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Innovation Systems for R&D in Genomics

Transforming CSIR to Council for Scientific & Innovative Research. Innovation Systems for R&D in Genomics. Prof. Samir K. Brahmachari. Director Institute of Genomics and Integrative Biology Council of Scientific & Industrial Research Delhi 110007, INDIA. Meeting on

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Innovation Systems for R&D in Genomics

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  1. Transforming CSIR to Council for Scientific & Innovative Research Innovation Systems for R&D in Genomics Prof. Samir K. Brahmachari Director Institute of Genomics and Integrative Biology Council of Scientific & Industrial Research Delhi 110007, INDIA Meeting on National Innovation Systems (NIS) of India New Delhi, 19th September, 2006

  2. What do innovators do? • Connect unconnectable • See beyond what is visible • Expect the unexpected • Celebrate naiveté: do not know, can not be done • Enjoy contradictions, shun consistency • Remember: Experiments never fail, mind does

  3. DREAMS STRATEGY & INNOVATION PASSIONATE DESIRE ACTION REALITY

  4. Key Elements of Success Creativity counts Knowledge matters • innovations transform • incentives inspire

  5. Innovations in R&D Strategy Case Studies: • Human Genome Project: Dream to Reality • Transformation of IGIB: From importer of chemicals and R&D support service centre to leading Institute in genomics

  6. Genomics: Opportunities and Challenges in India Indian Resource for Genomics Large Population Extended Families Genetic Diversity Rich Traditional Knowledge Computational Skill Genome Informatics Molecular Genetics Functional Analysis of Genome sequence

  7. Evolution of IGIB • Institute of Genomics & Integrative Biology • Focus on knowledge generation and dissemination in the area of Genomics & Bioinformatics Establishment of Functional Genomics Unit (FGU) at CBT • Center for Biochemical Technology • Focus on Reverse engineering • Centre for Biochemicals • Focus on chemical import substitutes 2002 1998 1992 Institute has transformed from an isolated laboratory working in the area of biochemical research to a laboratory dedicated to genomics research. 1977

  8. Busiworld(Genome Function) 7 - 21 JULY 1998

  9. Business World(Housed in small) 7 - 21 JULY 1998 ...

  10. Business World( ... 7 - 21 JULY 1998

  11. Bussiness World November,2002

  12. IGIB’s Transformation Story 1998 2000 2002 2003 2004 2005 2005 2005 2005 2005 2005 2006 2005-2006 • IGIB established largest clinical network in India • First Knowledge Alliance ‘GenoMed’ with NPIL • G.N. Ramachandran Knowledge Centre for Genome Informatics established through private funding to attract IT Professionals • First Bioinformatics Software of CSIR Commercialized • Largest Private – Public partnership TCGA (The Centre for Genomic Application co-shared facility) established • First Genomic marker for drug response discovered • Largest High Performance Computing facility (4.7 tera flops) established • India’s highest number of co-authored (158) paper published • First Recombinant Growth Factor drug REGEN-D launched (Technology Award 2006) • HP Centre of Excellence in Bioinformatics in Asia. • IGIB among the World’s best Bioinformatics Institutes for developing PML 2 protocol • First Bioincubator “Eclosion” being established • IGIB attains highest number of paper, total IF, Patents and ECF per scientist

  13. Improvement in Quality of Publications

  14. IF > 2 IF > 4 Average Quality of Publications (IF> 2 and IF>4) Number

  15. Synergistic Growth of Young Scientific Man Power at IGIB 1997-2006

  16. R&D & TECHNOLOGY MANAGEMENT: APPROACH & STRATEGY B2. Setting up New R&D Models : G.N. Ramachandran Knowledge Centre The G.N. Ramachandran Knowledge Centre has been established at IGIB for promotion of human resource development in the field of Bioinformatics. The Centre utilizes the philanthropic funds from the industrial concerns, like The Chatterjee Group, for granting scholarships to the deserving and bright students. The objective is to retain young bright minds in the country by offering them fellowships at competitive rates and to develop the human resource for future needs of the country. The BTech students with IT expertise from the best institutions like IIT Kanpur were attracted & join the centre. Leading Indian scientists like Prof. C. Ramakrishnan FNA, Molecular Biophysics Unit, IISc has become a distinguished fellow of the GNR Knowledge Centre at IGIB to teach and help our scientists and students in the area of Structural Biology. Need to Set Up Knowledge Center in CSIR Labs Students at Work in G.N.Ramachandran Knowledge Centre, IGIB Our strength Convergence of a large team of research students from various fields of Life Sciences and IT professionals Our lab is equipped with supercomputer, linux cluster, workstations and PCs with all types of operating systems

  17. Our strength: Convergence of a large team of research students from various fields of Life Sciences and IT professionals Our lab is equipped with supercomputer, linux cluster, workstations and PCs with all types of operating systems Institute of Genomics and Integrative Biology (Formerly known as Centre for Biochemical Technology) Council of Scientific and Industrial Research Mall Road, Delhi-110007, India G.N Ramachandran Knowledge Center for Genome Informatics Functional Genomics Unit • Genome Informatics activities: • Genome analysis • Repetitive Sequences analysis • Nucleosomal Positioning • In silico Gene Prediction • SNP Prediction • In silico Proteomics • Proteome Profiling insilico • Structural Genomics • Pathways Modeling • Comparative Genomics • Identification of virulence factors and drug target -SEEPATH • PLHOST-Function Prediction • PROFASE-Function assignment • Genome Calculator-Repligen Genome Analysis Insilico Proteomics Comparative Genomics Genome Informatics Pathway Modeling Structural Genomics “G.N.Ramachandran Knowledge Centre for Genome Informatics“ The Bioinformatics unit in the Institute of Genomics and Integrative Biology

  18. Networking with Industries for Bioinformatics Parallel Computing on Linux Cluster (Bio Tools) Edutech Informatics Delhi E-Learning Jalaja Technologies Bangalore ? System Biology IGIB Bioinformatics Software (TATA-BIOSUITE) IT Consortium TCS / NMITLI Microarray Design & Analysis SILICOGEN Delhi/Calcutta Genotypic Technologies Bangalore Genomed Mumbai / Delhi Bioinformatics support to Molecular Medicines HTSSS

  19. PLHOST : The First Bioinformatics product from CSIR The first bioinformatics tool from CSIR released in May 2003. This novel software will speed up the process of understanding the role of unknown proteins in various living organisms. It could also help identify new drug targets against disease-causing microorganisms.

  20. CSIR: Public Private Partnership LinearModels Old Model New Process or Product Generation Student/Scientist Curiosity driven project selection Marketing Human Resource is Exported Not Marketable Present Model Business driven R&D Marketing Wealth Creation Invention of New Process/ Product Domain Knowledge From direct R&D Job Creation

  21. CSIR: Public Private Partnership FutureModels Alliance Model Industries Market Intelligence Alliance Co-development of projects executed by Industrial partner Lab’s Domain Knowledge Part flows back as Royalty Increase of New Process/Product Industry Wealth Creation by Industry HR absorbed by Industry Marketing R&D Service Model Knowledge Based Service Centres Managed by Industries with Lab’s equity in IPR/ Services Industries Marketing Skill, Manpower & Operating Expenses Alliance Lab’s Capital Facility, Knowledge and Expertise Services IPR Generation Industries in Core Sectors: Pharma, Genomics, Bioinformatics etc benefits Part flows back as Royalty/Services Marketing of IPR for Wealth Generation

  22. IGIB, NPIL CSIR the R & D Institution Project GenoMed An Independent R&D Entity IGIB-NPIL- Knowledge Alliance Knowledge through generation of ideas & formulation of commercially viable R & D plan for Genomic Medicine Brings in Finances, assets, H.R. & Management Knowledge Alliance Jointly Managed Advisory Board • Evaluation of lab-scale processes • Financial, Managerial & Infrastructure support • Commitment to commercialization Commitments to: • Provide technical services/training. • Provide spare capacity of facilities • Following standard CSIR/Industry contractual agreement. To Undertake Business Driven R & D in Genomic Medicine

  23. Normal Flow Chart of Projects (Applicable Research) Functional Genomics Strategy : Why Genomed Based on Resource Planning Dynamic work plan based on Global Development 1. What to do... 1. What to do... 2. How to do... 2. How to do... Networking & Innovative Ideas Cost Effective Way 3. To do... 3. To do... Publication New Project 4.To Generate Knowledge,Sell/Market/ Technology Transfer 4. To Generate Knowledge Genetic Resource Further Research FGU IPR To be Licensed Knowledge Alliance Industry IPR Absorbed Human Resource Human Resource 5. What to do that sells... B.D.R.D. G E N O M E D Technology & Knowledge Transfer Brain Drain 6. Teach How to do... G E N E Q U E S T 7. Industry Implements... 8. Industry Markets...

  24. Council of Scientific & Industrial Research Department of Science & Technology Institute of Genomics & Integrative Biology Drugs & Pharmaceutical Research Program The Chatterjee Group The Centre for Genomic Application

  25. TCGA aims to….. Create research facilities, infrastructure and work ambience of international quality to support R&D Institutions, Universities and Industry to carry out cutting edge research and make new discoveries. Liberate scientists from mundane day to day activities of managing research facilities by enabling usage of such facilities on a “charge for service basis”. Centralize operations of major facilities to optimize utilization on a time share basis.

  26. TCGA aims to….. Optimize governmental expenditure in future by replacing capital expenditure with operational expenditure. Nurture the growth of Biotechnology/Pharmaceutical Industry in the country through incubation facilities for start-up entrepreneurs. Catalyze genomic revolution in Indian R&D sector to bring affordable healthcare benefit for the people of India.

  27. TCGA : Present and Future Now….. Speeding up research:Core Share facility for Genomics and Proteomics Services In Future….. Nurturing Entrepreneurs:Incubation Laboratories for start up entrepreneurs Enabling Discovery:Laboratory Facilities to scientists of national and international fame to implement their vision

  28. TCGA: a New Tourist Destination in Delhi Some important Visitors at TCGA, 2006 Lord David Sainsbury, Ministry of Science & Innovation U.K.Dr.Tony Rahilly, National Research Council, Canada and team David E. Thompson, Eli Lily Asia,Inc., USA and team Dr.Gilbert S. Omenn, The Universtiy of Michigan Medical School, USA Dr. Maria C. Freire, CEO, Global Alliance for Development, USA Prof. Richard Larkins, VC & President, Monash University, Australia and team Adam Saffer, Research Triangle Institute, USA Dr. John G. Houston, Birstol-Myers Squibb Company, USA and team Dr.Huanming Yang, Beijing Genomics Institute, China and team Dr. Jun Wang, Beijing Genomics Institute, China Prof. Nadav Liron, Samuel Neiman Institute, Israel and team Dr. Yukata Akiyama, CBRC, Japan and team Dr. Kuber T. Sampath, VP, Genzyme Corporation, USA Vinod K. Goel, The World Bank, USA …and many more Lal Qila Connaught Place Qutab Minar The Centre for Genomic Applications Lotus Temple

  29. “ECLOSION” Bioincubator @ IGIB/TCGA Road map

  30. Nodal Laboratory: Institute of Genomics & Integrative Biology, Delhi Project planning Samir K. Brahmachari, Abhay Sharma, Mitali Mukerji (IGIB); Kunal Ray, Susanta Roychoudhury (IICB); Lalji Singh, G. R. Chandak, K. Thangaraj (CCMB); Saman Habib (CDRI) D. Parmar (ITRC); Partha P. Majumder (ISI) Implementation Samir K. Brahmachari, Mitali Mukerji, Shantanu Sengupta, Dwaipayan Bharadwaj, Debasis Dash (IGIB); Kunal Ray, Susanta Roychoudhury (IICB); G. R. Chandak (CCMB); Saman Habib, Srikanta K. Rath (CDRI); D. Parmar, R. Shankar (ITRC); Jagmohan Singh (IMTECH) Population identification Partha P. Majumder (ISI); Mitali Mukerji, Komal Virdi, Samira Bahl (IGIB); V. R. Rao, K. Thangaraj (CCMB); Saman Habib, Srikanta Rath, Swapnil Sinha, Ashok Singh, Amit Mitra, Shrawan K. Mishra (CDRI); D. Parmar (ITRC); B. R. K. Shukla (Lucknow University) Sample collection Shantanu Sengupta, Dwaipayan Bharadwaj, Mitali Mukerji, Qadar Pasha, Souvik Maiti, Abhay Sharma, Samira Bahl, Komal Virdi, Amitabh Sharma, Jitender Kumar, Aarif Ahsan, Tsering Stobdan, Chitra Chauhan, Saurabh Malhotra, Ajay Vidhani, S. Siva, Aradhita Baral, Rajesh Pandey, Ravishankar Roy, Mridula Singh, S. P. Singh (IGIB); Nitin Maurya (University of Delhi); Arun Bandyopadhyay, Susanta Roychoudhury, Ganga Nath Jha, Somnath Dutta, Gautam Ghosh, Tufan Naiya (IICB); K. Thangaraj, G. R. Chandak, Manoj Jain (CCMB); Saman Habib, Srikanta Rath, Swapnil Sinha, Ashok Singh, Amit Mitra, Shrawan K. Mishra, J. P. Srivatava, J. R. Gupta (CDRI); Vinay Khanna, Alok Dhawan, Mohini Anand, R. Shankar, R. S. Bharti, Madhu Singh, Arvind P. Singh, Anwar J. Khan, D. Parmar (ITRC); Kamlesh Kumar Bisht, Ashok Kumar (IMTECH) SNP discovery Shantanu Sengupta, Dwaipayan Bharadwaj, Mitali Mukerji, Qadar Pasha, Balaram Ghosh, Abhay Sharma, Swapan Kumar Das Taruna Madan, Chitra Chauhan, Ranjana Verma, Uma Mittal, Samira Bahl, Amitabh Sharma, Jitender Kumar, Anubha Mahajan, Sreenivas Chavali, Rubina Tabassum, Vijaya Banerjee, Jyotsna Batra, Rana Nagarkatti, Shilpy Sharma, Mamta Sharma, Rajshekhar Chatterjee, Jinny A. Paul, Pragya Srivastava, Rupali Chopra, Aradhita Baral, Ankur Saxena, Charu Rajput, Prashant Kumar Singh, Aarif Ahsan, Tsering Stobdan, Mudit Vaid (IGIB); Kunal Ray, Susanta Roychoudhury, Sumantra Das, Keya Chaudhuri, Rukhsana Chowdhury, Arun Bandyopadhyay, Arijit Mukhopadhyay, Moulinath Acharya, Ashima Bhattacharyya, Atreyee Saha, Arindam Biswas, Moumita Chaki, Arnab Gupta, Saibal Mukherjee, Suddhasil Mookherjee, Ishita Chattopadhyay, Taraswi Banerjee, Meenakshi Chakravorty, Chaitali Misra, Gourish Monadal, Shiladitya Sengupta, Ishani Deb, Arunava Banerjee, Rajdeep Chowdhury, Amalendu Ghosh, Kalidas Paul, Priyanka De, Sumita Mishra (IICB);G. R. Chandak, K. Thangaraj, Rachna Shukla, G. S. Ramalakshmi, Pankaj Khanna, M. Mohd. Idris, K. Radha Mani, Seema Bhaskar, Swapna Mahurkar, Shalini Mani Tripathi, V. N. S. Prathyusha, V. Prasad Kolla, J. Hemavathi, Nikita Thakur (CCMB);Swapnil Sinha, Ashok Singh, Amit Mitra, Shrawan K. Mishra (CDRI); Madhu Singh, Arvind P. Singh, Anwar J. Khan, R. Shankar, Deepa Agarwal, D. Parmar (ITRC); Jagmohan Singh, Rupinder Kaur, Kamlesh Kumar Bisht, Ashok Kumar (IMTECH)  Repeat discovery and analysis Mitali Mukerji, Komal Virdi, Uma Mittal, Aradhita Baral, Rajesh Pandey (IGIB); Kunal Ray (IICB) HTSSS implementation Samir K. Brahmachari, Mitali Mukerji, Debasis Dash, Manoj Hariharan, Shantanu Sengupta, Siddharth Singh Bisht, Dipayan Dasgupta, Mridula Singh, Sangeeta Khanna (IGIB); Keya Chaudhuri, Susanta Roychoudhury, Kunal Ray (IICB); Saman Habib (CDRI); Ranjan Basu, Biswajit Das, Shuvankar Mukherjee, Jhuma Mukherjee, Debasish Saha (Silicogene); Pallab Banerjee, Bijoyesh Saha, Anirban Chatterjee, S. R. Moquim, Navneet Kwarta, Manish Kumar, Debkumar Sinha (Labvantage Asia) Data analysis, monitoring and database development Partha P. Majumder (ISI); Mitali Mukerji, Swapan Kumar Das, Chitra Chauhan, Samira Bahl, Komal Virdi, Uma Mittal, Ranjana Verma, Debasis Dash, Manoj Hariharan, Mridula Singh, Rajesh Pandey, Shantanu Sengupta, Dwaipayan Bharadwaj, Balaram Ghosh, Qadar Pasha, Taruna Madan, Samir K. Brahmachari (IGIB); Kunal Ray, Susanta Roychoudhury, Sumantra Das, Keya Chaudhuri, Rukhsana Chowdhury, Arun Bandyopadhyay (IICB); Shrish Tewari, G. R. Chandak, Lalji Singh (CCMB); Swapnil Sinha, Ashok Singh, Amit Mitra, Shrawan K. Mishra (CDRI); Madhu Singh, Arvind P. Singh, Anwar J. Khan, R. Shankar, A. Dhawan, V. K. Khanna, D. Parmar (ITRC); Jagmohan Singh, Balvinder Singh, G. P. S. Raghava (IMTECH) Genotyping, sequencing, primer synthesis management Mitali Mukerji, Shantanu Sengupta, Neelam Makhija, Abdur Rahim (IGIB); K. Narayanasami, Arindam Maitra, Sangeeta Sharma, Ruchi Chawla, Suruchika Soni, Preeti Khurana, Sushanta Das Sutar, Amit Tuteja, Mohd. Nadeem Khan, Abhishek Chandragupta, Pooja Rana, M. Chidambaram (TCGA); Kunal Ray, Susanta Roychoudhury, Sumantra Das, Keya Chaudhuri, Rukhsana Chowdhury, Arun Bandyopadhyay, Arijit Mukhopadhyay, Moulinath Acharya, Ashima Bhattacharyya, Atreyee Saha, Arindam Biswas, Moumita Chaki, Arnab Gupta, Saibal Mukherjee, Ishita Chattopadhyay, Taraswi Banerjee, Meenakshi Chakravorty, Chaitali Misra, Gourish Monadal, Shiladitya Sengupta, Ishani Deb, Arunava Banerjee, Rajdeep Chowdhury, Amalendu Ghosh, Kalidas Paul, Priyanka De, Sumita Mishra (IICB); K. Thangaraj, G. R. Chandak (CCMB); Swapnil Sinha, Ashok Singh, Amit Mitra, Shrawan K. Mishra, Bipin C. Mishra (CDRI); Madhu Singh, Arvind P. Singh, Anwar J. Khan, Deepa Agarwal, R. Shankar, D. Parmar (ITRC); Jagmohan Singh (IMTECH) The Indian Genome Variation Database Consortium 158 Author paper from CSIR

  31. 4.7Teraflops Compute Power CSIR HQ HP XC3000 288 Node Cluster The Facility Ranked 158th among Worlds TOP 500 Supercomputing Facilities and Listed in Top 10 in Life Science category Cluster Consists of 8 Head Nodes 4 Storage Node 276 Compute Nodes 10 Terabyte Central Storage 288 Port Voltaire IB Switch Established the VPN Network Physical networking of CSIR Institutes brings scientists shoulder to shoulder

  32. 4.7Teraflops Compute Power HP XC3000 288 Node Cluster Cluster Consists of 8 Head Nodes 4 Storage Node 276 Compute Nodes 10 Terabyte Central Storage 288 Port Voltaire IB Switch Each Node Consists of Intel XeonR2 Dual Core 3.6 GHz Processors 1 MB Cache Each CPU 2 GB REG. Memory Infiniband Interconnect Fabric Interconnect Gigabyte Ethernet interconnect The Facility Ranked 158th among Worlds TOP 500 Supercomputing Facilities.

  33. LAB BENCH TO BED SIDE…1997-1999-2005 Diabetic Foot Ulcer Burn Wound IGIB – Bharat Biotech Collaboration Work Done & Technology Transferred: IX th Plan Outcome:X th Plan National Technology Award, 2006

  34. Pre competitive positioning of CSIR's Knowledge and Technology Base Market demand Exists Market Exists Market may evolve No clue about market 1 2 3 4 Knowledge exists, Technology exists A Knowledge exists, Technology needs to be developed B Knowledge exists, No clue about Technology C D Role of MBA Potato chips Pringles Chips Development of Predictive Medicine (i) in 1997 (ii) in 2003 RISK Role of S & T Personnel ii Problem exists, Knowledge needs to be developed Pure water at 50p/lit Low Cost Solar cell i Designed microbes as Industrial warker eg.Creating H2 Fuel eg.CO2 + H2O > Glucose& Sucrose

  35. Dream Dream Dream Dreams Transform into thoughts And thoughts result into action

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