Evolution of Biotechnology in Brazil: The Role of Information Technology

1. Evolution of Biotechnology in Brazil: The Role of Information Technology Renato M.E. Sabbatini, PhD UNICAMP

2. Topics • The role of information technology in biotechnology • ; of biomedical computing in Brazil; • The history of bioinformatics in Brazil: the pioneers; • Genomics projects in Brazil and the role of bioinformatics; • Education and training in bioinformatics: the current bottleneck; • Job market for bioinformatics in Brazil.

3. Historical Antecedents • The field of Biomedical Informatics enjoyed earlier development than Bioinformatics in Brazi, by establishing na important base of research centers, educational initiatives and specialists: • 1973-77: first centers are formed (COPPE-UFRJ, FMRPUSP, INCOR-USP, FMUFRGS) • 1983: Center for Biomedical Informatics of UNICAMP • 1985-6: Establishment of the Brazilian Health Informatics Society, 1st Brazilian Congress of Health Informatics and the first Brazilian Journalof Health Informatics.

4. History of Bioinformatics in Brazil • Pioneering Groups • Renato M.E. Sabbatini and Marcos A Piani start bioinformatics software projects in the Center for Biomedical Informatics of UNICAMP - 1986 • Goran Neshich establishes the first Brazilian laboratory of bioinformatics at the National Center for Genetic Resources (CENARGEN) – 1993 • Computer scientistsJoão Meidanis and João Setúbal start the first university-based bioinformatics group at NICAMP – 1992 and write the first book: "Introduction to Computational Molecular Biology"

5. Genomics Projects (1) • In 1997 a great qualitative and quantitative leap is reached by the start of the FAPESP Genome Project (Research Support Agency of the State of São Paulo), with a record dotation of US$ 25 million • A collaborating network of 21 laboratories across the state is organized (ONSA: Organization for the Sequencing and Analysis of Nucleotides) or the Virtual Genomics Institute • The initial goal was to learn by completely sequencing the genome of Xyllela fastidiosa (a phytopathogenic bacterium of economica importance for the state, causing a citrus disease

7. Genomics Projects (2) • In 1998, the Laboratory of Bionformatics of the Computer Sciences Institute, in collaboration with the Center for Molecular Biology and Genetic Engineering of UNICAMP is charged with the responsibility of coordinating data collection and analysis for the ONSA • New methods and techniques were developed: ORESTES - Open Reading Frames EST Sequences by Andrew Simpson (Ludwig Institute) • Sequencing was completed in 2000 and tinal result published in Nature. It wasthe first time ever that a developing country was able to do this, and the the first sequenced genome of a phytopathogen in the world.

8. “The genome sequence of a strain of the bacterium Xylella fastidiosa, which causes citrus variegated chlorosis (CVC), a serious problem for commercial orange growers in Brazil, is reported this week. X. fastidiosa is emerging as a pathogen of increasing economic importance worldwide, as the cause of CVC and of Pierce's disease of grapevine in the United States. This is a landmark achievement in plant pathology - this first plant pathogen, and the first plant - associated bacterium, to have been sequenced.”

9. Genomics Projects (3) • With this first success, the Virtual Genomics Institute rapidly expanded its goals and the number of projects: • Human cancer genomes • Sugar cane genome • Schistosoma mansoni genome • Xanthomonas axonopodis (citric cancer) genome • First external contracts were celebrated (the wine grape Xylella) • The network of research laboratories was expanded to more than 50 group • Bioinformatics work was decentralized to two more laboratories in the state of São Paulo, using the same software tools

10. UNICAMP’s Bioinformatics “the exceptionaly high level of professional competency demonstrated by the two leaders of bioinformatics, combined with a willing to always help to solve problems”. International Steering Committee. Projeto Genoma FAPESP

11. Brazilian Bioinformatics Labs • Grupo de Bioinformática do Laboratório de Biologia Molecular, Instituto Ludwig de Pesquisa sobre o Câncer, São Paulo • Laboratório de Bioinformática, Instituto de Química da USP, São Paulo • Núcleo de Pesquisa em Bioinformática, Instituto de Matemática e Estatística da USP, São Paulo • Laboratório de Bioinformática do LIKA/UFPE, Recife, PE • Laboratório de Evolução Molecular e Bioinformática da UNIFESP, São Paulo • Centro de Bioinformática, Laboratório Nacional de Computação Científica (LNCC), Rio de Janeiro

12. Brazilian Bioinformatics Labs • Grupo de Bioinformática da Faculdade de Ciências Agrárias e Veterinárias da Unesp de Jaboticabal, SP • Laboratório de Bioinformática do Instituto de Informática da UFRGS • Laboratório de Bioinformática do Departamento de Informática da UFPE • Laboratório de Bioinformática da USP de Ribeirão Preto • Laboratório de Bioinformática da Universidade Católica de Brasilia • Laboratório de Bioinformática do CENARGEM/EMBRAPA, Brasilia, DF • Projeto de Bioinformatica do CNPTIA/EMBRAPA, Campinas, SP

13. National Genomics Project • The National Genomics Project Network has been established by the National Research Council/Ministry of Science and Technology, and aims at integrating 25 laboratories which are affiliated to federal and state universities and research centers, including one bioinformatics

14. National Bioinformatics Aims • To support the development of new knowledge in computational bioinformatics; • To strenghten and consolidate existing bioinformatics groups; • To support the development of software for genomics, proteomics and metabolomics research; • To develop specialized services; • To further the creation and expansion of private bioinformatics enterprises

15. Education in Bioinformatics • There are no bioinformatics courses at undergraduate level in Brazil; only isolated disciplines in a few biology and informatics courses; • There are very few graduate courses, with a small number of masters and doctoral • No private companies have systematic training programs • The professionals required for this area must have na interdisciplinary vocation; • There is a clear need to expand the number of courses and available places and to decentralize in geographic terms; • However, the work market is still undefined in Brazil, but there is a recognized potential for it.

16. Example of Interdisciplinary Courses The Biology and Computer Sciences Instuttes of UNICAMP have established na educational partnership for mutual teaching of courses: • Molecular Biology for Exact Sciences Students • Algorithms, Data Structures and Computer Programming for Biologists • Introduction to Computational Biology

17. The Center for Biomedical Informatics • The Center for Distance EducationIts mission is to support the development of on-line courses in biology and health and to investigate new technologies • The e*pub Group of Electronic Publications in Biology and MedicineIts mission is to publish journals, books and magazines in electronic and on-line format and to investigate new models and technologies • The Internet Bionformatics ProjectAims at exploring and developing new tools and techniques to revolutionize computational biology using the Internet

18. Internet Application Ideas • High performance remote database mining • Automated discovery and intelligent agents in distributed networks • Artificial neural networks over the Web • Dynapaper: dynamic electronic papers in biotechnology • Distance education in bioinformatics, molecular biology and genetic engineering

19. Conclusions