OPPORTUNITIES FOR THE PAKISTANI IT INDUSTRY WITHIN BIOINFORMATICS MINISTRY OF INFORMATION TECHNOLOGY GOVERNMENT OF PAKISTAN ISLAMABAD DECEMBER 2005 Copyright © 2005 Pakistan Software Export Board (G) Ltd. Ministry of Information Technology Government of Pakistan Printing December 2005 Printed by Roohani Art Press Blue Area Islamabad. Ph: 051-2873274-2206849 Published by Pakistan Software Export Board The Funding Agency The research study “Opportunities for the Pakistani IT Industry within Bioinformatics” is funded by the Pakistan Software Export Board (PSEB). PSEB is the entity within Government charged with the task of enhancing exports of software and IT enabled services (ITES) from Pakistan. PSEB is a guarantee limited company totally owned and funded by the Government of Pakistan. Any questions or comments about this report may be directed to PSEB Islamabad at 92-51-111-333-666 or through e-mail at [email protected] . Disclaimer The report is published by PSEB for the use of its members, the Pakistani IT industry, people working in bioinformatics and other relevant stakeholders. This report is the culmination of a project undertaken by the consultant with support from PSEB to conduct research on the field of Bioinformatics, its application areas and the role of IT, specifically with reference to Pakistan. The study incorporates feedback from PSEB, Ministry of IT and Telecom (MOITT), academia and leading research organizations working in the field of Bioinformatics. It faithfully reports what the consultant found to be the on-the-ground reality of the business opportunities for the Pakistani IT Industry within Bioinformatics and accurately reflects (and wherever possible attributes to others) the opinions the consultant was able to form on the basis of discussions and onsite visits to research organizations, educational institutes, and companies. To that effect, the report solely reflects the views of the consultant and may or may not reflect those of Pakistan Software Export Board (PSEB), the Ministry of IT and Telecom (MOITT), or the Government of Pakistan (GOP). The study advisors or the contributors are not responsible, in any way possible, for the errors/omissions in this report. This report is a best intentioned effort to disseminate information about the state of bioinformatics as an industry in Pakistan and should not be used as a sole means of advice for making investment decisions. PSEB does not accept any liability for any direct and consequential use of this report or its contents. The contents of this report may be reproduced only after prior permission from PSEB. C o n t e n t s Page # Executive Summary 1 1- Introduction to Bioinformatics What is bioinformatics 6 The Human Genome Project 6 Utility of the Genome Data 6 Biotechnology and Bioinformatics 7 2- Applications of Bioinformatics 8 3- A Classification of Tasks in Bioinformatics 9 4- Industry Characteristics Estimation of Bioinformatics Market 10 Estimation of the Size of Industry 10 Market Estimate Based upon Sales 10 Segment-wise application of Bioinformatics 11 Bioinformatics and Drug Discovery 12 Drug Discovery Steps involved in bringing a Drug to Market Role of Information Technology in Drug Development The Need for Bioinformatics in Pharmaceutical Research 5- The Role of IT in Bioinformatics Summary of IT Processes in Bioinformatics 14 Electronic Data Capture 14 Data Mining 15 Data Warehousing 15 Data Visualization 15 Customized Software 15 Bioinformatics Products 15 6- Application Areas in Bioinformatics and the use of IT Genomics 17 Functional Genomics and Microarray Technology 19 Organizing Biological Knowledge in Databases 20 Mirror Databases / Mirror Sites Structural Bioinformatics 21 Drug Discovery 22 Proteomics 24 Pharmacogenomics and the Era of Personalized Medicine 25 7- Fields at the Periphery of Bioinformatics Laboratory Information Management Systems (LIMS) 27 Laboratory Automation 28 Medical Informatics and Bioinformatics 30 Clinical Trials Business 32 Case Study: Quintiles India 8- Business Models in Bioinformatics Industry Outsourcing 35 Proposed Model for Informatics-enabled Solutions 36 Reverse Brain Drain 38 Essential Components of a Bioinformatics Company 38 Possible Partnership 39 Partnership Challenges 40 Strengths of Developing Countries 41 Weaknesses of Developing Countries 42 9- Building Bioinformatics Capacity Building Bioinformatics Infrastructure 44 Trends for the Future 44 10- Bioinformatics Business in India and its Comparison with Pakistan Government Policies on Bioinformatics 46 Biotechnology Information System Network (BTISnet) 47 Research and Development 48 Databases and Mirror Sites 48 Biogrid India 48 India’s scientific workforce 49 India’s workforce in bioinformatics 49 Pharmaceutical and biotech industry 50 Investment in Biotechnology and Bioinformatics 50 Bioinformatics Companies in India 50 11- Bioinformatics Education Institutes in India 61 12- Bioinformatics Business and Education Institutes in Canada 66 13- Bioinformatics Business and Education in Selected Countries Australia 77 Japan 79 Europe 80 Bioinformatics in Denmark 81 Bioinformatics Education in United Sates 82 14- Bioinformatics Education in Pakistan 83 Mohammad Ali Jinnah University, Islamabad International Islamic University, Islamabad COMSATS University, Islamabad Baluchistan University of Information Technology and Management Sciences, Quetta 15- Possible Partners in Bioinformatics Business HEJ Research Institute of Chemistry, Karachi 86 Panjwani Centre for Molecular Medicine and Drug Research, Karachi 87 NIBGE, Faisalabad 88 Centre for Excellence in Molecular Biology, Lahore 90 Aga Khan University, Karachi 92 16- Use of Agricultural Biotechnology for Pakistan 93 17- Results of the Survey of Stake Holders 95 18- Opportunities and Threats 106 19- Recommendations Awareness 111 Business Model Development 111 Development of Human Resources 117 Appendices Appendix 1 Course Outlines of Bioinformatics Educational Institutes 121 Appendix 2 List of Scientists Working in Biotechnology in Pakistan 130 Appendix 3 List of projects in Biological Sciences funded by HEC 133 Appendix 4 Databases produced by Pakistan Agriculture 144 Research Council Appendix 5 List of on going projects at Aga Khan University 146 Appendix 6 Bioinformatics tools and Softwares 151 Glossary of important terms 156 Bioinformatics Workshop – List of Participants 164 About the Authors and the Team 165 Executive Summary An Overview of the Project The present report explore the question ‘whether bioinformatics can be considered as a potential business opportunity for the Pakistani IT Industry’, ‘what are the existing competencies of biologists that can be cashed upon in this respect’ and ‘what are the potential problems that will be faced by Pakistan in the process’. It provides an overview of the global bioinformatics industry, its segmentation, educational institutions, bioinformatics products and leading companies. The report also presents bioinformatics industry in India, Canada and a few other countries and explores the reasons behind emergence of India as a global bioinformatics hub in the developing world. Finally, it concludes with a list of suggestions compiled in consultation with a group of about 50 biological scientists, IT professionals and bioinformatics education providers, on the steps that should be taken by Pakistan to develop bioinformatics potential. Key objectives of the project were the following: i. Review of available information and data to develop a comprehensive understanding of the status and potential of IT within bioinformatics as a discipline in Pakistan. ii. Assessment of issues and constraints in the development of bioinformatics, both as a discipline and industry and identification of key factors for developing this field in Pakistan. iii. Identification of opportunities for Pakistan’s IT industry for collaborative ventures to enable them to obtain a share of the global bioinformatics business. iv. Identifying the enabling measures to facilitate the development and growth of bioinformatics and IT industry to develop in this field. v. Preparing a medium term strategy to this end. These objectives were achieved by using a combination of primary and secondary data. The primary data was collected by conducting in-depth interviews while secondary data was collected by conducting desk research. An initial desk research was carried out to gain background knowledge of the subject as well as to identify the stakeholders in bioinformatics business. Major part of objectives i, iii and iv were covered by conducting desk research. For this purpose published reports and statistics either electronic or in hardcopy were utilized through scientific journals, business reports, industry and technological magazines and online databases. A multidisciplinary team of researchers having background in Bioinformatics, Computer Science, Social Sciences and Biology was deployed for the purpose. A survey of potential stakeholders of bioinformatics business was done to estimate the current state of biological research in the country, research interests of different groups, opinion on bioinformatics, use of bioinformatics software and identification of opportunities in local and international markets. Opportunities for the Pakistani IT Industry within Bioinformatics 1 For the in-depth interviews, the sample was divided into 4 groups. Group 1. Scientists working in biological sciences/ medicine. Group 2. Information