NATIONAL INSTITUTE OF TECHNOLOGY, ARUNACHAL PRADESH, YUPIA, Pin-791112
(Established by MHRD, Govt. of India)
Website : www.nitap.in, Fax No: (0360) 2284972
E-Mail: [email protected] / [email protected]
Exercises Proposed for teaching in (July – December, 2016 Semester)
1. Name of the Teacher: Dr. Shantonu Roy
2. Department:
Biotechnology & Chemical Engineering
3. Course Title:
Bioinformatics
4. Course code:
BT-502
5. Course Hands out (in reference to framed & approved syllabus) (maximum 500 words)
Contents
Class estimate
Unit I:
Introduction to Bioinformatics: Definition and History of Bioinformatics,
Internet and Bioinformatics, Introduction to Data Mining, Applications of
Data Mining to Bioinformatics Problems and Applications of Bioinformatics
8 classes
Unit II:
12 classes
Bioinformatics Softwares: Clustal V, Clustal W 1.7, RasMol, Oligo,
Molscript, Treeview, Alscript, Genetic Analysis Software, Phylip
Unit III:
8 classes
Biocomputing: Introduction to String Matching Algorithms, Database
Search Techniques, Sequence Comparison and Alignment Techniques, Use
of Biochemical Scoring Matrices, Introduction to Graph Matching
Algorithms,
Automated Genome Comparison and its Implication,
Automated Gene Prediction, Automated Identification of Bacterial Operons
and Pathways;
Introduction to Signalling Pathways and Pathway
Regulation. Gene Arrays, Analysis of Gene Arrays
Unit IV:
Markov chains and applications: Systems Biology-an introduction
Machine Learning Methods, Hidden Markov models, Applications of HMM
in gene identification and Profiles HMMs, Neural Networks and Support
Vector machines.
5. Books/Literature to be followed:
(a) Books (Min. 2 texts + 3 references)
(i)
Title
Data Mining For Bioinformatics Application
Author
He Zengyou
Publisher
Elsevier Science
(ii)
Title
Bioinformatics: Database Tools & Algorithms
Author
Orpita Bosu
Publisher
Oxford University Press
(iii) Title
Evolutionary Computation in Bioinformatics
12 classes
NATIONAL INSTITUTE OF TECHNOLOGY, ARUNACHAL PRADESH, YUPIA, Pin-791112
(Established by MHRD, Govt. of India)
Website : www.nitap.in, Fax No: (0360) 2284972
E-Mail: [email protected] / [email protected]
(iv)
(v)
(b)
1.
2.
3.
4.
5.
Author
Publisher
Title
Author
Publisher
Title
Author
Publisher
Gary Forgel
Morgan Publisher
Intro To Math Method In Bioinformatics
Alexander Isave
Springer
Bioinformatics & Function Genomic
Jonathan Pevsner
Wiley Blackwell
Magazines/Journals (Minimum 5)
IEEE/ACM Transactions on Computational Biology and Bioinformatics, United State
Genomics, Proteomics & Bioinformatics, Elsevier, , Netherlands
Genomics Research, Elsevier, Netherlands
Genomics , Elsevier, Netherlands
Briefings in Bioinformatics, Oxford Journal
7. Mode of Teaching: J.C Bose √ / S. N. Bose (please tick).
8. If the course is of practices, list the experiments to be offered.
1. (i)
Handling of different databases (primary and secondary database)
2. Processing, storing and analyzing of DNA sequences from chromatogram
a. Open the chromatogram
b. Obtain the sequence in FASTA format
c. Annotate the sequence
d. Conversion of sequence in different format
3. Alignment of gene sequences for predicting similarities
a. Pair wise alignment using BLAST and ClustalW
b. Multiple sequence alignment using ClustalW
4. Phylogenetic analysis
5. Functional gene identification from genomic database
a. Find ORF and six frame translation product
b. Find out the conserved domain
6. Protein structure prediction
7. Drug designing and molecular docking
8. Basic of Perl Language
Are the manuals ready for the experiments to be conducted? Yes √ /No (please tick)
NATIONAL INSTITUTE OF TECHNOLOGY, ARUNACHAL PRADESH, YUPIA, Pin-791112
(Established by MHRD, Govt. of India)
Website : www.nitap.in, Fax No: (0360) 2284972
E-Mail: [email protected] / [email protected]
If “No”, the reasons there of and fixing responsibility
__________________________________________
__________________________________________
__________________________________________
__________________________________________
Remarks/ Endorsement by the HoD
With his /her signature with date
Name of the Teacher: Dr. Shantonu Roy
Designation: Assistant Professor (DST
INSPIRE)
Signature with Date:
NATIONAL INSTITUTE OF TECHNOLOGY, ARUNACHAL PRADESH, YUPIA, Pin-791112
(Established by MHRD, Govt. of India)
Website : www.nitap.in, Fax No: (0360) 2284972
E-Mail: [email protected] / [email protected]
Exercises Proposed for teaching in (July – December, 2016 Semester)
1. Name of the Teacher: Dr. Shantonu Roy
2. Department:
Biotechnology
3. Course Title:
Life Science
4. Course code:
BIO 101
5. Course Hands out (in reference to framed & approved syllabus) (maximum 500 words)
Contents
Unit I:
Origin of Life: History of earth, theories of origin of life and nature of
the earliest organisms.
Varieties of life: Classification, Five kingdoms, viruses (TMV, HIV,
Bacteriophage),
Prokaryote
(Bacteria-cellstructure,
nutrition,
reproduction), Protista, Fungi, Plantae and Animalia.
Chemicals of life: (Biomolecules)- Carbohydrates lipids, amino acids,
proteins, nucleic acids and identification of biomolecules in tissues.
Unit II:
Cell: Cell concept, structure of prokaryotic and eukaryotic cells, plant
cells and animal cells, cell membranes, cellorganelles and their
function, Structure and use of compound microscope.
Histology: Maritimes (apical, intercalary, lateral) and their function;
simple tissue (parenchyma, collenchymas, sclerenchyma); Complex
tissue (xylem and phloem); Tissue systems (epidermal, ground,
vascular); primary body and growth (root, stem, leaf); Secondary
growth (root, stem). Animal tissues (Epithelial, connective, muscle
and nervous tissues) and their functions in the body.
Unit III:
Transport: Plant water relationships, properties of water, diffusion,
osmosis, imbibition, uptake of water by roots and theories of transport
of water through xylem (ascent of water in xylem, cohesion- tension
theory), apoplast and symplast theory; Transpiration-structure of leaf,
opening and closing mechanisms of stomata, factors affecting
transpiration and significance of transpiration.
Nutrition: Mineral Nutrition in plants, Heterotrophic nutrition in
plants; Photosynthesis (Autotrophic- forms of nutrition), Chloroplast
structure, two pigment systems, photosynthetic UNIT, light absorption
by chlorophyll and transfer of energy, phosphorylation and electron
transport system, Calvin-Benson Cycle (C3), Hatch Slack Pathway
Class estimate
10 classes
6 classes
12 classes
NATIONAL INSTITUTE OF TECHNOLOGY, ARUNACHAL PRADESH, YUPIA, Pin-791112
(Established by MHRD, Govt. of India)
Website : www.nitap.in, Fax No: (0360) 2284972
E-Mail: [email protected] / [email protected]
(C4), Crassulacan Acid Metabolism (CAM), factors affecting
photosynthesis.
Unit IV:
Energy Utilization: (Respiration) - Structure of mitochondria, cellular
respiration, relationship of carbohydrate metabolism to other
compounds, Glycolysis, fermentation, formation of acetyl co-A, Kreb
cycle, Electron Transport System and Oxidative Phosphorylation,
ATP, factors affecting respiration;
Elementary canal in humans, nervous and hormonal control of
digestive systems, fate of absorbed food materials; Nutrition in
humans, Reference values; General characteristics of blood vascular
system, development of blood systems in animals, Composition of
blood, circulation in blood vessels, formation of tissue fluids, the
heart, functions of mammalian blood, the immune system.
12 classes
6. Books/Literature to be followed:
(a) Books (Min. 2 texts + 3 references)
(i)
Title
College Botany (Volume I & II)
Author
B.P. Pandey
Publisher
S. Chand Publisher, New Delhi, 2012
Edition
Revised
(ii)
Title
Plant Physiology
Author
H.S. Srivastava
Publisher
Rastogi Publishers, Meerut, 1998
Edition
Revised
(iii) Title
Plant Anatomy
Author
B.P. Pandey
Publisher
S. Chand & Company Ltd., New Delhi, 1997
Edition
Revised
(iv)
Title
Biology
Author
N.A. Campbell and J.B. Reece
Publisher
Person Education, Inc & Dorling Kinderley Publishing, Inc.
Edition
Revised
(b) Magazines/Journals (Minimum 5)
(i)
Journal of Biology, BioMed Central Ltd, London, England.
(ii)
Annals of Botany, Oxford JOURNALS, USA.
(iii) Plant and Cell Physiology, Oxford JOURNALS, USA.
(iv)
National Geographic Channel, http://science.nationalgeographic.co.in/science/earth
(v)
Wikipedia, The Free Encyclopedia, http://www.bbc.co.uk/science/earth
NATIONAL INSTITUTE OF TECHNOLOGY, ARUNACHAL PRADESH, YUPIA, Pin-791112
(Established by MHRD, Govt. of India)
Website : www.nitap.in, Fax No: (0360) 2284972
E-Mail: [email protected] / [email protected]
7. Mode of Teaching: J.C Bose / S. N. √ Bose (please tick).
8. If the course is of practices, list the experiments to be offered.
Are the manuals ready for the experiments to be conducted?
Yes /No (please tick)
If “No”, the reasons there of and fixing responsibility
__________________________________________
__________________________________________
__________________________________________
__________________________________________
Remarks/ Endorsement by the HoD
With his /her signature with date
Name of the Teacher: Dr. Shantonu Roy
Designation: Assistant Professor (DST
INSPIRE)
Signature with Date: