NATIONAL INSTITUTE OF TECHNOLOGY, ARUNACHAL PRADESH, YUPIA, Pin-791112

(Established by MHRD, Govt. of India)

Website : www.nitap.in, Fax No: (0360) 2284972

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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:
Bioinformatics Softwares: Clustal V, Clustal W 1.7, RasMol, Oligo, Molscript, Treeview, Alscript, Genetic Analysis Software, Phylip / 12 classes
Unit III:
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 / 8 classes
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. / 12 classes

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

Author Gary Forgel

Publisher Morgan Publisher

(iv)  Title Intro To Math Method In Bioinformatics

Author Alexander Isave

Publisher Springer

(v)  Title Bioinformatics & Function Genomic

Author Jonathan Pevsner

Publisher Wiley Blackwell

(b) Magazines/Journals (Minimum 5)

1.  IEEE/ACM Transactions on Computational Biology and Bioinformatics, United State

2.  Genomics, Proteomics & Bioinformatics, Elsevier, , Netherlands

3.  Genomics Research, Elsevier, Netherlands

4.  Genomics , Elsevier, Netherlands

5.  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)

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:

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 / Class estimate
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. / 10 classes
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. / 6 classes
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 (C4), Crassulacan Acid Metabolism (CAM), factors affecting photosynthesis. / 12 classes
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

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: