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BANASTHALI VIDYAPITH, BANASTHALI


About the Bioinformatics Centre
 

In view of rapidly growing importance of Information Technology in Biotechnology teaching and research, communication etc., Centre for Bioinformatics (a sub-DIC under BTIS programme) at Banasthali University was sanctioned by Department of Biotechnology, Govt. of India in November, 1998. Over the last fifteen years, this centre has acquired many databases and software’s and has round the clock Internet connectivity. The Centre has 3 servers, 42 PCs, 2 scanner, 13 printers, 1 LCD projector, 2 IBM & 2 HP Laptops, 4 Web Camera, 2 Digital Camera, 3 External CD/DVD Writers, 2 Photocopier machines, several software and databases. All computers are connected to Internet through 2 MBPS lease line under campus networking. Centre is providing services to the PG students in Biotechnology, Bioscience and Bioinformatics, Ph.D. students and the teaching faculty in the following ways:

  • Searching literature/databases of their own research interest
  • Computational work
  • Application of available software in the centre
  • Usage of design databases by the centre

Some of the important databases in Biological Sciences that are currently available are: Medline Standard, Agris, Agricola, Chrome Circle Application, Biotechnology Abstracts and Indian Forester Information System.  To cater to the regional and national needs, the Centre has also developed database on "Biotechnological Industries of Rajasthan", “SSRDatabase of Citrus sinensis,”, “Database for Simple Sequence Repeats of Takifugu rubripus”, “Database of Diterpene Synthase Gene” and "Flora of Indian Desert". “Database of Plant Host-Pathogen Interaction” is in progress. Further, Centre is actively involved in research work in bioinformatics. Various research papers have published in several reputed national and international journals. Since from its inception 7 workshops and training programs has been held in the centre. Around 500 participants from several institutions have been trained including faculty members, research scholars and PG students.

Since from its inception the centre has been coordinated by Prof. Vinay Sharma, Dean, Faculty of Science & Technology, HOD, Dept. of Bioscience and Biotechnology.

 
Centre for Bioinformatics, Banasthali University
 
Bioiformatics Lab, Banasthali University
Bioiformatics Lab, Banasthali University
 
Area of Specialization:
I. Information Dissemination in Biotechnology
II. Bioinformatics Human Resource Development;
III. Research in the following areas is:
  • Plant Genomics & Proteomics
  • Chloroplast and Mitochondrial Genomics & Proteomics
  • Molecular Modeling & Computational Aided Drug Designing
 
Objectives
  • More Interaction with Bioinformatics Industry
  • Continue to Train Human Resources in Bioinformatics
  • To cater to the regional and national needs, the work on the specific databases being currently developed by the Center will continue.
  • The R & D activities will be strengthened in Bioinformatics.
 
Achievements at a glance
  • Research in the following above mentioned 3 areas is in progress and several research papers have been published.
  • Acquired additional infrastructure facilities including hardware’s, software’s and database.
  • To provide services for the analysis of biological data, bibliographic references to published literature in science and technology (including databases and patents).
  • Training programmes held in Bioinformatics.
  • The PG course (M.Tech) in Bioinformatics specialization has been introduced this year; however this is an independent activity of the university.
 
Current Area of Research
 

In the centre of bioinformatics the current research is focused on the following specialized area:

 
Phylogenetic anaylysis using organelle genome (Chloroplast & Mitochondria)

The phylogenetic analysis of plants using organelle genome sequences is an interesting research area to know the evolution of land plants. Therefore research is focused on organelle genome sequences to elucidate plant phylogeny by applying methods including Maximum likelihood and Bayesian analysis used for phylogenetic tree reconstruction. The maximum-likelihood analysis consists of three parts. First a model of evolutionary change for nucleotides or amino acids is specified. Then, based on this model, different hypotheses about the evolutionary history are evaluated in terms of the probability that the hypothesized history would give rise to the observed data. Finally, the hypothesis is selected that shows the highest probability Maximum-likelihood often yields estimates with a lower variance than other methods, and it is frequently the estimation method least affected by sampling error. Bayesian inference in phylogeny generates a posterior distribution for a parameter, composed of a phylogenetic tree and a model of evolution, based on the prior for that parameter and the likelihood of the data, generated by a multiple alignment.

  1. The objectives of the research are to the phylogenetic analysis of bryophytes using organelle genome sequences (chloroplast and mitochondrial) from NCBI to know the evolution and tree reconstruction of early land plants.
  2. Applying the statistics probability methods including Maximum likelihood and Bayesian analysis for phylogenetic tree reconstruction.
 
Comprehensive study of mitochondrial genome with respect to SSRs
Research involved in mitochondrial genomics and proteomics using bioinformatics approaches including with the advent of advanced technologies the sequenced genome data has increased with a greater pace and provided us the opportunity to identify hidden trends and patterns.
  • Objectives of research is focused on phylogeny of mitochondrial genomes, because mitochondrial genome is very diverse in terms of number of genes and also in genome sizes as compared to other organelle genome i.e. chloroplast. The variation is also represented in the form of arrangement pattern of genes in the genome which is in contrast with chloroplast and also with nuclear genome. Trying to justify the patterns behind the whole thing her focus of research is to identify the patterns of mitochondrial genome evolution.
  • Further, objective is to analyze the applications and the effect of simple sequence repeat patterns on gene functionality in mitochondrial genomes. SSRs play a major role in proper functionality of genes as well as proteins and can be used to analyze the polymorphism associated with the genes and genomes and can be used as markers.
 
Molecular Modeling & Computational Aided Drug Designing

Primary research focused on to understand the nature and mechanism of molecular recognition and binding free energy determination, further in the development of novel approaches to improve the research and discovery of new molecules and to investigate the intricate relationship between structure and function in biomolecules using in silico tools. By using standard cheminformatics and molecular modeling approaches including Virtual Screening, Pharmacophore mapping, Molecular docking (Protein-ligand, protein-protein, protein-DNA), 3D-QSAR (CoMFA and CoMSIA), Molecular dynamics and Homology and ab initio modeling, Binding Free Energy calculations, Similarity and Diversity Analysis, Structural Descriptors, machine learning methods among others techniques.
In the centre further research is ongoing in the projects including following objectives:

  • To the Prediction of protein structures from sequence, investigating of structure activity relationships responsible for the recognition and binding of the known inhibitor analogs using 3D-QSAR methods.
  • Analyzing and predicting intermolecular binding affinities using molecular docking methods.
  • Developing new virtual screening workflow integrating different ligand and structure based virtual screening methods in addition to machine learning methods to efficiently identify the lead compounds from the library of drug-like compounds and implicating the possible determinants of inhibitor’s specificity using the molecular modeling and dynamics studies. 
 
Database, Flora of Indian Desert developed by Centre for Bioinformatics.
 
 
Infrastructure facilities in the Bioinformatics Centre
  • Branded Dell/HP – 4 Nos.
  • Branded Apple iMac – 2 Nos.
  • HP Elite Book 8560w Notebook – 1 No
  • Blu-Ray Disc Writer Internal – 2 Nos.
  • HP color LaserJet M 451 DN – 1 No
  • Digital Heavy duty Photocopier make Sharp Ar-5623N build in duplex with complete accessories and stabilizer.- 1 No
  • Switch 24 port D-Link – 2 Nos.

Software’s:Adobe CS6 Design Premium 6.0 DVD Academic, Red Hat Enterprise Linux Server- AP Standard, Red hat Desktop 1 year basic, Media for Red Hat Products, Oracle 11 g Standard ONE Edition.

 
Databases:
  • Agricola Database (12 month subscription with Quarterly Updates 1984+)
  • Agris
 
Faculty Members
Coordinator, Bioinformatics Centre: Prof. Vinay Sharma, Dean, Faculty of Science & Technology
 

The staff members working in the centre are:

Name of the Staff

Designation

Educational Qualification/ Specialization

Ms. Mugdha Agarwal

Information Officer

M.Sc. Bioinformatics

Mrs. Kiran Shanti

Technical Assistant

P.G.D.C.A., M.Sc. Botany

Mr. S. R. Choudhary

Computer Operator

M.C.A.,  M.Sc. Bioinformatics, I.T.

Mr. Amit Goyal

Data Entry Operator

‘O’ Level, MCSE, CCNA, M.A.

Mr. Chandresh Kumar

Junior Technical Assistant

MCA

 
For More information:
 
Visit: banasthali.org
 


About the Institution
 

Banasthali University is a national institute exclusively for women’s education. It was founded by (Late) Smt. Ratan Shastri and (Late) Pandit Hira Lal Shastri on October 6, 1935 to fill the vacuum caused by the sudden demise of their highly talented and promising daughter Shantabai. On October 25, 1983 the Government of India, on the advice of University Grants Commission, New Delhi notified the Banasthali as an Institution Deemed to be University.
The Institution aims at the amalgamation of spiritual values and scientific achievements. Considering its relatively short existence as a University, the institution has made phenomenal progress. At present, it has around 31 teaching departments, over 427 teachers and nearly 9500 students. The institute offers several human resource development oriented programmes which include advanced courses at undergraduate and postgraduate levels in the new emerging areas of management, biotechnology, bioinformatics, computer science, information technology and electronics besides various courses in humanities, social sciences, home science, education and fine arts.
Department of Bioscience & Biotechnology
 
Databases/Applications Developed

Name of Database

Functional Area

Completion Status

Biotechnological Industries of Rajasthan

Biotechnology

Completed

SSRDatabase of Citrus sinensis

Bioinformatics

Completed

Database for Simple Sequence Repeats of Takifugu rubripus

Bioinformatics

Completed

Database of Diterpene Synthase Gene

Bioinformatics

Completed

Database of Flora of Indian Desert

Biodiversity

Completed

Database of Plant Host-Pathogen Interaction

Biodiversity

In Progress

 
Database, Biotechnological Industries of Rajasthan developed by Centre for Bioinformatics
 
Database, Biotechnological Industries of Rajasthan developed by centre for Bioinformatics
 
Database, Flora of Indian Desert developed by Centre for Bioinformatics
 
Portal and Website Development
The Centre has a website Link (http://www.banasthali.org) at website of the institution.
 
Network Connectivity
A total of 11 Mbps Leased line and 1 Gbps BSNL Link is being shared amongst 2700 nodes in Banasthali University. During 900 am to 600 pm, only c. 600 nodes are active.
 
Long Term Courses
 

M.Tech Bioinformatics
M.Sc. Bioinformatics
PG Diploma in Bioinformatics

 
Inter Institutional Collaboration
 

Industry Interactions:
The centre remains in contact with some Bioinformatics firms, viz. Mascon Life Science; MRD Life Sciences; Cadilla Pharmaceuticals; CSRD People’s group, Bhopal; HH BioTechnologies Pvt Ltd etc.  However the interaction needs to be further promoted.

 
Interactions with Other Institutions/Centers:
  • Centre is having contact with the following Educational Institutes leading in Bioinformatics:  Jaipur National University
  • BISR
  • Institute of Cytology & Preventive Oncology, Noida
  • CIMAP, Lucknow
 
Recent Publications
 

    Raghav, D., Sharma, V., and Agarwal, S.M., 2013. Structural investigation of deleterious non-synonymous SNPs of EGFR gene. Interdisciplinary Sciences: Computational Life Sciences, 5(1): 60-68. {9, DOI: 10.1007/s12539-013-0149-x.

    Raghav, D., and Sharma, V., 2013. An in-silico evaluation of deleterious non-synonymous SNPs in ErbB3 oncogene. BioResearch Open Access. 2(3): 206–211.

    Kuntal, H., and Sharma, V., 2013. SNP analysis in core mitochondrial genes of Chlorophytes. International Journal of Computational Bioinformatics and In Silico Modeling, 2(5): 234-238.

    Sekhwal, M.K., Sharma, V., and Sarin, R., 2013. Annotation of glycoside hydrolases in Sorghum bicolor using proteins interaction approach. Journal of Proteome Science Computational Biology, 2(1): 1-8. doi: 10.7243/2050-2273-2-2.

    Shanker, A., 2013. Paraphyly of bryophytes inferred using chloroplast sequences. Archive for Bryology 163: 1-5.

    Shanker, A., 2013.Inference of bryophytes paraphyly using mitochondrial genomes. Archive for Bryology 165: 1-5.

    Shanker, A., 2013. Combined data from chloroplast and mitochondrial genome sequences showed paraphyly of bryophytes. Archive for Bryology 171: 1-9.

    Sharma, V., Sekhwal, M.K., Swami, A.K. and Sarin, R. 2012. Identification of drought responsive proteins using gene ontology hierarchy. Bioinformation, 8(13): 595-599.

    Sharma V, Kuntal H, Katara P, Sharma S. Identification of SSRs in EST sequences of  Lolium and Agrostis species.International Journal of Integrative Research, 13(2): 80-87.

    Shanker, A.  and Sharma, V. 2012. Efficacy of maximum likelihood method and longer sequences in phylogenetic analysis. Res. J. Biotech. 7: 114-118.

    Shanker A and Sharma V. 2012. Chloroplast genome analysis to detect transition link between bryophytes and pteridophytes: A Bioinformatics Approach. Archive for Bryology. 121: 1-8.

    Katara P and Sharma V. 2012. In Silico Approaches to Predict Gene Distribution Patterns. International Journal of Biomedical Research. 5 (2): 71-74.

    Katara P, Grover A and Sharma V. 2012. In Silico Prediction of Drug Targets in Phytopathogenic Pseudomonas syringae pv. phaseolicola: Charting a Course for Agrigenomics Translation Research. OMICS: A Journal of Integrative Biology. 16(12): 700-706.

    Kuntal H, Sharma V and Daniell H. 2012. Microsatellite analysis in organelle genomes of Chlorophyta. Bioinformation. 8(6): 255-259.

    Sekhwal, M.K., Swami, A.K., Sarin, R. and Sharma, V. 2012. Identification of salt treated proteins in sorghum using gene ontology linkage. Physiology and Molecular Biology of Plants, 18: 209-216.

    Sekhwal, M.K., Sharma, V. and Sarin, R. 2012. Identification of MFS Proteins in Sorghum Using Semantic Similarity. Theory in Biosciences, DOI: 10.1007/s12064-012-0174-z

    Katara P, Grover A, Sharma V. 2011. Phylogenetic footprinting: a boost for microbial regulatory genomics. Protoplasma.  Nov 24.

    Shanker, A., Sharma, V. and Daniell, H. 2011. Phylogenomic evidence of bryophytes’ monophyly using complete and incomplete data sets from chloroplast proteomes. J. Plant Biochem. & Biotechnol. 20: 288-292.

    Kuntal H. and Sharma V. 2011. In silico analysis of SSRs in mitochondrial genomes of plants. OMICS: A Journal of Integrative Biology 15(11): 783-789.

 
Contacts:
 

Coordinator            :      Professor VINAY SHARMA
Phone                      :      01438-228302, 01438-228341
Ext                          :      380 (O)
Fax                          :      01438-228365
E-mail                      :     vinaysharma30@yahoo.co.uk; bv.bioinfo@gmail.com                                                    banasthali.btisnet@nic.in
Web –Address            www.banasthali.org

 
Coordinator, Centre for Bioinformatics, Banasthali University, Professor Vinay Sharma
 
 
 
 
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