Systems Biology @Knowmics
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This document provides a project proposal for systems biology research at NIPER. It outlines an academic program involving systems biology courses for biotechnology students and research projects on targets for lifestyle diseases like oxidative stress and aging as well as communicable diseases. The proposal describes procuring hardware, software, and equipment needed for the research. It presents a workflow for systems biology moving from omics data to target identification using both wet lab and in silico methods along with the relevant software tools.
Systems Biology @Knowmics
- 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