1. A
PROGRRAM PROJECT PROPOSAL FOR SYSTEMS
BIOLOGY RESEARCH AT NIPER
Research project funded under XI five year plan
Controller & Coordinator: Nilanjan Roy PhD

2. Why
What
How

3. Why
lifestyle Communicable Others 120
Source: World Health Organization. 100
80
Millions
60
40
20
0
'
1'
'
'
'
'
'
'
'
'
'
-9
19
29
49
69
79
89
99
39
59
'<
'5
5-
5-
5-
5-
5-
5-
5-
5-
5-
'1
'2
'3
'4
'5
'6
'7
'8
'9
Distribution of Indian population, 2001

4. Vision 2020; Indian paradox
Times of India, March 18, 2007
Source: “2006 World Population Prospects”
A report by UN Department of Economics and Social Affairs

5. Systems Biology at a glance
Genome Analysis Expression Analysis Proteome analysis
Interactome Analysis Pathway analysis Flux Balance Analysis
Sequence analysis Structural analysis

6. What
5.1 INSTITUTIONAL
Following institutional academic and research activity will be carried out in the
proposed program.
5.1.1 ACADEMIC PROGRAM:
Systems Biology course (M.S. Pharm.) in Biotechnology. Students from the
biotechnology department will be trained in this facility apart from their
departmental program.
5.1.2 RESEARCH
Following projects has been taken up under the scheme
Target discovery
1. Target for lifestyle diseases
a. Oxidative stress and Aging
b. Ischemic reperfusion injury
2. Targets for communicable diseases
a. Anti-protozoal
b. Anti-fungal

7. 5.1.1 ACADEMIC PROGRAM:
Systems Biology course (M.S. Pharm.) in Biotechnology. Students from the
biotechnology department will be trained in this facility apart from their
departmental program.
BT-540 SEQUENCE ANALYSIS (2 CREDITS)
1.Basics of computational biology
2.DNA & protein Sequence Analysis
3.Various methods of DNA and Protein comparison
4.Phylogenetic Analysis.
BT-660 SYSTEMS BIOLOGY (2 CREDITS)
1.Computational methods for Omics biology
2.Network construction and FBA
3.Computational methods for protein structure prediction
4.Computational methods for target based drug screening

8. 5.1.2 RESEARCH

9. E. Procurements
E.1 HARDWARE:
HPC Server, IBM workstation, MacPro work station, Storage & networking
hardware .
E.2 SOFTWARE
Scanarray Express, Pathway Studio, Matlab, Vector NTI, MOE, Sybyl,
Schrondiger & PBSPro.
E.3 EQUIPMENT:
Bio-analyzer, Microarray hyb station, Real-time PCR, liquid handling Robot
& Flow-cytometer.
E.4 FURNITURE AND LAB REMODELING

10. How
System biology Work flow
From Omics to Target
Data from
Wet lab Insilico lab I Insilico lab II Insilico lab III
other lab 1. Microarray 1. Pathway analysis 1. Sequence analysis 1. Protein modeling
can also be 2. 2D-Gel Proteomics 2. Identification of 2. RT-PCR, Cloning 2. SAR, Active site
feed in key regulators support identification
System
biology
pipeline Software Software Software Software
R, ScanArray, Avadis, Pathway Studio, Chromas, GCG, MOE, Sybyl
PD Quest Matlab Vector NTI Schrodinger