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Bioinformatics Centre - A Profile Commissioning of the Centre 1992-93 Phone : +91 413 2655212 Fax : +91 413 2655211/265

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Presentation on theme: "Bioinformatics Centre - A Profile Commissioning of the Centre 1992-93 Phone : +91 413 2655212 Fax : +91 413 2655211/265"— Presentation transcript:

1 Bioinformatics Centre - A Profile Commissioning of the Centre Phone : Fax : /265 University webpage: Centre website: BIOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSITY

2 About University Pondicherry University is a Central University established by an Act of Parliament No. 53 of 1985 fully supported by the University Grants Commission. Pondicherry University was the first to provide the students with the Choice Based Credit System (CBCS) BIOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSITY

3 School of Life Sciences The University is organized at several levels for efficient functioning (Schools/Departments/Centres). The School of Life Sciences comprises the following Departments / Centres viz., Department of Biochemistry & Molecular Biology, Department of Biotechnology, Department of Ecology and Environmental Science, Department of Ocean Studies & Marine Biology, Centre for Pollution Control & Energy Technology and Bioinformatics Centre. BIOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSITY

4 Bioinformatics Centre Centre was established as Sub-Distributed Information Centre (Sub-DIC) with support of DBT 1995Service provider with facilities for sequence retrieval and analysis and abstract services 2001Started one year Advanced Post Graduate Diploma course in Bioinformatics 2004Sub-DIC was upgraded as a full-fledged center with DIC Status 2005Started Molecular Modeling facility (Silicon Graphics System with Insight-II & DS Modeling server) and Linux based Beowulf type Clustering BIOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSITY

5 Personnel Teaching Teaching Coordinator Prof. P.P. Mathur Reader1 No. (Vacant) Lecturer Dr. D. Sundar Lecturer 1 No. (Vacant) Temporary Faculties 3 Nos. Technical Technical Information Officer Mr. M. Sundara Mohan Technical AssistantMs. V. Amouda Computer Operator Mr. E. Selvakumar Computer Operator Ms. N. Shanthi Data Entry Operator 1 No. (Vacant) Office Office Attendant Mr. T. Gopy Temporary positions Temporary positions DBT-JRF1 No. (Vacant) DBT-Traineeship2 Nos. (Vacant) DBT-Studentship2 Nos. (Vacant) BIOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSITY

6 Activities Teaching Teaching Regular M.Sc Program in Bioinformatics (applied to UGC) Advanced PG Diploma in Bioinformatics (since 2001) Training Training Regular Training Programs (Short term & Long term) Research Research Molecular Dynamics simulation of Human Transferrin Protein Engineering of DNA-binding Proteins Database and Software Development Extension Extension Development of E-Learning modules in Bioinformatics BIOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSITY

7 Teaching Program o o The Centre has been offering an Advanced Post Graduate Diploma Course in Bioinformatics since the Academic year with the support from Department of Biotechnology, New Delhi o o The students are selected through a competitive examination conducted at the All India Level in 14 Centres in the month of June followed by a personal interview o o Only those candidates who have Master’s degree in any branch of Biological Sciences, Molecular Biology/ Biotechnology/ Biochemistry/ Biophysics/ Microbiology/ M.B.B.S/ Life Sciences/ Botany/ Zoology are currently eligible to join the Advanced PG Diploma program in Bioinformatics. o o A sum of Rs. 5000/- per month is offered as a stipend to the selected students. BIOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSITY

8 Students Placements o o Johns Hopkins University, Baltimore, USA o o HCL Technologies Limited o o Institute of Bioinformatics, Bangalore o o Protein Lounge, Orissa o o Central Sericulture Research & Training Institute, Mysore o o Vector Control Research Centre, Pondicherry o o Orissa Agricultural University, Orissa o o HNB Garhwal University, Srinagar o o University of Madras, Chennai o o Pondicherry University, Pondicherry BIOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSITY

9 Training Program o Training Programs (Short term) The Bioinformatics Centre regular short term training program every year during Jan-Feb. We have so far conducted 18 National Level Seminars / Workshops / Training Programs since o Training Programs (Long term) The Centre accepts students who have qualified the DBT-Junior Research Fellowship All India Examination for the Ph.D. program in Bioinformatics. DBT has sanctioned two positions each for Traineeship and Studentship in Bioinformatics every year. The students selected under these two schemes will be awarded a stipend of Rs per month. BIOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSITY

10 Forthcoming Seminars National Seminar on "Intellectual Property Rights in Bioinformatics & Biotechnology" to be organized by our Centre during September 15-16, National Seminar on "Advances in Nanosciences and Nanobiotechnology" to be organized by our Centre during December 05-06, National Seminar on "Bioinformatics and Functional Genomics" to be organized by our Centre during February 15-17, BIOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSITY

11 Infrastructure - Hardware Servers WiproProcessor: Ghz; RAM: 1 GB; HDD: 120 GB; OS:Red Hat Linux 9; 12/24GB-DAT drive 1 HCL (AMD Opteron 64 BIT) Processor: AMD 8131/8111 Motherboard (Dual Processor Capable); RAM: 1 GB; HDD: 100 GB; OS:Windows 2003 Server; 12/24GB-DAT drive; 1 HP-VectraProcessor: Pentium Mhz; RAM:128 MB; HDD:30 GB; OS: Red Hat Linux 9 1 Specialized Workstations Silicon Graphics (Onyx3 Fuel) Processor: 800Mhz. MIPS R16000 (IP35) with MIPS R16000 FPU; RAM: 1 GB; HDD:176 GB; OS: IRIX64 Release 6.5; Graphics: V10) 1 DSM Modeling Server Processor: Pentium Ghz.; RAM: ; HDD:40 GB; OS:Windows XP; CD-RW; DVD- RW 1 Workstation ClusterBeowulf type Cluster (Linux based) 1 Master + 5 Slaves BIOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSITY

12 Infrastructure - Hardware Workstations Workstations 25 Workstations Intel Pentium IV with Dual Operating Systems (Red Hat Linux 9 & Windows XP Professional). All workstations are connected with a domain name server on Windows 2003 server. Printers Printers HP 4600 DN Color Laser, HP 2200DN Laser printer, HP 1150 Laser Printer, HP 4P-Laser printer, HP Inkjet 5748, 810 & 670 C Accessories Accessories Sony DVD Writer, HP CD-Writer, HP Scanner, Modem, Infocus LCD Projector, Kodak Digital Camera, Sony Internal Cd-Writers, Web Camera, Toshiba Multifunctional Copier, Toshiba Multifunctional Fax and Hitachi Hi-Fax, Uninterrupted power supply (10 KVA – 1 no. & 5.0 KVA- 2 nos., 0.6 KVA UPS – 4 nos.) BIOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSITY

13 Infrastructure - Software Academic Licensed Academic Licensed Amber- Molecular Dynamics simulation AutoDock- Molecular Docking (Flexible Ligand docking) Dock- Molecular Docking (Rigid docking) GROMOS96- Molecular Dynamics simulation Modeller - Homology Modeling Phred, Phrap, Consed - Sequence Analysis Whatif- Protein Structure Modeling & validation suite Vendors Licensed Vendors Licensed Insight II 2005 (single user with 5 years term license) Affinity, Discover Bundle, Biopolymer, Homology, Ludi DS Modeling Suite 1.5 (single user with 5 years term license) Visualizer, Project KM plus, Analysis, Biopolymer, CHARMm, Delphi, LigandFit, Ligand Score, Ludi, Modeler, MS Search, Protein Families, Protein Health, Protein Similarity Search Trends Micro's Enterprise Solution (Neat Suite) Endnote Statistica BIOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSITY

14 Infrastructure - Software Academic free & Open Source suites Academic free & Open Source suites BIOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSITY

15 Infrastructure - Communication Internet Internet A 4 Mbps (Megabit per second) leased circuit Radio Link Internet connectivity from the Software Technology Parks of India (STPI), Pondicherry provides round the clock internet access. The computing facilities in the Bioinformatics Centre are available to the students round the clock on 24 hours/day, 365 days/year basis. Intranet Intranet All the buildings in the Campus are interconnected through a Fiber Optic backbone with CISCO switches and routers. The connectivity to workstations is using UTP Cable ensuring a dedicated 100 Mbps bandwidth at desktop level. The intranet acts as a platform for Internet, UGC-Infonet, Library services and University automation functions BIOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSITY

16 Bioinformatics Centre Library The INFLIBNET Centre, Ahmedabad is providing access to the scholarly e-journals under UGC-Infonet E-Journals Consortium. As part of the consortium, access to the Electronic databases/ Journals of the Science Direct is also provided through the campus-wide Intranet to our Bioinformatics Centre. The Central Library of Pondicherry University has a collection of over books and several scientific journals. The Bioinformatics Centre subscribes to several important Journals like Bioinformatics, Journal of Bioinformatics and Computational Biology (JBCB), Briefings in Bioinformatics, Nature, Nature Structural Biology, Science, Scientific American, Linux for You for its departmental library. The Bioinformatics Centre library holdings include Books (300) and Journals (8). BIOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSITY

17 Bioinformatics Centre e-Library

18 Collaborating Department The Centre has a close collaboration with the Department of Biochemistry & Molecular Biology within the School of Life Sciences. This Department is recognized for special funding under DST-FIST program and has also attracted extramural funding worth several lakhs. The Departmental Faculty has established research collaborations with foreign investigators as well as with the Bioinformatics Centre in teaching and wet-lab research. BIOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSITY

19 Infrastructure - Wet Lab UV-Visible Spectrophotometer ShimadzuUV-1700 Pharmaspec High Speed CentrifugeHitachiHimach CR 26H SorvallRC 5C Plus UltracentrifugeSorvallRC 90 Gel Documentation SystemSyngeneIngenius Gamma CounterLKB Wallac1275 Mini Gamma Liquid Scintilation CounterLKB Wallac1209 Rack Beta ELISA ReaderMultiscope Laminar Flow ChamberYorco HomogenizerPolytronPT 3000 CO 2 IncubatorVWR scientificModel 2100 Thermo FormaModel 311 BIOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSITY

20 Phase Contrast MicroscopeLeicaDM IL LynxVision 2000 PCREppendorf Deep Freezer -80°CSanyoMDF U6086S Ultrasonication (Sonifier)Branson450D MicrofugeFisherModel 235A Nitrogen AnalyzerKjel PlusDistil –M Metabolic Shaker IncubatorOrbitek Gel ElectrophoresisBioRad / Hoefer Fraction CollectorBio Rad / Hoefer Infrastructure - Wet Lab BIOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSITY

21 Research Collaborations Johns Hopkins University, Baltimore, USA Johns Hopkins University, Baltimore, USA Protein engineering of DNA recognition motifs, artificial ZF-transcription factors/repressors and in particular Zinc Finger Nucleases (ZFNs) to target and achieve highly efficient and permanent genome modification of plants and mammals including the humans. Anna University – Chennai Anna University – Chennai Molecular Modeling & High Performance / Cluster Computing Central Leather Research Institute – Chennai Central Leather Research Institute – Chennai Molecular Dynamics Simulations Kern Labs Private Limited, Chennai Kern Labs Private Limited, Chennai Development of e-learning modules in Bioinformatics Possible collaboration with Ecole Superieure De Physique et Chimie Industrielles, Paris, France Possible collaboration with Ecole Superieure De Physique et Chimie Industrielles, Paris, France Prof. Brigitte Quenet Neural Networking (Formal modeling with multistate neurones and multidimensional synapses) BIOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSITY

22 Research Collaborations Biogrid India Our centre will be soon connected to Biogrid (a Virtual Private Network of the Department of Biotechnology, Govt. of India) enabling access by student and scientific community from across the country. It is envisioned that the Biogrid will span all the 60+ Bioinformatics centres of the Department of Biotechnology with Gbps bandwidth and 10+ Teraflops of computational power..

23 Research Focus Database & Software Development Database & Software Development EST & SNP database Analytical tools for Genome analysis Molecular Modeling studies Molecular Modeling studies Molecular Dynamics simulation of human serum Transferrin as a heavy metal transporter – an approach for targeted drug delivery Protein Engineering of DNA-binding Proteins Protein Engineering of DNA-binding Proteins BIOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSITY

24 Research Publications (2004) Swarnalatha, M., Jutur, P.P., Amouda, V., Mathur, P.P., A.R. Reddy (2004) Prediction of Transcriptional Regulation by Dlx and Msx homeodomain proteins. Online J. Bioinformatics 5: Mathur, P.P. (2004) Bioinformatics: From Pre-Genomic to Post-Genomic Era, Advanced Biotech. 3: Kumaran, K. and Mathur, P.P. (2004). Computational analysis reveals potential vaccine candidates for SARS Coronavirus, Asia Pacific Bioinformatics Conference conducted by the Institute of Infocomm Research, Singapore, January Sundar D, A.D. Bosley, A.B. Abulencia, S. Chandrasegaran and M. Ostermeier (2004). A bacterial one-hybrid selection system for interrogating zinc finger-DNA interactions. FASEB Journal 18(8): C174. Kandavelou, K., M. Mani, Sundar D. and S. Chandrasegaran (2004). Engineering and applications of chimeric nucleases. In: Nucleic Acids & Molecular Biology, Vol. 14, A. M. Pingoud (Ed.). Restriction Endonucleases, pp , Springer-Verlag, Berlin, Heidelberg, Germany. BIOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSITY

25 Mani, M., K. Kandavelou, Sundar D. and S. Chandrasegaran (2005). Design, engineering and characterization of zinc finger nucleases for gene targeting. Biochemical & Biophysical Research Communications 335: Sundar D., A.D. Bosley, A.B. Abulencia, S. Chandrasegaran and M. Ostermeier (2005). A bacterial one-hybrid selection system for interrogating zinc finger-DNA interactions. Combinatorial Chemistry & High Throughput Screening (in press). Kandavelou, K., M. Mani, Sundar D. and S. Chandrasegaran (2005). “Magic” scissors for genome surgery. Nature Biotechnology 23(6): Sundar D., Kandavelou, K., M. Mani, M. Porteus and S. Chandrasegaran (2005). Zinc finger nucleases: custom-designed molecular scissors. Nucleic Acids Research (Invited article, submitted) Amouda, V. Shanthi, N. and Palanivelu. K (2005) Aspect-Oriented Programming: A new approach for biological database, Advances in Bioinformatics and Computational Biology (submitted). Arul Prakasam, P., Lakshminarayanan, S., Selvakumar, E. and Mathur, P.P. (2005). Three Dimensional Structure of Human 15-Lipoxygenase predicted by homology-based modeling - a potential target for atherosclerosis and cancer. Journal of Molecular Modeling (submitted). Balamurugan. R, Selvakumar, E. and Mathur, P.P. (2005) Molecular Dynamics Simulation of Human Serum Transferrin as a heavy metal transporter - An approach for targeted drug delivery. Journal of Molecular Modeling (submitted). Research Publications (2005) BIOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSITY

26 For more details please visit… BIOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSITY

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