department of bioinformatics chhatrapati shahu ji maharaj ... of department of bioinformatics...
TRANSCRIPT
Department of Bioinformatics
Chhatrapati Shahu Ji Maharaj University
Kanpur
(NAAC Reaccredited in 2015)
(UP State Govt. University)
Mission of Bioinformatics
The Department of Bioinformatics was established in 2004 year in University Institute of Engineering
and Technology, CSJM University. Bioinformatics is the integration of biological sciences,
information technology and computer sciences and has become an essential tool of all biological
research activities. At the Department of Bioinformatics, UIET, CSJM University Kanpur, it is our
goal to train young minds to contribute to this now burgeoning field of science. We strive to provide
them with excellent teaching and laboratory facilities as well as an environment that grooms them to
be leaders in the field.
We have a distinguished core Bioinformatics faculty whose varied research interests include drug
designing, molecular structure prediction and visualization, genomics, transcriptomics and
proteomics, metabolic modeling and system biology. The program is truly interdisciplinary with
collaborating faculty from Computer Science, Biological Sciences, Information Technology and
Mathematics. The program also benefits immensely from intellectual interactions with premier
institutes such as the Indian Institute of Technology and Indian Institute of Pulses Research in its
vicinity.
. We invite you to explore the program in more detail through this web-site and encourage you to
personally visit the campus. Thank you for your interest in our program
Bioinformatics is the use of information technology in the field of Biotechnology, Biochemistry, Life
Sciences, Medical Sciences and Computer Sciences. It utilizes the application of computer
technology for scrupulous analysis and management of biological data. It is emerging
interdisciplinary research field and is increasingly more being used to get better the quality of life.
At present huge amount of data is being generated in the field of biological sciences, so computers
are used to pull together, analyze, accumulate and combine the biological data which can improve
the living standards of human beings.
Courses offered by Department of Bioinformatics
Year of Establishment 2004
1- M.Sc. Bioinformatics
Duration: 2 years (Four Semester).
No of seat: 40
Mode of Admission: - Through University Entrance Examination
Eligibility Criteria: Bachelor's Degree in Science( Special or General with Biochemistry,
Biotechnology, Bioinformatics, Microbiology, Electronics, Computer Science, Agriculture Science,
Pharmacy, Botany, Zoology, Mathematics, Physics) or equivalent with minimum 50% of marks for
General/OBC categories and 5% relaxation for SC/ST.
2- Advanced Post Graduation Diploma in Bioinformatics
Duration: 1year (Two Semester)
No of seat: 20
Mode of Admission: - Through University Entrance Examination
Eligibility Criteria: Master's Degree in Sciences (Special or General with Biochemistry,
Biotechnology, Bioinformatics, Microbiology, Life Science, Botany, Zoology, Mathematics,
Physics, Electronics, Computer Science, Agriculture Science, Pharmacy, B. Tech (In any engineering
branch), MBBS, BDS, BAMS, BUMS or equivalent with minimum 50% of marks for General/OBC
categories and 5% relaxation for SC/ST.
Availability of Entrance Form: February to Last Week of March, for admission queries kindly visit
the University Website. www.kanpuruniversity.org
http://www.uietkanpur.com/bi.php
Fee Structure of Courses
Fee M.Sc. Bioinformatics-
First Year
(I & II Semester)
M.Sc. Bioinformatics-
Second Year
(III & IV Semester)
Advanced P.G. Diploma in
Bioinformatics
One year (I & II Semester)
Tuition Fee 25,000/- 25,000/- 25,000/-
Examination Fee 3,000/- 3,000/- 3,000/-
Enrolment Fee 100/- ------ 100/-
Examination
Form Processing Fee
100/- 100/- 100/-
Group Insurance 443/- 443/- 443/-
Total 28,643/- 28,543/- 28,643/-
Hostel Availability and Allotment
The University has three well-furnished girls’ hostels with a total capacity of 500 inmates, a boy’s
hostel with the capacity of 400 inmates. All the hostels have mess facilities at very moderate rates,
24 hour power supply, common hall, TV room, reading rooms, telephone, recreational and sports
facilities with a tight security system. The students are allowed to use their own computer in the
rooms. Institute has limited hostel facility and therefore hostel cannot be made available to all newly
admitted students. In view of shortage of Hostel, the students belonging to Kanpur District are not
eligible for allotment of Hostel as a matter of policy.
Boys Hostel Fees : Rs. 18050/- per year (Rent only)
Girls Hostel Fees : Rs. 18000/- per year (Non-attached bathroom)
: Rs. 20000/- per year (Attached bathroom)
: Rs. 12000/- per year (For low income, after producing income certificate)
: Rs. 1500/- Security money for girls
Rs. 50/- Form fees for girls
Note: Mess fees as per actuals and seprate from the above
Scholarship: Scholarship and Fee Reimbursement is provided as per Govt. Rule.
(http://scholarship.up.nic.in/)
Facilities
Hardware
Items Qty. Configuration
High
Performance
01
Master
2 * Intel Xeon Quad Core
3.00GHZ/12MB L2
Cache/1333Mhz FSB (x5450),
Intel 5000x chipset based Intel
Computing
Cluster Server
motherboard 8*2 GB DDR2 FB
DIMM RAM (667Mhz), 1*146 GB
3*300 GB SAS HDD, 19” TFT
LCD Monitor, 107 Keys
Mechanical Keyboard & 3 Bt
Optical Mouse.
Cluster Server
Workstation
03
Slave
Intel Core 2 duo Processor
[email protected], 6MB L2 Cache,
1333Mhz FSB, Intel G31 express
Chipset or better, 2*1GB DDR II
RAM(800Mhz) 4DIMM slots,
160GB SATA HDD(3.0gbps),
DVD-RW, 19’’ TFT LCD wide
screen Monitor, 107 Keys
Mechanical Keyboard, Optical
mouse, Integrated LAN Ethernet
Network card 10/100/1000
Workstation 02
2 * Intel Xeon Quad Core 3.00
GHZ/12 MB L2 Cache/1333Mhz
FSB (5450), 8*2 GB DDR2 FB
RAM (667Mhz) 3*300 GB SAS 15
krpm Hot plugable HDD Nvidia
QUADRO FX 1700,
512MB Graphics card, 19” TFT
LCD wide screen Monitor, DVD-
ROM
Printer 02 HP Laser jet (black and white) and
Office jet (colour)
LCD Projector
with screen tripod
screen
01
High pressure mercury lamp 210
W, power consumption 310 W,
zoom ratio 1.6X,3000 ANSI lumen,
resolution 1024x768, XGA contrast
=400x1 radian
UPS 02 30KVA
Laboratory
Bioinformatics
& Basic
Programming
Lab (BI-301)
40
Intel P4 Processor
[email protected] CPU , 1 GB
RAM, 80 GB HDD
Internet Facilities
24 Hours High bandwidth Internet Facilities and fully A.C. Laboratory
Softwares
CADD &
Molecular
Modelling Lab
(BI-302)
40
CPU: Intel Core 2 duo Processor
[email protected], 2 GB RAM, 160
GB HDD
S.No. Public Domain Softwares
1. Molecular Visualization
Software
Rasmol, Pymol, Cn3d
2. Structure Prediction &
validation
Swiss PDB Viewer, GOR, Swiss model
3. Homology modeling Geno3D, Modeller
4. Submission Tool Sakura, Bankit, Webin
5. Alignment Tools BLAST, Clustal package, Tree view, Jalview, T-coffee
6. Docking Software Hex , Molegro, Auto Dock
7. Molecular modeling
software
DTMM, ChemSketch, Viewer Light
8. Editing tool Bio-Edit
9. Chromatogram trace
viewer
FentchTV
10. Phylogenetic analysis Treeview, Phylip, Clustal W/X/Omega
11. Online Databases NCBI, DDBJ, EMBL, GenBank, PIR, Swissprot, PROSITE,
Print, Block, PDB, CATH, SCOP, P-fam
12. Systems Biology &
Metabolomics
Cytoscape, Cell Designer, Copasi, Gepasi, Systems Biology
Workbech (SBW)
13. Others Gene Designer, E-Cell, V-Cell, ORF Finder. MFOLD, RNA
FOLD, EMBOSS, GROMAC, GROMOS, AMBER, R
(STATISTICAL PACKAGE), GENESIS, CLUSTAL W,
Chime, CELL-DESIGNER, LUDI, MOLMAKER, System
Faculty
Name of Faculty Designation Qualification Department Area of Interest
Er. Mamta Sagar E.mail [email protected]
M.No.- 7499292773
Assistant
Professor &
Head
Ph.D. Bioinformatics
(Pursuing),
M.Tech I.T.(Bioinformatics)
IIIT-Allahabad,
M.Sc. (Microbiology), CCS
University , Meerut
CSIR- NET, GATE
Bioinformatics
Modelling and visualization
of protein conceived to act
as drug target, structure-
based drug design, in silico
vaccine design for Liver
cancer and HIV and
application of agent based
models, artificial neural
networks.
Dr. Manish Kumar Gupta E.mail
M No.- 9307267812
Assistant
Professor
Ph.D. in
Bioinformatics Dr.
APJ Abdul Kalam
Technical University,
Lucknow M.Tech in
IT (Bioinformatics)
IIIT-Allahabad,
M.Sc.(Biotechnology)
University of
Hyderabad,
Qualified CSIR-
JRF_NET, GATE
Bioinformatics
Systems Biology, Rnomics,
RDD, Database Design and
Development.
Er. Brijendra Singh
Mob. no.- 8005384692
Assistant
Professor
Ph.D. Bioinformatics
(Pursuing), M.Tech
I.T. (Bioinformatics)
IIIT-Allahabad, M.Sc.
(Microbiology) Dr.
RMLA University
GATE
Bioinformatics
Drug Design And Molecular
modelling, microarray
analysis.
Dr. Varsha Gupta
Associate
Professor
(Adjunct
Faculty)
Ph.D. (Mathematics) Mathematics Engg. Mathematics.
Dr. Dharmendra Kumar Singh
Assistant
Professor
(Adjunct
Faculty
Ph.D. (Mathematics) Mathematics Biostatistics, Mathematics.
Dr. Manoj Kumar Singh
Assistant
Professor
(Adjunct
Faculty)
Ph.D. (Mathematics) Mathematics Biostatistics, Mathematics.
Er. Manish Dua
Assistant
Professor
(Adjunct
Faculty)
M.Tech (Computer
Science.) CSE JAVA Programming.
Technical Staff
Biology Markup Language & BSML,Vector Alignment
Search Tool, Ligplot
Mr. Luxman
Rajput
(Technical
Assistant)
B.Sc. (Math), M.A., DCA
(Hardware Networking) [email protected] Mob. no.-9956096532
Career@ Bioinformatics
Bioinformatics has profound impact in various fields like human healthiness, environment,
Biotechnology agriculture and energy to enhance the biomedical research and development. It is also
used in the area of molecular medicine for Drug designing which can cure many lethal Diseases.The
ultimate goal of bioinformatics is to uncover the prosperity of biological information hidden in
sequences, structure, literature and other biological data. It obtains a clear insight into the
fundamental biology of organisms and to use this information to enhance the standard of life for
human being.
Today, Bioinformatics is speedily growing field all over the world. Hence, one can begin a career in
Bioinformatics and find out employment opportunities in Biotechnology, Bioengineering,
Biomedical and pharmaceutical sciences, software development, in industries, hospitals and research
institutions.
According to the new market research report from Industry Experts ‘Bioinformatics – A Global
Market Overview', global market for bioinformatics is estimated at about $2.4 billion in 2011 and
further projected to reach $7.6 billion by 2017 registering a CAGR of 18.3% during the period 2007-
2017.
Scope of Bioinformatics
Due to increasing demand of Bioinformatics candidates, a career in Bioinformatics offer good
prospects. Bioinformatics specialists have a variety of career opportunity. Most of these trained
persons are absorbed in pharmaceutical and Biotech companies. They can also work with leading
scientific research organization of public and private sector. They can also occupy with government
and private hospitals. These experts also can find employment in industries manufacturing different
biomedical products. One can also take up teaching jobs in public and private University/Institute
offering bioinformatics as a subject. The extent of bioinformatics is in areas like database design and
maintenance, sequence assembly, proteomics, clinical pharmacologist, sequence analysis,
bioinformatics software developer and bio-analytics.
Bioinfomatician
Pharma Industry/Biotechnology Industry/Software Industry/
Database Designing and Management
Research Organization(CSIR, ICMR, ICAR, Biotech
Park)/Teaching Organization
Job Opportunities and Bioinformatics Companies
Excellent job opportunities are available for bioinformatician in Biotech, Pharmaceutical, Software
development companies in India as well as abroad. The names of some of the companies are:-
Tata consultancy services (TCS), Bigtec , Strand genomics, Wipro, Mphasis, Bioworld, Zensar,
Satyam computer services, Avestha gengraine technologies, Metahelix life sciences, IBM india
Research labs (irl), Sun Microsystems, Dr.Reddy's laboratories limited, Ranbaxy, Nicholas Piramal,
Biocon/syngene/clingene, Jubilant biosys ltd. (JBL), Molecular connections, Accelrys, Ocimum bio,
Reliance life sciences, Mathworks, Schrodinger, GVK Biosciences, DSQ Biotech, Centre for
Development of Advanced Computing (C-DAC), AstraZeneca Research Centre, Silicon Genetics
and Tessella, Vlife, Tripos :A Certara™ Company
Govt. Of India Initiative in the field of Bioinformatics
The Department of Biotechnology (DBT), Government of India has instituted Bioinformatics
National Certification (BINC) (http://binc.scisjnu.ernet.in/) in 2005 and conduct examination every
year in the month of February with the objective of evaluating the Bioinformatics knowledge & skills
of students. The qualifying candidates will be awarded a certificate. This certification would facilitate
industries and potential employers in recruiting Bioinformatics professionals.
After Qualifying this examination, the Students can be benefited by:-
Cash awards to the top ten candidates in the merit list.
DBT BINC junior research fellowships (DBT-BINC-JRF) to all qualified candidates.
Department of Biotechnology (DBT), Ministry of Science and Technology, Government of India,
Biotech Consortium India Limited (BCIL) ( http://www.bcil.nic.in/) is coordinating a scheme of
practical industrial training for B.Tech./ B.E./ M.Sc./ M.Tech./ Advanced Post Graduate Diploma in
Bioinformatics and BINC qualified students. The students are placed for training in Bioinformatics
& Biotechnology companies willing to impart practical training to these candidates. The training is
for a period of six months during which every trainee is paid a stipend of Rs. 8000/- per month.
Remuneration
It is a very much remunerative career choice. Persons working in government research organization
and hospital get pay as fixed by government. It can be Rs 24,000 to Rs 36,000 depending upon job
profile and experience. Professors working in University/Institute can get basic pay of Rs 40000 to
Rs 60000 per month at entry level. Those working in private sector Pharma companies or
Multinational companies get a pay of Rs 4, 50,000 - Rs 6, 00,000 per annum.
Placement at the Department
Placement Organization Name of Organization
Research Organization in
India IIT-Italy, Institute of Veterinary Science-Viana,Austria.
Universities
Sharda University-Meerut, GB Pant University-Pantnagar, CSJM University Kanpur,
Lucknow University, Central University Hyderabad, IIIT-Allahabad, Amity University-
Lucknow & Noida, Hindustan college of management science.
Pharmaceutical Industry Zydus cadila, Ranbaxy, K life Sciences, Kusum Pharmaceutical.
Chemicals industry Aroma Chemicals, Tansy Chemicals, Cremaline Chemicals.
Software and BPO
Industry
IBM, TCS, Wipro, Genpact, Cell work, Biocon, ACME Telepower,Tova optics India
Pvt. Ltd.
Banking Sector Punjab National Bank, State Bank of India, ICICI Bank.
Research Publication Ocimum Publication Group
Projects
Area of
Research
Projects
Software Development, Database Development, Rational Drug Designing, Molecular Docking and Virtual
Screening, System Biology, Pathways Modeling and simulation analysis, RNA Secondary Structure
Prediction, Rational Design of siRNA and miRNA, QSAR, Metabolomics, Molecular Modelling and
Visualization, in silico Vaccine Design, Agent Based Models, Artificial Neural Networks, Next Generation
Sequencing, Microarray Analysis.
List of Publications Department of Bioinformatics:
Research Article:
1. Mamta Sagar, Rajesh Kumar Pathak, Rishi Kumar Pandey, Dev Bukhsh Singh, Neetesh Pandey, Manish
Kumar Gupta (2014) Binding affinity analysis and ADMET prediction of epigallocatechine gallate
(EGCG) derivatives for AP-1 protein: a drug target for liver cancer. Network Modeling Analysis in Health
Informatics and Bioinformatics 3:66 (ISSN: 2192-6662 ; Online ISSN: 2192-6670)
2. Gupta MK, Misra K (2014) Atom based 3D-QSAR, molecular docking and molecular dynamics
simulation assessment of inhibitors for thyroid hormone receptor α and β. Journal of Molecular Modeling
20:2286 (Print ISSN:1610-2940 ; Online ISSN:0948-5023 )
3. Manish Kumar Gupta, Dev Bukhsh Singh, Rohit Shukla, Krishna Misra (2013) Comprehensive metabolic
modeling of thyroid pathway.in relation to thyroid pathophysiology and therapeutics. OMICS: A Journal
of Integrative Biology. 17(11):584-593 (Print ISSN: 1536-2310 Online ISSN: 1557-8100)
4. Dev Bukhsh Singh, Manish Kumar Gupta , Durg Vijay Singh, Sushil Kumar Singh, Krishna Misra (2013)
Docking and In silico ADMET studies of noraristeromycin, curcumin and their derivatives with
Plasmodium falciparum SAH hydrolase: A molecular drug target against malaria. Interdisciplinary
Sciences: Computational Life Sciences. 5:1-12 (ISSN: 1913-2751; Online ISSN 1867-1462)
5. Singh DB, Gupta MK, Misra K, (2013) Comparative Docking and ADMET Study of Some Curcumin
Derivatives and Herbal Congeners Targeting beta-Amyloid. Journal of Network Modeling Analysis in
Health Informatics and Bioinformatics. 2(1):13-27 (ISSN: 2192-6662 ; Online ISSN: 2192-6670)
6. Gupta MK, Misra K, (2013) Modeling and Simulation Analysis of Propylthiouracil (PTU), an Anti-thyroid
drug on Thyroid Peroxidase (TPO), Thyroid Stimulating Hormone Receptor (TSHR) and Sodium iodide
Symporter (NIS) based on Systems Biology Approach. Journal of Network Modeling Analysis in Health
Informatics and Bioinformatics. 2(1): 45-27 (ISSN: 2192-6662 ; Online ISSN: 2192-6670)
7. Gupta MK, Agarwal K, Prakash N, Singh DV, Misra K, (2012) Prediction of miRNA in HIV-1 genome
and its targets through artificial neural network: a bioinformatics approach. Journal of Network Modeling
Analysis in Health Informatics and Bioinformatics. 1(4):141-151 (ISSN: 2192-6662 ; Online ISSN: 2192-
6670)
8. Kumar GM, Singh Dev Bukhsh, Krishna M (2012) Metabolic Modeling and Simulation Analysis of
Thyroid Disorder Pathways. J Comput Sci Syst Biol. 5(2):52-61 doi:10.4172/jcsb.1000090 (ISSN: 0974 -
7230)
9. Kumar GM, Prakash N, Pragya C, Krishna M (2011) Computational Analysis of SNPs in 10 kb Region of
Human Chromosome 1. J Comput Sci Syst Biol. 4: 033-034. doi:10.4172/jcsb.1000073 (ISSN: 0974 -
7230)
10. Gupta SK, Singh S, Gupta MK, Pant KK, Seth PK (2010) Definition of Potential Targets in Mycoplasma
Pneumoniae Through Subtractive Genome Analysis. J Antivir & Antiretrovir 2: 038-041 (ISSN: 1948-
5964)
11. Singh S, Gupta SK, Sabir G, Gupta MK, Seth PK (2009) A database for anti-diabetic plants with clinical
/ experimental trials. Bioinformation. 31;4(6):263-268 (Online ISSN 0973-2063; Print ISSN 0973-8894)
12. Mamta Sagar, Padma Saxena, Neetesh Pandey and Dev Bukhsh Singh, (2013) Modelling transmembrane
region in G8 protein of Human and other organisms. Int J Comput Bioinfo In Silico Modeling 2(4): 152-
157.
13. Pramod Kumar Yadav, G. Singh, B. Gautam. S. Singh, Brijendra Singh (2013) Molecular modeling,
dynamics studies and virtual screening of fructose 1,6 biphosphate aldose – II in community acquired
methicillin resistant Staphylococcus aureus (CA-MRSA). Bioinformation, 9(3):158-164.
14. Shrasti Gupta, Vijay Laxmi Saxena, Brijendra Singh (2013) Homology Modeling and Docking Studies of
Neuraminidase Protein of Influenza a Virus (H1N1) virus with Select Ligand – A Computer Aided
Structure Based Drug Design. International Journal of Pharmaceutical Science Invention, 2(6):35-41.
15. Mamta Sagar, Neetesh Pandey, Naseha Qamar, Brijendra Singh, Akanksha Shukla (2014) Domain
analysis of 3 keto acyl-CoA synthase using sequence and structure alignment approach in Vitis vinifera
and Oryza brachyantha. Interdisciplinary Sciences--Computational Life Sciences, 6: 1-14.
Review Article:
1. Singh Dev Bukhsh, Gupta Manish Kumar, A Kesharwani, Rajesh Kumar, Sagar Mamta, Dwivedi Seema;
Misra Krishna (2014) Molecular drug targets and therapies for Alzheimer’s disease. Translational
Neuroscience 5(3): 203-17 (Print ISSN:2081-3856 Online ISSN:2081-6936)
2. Gupta MK, Misra K (2016) A holistic approach for integration of biological systems and usage in drug
discovery. Journal of Network Modeling Analysis in Health Informatics and Bioinformatics. 5(4) (ISSN:
2192-6662; Online ISSN: 2192-6670)
Photo Galleries (Laboratories)
(Seminar/Workshop/Conferences/Symposium)
Workshop on “Current Trend in Computing and Bioinformatics” in 2007. The chief guest of
the event was father of bioinformatics in India known as Prof. A.S Kolaskar, Former Vice-
Chancellor of Pune University. The Patron of the event was Prof. S.S. Katiyar Former Vice-
Chancellor of CSJM University kanpur.
National Educatin Day 2009 was celebrated on theme “ Education System in india:
Introspection” .The chief guest of the event was Prof. H.C Verma from IIT Kanpur.
National Educatin Day 2011
National Educatin Day 2011 was celebrated on theme “ Recent Trendes in Biosciences and
Bioengineering” .The chief guest of the event was Prof. R.Shankarramakrishnan, Dept of
Biosciences and Bioengineering , IIT Kanpur . Prof. Krishna Misra was guest of honour from
Indian Institute of Information Technology Allahabd . Special lecture was taken by Por.
Thesoun Bharoun from University of Mauritius.
National Education Day 2014
Bhabha Atomic Research Centre, Mumbai, Department of Atomic Energy, Govt. of
India, Organized A Seminar On “Many Dimensions Of Indian Atomic Energy
Programme” and Exhibition on “BARC Technologies” on February 25, 2015. The Chief
Guest of the event was Prof. Indiranil Manna, Director IIT Kanpur.
Contact Us
Department of Bioinformatics
University Institute of Engineering and Technology
CSJM University Campus – Kanpur
Email: [email protected]
M.No.: 9307267812
8005384692