Course

Unit 1

Introduction to nucleic acid and protein sequence, structure, and function – introduction of drug molecules – Scripting language / Linux command to handle big biological data files (sequence and structure) – programming using python and R – Linux commands.

Unit 2

Explore different biological databases (RCSB, GenBank, DrugBank etc.) – introduction to protein family and onotology – protein functional database (Pfam, GO etc.) – extract data from database using scripting languages (awk, bash) 

Unit 3

Biomolecular sequence descriptors – presents biomolecular structure using graph – quantify dynamics natures of biomolecules – scoring matrices to describe evolution relationship – fundamental of biomedical image analysis using python and MATLAB (CT scan, mammography, MRI etc.) – biomedical signal (ECG, EEG etc.) visualization and annotation using MATLAB -Virtualization software (PyMol, VMD etc) – TCL and Python programming to write code for PyMol and VMD.

Unit 4

Application of AI and machine learning to predict biological activity of biomolecules (regression) – AI-based biomolecular structure prediction models – Binary and multi classification problems related to biological data.. 

Course Objectives

• The course is aimed at educating students on fundamentals concept of biomolecules (sequence, structure, conformational state and functions) and the central dogma of biology.
• To teach them how to read /write molecular structure and sequence from specific file using scripting language (like awk, LINUX command vim) and introduced with LINUX system.
• It will explore different biological databases (Uniport, RSCB, GeneBank, PDBbind etc) and teach how to extract data from those databases.
• Ontology: Storing data in a structured manner through ontologies
• Teach fundamental concept to process the bio-signal and biomedical images.
• The fundamental concept of regression and classification will be introduced using example of biological data set.
• Introduced students with the biological visualization software (PyMol, VMD, ChemDraw, Arena3D etc.) and different webservers.

Course Outcomes

After completing this course, students will be able to

Evaluation Pattern

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Text Books / References

“Introduction to Protein Structure” by Carl Ivar Branden, John Tooze

Ramachandran, G.N., and Sasisekharan, V. Advances in Protein Chemistry, Vol. 23, Academic Press, P. 283 (1968).

Schulz and Schirmer, Principles of Protein Structure, Springer-Verlag (1979).

Wolfram Saenger. Principles of Nucleic Acid Structure (19840).

UNIX: Concepts and Applications Sumitabha Das

“Bioinformatics: Sequence and Genome Analysis” by David mount 

“Bioinformatics algorithm, An active learning Approach”, Phillip Compeau and Pavel Pevzner, Vol.1. and Vol.2, 2015.

“”Bio-Inspired Computation and Applications in Image Processing”” by João Paulo Papa and Xin-She Yang Professor

ECG Signal Processing, Classification and Interpretation: A Comprehensive Framework of Computational Intelligence”” by Witold Pedrycz and Adam Gacek.

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