expresion Arrays-CGH Class Prediction Functional Annotation RIDGE analysis

Usage statistics More than 150, 000 experiments analysed during the last year. More than 500 experiments per day. 24 h usage map as of June 8, 2006

Courses: http: //bioinfo. cipf. es/docus/courses. html • 22 - 24 March 2006 II - Course on Microarray Data Analysis. Centro de Investigación Príncipe Felipe - Valencia • 19 -21 April 2006 EMBO Practical Course on Comparative Genomics and SNP Analysis using the Ensembl Genome Browser. Centro de Investigación Príncipe Felipe - Valencia • 15 - 19 Mayo 2006 Evolución Molecular, Filogenia y Filogenómica. Centro de Investigación Príncipe Felipe - Valencia • 22 nd-24 th May 2006 Course on Microarray Data Analysis. Graduate School of Biological, Medical and Veterinary Sciences. University of Cambridge. UK • June 2006 Course on Microarray Data Analysis. Gulbenkian Inst. Lisbon (Portugal) • September 2006 Course on Microarray Data Analysis. Cape Town (SA) • November 2006 Course on Microarray Data Analysis. Las Palmas de Gran Canaria • November 2006 Course on Microarray Data Analysis. Graduate School of Biological, Medical and Veterinary Sciences. University of Cambridge. UK Increasing demand

The INB, a “Virtual” Institute Training F. Sanz - UPF With F. Martin ISCIII, F. Moran UCM Computational Node 2 X. Messeguer –UPC /Barcelona Supercomputer Center Bioinformatics and Genomics R. Guigo – IMIM/CRG Central Node Bioinformatics and Proteomics A. Valencia – CNB/CSIC Protein Structure M-Orozco – Univ. Barcelona Parc Cientific Barcelona Computational Node 1 J. M. Carazo – PCM Functional Genomics J. Dopazo – CIPF Integrated Bioinformatics O. Trelles – Univ. Malaga

INB Status Technological platform of Genoma España INB is organized as a Network Managed as a standard multi- institution project Total endowment to the project for 3 years: 4. 443. 358 €

There is a growing interest in Spain in microarray-based technologies Demand in training activities Genoma España is promoting the use of microarrays, by means of subsides. Bioinformatics and Ce. Gen (large-scale genotyping) are funded as virtual institutes

Future of CAMDA Itinerant international conference. Who is next? Dataset-driven or topic-driven? Maybe both. . . Proceedings? Selection of n* best papers for a section in an issue of a journal? Training: demos? Tutorials? Sponsors: companies, local/national government, etc. * n=10?