Bioinformatics Cluster A Allan Orozco. UCR, nov Training & Scientific Manager Spanish National Bioinformatics Institute- CNIO- Madrid- Spain

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1 Bioinformatics Cluster A Allan Orozco UCR, nov 2011 Training & Scientific Manager Spanish National Bioinformatics Institute- CNIO- Madrid- Spain

2 Qué es la Bioinformática? La bioinformática es el campo donde las ciencias biológicas, biomédicas, la ciencia de la computación, y la tecnología de información se funden en una disciplina. El objetivo principal es el descubrimiento de nuevos indicios biológicos, como también crear una perspectiva global de la cual poder unificar principios de la biología. (NCBI Education)

computación, y la tecnología de información se funden en una disciplina.

3 GENOMA BIOINFORMATICS relaciones gen-proteína PROTEOMA relaciones proteína-proteína METABOLOMA Relaciones metabólicas y celulares Citrate Cycle Dr J De Las Rivas 3

4 De la información clínica al diseño de fármacos con Bioinformática

5 ENSAYOS CLÍNICOS Medicina genómica con aplicación en clínica Investigación Básica Genoma Transcriptoma Proteoma Metaboloma Genotipado Haplotyping Genómica individualizada (SNPs y mutaciones) Variabilidad Humana Investigación Translacional Tecnología Datos Aplicaciones Diagnóstico Molecular Farmacogenética Aplicaciones Clínicas Medicina Personalizada DNA Microarrays acgh chip on ChIP Met arrays MS, 2D Bioinformática en Biomedicina Genómica Funcional Proteómica Nueva clasificación de enfermedades Farmacogenómica -Terapias individualizadas -Medicina preventiva Bases Moleculares de enfermedades

Farmacogenética Aplicaciones Clínicas Medicina Personalizada DNA Microarrays acgh chip on ChIP Met arrays MS, 2D Bioinformática en Biomedicina

6 De la genomica computacional a los ensayos clínicos

7 Aplicaciones bioinformáticas Secuenciación ADN Funcionalidad en estructura y enfermedades Determinación de motivos

8 NGS Next generation sequence

9 Workflows Automatización de tareas biomédicas

10 Para ello se amplifica el ADN obtenido a partir de una muestra de sangre o tejido de un paciente. Farmacogenómica y Bioinformática en la medicina clínica Fuente: Estos fragmentos de material genético pueden ser secuencias cortas llamadas oligonucleótidos, o de mayor tamaño, cdna (ADN complementario sintetizado a partir de mrna), o bien productos de PCR (replicación in vitro de secuencias de ADN mediante la reacción en cadena de la Polimerasa).

ser secuencias cortas llamadas oligonucleótidos, o de mayor tamaño, cdna (ADN complementario sintetizado a

11 PROJECTS

12 Web services INB MOBY-DEV Repository (402 services) Distances Clustering Repeat_Masking StructuralStudies SequenceAnalysis Base_Calling Database Biochemistry Translating Sequence_Assembly Annotations GeneExpression Alignment Sequence_Filtering Low_Complexity_Masking Displaying Alignment, 22% Converting, 9% Displaying, 2% INAB Repository (278 services) Parsing, 11% This is the collection of web services that we have at the INB, to solve by using different methods, problems of sequencing, prediction and functional gene annotation Distances, 4% Clustering, 1% 51 Structural Studies, 10% 34 GeneExpression, 3% Database, 19% Biochemistry, 1% Annotations, 5% Translating, 1% Sequence Analysis, 12% Distances Clusterin g Structural Studies Sequence Analysis Database Biochemi stry

services) 122 6 25 30 28 61 Parsing, 11% This is the collection of web services that we have at the INB, to solve by using different methods, problems of sequencing, prediction and functional gene

13 INB MOBY Services (+600) Stable Services (INAB) Unstable Services (MOBY-DEV) INBmassRegistry (473 without duplications) getmobywsdl (used by EMBRACE) Tester Database INBmassTester (periodically launched)

14 Tools Software

15 Sistema oncogenómico de empleo en biomedicina The bio-widgets are the functional elements of CARGO. Control and visualization elements, which can be individually selected by users and which organize themselves to form a web control panel via the user interface.

Control and visualization elements, which can be individually

16 Intogen De empleo en investigación del cáncer ; Integrative OncoGenomics (IntOGen), a discovery tool for cancer researchers, is a resource that integrates multidimensional OncoGenomics Data for the identification of genes and groups of genes (biological modules) involved in cancer development.

integrates multidimensional OncoGenomics Data for the identification of

17 BlastXP (Pharmacogenomics) BlastXP (BLAST Cross-Pharmacology) is an accessible web tool that identifies proteins which are pharmacologically related through the number of shared ligands between them.

18 Clustering (Microarrays) Microarrays para perfiles de expresión Génica para análisis de tratamiento y Dosificación de fármacos

19 Fuente: Jose Maria Fernandez, CNIO-INB ihop (Text Mining)

20 INB Technological Offer Implementation Cluster UCR Nelly Calendula

21 Grupo de Bioinformática- Escuela de Medicina- Universidad de Costa Rica (2006)

22 Creación de Red de Bioinformática en Centroamérica, 2011 Base: Cluster de medicina

23 Red Clara Red Centroamericana de Bioinformática

24 Also we have built a Central American net of Bioinformatics with a computational cluster named Nelly, in honor to my mother that struggled with me to find out what my field of interest was. The cluster was built thanks to the contributions of institutions such as Microsoft Research and the University of Washington. North America and South America Bioinformatics Net Red Clara GISELA We must remember that Central America has one of the most extraordinary biodiversity areas of the world. Others

25 RED NACIONAL DE BIOINFORMATICA Plataforma formación con casos de estudio Repositorios nacionales de información clínica

In Spain, the institute where I work is in charge of providing all the technology related with web services of it.

26 Propose: Bioinformatics American Network? RED CLARA For example, in Europe actually there is a bioinformatics infrastructure building going on, coordinated by the European Bioinformatics Institute. In Spain, the institute where I work is in charge of providing all the technology related with web services of it. This particular situation may extend bridges in the future for ELIXIR and other Latin American nets if we think about an American Bioinformatics Net. The INB is member of the steering committee of the ELIXIR project for the construction of the European Infrastructure for Bioinformatics. Window of opportunity: ELLA?

27 Training & Projects (Bioinformatics, Nanotechnology, Molecular BioCan net Medicine) RedCLARA Plataforma de educación en Bioinformática Spain ALICE2 CLARA RNP AmLight Investment: 30,000,000 Rio Porto Alegre Brasil

28 Finish: August 2011 GEANT2 & GISELA (CLARA) Bioinformatics & Nanomedicine Educational Platform Caléndula Caléndula

29 Nanorobots and Bioinformatics operating system As a central idea we could imagine the organization of development projects by thematic. But one of the greater bets would be to focus on a parallel way the development and research on nanotecnologies, bioinformatics and biomedicine..

30 Nanogenomics bioinformatics Leonardo Da Vinci Nuevos campos de aplicación en medicina genómica

31 Training-INB

32 Temática curso

33 Presencial y virtual servidores: ( BSc y INAB)

34 Students of several hospitals in Barcelona educating in our platforms located in BSC and the INB.

35 Caso Pionero en europa

37 Creación del primer Master de Bioinformática en Centroamérica-2011 (UCR)

38 Nanorobots and Bioinformatics operating system As a central idea we could imagine the organization of development projects by thematic. But one of the greater bets would be to focus on a parallel way the development and research on nanotecnologies, bioinformatics and biomedicine..

39 Nanogenomics bioinformatics Leonardo Da Vinci Nuevos campos de aplicación en medicina genómica

40 THANKS!!!

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