About our Centre
The Centre for Bioinformatics in Pondicherry University was started initially as Sub Distributed Information Centre of the Department of Biotechnology, Govt. of India (DBT) in 1991. The mandate of the Centre was to train manpower and conduct research in various areas of Bioinformatics. Recognizing the progress made by the Centre, DBT upgraded the Centre to a full Centre (DIC) level in 2002 The Centre was identified as a Centre of Excellence for Research and Training in the field of Bioinformatics by the Department of Information Technology, Govt. of India, New Delhi in 2007 and awarded a special grants.
The Centre is offering an M.Sc., program in Bioinformatics in 2007 supported by the University Grants Commission (UGC) under the scheme of “Innovative Programme - Teaching & Research in Interdisciplinary and Emerging Areas”. To advance research in Bioinformatics, the Centre started Ph.D. Programme in 2009. The Centre started offering a Network M.Sc., Computational Biology teaching programme fully funded by DBT in collaboration with Madurai Kamaraj University, Madurai and Anna University, Chennai in 2010. This programme will be first of its kind in the country. This programme has been upgraded to M.Tech,. Computational Biology from 2014 and offered in collaboration with Anna University. Most of the past students were placed in various leading research institutions and industries. Many of them are perusing higher studies abroad.
In the past few years, Centre has taken up research activities in the areas of sequence analysis, molecular modeling, structural biology, database development etc., and several papers have been published in peer-reviewed International and National Journals. The faculty and students have received projects/fellowships from various funding agencies like Department of Biotechnology, Department of Information Technology, University Grants Commission, Council of Scientific and Industrial Research-JRF/SRF, Department of Science and Technology, Bioinformatics National Certificate (BINC), DST-Innovation in Science pursuit for Inspired Research (INSPIRE) and Rajiv Gandhi Fellowship.
The University supported the Centre with a state of the art building of about 35000 sqft with complete UPS backup for all rooms and a solar power for the lighting load. The building is having 3 computational labs, 13 Faculty rooms, 13 individual research labs for faculty, common wet lab, common instrumentation room, Library, 3 class rooms and a seminar hall.
Highlights
- One of the Biggest Bioinformatics Centre in India
- 12 Faculty members with multi-disciplinary expertise
- Teaching programmes are supported by various funding agencies
- 24 hours computational lab facility for students and research scholars
- 240 Mbps Leased Line internet connectivity
- Internal webhosting facility for research tools and databases
- Well equipped computational labs and class rooms with ICT facility
- Well equipped wetlab for protein purification and crystallization
- High Performance Computing Servers and GPU computing facility for simulations
- Good Collection of reference books in department library
- Commercial and academic licensed software for biological research
- State of art new building exclusively for the Bioinformatics Centre
- Research publications in the high reputed journals
M. Sc. Bioinformatics (2007 onwards)
The Centre is offering an M.Sc. Bioinformatics course (72 credits) with the support of University Grants Commission (UGC), Govt. of India, under the scheme of Innovative Programme – Teaching and Research in Interdisciplinary & Emerging Areas. The students are selected through a competitive examination conducted by the university all over India. Candidates with 50% of marks in Bachelor’s degree in any branch of Biological Sciences/ Molecular Biology/ Biotechnology/ Biochemistry/ Biophysics/ Microbiology/ Computer Science/ Statistics and Mathematics are eligible.
M. Tech. Computational Biology (2015 onwards)
The Centre is offering an M. Tech. Computational Biology network teaching programme in collaboration with Anna University funded by DBT, Govt. of India. Selection will be based on a common entrance examination conducted by the Pondicherry Universities at National level. A stipend of Rs. 8,000/- per month is provided by the DBT to all the students admitted.
Ph.D. Bioinformatics (Full time) (2009 onwards)
The Centre offers a full-time Ph.D. program. Students are selected through a competitive entrance examination conducted by the university at National level and an Interview. A sum of Rs.8000 per month is offered by the university as stipend to the selected students. Students who have qualified CSIR/UGC-NET, DBT-BINC, ICMR-JRF examination are admitted directly for Ph.D. full-time program without entrance examination.
M. Sc. Computational Biology (2010-2015)
The Centre was offering an M. Tech. Computational Biology network teaching programme in collaboration with Anna University and Madurai Kamarajar University funded by DBT, Govt. of India. Selection was based on a common entrance examination conducted by Pondicherry Universities at National level. A stipend of Rs. 5,000/- p.m. was provided by the DBT to all the students admitted.
Modular Course in Bioinformatics (2009 onwards)
The Modular course offered under the Centre of Excellence grant comprises of four modules. A certificate will be awarded on completion of each Module. The candidates will be awarded a P.G. Diploma in Bioinformatics on successful completion of all four modules.
Advanced Post Graduate Diploma in Bioinformatics (2001-2008)
The Centre offered an Advance Post Graduate Diploma course in Bioinformatics (APGDB) (46-credit) with the support of Department of Biotechnology (DBT), Government of India between 2001-08. All the passed out students are placed well in the industries and various research institutions national and international wide.
Softcore
The Centre is also offering a softcore in Bioinformatics to the students of M.Sc (Biochemistry & Molecular Biology), M.Sc (Biotechnology), M.Sc (Environmental Science) M.Tech (Computer science) in the University.
DBT Studentship / Traineeship
The Centre offers Traineeship and Studentship (4 Nos.) in Bioinformatics every year. The Students selected under these two schemes are awarded a stipend of Rs.5000/- per month for a period of one year.
Unique Features
- ICT & Video Conferencing enabled teaching facility.
- 24x7 lab facility for all the students.
- Uninterrupted power back up for systems.
- Wi-Fi facility for mobile devices is enabled for the student.
- Centre will assist for the Industrial Placement and career.
- Common facility like printer, copier & scanners on local area network for immediate need of students.
- Reference Library along with photo copier facility
- Technical Assistance for system, laptop and for software programing
- Centralized Air Conditioning for labs and class rooms
- High sophisticated wetlab instruments and HPC servers for biological simulation studies.
| Sl. No. | Name of the Faculty | Total no. of publication |
|---|---|---|
| 1 | Dr. H. Surya Prakash Rao | 125 |
| 2 | Dr. Basant K. Tiwary | 18 |
| 3 | Dr. Dinakar Ampasala | 19 |
| 4 | Dr. P.T.V. Lakshmi | 25 |
| 5 | Dr. R. Krishna | 37 |
| 6 | Dr. M. Suresh Kumar | 6 |
| 7 | Dr. Archana Pan | 13 |
| 8 | Dr. R. Amutha | 14 |
| 9 | Dr. B. Syed Ibrahim | 7 |
| 10 | Dr. A. Murali | 33 |
| 11 | Dr. S. Mohane Coumar | 35 |
| 12 | Dr. V. Amouda | 19 |
| 12 | Prof. P. P. Mathur (1991-2012) | 111 |
Research Projects
In the past few years, the Centre has taken up research activities in the areas of sequence analysis, molecular modeling, database development etc., and several papers have been published in peer-reviewed international and national journals.
University Grants Commission (UGC)
| Sl No | Title | PI | Year | Amount (in Lakhs) |
|---|---|---|---|---|
| 1 | Structure of Qbeta replicase in different ionic strengths using single particle analysis | Dr. A. Murali | 2012-15 | Rs.14.25 |
| 2 | Targeted anti-cancer agents: Structural Bioinformatics approach to the Design & Development of allosteric Kinase inhibitors | Dr. S. Mohane Coumar | 2012-15 | Rs.10.10 |
| 3 | Searching for potential therapeutic targets in human pathogens (food- and water-borne) using comparative genomics approach: molecular modeling, docking and simulation studies | Dr. Archana Pan | 2011-14 | Rs.7.818 |
| 4 | Structure based drug design for acidic Sphingomyelinase | Dr. M. Suresh Kumar | 2010-13 | Rs. 10.45 |
| 5 | Hydration Studies on Proteins: Study of dehydrated/rehydrated x-ray crystal structural of Rhida-rest and structural determination of horosapiens gamma- Synuclein | Dr. R. Krishna | 2010-13 | Rs. 10.60 |
Department of Information Technology (DIT), Govt. of India
| Sl No | Title | PI | Year | Amount (in Lakhs) |
|---|---|---|---|---|
| 1 | iAligner: A Novel Approach using self-organizing Genetic Algorithm for MSA to discover intron pattern | Dr. V. Amouda | 2011-13 | Rs. 17.6 |
Department of Biotechnology (DBT), Govt. of India
| Sl No | Title | PI | Year | Amount (in Lakhs) |
|---|---|---|---|---|
| 1 | Computational and biochemical approaches for in-silico screening and discovery of drug-like leads: Anti-diabetic and anti-hypertensive compounds from Clerodendrum spp. occurring in North East India | Dr. S. Monahe Coumar | 2012-13 | Rs. 11.83 |
| 2 | Structure based Inhibitor for Protein Disulfide Isomerase | Dr. M. Suresh Kumar | 2011-14 | Rs. 44.00 |
Department of Science & Technology (DST), Govt. of India
| Sl No | Title | PI | Year | Amount (in Lakhs) |
|---|---|---|---|---|
| 1 | Design and discovery of aurora kinase inhibitors as anti-cancer drugs: Application of computer aided drug design | Dr. S. Mohane Coumar | 2012-15 | Rs. 24.30 |
| 2 | DST-SERC-FAST track Young Scientists programme | Dr. R. Amutha | 2012-15 | Rs. 19.00 |
University Startup Grant
| Sl No | Title | PI | Year | Amount (in Lakhs) |
|---|---|---|---|---|
| 1 | Structure and Biochemical characterization of Factor V activating enzyme (FVA) from snake venom towards drug designing | Dr. B. Syed Ibrahim | 2011-12 | Rs. 3.00 |
Schemes & Funding Agencies
The Centre is identified as a Centre of Excellence in Bioinformatics Teaching and Research by the Department of Information Technology, Govt. of India, New Delhi in 2007 and awarded a special grant of around 3.79 crores. The Centre has taken up research projects and offering of modular courses under this Grant. The Centre has so far received grants to the tune of more than 4 crores from DBT and 30 lacs from the UGC in addition to Rs.3.79 crores from the DIT. The University is extending full support for the development of the Centre and the Centre will achieve newer heights and will soon become a leading Centre for Bioinformatics teaching and research in this part of the world.
Fund Sanctioned by varies Agencies
| Sl No. | Scheme | Funding Agency | Amount | Period |
|---|---|---|---|---|
| 1 | Fund for Improvement of S&T Infrastructure (FIST) | Dept. of Science and Technology(DST), Govt. of India | 100.00 Lakhs | 2015-2020 |
| 2 | Special Assistant Program (SAP) | University Grants Commission(UGC), Govt. of India | 75.00 Lakhs | 2012-2017 |
| 3 | Distributed Information Centre (DIC) | Dept. of Biotechnology (DBT), Govt. of India | 4.00 Cr | 1991 - Till date |
| 4 | NetworkComputational Biology | Dept. of Biotechnology (DBT), Govt. of India | 1.30 Cr | 2010 - Till date |
| 5 | Innovative Programme - Teaching & Research in Interdisciplinary and Emerging Areas | University Grants Commission(UGC), Govt. of India | 30 Lakhs | 2007 - Till date |
| 6 | Centre of Excellence (CoE) | Dept. of Information Technology (DIT), Govt. of India | 3.79 Cr | 2007-2013 | 7 | Advanced P.G. Diploma in Bioinformatics | Dept. of Biotechnology (DBT), Govt. of India | 80 Lakhs | 2001 - 2008 |
Collabrations
Universities/ Institutions
- Anna University, Chennai
- Madurai Kamaraj University, Madurai
- Indian Institute of Technology, Madras
- Indian Institute of Chemical Technology, Hyderabad
- JIPMER, Pondicherry
- Vector Control Research Centre, Pondicherry
Non-Government Organizations
- Institute of Bioinformatics (IoB), Bangalore
Under MoU the following Faculty are recognized supervisor for Ph.D. programme
-
Institute of Bioinformatics (IoB), Bangalore
- Dr. Akhilesh Pandey, Ph.D.
Specialization: Genomics, Proteomics, Bioinformatics, Molecular Biology. - Dr. T.S. Keshava Prasad, Ph.D.
Specialization: Bioinformatics, Genomics & Proteomics.
-
Indian Institute of Chemical Technology, Hyderabad.
- Dr. G. Narahari Sastry, Ph.D. [MoU through IOB]
Specialization: Bioinformatics, computational biology, computational chemistry.
Inter-Departmental
- Interdisciplinary Programme in Life Sciences for Advanced Research and Education (IPLS) funded by DBT - (Centre for Bioinformatics, Dept. of Biotechnology, Dept. of Biochemistry & Molecular Biology)
- PURSE Programme, funded by DST
Hardware
Servers -11
Super Micro Zeon quad core (Tesla Server), HCL Zeon quad core (Web server), HCL Zeon quad core (Database server), HCL Zeon quad core (DNS server), HCL Zeon quad core (DBT Web server), HCL Zeon dual core (Linux dedicated cluster server), HCL Itanium2 (Mail server) and Wipro (Active Directory Server), HCL AMD Opteron 64 BIT (File Server)
Specialized Workstation - 8
HP quad core workstations(5), Apple iMac(2), SGi Silicon Fuel workstation.
Workstations -146
HCL Intel Core 2 Dual Workstations with 2 to 4 GB of memory and 160 to 320 GB Storage and with Gigabit Ethernet.
Software
Vlife, Schrodinger Mastero 2011, Tripos Sybyl 8.1, Discovery Studio 3.1, Kaspersky 6.0, SPSS 10, Endnote 11, Amber 11, Autodock, Dock, Modeller, Gromos 96, Whatif, EMBOSS, BioEdit, Phred, Consed, GeneScan, Statistica, R
Wetlab
The Centre has developed a separate wet lab facility. The lab is functional with the following equipments: HPLC System AKTA PURIFIER 10, UV-Visible Spectrophotometer Shimadzu Model - Uv-1800, ELISA Reader Versamax Model 2020, Gel Documentation System Syngene GBOX/EF, Thermo Cycler Bangalore Genei, -80C Deep Freezer Premium Upright Model: U410, -20C Deep Freezer Carrier Model HF300, Refrigerated Centrifuge 5415 Eppendorf, Cooling Centrifuge Revolutionary table top REMI Model: C24BL), Bio-safety cabinet BIOBASE BIOTECH , Bench Top Freeze Dryer ILSHIN - TFD5505 Table top model, Water purification system PURELAB OPTION-Q 7/15, Cold cabinet UNICHROMAT 1500-PRO.
The Centre is in a process of establishing a cell culture facility.
Library
Books
600 books available in the reference library of the Centre.
A separate E-books intranet server is available with more than 250 ebooks in the Centre.
Journals
Science, Nature, Scientific American, Briefings in Bioinformatics, Bioinformatics, Nature Structural and Molecular Biology, Nature Chemical Biology, Cell, Bioinformatics Trends, Current Science, Chem informatics,
Magazines
Linux for U, PC Quest, PC World, Chip, Biospectrum
Access to E-Journals
The Centre, through the University network has access to UGC Infonet Journals, Science Direct, Blackwell Publishers, EBSCO Databases
Network
Internet
The Centre has a dedicated 11 Mbps Internet connectivity exclusively from BSNL, Puducherry in addition to the Internet Connectivity provided by the University.
Intranet
The Centre is completely interconnected through 10 manageable Gigabyte switches with CISCO Routers for internet and intranet connection. Through the 1000baseT Local area back bone network user can be connected to the Internet and also access to the local resources like E-Journals, ebooks, ftp, print share, backup storage, token license server, anti-virus protection support, etc., A Wifi facility will also be provided to the students round the clock in the vicinity.
Hardware
| Vendor | Usage | Configuration | Nos | |
|---|---|---|---|---|
| Servers | ||||
| Super Micro Performance: 4 TF |
Terminal Server (Tesla Server) |
Processor: 2 x Intel Xeon processor E562020 (Quad-Core/2.4GHz/12M L3 Cache) Memory: 64 GB DDR3 Storage: 6 x 1000GB, 7200 RPM, SATA Raid: SAS RAID controller with 128MB cache supports Hardware RAID 0, 1, 10, 5 & 6 Display: 24" TFT LED Color Monitor Graphics: 2 x NVIDIA Tesla C2050 (448 cores) OS: CentOS |
1 | |
| HCL | Web Server | Processor: 2 x Xeon Quad Core @1.6GHz Memory: 4 GB Storage: 6 x 146GB with RAID Display: 15” Integrated KVM LCD Display OS: RHEL 5 |
1 | |
| HCL | Proxy Server | Processor: 2 x Xeon Quad Core @1.6GHz Memory: 4 GB Storage: 6 x 146GB with RAID Display: 15” Integrated KVM LCD Display OS: RHEL 5 |
1 | |
| HCL | Database Server | Processor: 2 x Xeon Quad Core @1.6GHz Memory: 4 GB Storage: 6 x 146GB with RAID Display: 15” Integrated KVM LCD Display OS: RHEL 5 |
1 | |
| HCL | Zinc Finger Database Server | Processor: 2 x Xeon Quad Core @1.6GHz Memory: 4 GB Storage: 6 x 146GB with RAID Display: 19” Integrated KVM LCD Display OS: RHEL 5 |
1 |
|
| HCL | Cluster Server (Master) | Processor: 2 x Intel Xeon @3.2GHz Memory: 4 GB Storage: 6 x 146GB with RAID Display: 19’’ LCD Display with KVM Switch OS: RHL Advanced Server 4 |
1 | |
| HCL | Cluster Server (Node) | Processor: 2 x Intel Xeon @3.2GHz Memory: 4 GB Storage: 2 x 144GB with RAID Display: 19’’ LCD Display with KVM Switch OS: RHL Advanced Server 4 |
2 | |
| HCL | Mail Server | Processor: 2 x Itanium 2 @1.7GHz Memory: 4 GB Storage: 6 x 146GB with RAID Display: 19’’ LCD Display with KVM Switch OS: RHL Advanced Server 4 |
1 | |
| Wipro | Domain Name System | Processor: Xeon @3.0Ghz Memory: 1 GB Storage: 120 GB Drives: 12/24GB-DAT drive OS:RHL9 |
1 | |
| HCL | Domain Controller | Processor: AMD 8131/8111 Motherboard Memory: 1 GB Storage: 100 GB Drives: 12/24GB-DAT drive OS: Windows 2003 Server |
1 | |
| Desktop Computers | ||||
| HCL | M. Sc –I (LAB) (Bioinformatics) |
Processor: Pentium Core 2 Duo@2.80GHz Memory: 4 GB DDR2 Storage: 320 GB Display: 19’’ Wide LCD OS: Windows XP & RHEL5(Dual boot) |
40 | |
| HCL | M. Sc –II (LAB) (Bioinformatics) |
Processor: Pentium Core 2 Duo@2.80GHz Memory: 4 GB DDR2 Storage: 320 GB Display: 17’’ Wide LCD OS: Windows XP & RHEL5(Dual boot) |
45 | |
| HCL | Research Scholars Lab | Processor: Intel core 2 Duo@ 1.8 GHz Memory: 3 GB DDR2 Storage: 160 GB Display: 15’’ LCD OS: Windows XP & RHEL5(Dual boot) |
14 | |
| HCL | Faculty Systems | Processor: Intel core 2 Duo@ 1.8 GHz Memory: 1 GB DDR2 Storage: 160 GB Display: 17’’ LCD OS: Windows XP & RHEL5(Dual boot) |
6 | |
| HCL | M. Sc –I (LAB) (Computational Biology) |
Processor: Pentium D@3.00GHz Memory: 3 GB DDR2 Storage: 160 GB Display: 15’’ LCD OS: Windows XP & RHEL5(Dual boot) |
20 | |
| HCL | Staff Systems | Processor: Pentium D@2.80GHz Memory: 1 GB DDR2 Storage: 160 GB Display: 17’’ LCD OS: Windows XP & RHEL5(Dual boot) |
7 | |
Network
Internet
The Centre has a dedicated 11 Mbps Internet connectivity exclusively from BSNL, Puducherry in addition to the Internet Connectivity provided by the University.
Intranet
The Centre is completely interconnected through 10 manageable Gigabyte switches with CISCO Routers for internet and intranet connection. Through the 1000baseT Local area back bone network user can be connected to the Internet and also access to the local resources like E-Journals, ebooks, ftp, print share, backup storage, token license server, anti-virus protection support, etc., A Wifi facility will also be provided to the students round the clock in the vicinity.