Objetivo del Proyecto

Coordinator: Dr. Sathish Mundayoor

The Bioinformatics Centre (DISC) at RGCB funded by Department of Biotechnology, Govt of India, under the National Bioinformatics Network program started functioning from May 2002 with a view to catering to the needs of the scientific community. The main function of the Centre is to act as a member of Bioinformatics Network System for providing informa- tion and technology inputs to the interested users on topics pertaining to the relevant areas of Biotechnology, especially genomics and proteomics.

Major activities

Development of Centre to cater the needs for the researchers, students related to biotechnology, bioinformatics and computer technology. Initiated and enriched the research environment which resulted in:

 Publications (peer reviewed): 04

 Poster Presentations: 02

 Training: B.Tech: 04, M.Sc: 07, M.Tech: 04,

 Development of database archives and softwares.

 R&D activities in Bioinformatics

 Hypotheses generation and validation of possible outcomes

Infrastructure facilities

Computer hardware/ Communication facilities

To keep in pace with the developments in bioinformatics field, impetus is given to set up the necessary computational infrastructure and resources for the research community. The centre has upgraded its computational resources by setting up high performance computing facility. Twelve Intel Core-i7 processors (customized for cluster computing), three Dell PowerEgde T300 Workstations and five Dell Vostro 400 computers are available for computational research activities. The centre have 10 Mbps managed leased line connectivity and computers are well connected through LAN.

Scientific Software packages

The molecular modeling package Accelrys Discovery Studio 2.5 was purchased on DBT grand, is used for molecular modeling, docking and simulation studies. Apart from commercial packages, the centre maintains latest version of free bioinformatics softwares such as: - EMBOSS, Autodock, WHATIF, MODELLER, ClustalW, Phylip, Cn3D, Rasmol, SOAP, Bowtie, HMMER, MEGA4, XMGRACE, GROMACS, FTDOCK, PyMOl, Z-dock etc.

Websites/Web servers

The Centre is actively involved in creating softwares and integrated knowledgebases for those who are working in the areas of plant bioinformatics. Some of the databases and webservers developed at the centre are: PKSIIIexplorer[http://type3pks.in/ tsvm/pks3/], PKSIIIpred [http://type3pks.in/prediction/], TypeIII Polyketide Synthase Database [http://type3pks.in].

Services provided

Data retrieval, Next-Generation Sequencing analysis, Molecular modeling, Drug design and Virtual screening services are offered. This facility provides project works to students undergoing B.Tech/M.Tech/M.Phil/M.Sc courses from a large number of universities/institutes.

Publications

1. Deepa Rajan S, Rejimoan R, Sivakumar KC, Sathish Mundayoor.,An SVM based Tool for the Prediction of

Nitrogen Fixing Proteins. IJCA., June 2012., 0975 – 8887.

2. Anitha Jose, Rejimoan R, Sivakumar Kc,Sathish Mundayoor., Prediction of Extracellular Matrix Proteins using

3. Thasni KA, Ratheeshkumar T, Rojini G, Sivakumar KC, Rakesh Sathish N, Srinivas G, Asoke B, Veena S, Priya S., Structure activity relationship of plumbagin in BRCA1 related cancer cells. Mol Carcinog. 2012 Jan 30. doi: 10.1002/mc.21877.

Presentations

1. Mallika V, Aiswarya G, Sivakumar KC, Soniya EV.,” Structural analysis of chalcone synthase proteins from

selected members of Zingeberabceae: An insilico approach.” In the International Conferences on Advances in Biological Sciences (ICABS 2012) held at Kannur, Kerala, March 15-17, 2012.

T.M. Bhagalpur University, Bhagalpur

Coordinator: Prof. (Dr.) A.K. Roy

Summary of the progress made by the Centre from its inception:

The Centre is an established unit of T.M. Bhagalpur University and it has been engaging regular classes on Computer application & Bioinformatics for the Post & Under graduate students of Science faculty and also providing information to the teachers & research scholars for Ph.D. works since its inception. As such it has been acting as integrated information resource on all aspects of research, Molecular biological data and Data Mining of Biological resource. The centre has developed adequate infrastructure with good dry lab which has been availed by the teachers, staffs & students of this University. An attendance register has been maintained daily for the users. Record clearly shows that about approx 100-150 users are taking benefit of it in a month. The centre has also its own research activities on different aspects of plant science & arranging workshop at local, regional & national level.

Major research activities in biotechnology and its related fields :

 Cytogenetic studies of selected plant species.

 Data Mining of Medicinal Plants & their diseases of Bhagalpur & Jharkhand region.

 Data mining of endangered & endemic plants of Bihar & Jharkhand region.

Area of Specialization of the centre:

 Dynamics of genes and proteins

 Generation of database.

Major achievements of the centre during the year 2012-13:

 Database developed on “Medicinal Plant of Bihar & Jharkhand region”. Anyone can see uses of particular

plants, disease symptoms of medicinal plants and what fungi are responsible for its disease condition.

 Regular theory and practical classes to the M.Sc. Biotechnology and other students of science faculty on Computer Applications & Bioinformatics.

 Assisting research scholars of different department to collect the information from Internet.

 Manage & updating of University website (www.tmbu.org) and assist University in computer related works.

 Developed a database on “Katarni” a local race of Oryza sativa which is famous for its aroma and fineness.

Infrastructure facilities in the Bioinformatics Centre:

A. Computer & Communication facility: 3 Servers (Web, Mail and Database), 22 clients workstation, One

Laptop Intel P-M Processor 1.66 Hz., One Multimedia Projector (Sony). Networking Equipments: Modem: One

External, Internet Connection: 512 kbps BSNL Broadband Connectivity, Sony Digital Camera

B. Scientific Software Packages: Exome, Exome Blast, Exome – ED, Widows 2003 Server with xp clients, Red Hat

Linux server ad. Std

C. Databases and other Information resources: 100 books covering various fields of bioinformatics & Database of

Details about staff members working in the Centre:

Name Designation Area of Specialization Period of working

Prof.(Dr.) A.K. Roy Coordinator Microbiology, Biotech. since 08-12-2011

Dr. Rakesh Ranjan Technical Assistant* Statistics & Comp. Appl. since 22-06-2006*

Mr. Saket Vinayak Data Entry Operator* Comp. Appl. since 28-06-2006*

Ms. Archana Dixit Traineeship Bioinformatics since 28-08-2012

*University has already taken suitable steps for the Manpower absorption issue in consultation with HRD, Govt. of Bihar (vide University

Latter No. B/9835 dated 7/08/2012). It is expected that the issue will be settled within one year. Educational activities:

 Assisted faculties and students from neighboring science departments and college/Institutions in updating

their knowledge through different databases / software available in the centre.

 Regular theory and practical classes of Bioinformatics and computer papers of M.Sc. Students of DBT spon-

sored P.G. Dept. of Biotech and UG Students of college of this University.

 P.G. Diploma in Bioinformatics will begin in the Centre from the coming academic session. Approval of syllabi and duration of the course is awaited for the assent of the Chancellor’s office of Bihar.

Papers published or presented in the conferences with reference (2012-13):

 Database of unreported diseases of medicinal plants.

Initiation of R & D activities in Bioinformatics:

 Near Bhagalpur, a primitive tribal community of Dravidian origin called “Paharias” residing in and around the

Rajmahal Hills of Santhal Pargana. This isolated patch of human genome has been selected for investigation and with the objective to identify the genetic reasons for the gradual decrease in the population.

Details of Training /workshop organized and the total number of user trained:

 Training Course on “Basics of Bioinformatics & Computer Application” for the UG Biotech students of re-

gional colleges was organized on March 23 & 24, 2012. 31 participates were participated in Training Course Batch-I. (Report submitted to DBT office)

 Training Course on “Basics of Bioinformatics & Computer Application” for the UG Biotech students was

organized on April 9 & 10, 2012 at University level. 29 UG Biotech students were participated in Training Course Batch-II. (Report submitted to DBT office)

 Training Course on “Basics of Bioinformatics & Computer Application” for the UG & PG Biotech students was organized on May 7 & 8, 2012 at University level. Twenty-seven (27) UG & PG Biotech students were partici- pated in Training Course Batch-III. (Report submitted to DBT office)

 National Training Course on “Basics of Bioinformatics & Computer Application” in collaboration with T.N.B.

Contact details:

Name of the Coordinator Prof. (Dr.) A.K. Roy

Postal Address Coordinator Sub-DIC, University Centre of Bioinformatics, T. M. Bhagalpur

University, Bhagalpur- 812007

Phone Number 0641-2501382, Mobile: +91(94312)04572

Email [email protected]

Website www.bioinformatics-tmbu.org.in