BSC Syllabus

L T P C
Basics in Programming (AEC)

3 0 0 2
Course Objective:
1. To Introduce programming language and aware the students about programming paradigm
2. To Focus Fundamentals of Computers and Peripherals
3. To Focus Concept and Methodology of Programming
Course Outcome:
The students will be able to
1. Apply computer programming concepts to new problems or situations.
2. Demonstrate appropriate design, coding, testing, and documenting of computer programs
that implement project specifications and requirements.
3. Develop projects that utilize logical algorithms from specifications and requirements
statements.
4. Understand and use the fundamental concepts of data types, structured programming,
algorithmic design, and user interface design.
5. Categorize different programming languages and their uses.
6. Describe how data are represented, manipulated, and stored in a computer.
Module I
Introduction to Computers & Problem solving: Generation of computers; Computer system:

Basic Block Diagram, super, Main Frame, Mini & Personal computer, Nomenclature; Software:
Systems and Application; Hardware & Software hierarchy; Computing environment,
Algorithms: importance, essential features, design & classifications; Complexity: notation, time
& space
Module II
Number Systems & Arithmetic Number System: Positional, Non-positional, binary, octal,
decimal, hexadecimal and their representation; Methods of conversion from one base to another;
Unsigned, Signed, 1’s Complement, 2’s Complement, sign-magnitude and excess notation; range
of values
Module III
Boolean Algebra: Concepts prepositional logic; Two variable Boolean algebra definitions,
postulates, properties, simplification of logical expressions using properties and maps (up to 4-
variables), Minterm, Maxterm, expressions.
Module IV
C Programming : Introduction: Basic Structure, Character Sets, Keywords, Identifiers Constants,

Variable type declaration; Execution of some simple sample programs. Operators: Arithmetic,
Relational, Logical and Assignment, Increment, Decrement and Conditional; Operator
Precedence and Associations; Expressions in C; Expression evaluation and type conversion
Module V
Operating systems: What is OS; Concepts of Process, Files, Shell, System Calls. Structures:
Monolithic, Layered, Virtual, Client-Server Model. Concept of Synchronization: Semaphores,
Critical Regions, Monitor etc., Inter Process Communication Mechanisms. Processor; Message
Passing, Scheduling; I/O: Devices and Device Controllers; Interrupt handlers and Device drivers.
Module VI
DATA & FILE STRUCTURES: Definitions: Concepts of data types, Elementary Structure,
Words and their interpretation; Arrays: Types, Memory representation, Address translation,
Functions of single and multi dimensional arrays with examples; Linked Structures: Singly
linked list; List Manipulation with Pointers: Examples involving insertion and deletion of
elements
References
1. Manvino & Leach, TMH ;Digital Principal and Application. Seventh edition , Tata
McGraw –Hill Inc Newyork ., 2011.
2. Silberschatz, Abraham, Peter B. Galvin, and Greg Gagne. Operating system concepts.
John Wiley & Sons, 2006.
3. Tanenbaum, Andrew S. Structured computer organization. Pearson Education India,
2016.
4. E. Balagurusamy, TMH ;Programming in ANSI C.Seventh edition, McGraw –Hill Inc
Newyork ., 2017.
University in India: Manipal University
University Abroad: Duke University UK

L T P C
Bioinformatics
3 0 0 3
Course Objectives:
1. To apply basic principles of biology, computer science and mathematics to address complex
biological problems
2. To introduces the students to concepts in bioinformatics
3. To understand the computational challenges (and their solutions) in the analysis of large biological
data sets
Course Outcome:
1. Describe the history, scope and importance of Bioinformatics and role of internet in
Bioinformatics.
2. Explain about the methods to characterise and manage the different types of Biological
data.
3. Overview the structural organisation, structural properties and various techniques
employed in the structure determination of Biological macromolecules – DNA, Protein
and Carbohydrates
4. Interpret about Multiple Sequence Alignment, its significance, algorithms and tools used
for MSA
5. Simplify about microarray data sequence analysis and expression pattern finding tools
6. Explanation about various approaches in protein three dimensional structure prediction
Module I: Introduction to bioinformatics and data generation (7 Hours)

What is bioinformatics and its relation with molecular biology. Examples of related
tools(FASTA, BLAST, BLAT, RASMOL), databases(GENBANK, Pubmed, PDB ) and
software(RASMOL,Ligand Explorer). Data generation; Generation of large scale molecular
biology data. (Through Genome sequencing, Protein sequencing, Gel electrophoresis, NMR
Spectroscopy, X-Ray Diffraction, and microarray). Applications of Bioinformatics.
.
Module II: Biological Database and its Types (7 Hours)
Introduction to data types and Source. Population and sample, Classification and Presentation of
Data. Quality of data, private and public data sources. General Introduction of Biological
Databases; Nucleic acid databases (NCBI, DDBJ, and EMBL). Protein databases (Primary,
Composite, and Secondary). Specialized Genome databases: (SGD, TIGR, and ACeDB).
Structure databases (CATH, SCOP, and PDBsum)
Module III: Data storage and retrieval and Interoperability (8 Hours)

Flat files, relational, object oriented databases and controlled vocabularies. File Format
(Genbank, DDBJ, FASTA, PDB, SwissProt). Introduction to Metadata and search; Indices,
Boolean, Fuzzy, Neighboring search. The challenges of data exchange and integration.
Ontologies, interchange languages and standardization efforts. General Introduction to XML,
UMLS, CORBA, PYTHON and OMG/LIFESCIENCE.
.
Module IV: Sequence Alignments and Visualization (8 Hours)
Introduction to Sequences, alignments and Dynamic Programming; Local alignment and Global
alignment (algorithm and example), Pairwise alignment (BLAST and FASTA Algorithm) and
multiple sequence alignment (Clustal W algorithm). Methods for presenting large quantities of
biological data: sequence viewers (Artemis, SeqVISTA), 3D structure viewers (Rasmol, SPDBv,
Chime, Cn3D, PyMol), Anatomical visualization.
Module V: Gene Expression and and Representation of patterns and relationship (7 Hours)
General introduction to Gene expression in prokaryotes and eukaryotes, transcription factors
binding sites. SNP, EST, STS. Introduction to Regular Expression, Hierarchies, and Graphical
models (including Marcov chain and Bayes notes). Genetic variability and connections to
clinical data.
Module VI: Protein Tertiary structure prediction methods (8 Hours)

Homology Modeling, Fold Recognition, Abintio Method. Protein folding, Molecular Dynamics
of Protein, Molecular Docking of Protein, Small molecule and Nucleotide, Concepts of Force
Field
References
1. Letovsky, Stanley I., ed. Bioinformatics: databases and systems. Springer Science &
Business Media, 2006.
2. Sorin Draghici. Bioinformatics Databases: Design, Implementation, and Usage
(Mathematical & Computational Biology). CRC Press; 1st edition, 2013
3. Arthur M.Lesk. Data base annotation in molecular biology, principles and practices,
Wiley; 1st edition,2004
4. Tao, Jiang, Ying Xu, Michael Q.Zang; Current topics in computational molecular
biology, A Bradford Book. Cambridge 2002
University in India: Amrita University
University Abroad: University of Chicago

Lab Subjects
L T P C
Bioinformatics Lab
0 0 4 2
Course Objectives:
1. To comprehend the utility of tools & databases available in genomic & proteomics
2. To Store and Retrieve Bimolecular related information using online tools
3. To : Understand the principles and applications Computational technologies on new drug discovery
process.
Course Outcome:
1. Distinguish knowledge and awareness of the basic principles and concepts of
biology, computer science and mathematics.
2. Demonstrate existing software effectively to extract information from large databases
and to use this information in computer modeling
3. Extend problem-solving skills, including the ability to develop new algorithms and
analysis methods
4. Explain the intersection of life and information sciences, the core of shared concepts,
language and skills the ability to speak the language of structure-function
relationships, information theory, gene expression, and database queries
5. Applying the concepts involved in Computational technology on biomolecular analysis.
6. Executing the recent technology involved in bioinformatics.
Exercises
1. RETRIEVAL SYSTEM AND FILE FORMATS IN PRIMARY SEQUENCE

DATABASES
2. GENBANK
3. EMBL
4. PRELIMINARY ANALYSIS ON VIRAL AND BACTERIAL GENOMES
5. PRELIMINARY ANALYSIS OF C-MYC ONCO PROTEINS FROM SWISS-
PROT/TrEMBL
6. ANALYSIS OF PROTEIN SEQUENCES WITH PROTEIN INFORMATION
RESOURCE DATABASE.
7. ANALYSING THE STRUCTURAL FEATURES OF PROTEIN USING PROTEIN
DATABANK
8. ANALYSING THE GEOMETRY OF PROTEIN AND VISUAVALIZE THE PROTEIN
USING PROTEIN DATABANK AND SWISS-PDB VIEWER.
9. PROTEIN FAMILIES – SCOP, Pfam and CATH
10. BLAST - SIMILAR DNA SEQUENCES SEARCH
References
1. Baxevanis, Andreas D., and BF Francis Ouellette. "A Practical Guide to the Analysis of
Genes and Proteins." Second Edition ,Wily Interscience 2019 .
2. Bujnicki, Janusz M.” Practical Bioinformatics” Second edition, Springer .2004.
3. Shui Qing Ye, Bioinformatics .A practical Approach, Fourth edition , Chapman and
Hall/CRC.2019
University in India: Pondicherry University
University Abroad: University of Yale

BSC Syllabus

Uploaded by

Copyright:

Available Formats

BSC Syllabus

Uploaded by

Document Information

Original Description:

Original Title

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

BSC Syllabus

Uploaded by

Copyright:

Available Formats

L T P C

Basics in Programming (AEC)

Introduction to Computers & Problem solving: Generation of computers; Computer system:

C Programming : Introduction: Basic Structure, Character Sets, Keywords, Identifiers Constants,

University in India: Manipal University

University Abroad: Duke University UK

Module I: Introduction to bioinformatics and data generation (7 Hours)

Module III: Data storage and retrieval and Interoperability (8 Hours)

Module VI: Protein Tertiary structure prediction methods (8 Hours)

University in India: Amrita University

University Abroad: University of Chicago

5. Applying the concepts involved in Computational technology on biomolecular analysis.

6. Executing the recent technology involved in bioinformatics.

1. RETRIEVAL SYSTEM AND FILE FORMATS IN PRIMARY SEQUENCE

University in India: Pondicherry University

University Abroad: University of Yale

You might also like