Evolution of Biotechnology in Brazil: The Role of

Information Technology

Evolution of Biotechnology in Brazil: The Role of

Information Technology

Renato M.E. Sabbatini, PhDRenato M.E. Sabbatini, PhD

UNICAMPUNICAMPRenato M.E. Sabbatini, PhDRenato M.E. Sabbatini, PhD

UNICAMPUNICAMP

TopicsTopics

• The role of information technology in The role of information technology in biotechnologybiotechnology

• ; of biomedical computing in Brazil;; of biomedical computing in Brazil;• The history of bioinformatics in Brazil: the The history of bioinformatics in Brazil: the

pioneers;pioneers;• Genomics projects in Brazil and the role Genomics projects in Brazil and the role

of bioinformatics;of bioinformatics;• Education and training in bioinformatics: Education and training in bioinformatics:

the current bottleneck;the current bottleneck;• Job market for bioinformatics in Brazil.Job market for bioinformatics in Brazil.

• The role of information technology in The role of information technology in biotechnologybiotechnology

• ; of biomedical computing in Brazil;; of biomedical computing in Brazil;• The history of bioinformatics in Brazil: the The history of bioinformatics in Brazil: the

pioneers;pioneers;• Genomics projects in Brazil and the role Genomics projects in Brazil and the role

of bioinformatics;of bioinformatics;• Education and training in bioinformatics: Education and training in bioinformatics:

the current bottleneck;the current bottleneck;• Job market for bioinformatics in Brazil.Job market for bioinformatics in Brazil.

Historical AntecedentsHistorical Antecedents

• The field of Biomedical Informatics enjoyed The field of Biomedical Informatics enjoyed earlier development than Bioinformatics in earlier development than Bioinformatics in Brazi, by establishing na important base of Brazi, by establishing na important base of research centers, educational initiatives and research centers, educational initiatives and specialists:specialists:– 1973-771973-77: first centers are formed (COPPE-UFRJ, : first centers are formed (COPPE-UFRJ,

FMRPUSP, INCOR-USP, FMUFRGS)FMRPUSP, INCOR-USP, FMUFRGS)– 1983:1983: Center for Biomedical Informatics of UNICAMP Center for Biomedical Informatics of UNICAMP– 1985-6:1985-6: Establishment of the Brazilian Health Establishment of the Brazilian Health

Informatics Society, 1st Brazilian Congress of Informatics Society, 1st Brazilian Congress of Health Informatics and the first Brazilian Journalof Health Informatics and the first Brazilian Journalof Health Informatics.Health Informatics.

• The field of Biomedical Informatics enjoyed The field of Biomedical Informatics enjoyed earlier development than Bioinformatics in earlier development than Bioinformatics in Brazi, by establishing na important base of Brazi, by establishing na important base of research centers, educational initiatives and research centers, educational initiatives and specialists:specialists:– 1973-771973-77: first centers are formed (COPPE-UFRJ, : first centers are formed (COPPE-UFRJ,

FMRPUSP, INCOR-USP, FMUFRGS)FMRPUSP, INCOR-USP, FMUFRGS)– 1983:1983: Center for Biomedical Informatics of UNICAMP Center for Biomedical Informatics of UNICAMP– 1985-6:1985-6: Establishment of the Brazilian Health Establishment of the Brazilian Health

Informatics Society, 1st Brazilian Congress of Informatics Society, 1st Brazilian Congress of Health Informatics and the first Brazilian Journalof Health Informatics and the first Brazilian Journalof Health Informatics.Health Informatics.

History of Bioinformatics in Brazil

History of Bioinformatics in Brazil

• Pioneering GroupsPioneering Groups– Renato M.E. Sabbatini and Marcos A Piani start Renato M.E. Sabbatini and Marcos A Piani start

bioinformatics software projects in the Center bioinformatics software projects in the Center for Biomedical Informatics of UNICAMP - 1986for Biomedical Informatics of UNICAMP - 1986

– Goran Neshich establishes the first Brazilian Goran Neshich establishes the first Brazilian laboratory of bioinformatics at the National laboratory of bioinformatics at the National Center for Genetic Resources (CENARGEN) – Center for Genetic Resources (CENARGEN) – 19931993

– Computer scientistsJoão Meidanis and João Computer scientistsJoão Meidanis and João Setúbal start the first university-based Setúbal start the first university-based bioinformatics group at NICAMP – 1992 and bioinformatics group at NICAMP – 1992 and write the first book: write the first book: "Introduction to Computational "Introduction to Computational Molecular Biology" Molecular Biology"

• Pioneering GroupsPioneering Groups– Renato M.E. Sabbatini and Marcos A Piani start Renato M.E. Sabbatini and Marcos A Piani start

bioinformatics software projects in the Center bioinformatics software projects in the Center for Biomedical Informatics of UNICAMP - 1986for Biomedical Informatics of UNICAMP - 1986

– Goran Neshich establishes the first Brazilian Goran Neshich establishes the first Brazilian laboratory of bioinformatics at the National laboratory of bioinformatics at the National Center for Genetic Resources (CENARGEN) – Center for Genetic Resources (CENARGEN) – 19931993

– Computer scientistsJoão Meidanis and João Computer scientistsJoão Meidanis and João Setúbal start the first university-based Setúbal start the first university-based bioinformatics group at NICAMP – 1992 and bioinformatics group at NICAMP – 1992 and write the first book: write the first book: "Introduction to Computational "Introduction to Computational Molecular Biology" Molecular Biology"

Genomics Projects (1)Genomics Projects (1)

• In 1997 a great qualitative and quantitative leap In 1997 a great qualitative and quantitative leap is reached by the start of the FAPESP Genome is reached by the start of the FAPESP Genome Project (Research Support Agency of the State of Project (Research Support Agency of the State of São Paulo), with a record dotation of US$ 25 São Paulo), with a record dotation of US$ 25 millionmillion

• A collaborating network of 21 laboratories across A collaborating network of 21 laboratories across the state is organized (ONSA: Organization for the the state is organized (ONSA: Organization for the Sequencing and Analysis of Nucleotides) or the Sequencing and Analysis of Nucleotides) or the Virtual Genomics InstituteVirtual Genomics Institute

• The initial goal was to learn by completely The initial goal was to learn by completely sequencing the genome of sequencing the genome of Xyllela fastidiosaXyllela fastidiosa (a (a phytopathogenic bacterium of economica phytopathogenic bacterium of economica importance for the state, causing a citrus diseaseimportance for the state, causing a citrus disease

• In 1997 a great qualitative and quantitative leap In 1997 a great qualitative and quantitative leap is reached by the start of the FAPESP Genome is reached by the start of the FAPESP Genome Project (Research Support Agency of the State of Project (Research Support Agency of the State of São Paulo), with a record dotation of US$ 25 São Paulo), with a record dotation of US$ 25 millionmillion

• A collaborating network of 21 laboratories across A collaborating network of 21 laboratories across the state is organized (ONSA: Organization for the the state is organized (ONSA: Organization for the Sequencing and Analysis of Nucleotides) or the Sequencing and Analysis of Nucleotides) or the Virtual Genomics InstituteVirtual Genomics Institute

• The initial goal was to learn by completely The initial goal was to learn by completely sequencing the genome of sequencing the genome of Xyllela fastidiosaXyllela fastidiosa (a (a phytopathogenic bacterium of economica phytopathogenic bacterium of economica importance for the state, causing a citrus diseaseimportance for the state, causing a citrus disease

Genomics Projects (2)Genomics Projects (2)

• In 1998, the Laboratory of Bionformatics of the In 1998, the Laboratory of Bionformatics of the Computer Sciences Institute, in collaboration Computer Sciences Institute, in collaboration with the Center for Molecular Biology and with the Center for Molecular Biology and Genetic Engineering of UNICAMP is charged Genetic Engineering of UNICAMP is charged with the responsibility of coordinating data with the responsibility of coordinating data collection and analysis for the ONSAcollection and analysis for the ONSA

• New methods and techniques were developed: New methods and techniques were developed: ORESTES - ORESTES - Open Reading Frames EST SequencesOpen Reading Frames EST Sequences by Andrew Simpson (Ludwig Institute)by Andrew Simpson (Ludwig Institute)

• Sequencing was completed in 2000 and tinal Sequencing was completed in 2000 and tinal result published in Nature. It wasthe first time result published in Nature. It wasthe first time ever that a developing country was able to do ever that a developing country was able to do this, and the the first sequenced genome of a this, and the the first sequenced genome of a phytopathogen in the world. phytopathogen in the world.

• In 1998, the Laboratory of Bionformatics of the In 1998, the Laboratory of Bionformatics of the Computer Sciences Institute, in collaboration Computer Sciences Institute, in collaboration with the Center for Molecular Biology and with the Center for Molecular Biology and Genetic Engineering of UNICAMP is charged Genetic Engineering of UNICAMP is charged with the responsibility of coordinating data with the responsibility of coordinating data collection and analysis for the ONSAcollection and analysis for the ONSA

• New methods and techniques were developed: New methods and techniques were developed: ORESTES - ORESTES - Open Reading Frames EST SequencesOpen Reading Frames EST Sequences by Andrew Simpson (Ludwig Institute)by Andrew Simpson (Ludwig Institute)

• Sequencing was completed in 2000 and tinal Sequencing was completed in 2000 and tinal result published in Nature. It wasthe first time result published in Nature. It wasthe first time ever that a developing country was able to do ever that a developing country was able to do this, and the the first sequenced genome of a this, and the the first sequenced genome of a phytopathogen in the world. phytopathogen in the world.

“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.”

Genomics Projects (3)Genomics Projects (3)

• With this first success, the Virtual Genomics Institute With this first success, the Virtual Genomics Institute rapidly expanded its goals and the number of projects:rapidly expanded its goals and the number of projects:– Human cancer genomesHuman cancer genomes– Sugar cane genomeSugar cane genome– Schistosoma mansoni Schistosoma mansoni genomegenome– Xanthomonas axonopodis Xanthomonas axonopodis (citric cancer) genome(citric cancer) genome

• First external contracts were celebrated (the wine First external contracts were celebrated (the wine grape Xylella)grape Xylella)

• The network of research laboratories was expanded to The network of research laboratories was expanded to more than 50 groupmore than 50 group

• Bioinformatics work was decentralized to two more Bioinformatics work was decentralized to two more laboratories in the state of São Paulo, using the same laboratories in the state of São Paulo, using the same software toolssoftware tools

• With this first success, the Virtual Genomics Institute With this first success, the Virtual Genomics Institute rapidly expanded its goals and the number of projects:rapidly expanded its goals and the number of projects:– Human cancer genomesHuman cancer genomes– Sugar cane genomeSugar cane genome– Schistosoma mansoni Schistosoma mansoni genomegenome– Xanthomonas axonopodis Xanthomonas axonopodis (citric cancer) genome(citric cancer) genome

• First external contracts were celebrated (the wine First external contracts were celebrated (the wine grape Xylella)grape Xylella)

• The network of research laboratories was expanded to The network of research laboratories was expanded to more than 50 groupmore than 50 group

• Bioinformatics work was decentralized to two more Bioinformatics work was decentralized to two more laboratories in the state of São Paulo, using the same laboratories in the state of São Paulo, using the same software toolssoftware tools

UNICAMP’s BioinformaticsUNICAMP’s Bioinformatics

““the exceptionaly high level of the exceptionaly high level of professional competency professional competency demonstrated by the two demonstrated by the two leaders of bioinformatics, leaders of bioinformatics, combined with a willing to combined with a willing to always help to solve always help to solve problems”.problems”.

International Steering Committee. Projeto International Steering Committee. Projeto

Genoma FAPESPGenoma FAPESP

““the exceptionaly high level of the exceptionaly high level of professional competency professional competency demonstrated by the two demonstrated by the two leaders of bioinformatics, leaders of bioinformatics, combined with a willing to combined with a willing to always help to solve always help to solve problems”.problems”.

International Steering Committee. Projeto International Steering Committee. Projeto

Genoma FAPESPGenoma FAPESP

Brazilian Bioinformatics LabsBrazilian Bioinformatics Labs

• Grupo de Bioinformática do Laboratório de Biologia Grupo de Bioinformática do Laboratório de Biologia Molecular, Instituto Ludwig de Pesquisa sobre o Câncer, Molecular, Instituto Ludwig de Pesquisa sobre o Câncer, São PauloSão Paulo

• Laboratório de Bioinformática, Instituto de Química da Laboratório de Bioinformática, Instituto de Química da USP, São PauloUSP, São Paulo

• Núcleo de Pesquisa em Bioinformática, Instituto de Núcleo de Pesquisa em Bioinformática, Instituto de Matemática e Estatística da USP, São PauloMatemática e Estatística da USP, São Paulo

• Laboratório de Bioinformática do LIKA/UFPE, Recife, PELaboratório de Bioinformática do LIKA/UFPE, Recife, PE• Laboratório de Evolução Molecular e Bioinformática da Laboratório de Evolução Molecular e Bioinformática da

UNIFESP, São PauloUNIFESP, São Paulo• Centro de Bioinformática, Laboratório Nacional de Centro de Bioinformática, Laboratório Nacional de

Computação Científica (LNCC), Rio de JaneiroComputação Científica (LNCC), Rio de Janeiro

• Grupo de Bioinformática do Laboratório de Biologia Grupo de Bioinformática do Laboratório de Biologia Molecular, Instituto Ludwig de Pesquisa sobre o Câncer, Molecular, Instituto Ludwig de Pesquisa sobre o Câncer, São PauloSão Paulo

• Laboratório de Bioinformática, Instituto de Química da Laboratório de Bioinformática, Instituto de Química da USP, São PauloUSP, São Paulo

• Núcleo de Pesquisa em Bioinformática, Instituto de Núcleo de Pesquisa em Bioinformática, Instituto de Matemática e Estatística da USP, São PauloMatemática e Estatística da USP, São Paulo

• Laboratório de Bioinformática do LIKA/UFPE, Recife, PELaboratório de Bioinformática do LIKA/UFPE, Recife, PE• Laboratório de Evolução Molecular e Bioinformática da Laboratório de Evolução Molecular e Bioinformática da

UNIFESP, São PauloUNIFESP, São Paulo• Centro de Bioinformática, Laboratório Nacional de Centro de Bioinformática, Laboratório Nacional de

Computação Científica (LNCC), Rio de JaneiroComputação Científica (LNCC), Rio de Janeiro

Brazilian Bioinformatics LabsBrazilian Bioinformatics Labs

• Grupo de Bioinformática da Grupo de Bioinformática da Faculdade de Ciências Agrárias e Faculdade de Ciências Agrárias e Veterinárias da Unesp de Jaboticabal, SPVeterinárias da Unesp de Jaboticabal, SP

• Laboratório de Bioinformática do Instituto de Informática da Laboratório de Bioinformática do Instituto de Informática da UFRGSUFRGS

• Laboratório de Bioinformática do Departamento de Laboratório de Bioinformática do Departamento de Informática da UFPEInformática da UFPE

• Laboratório de Bioinformática da USP de Ribeirão PretoLaboratório de Bioinformática da USP de Ribeirão Preto• Laboratório de Bioinformática da Universidade Católica de Laboratório de Bioinformática da Universidade Católica de

BrasiliaBrasilia• Laboratório de Bioinformática do CENARGEM/EMBRAPA, Laboratório de Bioinformática do CENARGEM/EMBRAPA,

Brasilia, DFBrasilia, DF• Projeto de Bioinformatica do CNPTIA/EMBRAPA, Campinas, SPProjeto de Bioinformatica do CNPTIA/EMBRAPA, Campinas, SP

• Grupo de Bioinformática da Grupo de Bioinformática da Faculdade de Ciências Agrárias e Faculdade de Ciências Agrárias e Veterinárias da Unesp de Jaboticabal, SPVeterinárias da Unesp de Jaboticabal, SP

• Laboratório de Bioinformática do Instituto de Informática da Laboratório de Bioinformática do Instituto de Informática da UFRGSUFRGS

• Laboratório de Bioinformática do Departamento de Laboratório de Bioinformática do Departamento de Informática da UFPEInformática da UFPE

• Laboratório de Bioinformática da USP de Ribeirão PretoLaboratório de Bioinformática da USP de Ribeirão Preto• Laboratório de Bioinformática da Universidade Católica de Laboratório de Bioinformática da Universidade Católica de

BrasiliaBrasilia• Laboratório de Bioinformática do CENARGEM/EMBRAPA, Laboratório de Bioinformática do CENARGEM/EMBRAPA,

Brasilia, DFBrasilia, DF• Projeto de Bioinformatica do CNPTIA/EMBRAPA, Campinas, SPProjeto de Bioinformatica do CNPTIA/EMBRAPA, Campinas, SP

National Genomics ProjectNational Genomics Project

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

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

National Bioinformatics AimsNational Bioinformatics Aims

• To support the development of new To support the development of new knowledge in computational bioinformatics; knowledge in computational bioinformatics;

• To strenghten and consolidate existing To strenghten and consolidate existing bioinformatics groups; bioinformatics groups;

• To support the development of software for To support the development of software for genomics, proteomics and metabolomics genomics, proteomics and metabolomics research; research;

• To develop specialized services; To develop specialized services; • To further the creation and expansion of To further the creation and expansion of

private bioinformatics enterprises private bioinformatics enterprises

• To support the development of new To support the development of new knowledge in computational bioinformatics; knowledge in computational bioinformatics;

• To strenghten and consolidate existing To strenghten and consolidate existing bioinformatics groups; bioinformatics groups;

• To support the development of software for To support the development of software for genomics, proteomics and metabolomics genomics, proteomics and metabolomics research; research;

• To develop specialized services; To develop specialized services; • To further the creation and expansion of To further the creation and expansion of

private bioinformatics enterprises private bioinformatics enterprises

Education in BioinformaticsEducation in Bioinformatics

• There are no bioinformatics courses at undergraduate There are no bioinformatics courses at undergraduate level in Brazil; only isolated disciplines in a few biology level in Brazil; only isolated disciplines in a few biology and informatics courses;and informatics courses;

• There are very few graduate courses, with a small There are very few graduate courses, with a small number of masters and doctoral number of masters and doctoral

• No private companies have systematic training No private companies have systematic training programsprograms

• The professionals required for this area must have na The professionals required for this area must have na interdisciplinary vocation;interdisciplinary vocation;

• There is a clear need to expand the number of courses There is a clear need to expand the number of courses and available places and to decentralize in geographic and available places and to decentralize in geographic terms;terms;

• However, the work market is still undefined in Brazil, but However, the work market is still undefined in Brazil, but there is a recognized potential for it.there is a recognized potential for it.

• There are no bioinformatics courses at undergraduate There are no bioinformatics courses at undergraduate level in Brazil; only isolated disciplines in a few biology level in Brazil; only isolated disciplines in a few biology and informatics courses;and informatics courses;

• There are very few graduate courses, with a small There are very few graduate courses, with a small number of masters and doctoral number of masters and doctoral

• No private companies have systematic training No private companies have systematic training programsprograms

• The professionals required for this area must have na The professionals required for this area must have na interdisciplinary vocation;interdisciplinary vocation;

• There is a clear need to expand the number of courses There is a clear need to expand the number of courses and available places and to decentralize in geographic and available places and to decentralize in geographic terms;terms;

• However, the work market is still undefined in Brazil, but However, the work market is still undefined in Brazil, but there is a recognized potential for it.there is a recognized potential for it.

Example of Interdisciplinary Courses

Example of Interdisciplinary Courses

The Biology and Computer Sciences The Biology and Computer Sciences Instuttes of UNICAMP have Instuttes of UNICAMP have established na educational established na educational partnership for mutual teaching of partnership for mutual teaching of courses:courses:

• Molecular Biology for Exact Sciences Molecular Biology for Exact Sciences Students Students

• Algorithms, Data Structures and Computer Algorithms, Data Structures and Computer Programming for Biologists Programming for Biologists

• Introduction to Computational Biology Introduction to Computational Biology

The Biology and Computer Sciences The Biology and Computer Sciences Instuttes of UNICAMP have Instuttes of UNICAMP have established na educational established na educational partnership for mutual teaching of partnership for mutual teaching of courses:courses:

• Molecular Biology for Exact Sciences Molecular Biology for Exact Sciences Students Students

• Algorithms, Data Structures and Computer Algorithms, Data Structures and Computer Programming for Biologists Programming for Biologists

• Introduction to Computational Biology Introduction to Computational Biology

The Center for Biomedical Informatics

The Center for Biomedical Informatics

• The Center for Distance EducationThe Center for Distance EducationIts mission is to support the development of on-line Its mission is to support the development of on-line courses in biology and health and to investigate new courses in biology and health and to investigate new technologiestechnologies

• The e*pub Group of Electronic Publications in Biology The e*pub Group of Electronic Publications in Biology and Medicineand MedicineIts mission is to publish journals, books and magazines Its mission is to publish journals, books and magazines in electronic and on-line format and to investigate new in electronic and on-line format and to investigate new models and technologiesmodels and technologies

• The Internet Bionformatics ProjectThe Internet Bionformatics ProjectAims at exploring and developing new tools and Aims at exploring and developing new tools and techniques to revolutionize computational biology using techniques to revolutionize computational biology using the Internetthe Internet

• The Center for Distance EducationThe Center for Distance EducationIts mission is to support the development of on-line Its mission is to support the development of on-line courses in biology and health and to investigate new courses in biology and health and to investigate new technologiestechnologies

• The e*pub Group of Electronic Publications in Biology The e*pub Group of Electronic Publications in Biology and Medicineand MedicineIts mission is to publish journals, books and magazines Its mission is to publish journals, books and magazines in electronic and on-line format and to investigate new in electronic and on-line format and to investigate new models and technologiesmodels and technologies

• The Internet Bionformatics ProjectThe Internet Bionformatics ProjectAims at exploring and developing new tools and Aims at exploring and developing new tools and techniques to revolutionize computational biology using techniques to revolutionize computational biology using the Internetthe Internet

Internet Application IdeasInternet Application Ideas

• High performance remote database miningHigh performance remote database mining• Automated discovery and intelligent agents Automated discovery and intelligent agents

in distributed networksin distributed networks• Artificial neural networks over the WebArtificial neural networks over the Web• Dynapaper: dynamic electronic papers in Dynapaper: dynamic electronic papers in

biotechnologybiotechnology• Distance education in bioinformatics, Distance education in bioinformatics,

molecular biology and genetic engineeringmolecular biology and genetic engineering

• High performance remote database miningHigh performance remote database mining• Automated discovery and intelligent agents Automated discovery and intelligent agents

in distributed networksin distributed networks• Artificial neural networks over the WebArtificial neural networks over the Web• Dynapaper: dynamic electronic papers in Dynapaper: dynamic electronic papers in

biotechnologybiotechnology• Distance education in bioinformatics, Distance education in bioinformatics,

molecular biology and genetic engineeringmolecular biology and genetic engineering

ConclusionsConclusions