Bioinformatics Centre

- A Profile

Commissioning of the Centre 1992-93

Phone : +91 413 2655212 E-mail : bicpu2001@yahoo.co.in

Fax : +91 413 2655211/265

University webpage: http://www.pondiuni.org/bioinformatics.html Centre website: http://bicpu.edu.in

IOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSIT

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)

IOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSIT

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.

IOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSIT

Bioinformatics Centre
1991-1992 Centre was established as Sub-Distributed Information Centre (Sub-DIC) with support of DBT Service provider with facilities for sequence retrieval and analysis and abstract services

1995

2001
2004

Started one year Advanced Post Diploma course in Bioinformatics

Graduate

Sub-DIC was upgraded as a full-fledged center with DIC Status

2005

Started Molecular Modeling facility (Silicon Graphics System with Insight-II & DS Modeling server) and Linux based Beowulf type Clustering

IOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSIT

Personnel

Teaching
Coordinator Reader Lecturer Lecturer Temporary Faculties Prof. P.P. Mathur 1 No. (Vacant) Dr. D. Sundar 1 No. (Vacant) 3 Nos.

Technical
Information Officer Technical Assistant Computer Operator Computer Operator Data Entry Operator Mr. M. Sundara Mohan Ms. V. Amouda Mr. E. Selvakumar Ms. N. Shanthi 1 No. (Vacant)

Office
Attendant Mr. T. Gopy

Temporary positions
DBT-JRF DBT-Traineeship DBT-Studentship 1 No. (Vacant) 2 Nos. (Vacant) 2 Nos. (Vacant)

IOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSIT

Activities

Teaching

Regular M.Sc Program in Bioinformatics (applied to UGC) Advanced PG Diploma in Bioinformatics (since 2001)

Training

Regular Training Programs (Short term & Long term)

Research

Molecular Dynamics simulation of Human Transferrin Protein Engineering of DNA-binding Proteins Database and Software Development

Extension

Development of E-Learning modules in Bioinformatics

IOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSIT

Teaching Program
o

The Centre has been offering an Advanced Post Graduate Diploma Course in Bioinformatics since the Academic year 2001-2002 with the support from Department of Biotechnology, New Delhi 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 Only those candidates who have Masters 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. A sum of Rs. 5000/- per month is offered as a stipend to the selected students.

IOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSIT

Students Placements
o o

Johns Hopkins University, Baltimore, USA HCL Technologies Limited

o
o o o o o o

Institute of Bioinformatics, Bangalore

Protein Lounge, Orissa Central Sericulture Research & Training Institute, Mysore Vector Control Research Centre, Pondicherry Orissa Agricultural University, Orissa HNB Garhwal University, Srinagar University of Madras, Chennai

Pondicherry University, Pondicherry

IOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSIT

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 1991.

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. 5000 per month.

IOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSIT

Forthcoming Seminars

National Seminar on "Intellectual Property Rights in Bioinformatics & Biotechnology" to be organized by our Centre during September 15-16, 2005.
National Seminar on "Advances in Nanosciences and Nanobiotechnology" to be organized by our Centre during December 05-06, 2005. National Seminar on "Bioinformatics and Functional Genomics" to be organized by our Centre during February 15-17, 2006.

IOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSIT

Infrastructure
- Hardware
Servers
Wipro HCL (AMD Opteron 64 BIT) Processor: Xeon@3.0 Ghz; RAM: 1 GB; HDD: 120 GB; OS:Red Hat Linux 9; 12/24GB-DAT drive Processor: AMD 8131/8111 Motherboard (Dual Processor Capable); RAM: 1 GB; HDD: 100 GB; OS:Windows 2003 Server; 12/24GB-DAT drive; 1 1

HP-Vectra

Processor: Pentium III@833 Mhz; RAM:128 MB; HDD:30 GB; OS: Red Hat Linux 9

Specialized Workstations
Silicon Graphics (Onyx3 Fuel)
DSM Modeling Server Workstation Cluster

Processor: 800Mhz. MIPS R16000 (IP35) with MIPS R16000 FPU; RAM: 1 GB; HDD:176 GB; OS: IRIX64 Release 6.5; Graphics: V10)
Processor: Pentium IV@2.8 Ghz.; RAM: 512+256; HDD:40 GB; OS:Windows XP; CD-RW; DVDRW Beowulf type Cluster (Linux based)

1 Master + 5 Slaves

IOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSIT

- Hardware

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
HP 4600 DN Color Laser, HP 2200DN Laser printer, HP 1150 Laser Printer, HP 4P-Laser printer, HP Inkjet 5748, 810 & 670 C

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.)

IOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSIT

Infrastructure

- Software

Academic Licensed Amber AutoDock Dock GROMOS96 Modeller Phred, Phrap, Consed Whatif

Molecular Dynamics simulation Molecular Docking (Flexible Ligand docking) Molecular Docking (Rigid docking) Molecular Dynamics simulation Homology Modeling Sequence Analysis Protein Structure Modeling & validation suite

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

IOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSIT

Infrastructure

IOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSIT

Infrastructure
- Software

Academic free & Open Source suites

Internet

- Communication

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
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

IOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSIT

Infrastructure

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 96821 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).

IOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSIT

Bioinformatics Centre e-Library

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.

IOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSIT

Infrastructure
- Wet Lab
UV-Visible Spectrophotometer High Speed Centrifuge Ultracentrifuge Gel Documentation System Gamma Counter Liquid Scintilation Counter ELISA Reader Laminar Flow Chamber Homogenizer CO2 Incubator Shimadzu Hitachi Sorvall Sorvall Syngene LKB Wallac LKB Wallac Multiscope Yorco Polytron VWR scientific Thermo Forma PT 3000 Model 2100 Model 311 UV-1700 Pharmaspec Himach CR 26H RC 5C Plus RC 90 Ingenius 1275 Mini Gamma 1209 Rack Beta

IOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSIT

Infrastructure
- Wet Lab
Phase Contrast Microscope Leica Lynx PCR Deep Freezer -80C Ultrasonication (Sonifier) Microfuge Nitrogen Analyzer Metabolic Shaker Incubator Gel Electrophoresis Fraction Collector Eppendorf Sanyo Branson Fisher Kjel Plus Orbitek BioRad / Hoefer Bio Rad / Hoefer MDF U6086S 450D Model 235A Distil M DM IL Vision 2000

IOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSIT

Research Collaborations

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

Molecular Modeling & High Performance / Cluster Computing

Central Leather Research Institute Chennai

Molecular Dynamics Simulations

Kern Labs Private Limited, Chennai

Development of e-learning modules in Bioinformatics

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)

IOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSIT

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..

IOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSIT

Research Focus

Database & Software Development

EST & SNP database Analytical tools for Genome analysis

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

IOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSIT

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: 132-145. Mathur, P.P. (2004) Bioinformatics: From Pre-Genomic to Post-Genomic Era, Advanced Biotech. 3:27-31. 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 2005. 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. 413-434, Springer-Verlag, Berlin, Heidelberg, Germany.

IOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSIT

Research Publications (2005)

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: 447-457.
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): 686-687. 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).

IOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSIT

IOINFORMATICS CENTRE SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSIT

For more details please visit

http://www.bicpu.edu.in

Bioinformatics Centre, Pondicherry University