====== Oscar Restrepo ====== | University of Valle - Faculty of Engineering, School Systems Engineering and Computing.\\ Research group: [[http://bioinformatica.univalle.edu.co|Bioinformatics and Biocomputation]]. |{{:plazoleta-ingenieria.jpg?240}}|Mobile phone: +57-3007005383\\ Skype: orestrepov \\ E-mail: orestrepov[at]gmail[dot]com| ===== Short introduction and research interests ===== I am MSc student in engineering with emphasis on Systems Engineering and Computing of University of Valle; I have been working as a researcher in bioinformatics, software engineering and software development related projects for over four years. For my Master thesis I am currently developing a computational framework to extract, store, and analyze genomic information for retrovirus (HTLV-I) in the Laboratory of Bioinformatics and Computation the University of Valle. I am also involved in the development of bioinformatics workflows for analysis of samples of microbial DNA in extreme environments (Nevado del Ruiz, Colombia), in the Colombian Center for Genomics and Bioinformatics Extreme Environments, Gebix-COLCIENCIAS. I am also collaborating with the University of Bremen and Max Planck in the development of an annotation layer for a database of marine genome using web 2.0 technologies and ontologies. I have participated in others important projects related with research, bioinformatics and software developments in bioinformatics workflows, metabolic pathways, gene ontology, lims and web 2.0. My specific area of interest has been related to the bioinformatics, data mining and development algorithms and software to solve problems in life science. The technologies with which I have worked are J2EE, J2SE, PERL, C#, PHP, GWT Ajax Framework, Weka, Postgres, MySql, Oracle and others. Special Research Interests: Bioinformatics, Data Mining, Web 2.0, System Database, Software Engineering. ===== Education ===== Currently doing my Master degree in engineering. Special emphasis on Systems Engineering and Computing, University of Valle, Faculty of Engineering, School Systems Engineering and Computing, Cali.\\ Thesis, currently a work in progress: **A probabilistic model of classifier fusion for virus DNA sequences: retrovirus (HTLV-I), a case study.**\\ Subject: Bioinformatics and Data Mining. \\ \\ Systems engineer, University of San Buenaventura, Faculty of Engineering of Systems, Cali, 2003. \\ Undergaduate Thesis: **Extraction, transformation and load of data: a prototype.**\\ Subject: Database. ===== Teaching experience ===== Basics on information technologies for biologists, Bioinformatics Laboratory, ParqueSoft, 2005. ===== Journal, Conferences and workshop papers/Others publications ===== ==== Journal papers ==== Mercedes Salcedo, Oscar Restrepo, Felipe García (2011). **Using epidemiology and bioinformatics for studying HTLV-1 infectionassociated adult T-cell leukemia. ** REVISTA DE SALUD PÚBLICA · Volumen 13 (1), Febrero 2011: 129-140.\\ Fernando Barraza, Gustavo Salazar, Yesid Cuesta Astroz, Oscar Restrepo (2006). **Implementación de una Arquitectura Web para la Ejecución de Flujos de Trabajo en Bioinformática. ** Revista Ingeniería y Competitividad. Editorial Universidad del Valle. ISSN 0123-3033 Vol 8 Number 2 page 34-45. ==== Conferences and workshop papers ==== Gustavo Salazar, Oscar Restrepo, Yesid Cuesta Astroz, Fernando Barraza (2006). **Design and implementation of a centralized work environment for the execution of bioinformatics workflow. ** V Jornadas Peruanas de Computación. ISBN 9972-825-09-4 page 203-212.\\ Fernando Barraza, Oscar Restrepo, Gustavo Salazar, Yesid Cuesta Astroz (2006). **Desarrollo de una plataforma para la administración de ejecuciones de workflows en un entorno de trabajo en bioinformática. ** Congreso Latinoamericano de Estudio en Informatica, CLEI 2006. ISBN 956-303-028-1.\\ Oscar Restrepo, Gustavo Salazar, Yesid Cuesta Astroz, Fernando Barraza (2006). **Diseño e implementación de un entorno de trabajo centralizado para la ejecución de workflows en bioinformática. ** Latin-American Conference IEEE, ANDESCON 2006. ==== Other publications ==== Oscar Restrepo, Gustavo Salazar, Yesid Cuesta Astroz, Fernando Barraza (2006). **Implementation of a Web architecture for the execution of bioinformatics workflow. ** II Simposio de Investigación Universidad del Valle.\\ Oscar Restrepo, Gustavo Salazar, Rodriguez Fausto (2006). **GOMP, Gene Ontology and Metabolic Pathways. ** II Simposio de Investigación Univalle.\\ Fernando Barraza, Gustavo Salazar, Oscar Restrepo, Yesid Cuesta (2005). **Implementation of a Web architecture for the execution of bioinformatics workflow. ** I Jornadas Iberoamericanas de Bioinformatica.\\ Fernando Barraza, Gustavo Salazar, Oscar Restrepo, Yesid Cuesta (2005). **Nirvana: A Web Interfaz for running Workflows on Bioinformatics. ** Poster, Congreso Latinoamericano de Estudio en Informatica, CLEI 2005. ===== Projects in which I am involved, Work experience, Entrepreneurship experience ===== ==== Projects in which I am involved ===== **Researcher and Software developer**, Max Planck and Bremen University collaboration, Max Planck – Bremen University, February 2009 – present.\\ * Participation in the development of an annotation layer for a database of marine genome using web 2.0 technologies and ontologies. **Researcher, Laboratory of Bioinformatics and Computation**, Universidad del Valle, May 2008 – present. * Research and development of a Computational Framework for the extraction, storage, viewer and analysis of the genome information in the areas of integration of the retrovirus (HTLV-I) (Java – Data mining). **Researcher, Bioinformatics Laboratory**, ParqueSoft, 2004 - present. * Develop software tools for bioinformatics (J2SE y Perl). * Guide students in his graduation job. * Development and administration of the Web portal of the laboratory. **Researcher, Laboratory of research in software engineer (LIDIS)**, Universidad de San Buenaventura, 2002 – 2003. * Development of a flexible architecture for the construction of applications in different dominions from businesses, using technologies of Intranet and Internet with tools open source. * Production of the documentation of one of the components of the architecture. ==== Work experience ==== **Software developer**, Centro Colombiano de Genómica y Bioinformática de Ambientes Extremos, Gebix-Colciencias, June 2008 – present. * Participation in the development of Java applications for storage and analysis of biological data from the Colombian Center for Genomics and Bioinformatics Extreme Environments (JAVA).\\ **Software developer**, Integromics, Integromics España, September 2008 – December 2008 * Participation in the development of a display of metabolic pathways (C#).\\ **Software developer**, Databio, ParqueSoft, 2004\\ * Analysis and development of a Bioinformatics tool type LIMS – LIMSYS (PHP).\\ * Produce the whole documentation for the product. ==== Entrepreneurship experience ==== **Entrepreneur**, BIO - Bio Informatics Overture, ParqueSoft, 2005 - present. * Analysis, design and development of a tool based in the administration of workflows bioinformatics to help the bioinformatician job (J2EE). * Produce the whole documentation for the product. * Research new areas in which projects can be developed. * Define the projects of research of the company. ===== References ===== Pedro Moreno, pedroam[at]eisc[dot]univalle[dot]edu[dot]co, University of Valle, Colombia\\ Irene Tischer, irenetischer[at]gmail[dot]com, University of Valle, Colombia \\ Alexander Garcia, cagarcia[at]unibremen[dot]de, University of Bremen, Germany \\ Gustavo Salazar, gustavo[at]nbn[dot]ac[dot]za, NBN, University of Cape Town, South Africa \\