Computational Biology

Teacher

Jyoti Prakash Rath

Category

Core Courses

Course Attendees

Still no participant

Course Reviews

Still no reviews

Computational Biology

Code(Credit) : CUTM1435(3-1-0)

Course Objectives

Introduce students to the field of computational biology. To make them realize the importance of insilico databases and computational tools to understand biology in a better way.

Learning Outcomes

. To be familiar with the basic concepts of Computational Biology and its significance in biological data analysis.
. Learn and able to employ various computational tools for modern day research.

Course Syllabus

Module-I : Computational Biology Fundamentals and Biological Databases

1.1.Computational Biology: Basic Concepts, importance and application

1.2. Biological Databases: Classification and different types of Biological Database

1.3. DNA and Protein sequence analysis, Pairwise and multiple sequence alignment

1.4. Protein structural analysis, protein structure modeling and prediction

Practice : Demonstration and usage of web resources: EMBL, GenBank, ENTREZ

https://www.youtube.com/watch?v=Phxkg5H5Q6E

Module-II : Database Management Systems and Its Application in Computational Biology

2.1. Database Management Systems: Basic Concepts, importance and application

2.2. Database Models, relational database

2.3. SQL

2.4. Data mining: Fundamentals, Classification and applications of data mining

Practice : Retrieving sequence data from Entrez
http://vlab.amrita.edu/index.php?sub=3&brch=273&sim=1437&cnt=1

Module-III: Insilico Drug Design

3.1. Insilico Drug Design: Basic Concepts, importance and application

3.2. Molecular force fields and energy minimization

3.3. Molecular Dynamics Simulation methods

3.4. Methods of Insilico Drug Design: structure and ligand based drug design approach

Practice :  structure based drug design: Molecular docking using Biovia

Module-IV: Systems and Synthetic biology

4.1. Systems and Synthetic Biology : Basic Concepts, importance and application

4.2. Systems Modeling

4.3.  Formulating and Simulating Network Models in Biology

4.4. Potential Hazards of Synthetic Biology

Practice:  Mathematical modeling and simulating of Biochemical network
http://vlab.amrita.edu/index.php?sub=3&brch=276&sim=1457&cnt=1

Module-V: Algorithms in Computational Biology

5.1. Algorithms in Computational Biology: Algorithms and complexity, biological versus computer algorithms

5.2. recursive algorithms, iterative versus recursive algorithms

5.3. Overview of algorithm design techniques:  Dynamic programming

5.4. Markov Chains and Hidden Markov Models : Concept and application in computational biology.

Practice : 1. Pairwise Sequence Alignment using BLAST
http://vlab.amrita.edu/index.php?sub=3&brch=274&sim=1428&cnt=1
2. Aligning Multiple Sequences with CLUSTAL W
http://vlab.amrita.edu/index.php?sub=3&brch=274&sim=1438&cnt=1

Module-VI: Biopython and It's application in Computational Biology
6.1. Biopython: Introduction, important features and application of biopython in computational biology

6.2. Create a simple sequence in Biopython for DNA, RNA and Protein Alphabets

6.3. Sequence Alignment Tools in Biopython

6.4. PDB Module of Biopython

Practice: Align nucleotide/protein sequences using tools available in biopython
https://www.tutorialspoint.com/biopython/biopython_sequence_alignments.htm

Module-VII: Biojava and It's application in Computational Biology

7.1. Biojava: Introduction, importance and application of Biojava to computational biology

7.2. Protein structure module of Biojava and its use in manipulating structure of protein

7.3. Genome and sequencing module of biojava and its application for analyzing sequence data

7.4. Biojava alignment module and its application for pairwise and multiple sequence alignment

Practice : Study of protein structure using biojava
https://github.com/biojava/biojava-tutorial/blob/master/structure/img/4hhb_jmol.png

Reference Books

1. Bioinformatics: Sequence and Genome Analysis by Mount D., 2004, Cold Spring
Harbor Laboratory Press, New York.
2. Biological Sequence Analysis: Probabilistic models of protein and Nucleic
acids by Durbin
et al., 2007,Cambridge University Press.
3. Bioinformatics- a practical guide to the analysis of Genes and Proteins by
Baxevanis,A.D. and Francis Ouellellette, B.F., 1998, John Wiley & Sons, UK.
4.Introduction to bioinformatics by Teresa K. Attwood, David J. Parry-Smith,
1999,Pearson Education.
5.Arthur M.Lesk, Introduction to Bioinformatics, Oxford University Press, New Delhi, 2003.
6. D.Higgins and W.Taylor (Eds), Bioinformatics-Sequence, Structure and
databanks, Oxford University Press, New Delhi, 2000.

Session Plan

Session 1

Computational Biology: Basic Concepts, importance and application

https://www.youtube.com/watch?v=K9MqyU298uE

Session 2

Biological Databases, Classification and different types of Biological Database
https://www.youtube.com/watch?v=QjHKV2tkHSI

Session 3

DNA and Protein sequence analysis, Pairwise and multiple sequence alignment
https://www.youtube.com/watch?v=YVGpn-XNb58

Session 4

Protein structural analysis, protein structure modeling and prediction
https://www.youtube.com/watch?v=OEzVUrhtZ6s

Session 5

Practice : Demonstration and usage of web resources: EMBL, GenBank, ENTREZ

https://www.youtube.com/watch?v=Phxkg5H5Q6E

Session 6

Database Management Systems: Basic Concepts, importance and applicationhttps://www.youtube.com/watch?v=wR0jg0eQsZA

Session 7

Database Models, relational database
https://www.youtube.com/watch?v=diXxet0Bt3Q

Session 9

Data mining: Fundamentals, Classification and applications of data mining
https://www.youtube.com/watch?v=W44q6qszdqY

Session 10

Practice : Retrieving sequence data from Entrez
http://vlab.amrita.edu/index.php?sub=3&brch=273&sim=1437&cnt=1

Session 12

Molecular force fields and energy minimization
https://www.youtube.com/watch?v=lLFEqKl3sm4

Session 13

Molecular Dynamics Simulation methods
https://www.youtube.com/watch?v=5JcFgj2gHx8

Session 14

Session 15

Practice :  structure based drug design: Molecular docking using Biovia

Session 16

Systems and Synthetic Biology : Basic Concepts, importance and application
https://www.youtube.com/watch?v=rD5uNAMbDaQ

Session 17

Session 18

Formulating and Simulating Network Models in Biology

https://www.youtube.com/watch?v=hGR_gJjRWsc

Session 19

Potential Hazards of Synthetic Biology

https://www.youtube.com/watch?v=8DDgHq9ewOo

Session 20

Practice:  Mathematical modeling and simulating of Biochemical network
http://vlab.amrita.edu/index.php?sub=3&brch=276&sim=1457&cnt=1

Session 21

Algorithms in Computational Biology: Algorithms and complexity, biological versus computer algorithms
https://www.youtube.com/watch?v=48Xr-H05raA&t=29s

Session 22

Recursive algorithms, iterative versus recursive algorithms

https://www.youtube.com/watch?v=GJw6SO4vWnI

Session 23

Overview of algorithm design techniques:  Dynamic programming
https://www.youtube.com/results?search_query=dynamic+programming+mit+

Session 24

Markov Chains and Hidden Markov Models : Concept and application in computational biology
https://www.youtube.com/watch?v=d5NMrA2HkG4&list=PLUl4u3cNGP63uK-oWiLgO7LLJV6ZCWXac&index=10

Session 25

Practice: Pairwise Sequence Alignment using BLAST
http://vlab.amrita.edu/index.php?sub=3&brch=274&sim=1428&cnt=1

Session 26

Practice: Aligning Multiple Sequences with CLUSTAL W
http://vlab.amrita.edu/index.php?sub=3&brch=274&sim=1438&cnt=1

Session 27

Biopython: Introduction, important features and application of biopython in computational biology

https://www.youtube.com/watch?v=r66YCsA4YqM

Session 28

Create a simple sequence in Biopython for DNA, RNA and Protein Alphabets
https://www.youtube.com/watch?v=r66YCsA4YqM

Session 29

Sequence Alignment Tools in Biopython
https://www.youtube.com/watch?v=MxZCwiKusdE

Session 31

Cluster Analysis using Biopython
https://www.youtube.com/watch?v=1XqG0kaJVHY

Session 32

Practice: Align nucleotide/protein sequences using tools available in biopython
https://www.tutorialspoint.com/biopython/biopython_sequence_alignments.htm

Session 33

Biojava: Introduction, importance and application of Biojava to computational biology
https://www.youtube.com/watch?v=OxZ0NGYiVRo

Session 34

Protein structure module of Biojava and its use in manipulating structure of protein
https://github.com/biojava/biojava-tutorial/blob/master/structure/img/4hhb_jmol.png

Session 35

Genome and sequencing module of biojava and its application for analyzing sequence data
https://biojava.org/wiki/BioJava:CookBook3:FASTQ

Session 36

Practice :  Study of protein structure using biojava
https://github.com/biojava/biojava-tutorial/blob/master/structure/img/4hhb_jmol.png

Recent Comments

    Recent Comments

      Our Main Teachers

          Dr. Jyoti Prakash Rath is presently working as Assistant Professor (Botany), School of Applied Science, Centurion University of Technology and Management, Odisha (Bolangir campus). After earning his Bachelor’s degree in Botany and Master’s in LifeSciences, Dr. Rath moved to New Delhi for his higher studies and received his M.Phil.(Bioinformatics) from Jawaharlal Nehru University […]