CURRICULUM

OF

BIO INFORMATICS

BS/MS

(Revised 2015)

HIGHER EDUCATION COMMISSION

ISLAMABAD
1
 CURRICULUM DIVISION, HEC

Prof. Dr. Mukhtar Ahmed Chairman

Mr. Fida Hussain Director General (Acad)
Ms. Ghayur Fatima Director (Curr)
Mr. Rizwan Shoukat Deputy Director (Curr)
Mr. Abid Wahab Assistant Director (Curr)
Mr. Riaz-ul-Haque Assistant Director (Curr)

Composed by: Mr. Tanveer Ali, HEC

2
 CONTENTS

1. Introduction 6

2. Mission Statement 9

3. Scheme Of Studies For Four-Year Integrated 10

Curricula For Bachelor Degree In Bioinformatics
4. Scheme of Studies for BS (Bioinformatics) 13

5. Detail of Courses 17

MASTER OF SCIENCE (MS) in

6. 45
Bioinformatics

7. Scheme of Studies for MS Program in 46

Bioinformatics
8. Annexure A - F 50

9. Recommendations 71

3
 PREFACE

The curriculum, with varying definitions, is a plan of the teaching-learning

process that students of an academic programme are required to undergo.
It includes objectives and learning outcomes, course contents, scheme of
studies, teaching methodologies and methods of assessment of learning.
Knowledge in all academic disciplines is expanding and even new
disciplines are also emerging, it is imperative that curriculum are
developed and revised regularly.

University Grants Commission (UGC) was designated as the competent

authority to develop, review and revise curricula beyond Class-XII vide
Section 3, Sub-Section 2 (ii), Act of Parliament No. X of 1976 titled
“Supervision of Curricula and Textbooks and Maintenance of
Standard of Education”. With the repeal of UGC Act, the same function
was assigned to the Higher Education Commission (HEC) under its
Ordinance of 2002, Section 10, Sub-Section 1 (v).

In compliance with the provisions, the Curriculum Division of HEC

undertakes the revision of curricula after every three years through
respective National Curriculum Revision Committees (NCRCs) which
consist of eminent professors and researchers of relevant fields from
public and private sector universities, R&D organizations, councils,
industry and civil society nominated by their organizations.

In order to impart education at par with quality international standards,

HEC NCRCs have developed unified templates as guidelines for the
development and revision of curricula in the disciplines of Basic Sciences,
Applied Sciences, Social Sciences, Agriculture and Engineering in 2007
and 2009.

It is hoped that this curriculum document, prepared by the respective

NCRC’s, would serve the purpose of meeting our national, social and
economic needs, and it would also provide the level of competency
specified in Pakistan Qualification Framework to make it compatible with
international educational standards. The curriculum is also placed on the
website of HEC (www.hec.gov.pk).

(Fida Hussain)
Director General (Academics)
4
 CURRICULUM DEVELOPMENT PROCESS

STAGE-I STAGE-II STAGE-III STAGE-IV

CURRI. UNDER CURRI. IN FOLLOW UP

CONSIDERATION FINAL STAGE
DRAFT STAGE STUDY

COLLECTION OF APPRAISAL OF 1ST

DRAFT BY EXP. OF PREP. OF FINAL QUESTIONNAIRE
REC
COL./UNIV CURRI.

CONS. OF CRC. FINALIZATION OF INCORPORATION OF COMMENTS

DRAFT BY CRC REC. OF V.C.C.

PREP. OF DRAFT APPROVAL OF PRINTING OF REVIEW

BY CRC CURRI. BY V.C.C. CURRI.

Abbreviations Used: IMPLE. OF CURRI. BACK TO STAGE-I

CRC. Curriculum Revision Committee
VCC. Vice Chancellor’s Committee
EXP. Experts
COL. Colleges
UNI. Universities
ORIENTATION
PREP. Preparation COURSES
REC. Recommendations

5
INTRODUCTION

The final meeting of the National Curriculum Revision Committee in

Bioinformatics was held on May 17-19, 2014 at HEC, Regional Centre,
Karachi to review and finalize the curriculum for BS (4-years) and MS
(2-years) degree programs in Bioinformatics. Following members and
experts attended the meeting:

1. Dr. Nazeer Ahmed Convener

Professor / Chairman,
Department of Biotechnology & Informatics,
Balochistan University of Information Technology,
Engineering & Management Sciences,
Takatoo Campus, Airport Road, Quetta

2. Dr. Muhammad Ayub Member

Assistant Professor,
Department of Biochemistry,
University of Balochistan, Seriab Road, Quetta

3. Dr. Syed M. Jahangir Matti Member

CEO (Matti-K-Jahangir, Pvt Ltd.)
Family Suit # 8, Old MNA Hostel,
Sector G-5/1, Islamabad

4. Dr. Isharat Jabeen Member

Assistant Professor,
Department of Bioinformatics,
National University of Science & Technology,
Research Centre for Modeling & Simulation (RCMS),
H-12, Islamabad
5. Dr. Faisal F. Khan Member
Assistant Professor / Director,
Institute of Integrative Biosciences,
CECOS University of IT & Emerging Sciences,
Phase-VI, Hayatabad,Peshawar
6. Dr. Muhammad Inam ul Haq Member
Assistant Professor,
Department of Computer Sciences,
Khushal Khan Khattak University, Karak, KPK
7. Dr. Aftab Ali Shah Member
Assistant Professor,
Department of Biotechnology,
University of Malakand, KPK.
6
8. Dr. Shahida Hasnain Member
Professor / Vice Chancellor,
Department of Microbiology & Molecular Genetics,
The Women University, Katchery Road, Multan

9. Dr. Mehboob Ahmed Member

Assistant Professor,
Department of Microbiology & Molecular Genetics,
University of the Punjab,
New Campus, Lahore

10. Dr. Muhammad Wasim Member

Associate Professor,
Institute of Biochemistry & Biotechnology,
University of Veterinary & Animal Sciences, Lahore

11. Dr. Masroor Ellahi Babar Member

Professor,
Department of Bioinformatics,
Virtual University of Pakistan,
MA Jinnah Campus, Defence Road, Lahore

12. Dr. Samreen Amir Member

Associate Professor,
Hamdard Institute of Engineering & Technology,
Hamdard University,Madinat-al-Hikmah,
Shahrah-e-Madinat-al-Hikmah, Muhammad Bin
Qasim Avenue, Karachi-74600
13. Dr. Muhammad Arif Member
Assistant Professor,
Department of Biomedical Engineering,
Mehran University of Engineering & Technology,
Jamshoro, Sindh
14. Dr. Farhat Naureen Memon Member
Assistant Professor,
Institute of Mathematics & Computer Science,
University of Sindh, Jamshoro
15. Dr. Aziz Mithani Member
Assistant Professor,
Department of Biology,
Syed Babar Ali School of Science & Engineering,
Lahore University of Management Sciences,
Sector U, DHA, Lahore Cantt. 54792

7
16. Dr. Muhammad Nauman Aftab Member
Assistant Professor,
(Secretary NCRC 2011),
Institute of Industrial Biotechnology,
Government College University, Lahore

17. Ms. Iffat Farzana Anjum Member

Lecturer,
Department of Bioinformatics & Biotechnology,
Room # 11, Maryam Block,
International Islamic University, Islamabad

18. Mr. Rizwan Shaukat Member

Deputy Director (Curriculum Division)
Higher Education Commission,
Sector H-9,
Islamabad

19. Dr. Sajid Rashid Secretary

Assistant Professor,
National Centre for Bioinformatics,
Quaid-i-Azam University, Islamabad

8
Mission Statement
To train the next generation professionals and researchers to gain
advanced knowledge in the interdisciplinary field of Bioinformatics that is
required to design and implement novel methods and tools to provide a
better understanding of biological systems.

Program Objectives
At the end of four years BS program, the graduates should have
strong understanding of:

1. Various aspects of biological systems.

2. Different areas of computer science including programming
languages.
3. Existing bioinformatics tools and databases.
4. Computational applications related to biological systems.
5. Analysis and interpretation of biological data.

Learning outcomes
At the completion of this program, students are expected to know the
relationship between genes and proteins and use of computer to handle
biological data. . Students should have a deeper insight into various tools
and techniques commonly used in bioinformatics. Students should be able
to appreciate diversified areas and applications like genomics, drug
designing, agri- and health informatics, biotechnology, systems biology
and others.

Admission Requirements

Eligibility
Higher Secondary School certificate or equivalent (2 nd division with at least
50% marks) in pre-engineering/pre-medical/Intermediate in computer
sciences/relevant subjects

Duration
Four years program spread over 8 semesters, two semesters per year.

Course and Credit Requirements

A total of 124-136 credit hours are required to complete BS in
Bioinformatics.

9
 STANDARDIZED FORMAT/SCHEME OF STUDIES FOR
FOUR-YEAR INTEGRATED CURRICULA FOR
BACHELOR DEGREE IN BIOINFORMATICS
STRUCTURE

Sr. Categories No. of Credit

Courses Hours
Min – Max Min – Max

1. Compulsory Requirement (No 9–9 25 – 25

Choice)

2. General Courses to be chosen 7–8 21 – 24

from other departments

3. Discipline Specific Foundation 9 – 10 30 – 33

Courses

4. Major Courses including 11 – 13 36 – 42

research project/Internship

5. Electives within the major 4–4 12 – 12

Total 40 – 44 124 – 136

Total numbers of Credit hours 124-136

Duration 4 years
Semester duration 16-18 weeks
Semesters 8
Course Load per Semester 15-18 credit hours
Number of courses per semester 4-6 (not more than 3 lab/
practical courses)

10
LAYOUT

Compulsory General Courses Discipline

Requirements ( to be chosen from Specific
student has no other departments Foundation
choice) Courses

9 courses 7-8 courses 9-10 courses

25 Credit hours 21-24 Credit hours 30-33 Credit

hours

Subject Cr. Subject Cr. Subject Cr

hr. hr. .
hr.

1. English I 3 1. Data Structure 4 1. Linear Algebra 3

2. English II 3 and Algorithms and Differential
3. English III 3 2. Object oriented 4 Equations 4
4. Pak Studies 2 programming 2. Essentials of 4
5. Islamic 2 3. Programming 4 Genetics 3
Studies/ethics 3 Fundamentals 3. Cell Biology 4
6. Basic Calculus 3 4. Discrete 3 4. Bioinformatics 4
7. Computer Structures I 3
Fundamentals 3 5. Database 4 5. Bioinformatics 4
8. Basic Biology/ Management II 3
Basic 3 Systems 3 6. Biochemistry I
Mathematics 6. Social sciences 2 7. Biochemistry II
9. Chemistry subject 8. Molecular
7. Ethical and legal Biology
issues in 9. Recombinant
Bioinformatics DNA technology

25 24 32

11
 Major courses including Elective Courses
research project/internship within the major

11-13 courses 4 courses

36-42 Credit hours 12 Credit Hours

Subject Cr. hr. Subject Cr. hr.

1.Bioinformatics Computing I 4 Elective I 3

2.Genomics 3
3.Proteomics 3 Elective II 3
4.Graphics and Visualization 4
5.Bioinformatics Computing II 3 Elective III 3
6.Artificial Intelligence 3
7.Bioinformatics software 3 Elective IV 3
Engineering 3
8.Special topics in Bioinformatics 6
9.Research Project 3
10.Systems Biology 3
11.Modeling and Simulation 4
12. Probability and Biostatistics

42 12

12
 Scheme of Studies for BS (Bioinformatics)

Course Code Semester 1 Credit hours

Courses Lectures Lab

Hum-101 English Comprehension 3 0
Hum-105 Pakistan Studies 2 0

Hum-*** Islamic Studies/Ethics 2 0

Bio-101 OR Basic Biology* OR 2 1
MTH-101 Basic Mathematics* 3 0
Bio-102 Chemistry 2 1
CS-101 Computer Fundamentals 2 1
*Deficiency courses

Total Credit 13 3
Hours OR
14 2

Course Code Semester 2 Credit hours

Courses Lectures Lab

Bio-203 Probability and Biostatistics 3 1
Bio-103 Basic Cell Biology 3 1
CS-102 Programming Fundamentals 3 1
BSI-191 Basic Calculus 3 0
Bio-104 Biochemistry I 3 1

Total Credit 15 4
Hours

13
Course Code Semester 3 Credit hours

Courses Lectures Lab

Hum-201 Technical Report Writing 3 0
MTH-201 Linear Algebra and 3 0
Differential Equations
Bio-201 Essentials of Genetics 3 1
Hum-103 Communication skills 3 0
CS-201 Data Structure and 3 1
Algorithms

Total Credit 15 2
Hours

Course Code Semester 4 Credit hours

Courses Lectures Lab

BI-201 Bioinformatics I 2 1
Bio-204 Biochemistry II 3 0
Bio-202 Molecular Biology 3 1
CS-202 Object Oriented 3 1
Programming
SS-*** Social sciences subject 3 0

Total Credit 14 3
Hours

Course Code Semester 5 Credit hours

Courses Lectures Lab

CS-301 Discrete Structures 3 0
GEN-*** Recombinant DNA 2 1
technology
CS-302 Database Management 3 1
Systems

14
BI-202 Ethical and Legal Issues in 2 0
Bioinformatics
BI-301 Bioinformatics II 3 1
Bio-302 Genomics 3 0

Total Credit 16 3
Hours

Course Code Semester 6 Credit hours

Courses Lectures Lab

BI-302 Bioinformatics Computing I 3 1
CS-303 Modeling and Simulation 2 1
Bio-303 Proteomics 3 0
CS-304 Graphics and Visualization 3 1
Bio-304 Systems Biology 3 0

Total Credit 14 3
Hours

Course Code Semester 7 Credit hours

Courses Lectures Lab

CS-401 Artificial Intelligence 3 0
BI-402 Bioinformatics Software 2 1
Engineering
*** Elective I 3 0
*** Elective II 3 0
BI-403 Special Topics in 3 0
Bioinformatics
Research Project 0 3

Total Credit 14 4
Hours

15
Course Code Semester 8 Credit hours

Courses Lectures Lab

BI-401 Bioinformatics Computing II 3 0
*** Elective III 3 0
*** Elective IV 3 0
Research Project 0 3

Total Credit 9 3
Hours

Total Credit Hours 110 26

16
DETAIL OF COURSES

Semester-I

Hum-101 English Comprehension 3+0 Annexure - A

Hum-105 Pakistan Studies 2+0 Annexure - B

Hum-*** Islamic Studies/Ethics 2+0 Annexure - C

Bio-101 Basic Biology 2+1

Prerequisite: None
Specific objectives of the course:
To provide students with a biological foundation on which they can build a
graduate degree in natural and physical science.

Course Outline
Basic concepts of life science: origin of life; biological time scales,
branches of biology, prokaryotic and eukaryotic cells, viruses, structure of
viruses and bacteriophages, bacteria, bacterial structure and
classification; algae, fungi. Introduction to plant and animal biology, role
of biology in medicine.

Lab Outline
Study of plant and animal cell structure using compound microscope,
culture and staining of microorganisms, study of mitosis and meiosis,
study of flowers.

Recommended Books
Latest editions of following books
1. Campbell and Mitchell, “Biology: Concepts and connections”,
Wesley Longman Inc. New York.
2. Star C., “Biology Concepts and Applications”, Thomson.
3. Fogiel M., “The Biology Problem Solver”, Research & Education
Association.

MTH-101 Basic Mathematics 3+0

Prerequisite: None
Specific objectives of the course
This is a deficiency course for students who have not studied mathematics
at the intermediate level. The basic concepts of trigonometry, linear
algebra and vectors are introduced in this course.
17
Course Outline
Basic concepts of Linear Algebra, Introduction of Trigonometry, Using
graphs, Graph transforms, Combination and Permutations, Introductory
concepts in Integration and Derivatives, Exponentials, Logarithms, Basic
concepts related to Complex Numbers, Basic probability, Introduction to
Linear Equations and Algebraic Functions, Sequence and series,
Introductory concepts of Vectors and various applications of Vector
calculus.

Recommended Books
Latest editions of following books
1. Hebeorn and Littlewood, “Modular Math”, Heinemann,
2. Keith Pledger, “Core Mathematics”, Edexcel.

Bio-102 Chemistry 2+1

Prerequisite: None

Specific objectives of the course

This course will familiarize students with basic principles, concepts and
theories in chemistry.

Course Outline
Periodic table, nature of chemical bonding, state of matter, properties of
solutions; properties of liquid vapor pressure, surface tension viscosity,
optical activity, refractometry, liquid properties of water as solvent
structure and interaction, chemical reactivity, acid, bases, oxidation-
reduction reactions, chemical kinetics, first, second, and third order
reactions, influence of temperature on reaction rates, polymers and
colloids, introduction to organic chemistry.

Lab Outline
Preparation of molar and normal solutions, use of pH meter to determine
pH of various solutions, acid base titration, use of spectrophotometer to
determine the absorbance, determination of melting point and boiling
point.

Recommended Books
Latest editions of following books
1. Brown et al., “Chemistry: The central Science”, Pearson Printing
Hall.
2. Raymond Chang, “Chemistry”, McGraw Hill.
3. Christopher J. Crammer, “Computational Chemistry: Theories and
Models”, John Willey & Sons.

18
4. Philips / Mathews, “Advanced Chemistry: Physical and Industrial”,
Cambridge University Press.

CS-101 Computer Fundamentals 2+1

Prerequisite: None

Specific objectives of the course

This course focuses on introducing computing environments, general
application software, basic computing hardware, operating systems,
desktop publishing, Internet, software applications and tools and computer
usage concepts.

Course Outline
History, classification, computer and society, overview of numbering
system with various Boolean functions, flow chart techniques, storage,
programs & software, system software, application software, operating
systems, office automation tools: word processing, graphics packages,
databases and spreadsheets, various operating systems, current trends
and research prospects. Legal and moral aspects of computing.

Lab Outline
Computation of Number system, Implementation of Boolean Functions,
Basic machines organization including motherboard, memory, I/O cards,
Networking devices, Use of flow charts, Introduction to office tools,
overview of different browsers including open source browsers,
Introduction to various operating systems.

Recommended Books
Latest editions of following books
1. P.K Sinha, “Introduction to Computer Science”,
2. Glenn Brookshear, “Computer Science- An Overview”, Prentice
Hall.

Semester-II

Bio-203 Probability and Biostatistics 3+1

Prerequisite: None

Specific objectives of the course

This course introduces the concepts of statistical methods used in
analyzing biological data.

19
Course Outline
Frequency distribution and probabilities, measure of central tendencies
and dispersion, Elementary probability theory, Laws of Probability,
Conditional Probability, Introduction to Bayes Theorem Introduction to
Random Variable and Probability Distributions, Binomial Distribution,
Properties of binomial distribution, Poisson distribution, Normal
distribution area under the normal curves, Introduction to sampling and
various sampling design, Applications of Normal distributions and tests of
significance,. Test of independence or association, method related to one
and two means, variance and covariance, heritability and its uses, analysis
of variance (ANOVA), regression analysis, Pedcheck and merlin for LOD
score calculation.

Lab Outline
Collection of data, acquisition of random samples, graphical/tabular
representation of data, MS-Excel, SPSS/R, problems related to combining
probabilities, central tendencies and dispersion, problems related to chi-
square, problems of goodness of fit and independent events, verification
of genetic ratios and test of association.

Recommended Books
Latest editions of following books

1. Gravetter Frederick J., “Statistics for Behavioral Sciences”,

Wadsworth publishing.
2. Mead R Curnow R. N., “Statistical Methods in Agriculture and
Experimental Biology”. Chairman and Hall.
3. Mathews and Farewell, “Using and understanding Medical
Statistics”, Krager New York.
4. Ross, S., “Introduction to Probability Models”, Elsevier.
5. Bernard Rosner, “Fundamentals of Biostatistics”, Cengage
Learning.
6. Wayne W. Daniel, “Biostatistics: A Foundation for Analysis in the
Health Sciences”, Wiley.
7. Ronald E. Walpole, “Probability and Statistics for Engineering and
the Sciences”, Pearson.
8. Steel and Torrie, “Principles and procedures of Statistics: a
biometrical approach”, McGraw-Hill.

Bio-103 Basic Cell Biology 3+1

Prerequisite: None

Specific objectives of the course

20
This course provides the basic concepts of life science, with emphasis on
diversity of life, physical and chemical nature of living matter, the form and
function of the cell and organisms.

Course Outline
An introduction to cell biology, differences between prokaryotes and
eukaryotes, physio-chemical properties of protoplasm, cell wall, cell
membrane, structure and transport properties, fluid mosaic model,
organelles: mitochondria, endoplasmic reticulum, golgi bodies, plastids,
lysosomes, peroxisomes, cell internal structure, cytoskeleton,
microtubules, microfilaments, intermediate filaments, structure of
chromosomes, cell division and cell cycle.

Lab Outline
Study of cell structure using compound microscope and elucidation of
ultra-structure from electron microphotographs, measurement of cell size,
study of mitosis and meiosis by smear/squash method and from prepared
slides, study of chromosome morphology and variation in chromosome
number.

Recommended Books
Latest editions of following books
1. David M. P., “Methods in Cell Biology”, Academic Press London.
2. Lowery Sekivetz. “Cell Structure and Function”, John Willey and
Sons Publication.
3. Gerald Karp. “Cell Biology”, Wiley.
4. Lodish H. “Molecular Cell Biology”, Media Connected
5. Lewin B. “Genes X”, Pearson/Prentice Hall.
6. De Robertis, “Cell and Molecular Biology”, Lippincott Williams &
Wikins.
7. Sadava D. et al., “Life, The Science of Biology”, WH Freeman.
8. Bruce Alberts et al., “Molecular Biology of Cell”, Garland Science.

CS-102 Programming Fundamentals 3+1

Prerequisite: Basic Math

Specific objectives of the course

The course is designed to familiarize students with the basic programming
skills. It emphasizes upon problem analysis, algorithm designing, program
development and testing.

Course Outline
Overview of programming, overview of computer languages and
translators, basics of structured and modular programming, basics of
21
algorithms and problem solving logics, fundamentals of programming
constructs, translation of algorithms to programs, data types, control
structures, functions, arrays, records, files, pointers, program
development.

Lab Outline
Introduction to various programming paradigms, coding, executing and
debugging simple programs, implementation of simple control structures,
implementation of functions, arrays, records, file input / output techniques
implementation of pointers and memory allocation/deallocation.

Recommended Books
Latest editions of following books
1. R. P. Halpern, “C for Yourself – Learning C Using Experiments”,
Oxford University Press.
2. Yashwant Kanetkar, “Let us C”, Jones & Bartlett Learning.
3. Robert Lafore, “Turbo C. Programming for PC”, Prentice Hall.

BS-191 Basic Calculus 3+0

Prerequisite: None

This course will familiarize students with the basic principles of calculus
and their application to problem solving.

Course Outline
Introduction to Functions: Mathematical and physical meaning of
functions, graphs of various functions, Introduction to Limits: Theorems of
limits and their applications to functions. Derivatives: Introduction to
derivatives, Partial derivatives and their geometrical significance
Application problems (rate of change, marginal analysis) Higher
derivatives: Mean value theorem. Applications of derivatives: curvature
and radius of curvature, maxima and minima of a function Applications of
Partial Derivatives: Integral calculus: Methods of integration by
substitutions and by parts, reduction formulae, Applications of integral
calculus: Vector algebra: Introduction to vectors, Vector calculus: Vector
differentiation, vector integration and their applications.

Recommended Books
Latest editions of following books
1. Thomas Finney, “Calculus”, Penguin.
2. Doniel D. Benice, “Brief Calculus and its applications”, Houghton
Mifflin College Division.
3. Raymond A. Barnett, “Applied Calculus”, Prentice Hall.
22
4. Gerald L. Bradley, “Calculus”, Hoffman, McGraw Hill.
5. SM Yousaf, “Calculus with analytical geometry”, Ilmi Kitab Khana.

Bio-104 Biochemistry I 3+1

Prerequisite: None
Specific objectives of the course
The course will provide fundamental knowledge about chemistry of
biomolecules.

Course Outline
Water, pH and buffer systems, molecules of life: structure, function and
classification, nucleic acids as genetic material, lipids, bilayers and
membranes, saccharide chemistry, mono, di and polysaccharides, amino
acids the building block of proteins, levels of protein structures, protein
structure and folding, physiological role of proteins, role in catalysis and
signaling

Lab Outline
Hydrolysis of a protein and qualitative tests for amino acids; paper
chromatography of amino acids; estimation of proteins by Lowry’s, dye-
binding, titration curves of amino acids. Distinction between pentoses and
hexoses, reducing and non-reducing sugars, acid value, saponification
and iodine values of fat.

Recommended Books
Latest editions of the following books
1. Nelson and Michel, “Lehninger: Principles of Biochemistry”,
Freeman and Company.
2. Conn and Stumpf, “Outlines of Biochemistry”, John Willey and Sons.
3. Devlin and Thomas, “Text book of Biochemistry with Clinical
Correlations”, John Willey and Sons.
4. Campbell M. and Shawn F, “Biochemistry”, Cengage Learning.
5. Voet and Voet, “Biochemistry”, John Wiley and Sons.
6. Jeremy M. Berg, John L., T, STRYER L, “Biochemistry”, WH
Freeman & Co.

Semester-III

Hum-201 Technical Report Writing 3+0 ANNEXURE - A

Hum-103 Communication Skills 3+0 ANNEXURE - A

23
MTH-201 Linear Algebra and Differential Equations 3+0
Prerequisite: None
Specific objectives of the course
This course introduces matrices, determinants and differential equations
for solving linear equations.

Course Outline
Introduction to matrices, elementary row operations and vector spaces:
Brief introduction to matrices, system of linear equations, system of non-
homogeneous and homogeneous linear equation, introduction to
determinants, properties of determinants of order, axiomatic definition of a
determinant, multiple integrals, double integrals, differential equations of
first order, initial and boundary conditions, methods of solution of
differential equation of first order and first-degree, separable equation,
homogeneous equations, linear equations, Bernoulli equations,
applications of first order differential equations, Higher order linear
differential equations, homogeneous linear equations, solution of higher
order differential equations.

Recommended Books
Latest editions of following books
1. David C. Lay, “Linear Algebra and its applications”, Pearson
Addison Wesley.
2. Michael Greenberg, “Advanced Engineering Mathematics”,
Pearson.
3. Erwin Kreyszig, “Advanced Engineering Mathematics”, John Wiley
& Sons.

Bio-201 Essentials of Genetics 3+1

Prerequisite: Biochemistry 1
Specific objectives of the course
This course provides the basic principles of inheritance and students will
gain experience in variety of techniques used in gene analysis.

Course Outline
Introduction, heredity and variations, Mendelian and non-Mendelian
inheritance, chromosomal structure, chromosomal theory of heredity,
multiple allelic, linkage and gene mapping, polygenic inheritance, epitasis,
epigenetics, penetrance and expressivity, Sex-linked inheritance,
chromosomal aberrations, gene mutation, genetic disorders; DNA
polymorphism, cytoplasmic inheritance, population genetics [Hardy-
Weinberg equilibrium, selection, inbreeding and heterosis]

24
Lab Contents
Chromosome staining, Problems solving related to topics covered – ABO
blood grouping,

Recommended Books
Latest editions of following books
1. Strickburger, “Genetics”, Mac Millan.
2. Gardner, “Principles of Genetics”, John Wiley and Sons.
3. Griffith et al., “An Introduction to Genetics analysis”, W. H. Freeman.
4. William S. Klug, Michael Cummings, “Essentials of Genetics”,
Pearson/Prentice Hall.
5. Ricky Lewis, “Human Genetics”, McGraw Hill.

CS-201 Data Structure and Algorithms 3+1

Prerequisite: Programming Fundamentals
Specific objectives of the course
It describes data structures and explains some common data structures
and their implementation.

Course Outline
Introduction to data structures and algorithms, array based algorithms:
storage, retrieval and search, computational complexity, uses of arrays,
concept of binary and linear search, Stacks and queues, priority queues,
store, retrieve and search functionalities in stacks and queues, linked list,
double ended links, linked list efficiency, sorted list. Recursion application,
Triangular Numbers, Factorials, Trees, heaps, graphs and their
algorithms, sorting techniques: selection sort, insertion sort, bubble sort,
merge sort and quick sort. Comparison of sorting techniques and their
applications.

Lab Outline
Implementation of arrays, storing and searching data in arrays,
implementation of Linear Search, implementation of Binary Search in
Arrays, Using different sorting techniques on sample data, implementing
Stacks, Queues and priority queues , implementation of different types of
Linked Lists , tree and graph algorithms.

Recommended Books
Latest editions of following books
1. Neil C. Jones, Pavel Pevzner, “An introduction to Bioinformatics
Algorithms”, The MIT Press
2. Gary Benson and Roderic Page, “Algorithms in Bioinformatics”.
3. R. Sedgewick, “Algorithms in C”, Addison-Wesley.
4. S. Lipschutz, “Data structures with C”, Schaum Series.
25
Semester-IV

SS-*** Social sciences subject 3+0

BI-201 Bioinformatics-I 2+1

Prerequisite: Computer science 101

Specific objectives of the course
This course presents the basic principles and concepts in exploring
sequence storage, retrieval and analysis.

Course Outline
Introduction, history, timeline, databases, sequence storage, retrieval and
analysis, similarity and homology, creating alignments, local and global
alignment, pairwise and multiple sequence alignments, phylogenetic
analysis, dot matrix plots, dynamic programming algorithm, word (k-tuple)
methods, substitution matrices PAM and BLOSUM, scoring algorithms,
gap penalties, online tools BLAST, BLAT and FASTA, PDB file structure.

Lab Outline
Accessing NCBI, ENSEMBL, UniProt , Genbank, EMBL, SWISS-PROT,
Accessing structural databases including PDB, SCOP and CATH,
EXPASY and FASTA using tools for pairwise and multiple sequence
alignment, Phylogenetic analysis, Bioedit.

Recommended Books
Latest editions of following books
1. Arthur M. Lesk, “Introduction to Bioinformatics”, Oxford University
Press.
2. Ignacimuthu SJ, “Basic Bioinformatics”, Narosa Publishing House.
3. Yadav Neelam, “A Hand Book of Bioinformatics”, Anmal
Publications Pvt.Ltd.
4. Krawetz. Stephen A., “Introduction to Bioinformatics: A Theoretical
and Practical Approach”, Humana Press.

Bio-204 Biochemistry II 3+0

Prerequisite: Biochemistry I
Specific objectives of the course
This course focuses on macromolecules and their metabolisms with
emphasis on various cellular pathways.
Course Outline
Study of bioenergetics, introduction to metabolic pathways, metabolism of
carbohydrates, Glycolysis, Citric acid cycle, Pentose pathway, electron

26
transport chain, and oxidative phosphorylation, lipid metabolism, β-
oxidation, ketone bodies formation and biosynthesis of triglyceride, protein
metabolism, oxidative deamination and decarboxylation, transamination,
amino acids metabolism, urea cycle, nucleic acid metabolism, break down
and synthesis of purine and pyramidine bases

Recommended Books
Latest editions of following books
1. Nelson and Michel, “Lehinger Principles of Biochemistry”, Freedman
and Company.
2. Conn and Stumpf, “Outlines of Biochemistry”, John Willey and Sons.
3. Devlin and Thomas, “Text book of Biochemistry with Clinical
Correlations”, Wiley.
4. Campbell M and Shawn F, “Biochemistry”, Thomas Book Pub.
5. Voet and Voet, “Biochemistry”, John Wiley and Sons.
6. Jeremy M Berg, John L T, Stryer L, “Biochemistry”, MacMillan.

Bio-202 Molecular Biology 3+1

Prerequisite: Biochemistry 1
Specific objectives of the course
This course is designed to teach the students about organization of
genetic material, regulation of gene expression and translation.

Course Outline
Basic concepts about DNA, RNA and proteins with special emphasis on
nature of genetic material and its organization in viruses, prokaryotes and
eukaryotes, DNA replication, recombination, mutations and repair, Gene
structure, transcription, regulatory elements, regulation of gene
expression. RNA processing, splicing and editing, translation and post-
translational modifications, control of gene expression in prokaryotes and
eukaryotes. Introduction to plasmids and vectors.

Lab Outline
Isolation of plasmid and genomic DNA from eukaryotes and prokaryotes,
Primer designing, PCR, gel electrophoresis and its interpretation.

Recommended Books
Latest editions of following books
1. Robert Weaver, “Molecular Biology”, McGraw Hill.
2. Benjamin Lewin, “Genes XI”, Pearson/Prentice Hall.
3. Gerald Karp, “Cell and Molecular Biology concepts and
Experiments”, John Willey and Sons.
4. Brown T. A., “Molecular Biology Lab .FEX”, Academic Press
Publication.
27
5. Lodish H. et al., “Molecular Cell Biology”, W.H. Freeman.
6. Bruce Alberts et al., “Molecular Biology of Cell”, Garland Science.
7. Reece et al., “Campbell Biology”, Pearson.
8. David Clark, “Molecular Biology”, Elsevier.

CS-202 Object Oriented Programming 3+1

Prerequisite (s): Programming Fundamentals
Specific objectives of the course
The course focuses on object-oriented concepts, analysis and software
development.

Course Outline
Concept of object oriented programming (OOP), characteristics of OOP,
simple programs, dynamic initializing, scope and lifetime of variables, type
conversion and casting, the type promotion rules, arrays, string data type,
operator and its types. Introducing classes, declaring objects, object
reference, control access, specified, public, private, static, data member
and methods. Creating packages, constructors, function overloading,
constructor overloading, reference, members, inheritance, polymorphism,
dynamic method binding, inner class definitions, Friend function, virtual
functions, inline functions, Abstract classes, Interfaces, exception
handling.

Lab Outline: Programs formulation according to the Course outlines.

Recommended Book
Latest editions of following books
1. Ivor Horton, “Beginning Java”, Wrox.
2. Herbert Schildt, “Java: The Complete Reference”, Mcgraw-Hill
Osborne Media.
3. Robert Lafore, “Object Oriented Programming in C++”, Sams
Publishing.
4. Deitel & Deitel, “JAVA: How to Program”, Prentice Hall.

Semester V

CS-301 Discrete Structures 3+0

Prerequisite: Basic Calculus
Specific objectives of the course
28
Introduces the fundamentals of discrete mathematics as they apply to
Computer Science, focusing on providing a solid theoretical foundation

Course Outline
Logic and proofs, direct proofs, proof by contradiction, Sets,
combinatorics, sequences, formal logic, prepositional and predicate
calculus, methods of proof, mathematical induction and recursion, loop
invariants, relations and functions, Pigeonhole principle, trees and graphs,
elementary number theory, optimization and matching, Fundamental
structures, functions, relations (more specifically recursions), cardinality
and countability, probabilistic methods.

Recommended Books
Latest editions of following books
1. Kenneth H. Rosen, “Discrete Mathematics and Its Applications”,
McGraw Hill Book Co.
2. Richard Johnsonbaugh, “Discrete Mathematics”, Prentice Hall
Publishers.
3. Kolman, Busby and Ross, “Discrete Mathematical Structures”,
Prentice-Hall Publishers.
4. Ralph P. Grimaldi, “Discrete and Combinatorial Mathematics: An
Applied Introduction”, Pearson.
5. Prather R, “Elements of Discrete mathematics”, Houghton Mifflin.

GEN-507 Recombinant DNA technology 2+1

Prerequisite: None

Specific objectives of the course

The course objectives are to provide information on techniques used to
manipulate genetic materials; and to discuss applications of recombinant
DNA technology in medicine, agriculture and environment.

Course Outline
Basic concepts in recombinant DNA technology, Gel electrophoresis,
hybridization, PCR and gene transformation, Restriction and modification
system: types, enzymes, classifications, nomenclature and application:
isolation and purification of DNA, cutting of DNA molecules, ligation of
DNA molecules, blunt ends and cohesive termini, homopolymer tailing,
Cloning vectors: plasmids (bacteria and yeast), viruses (CMV, SV40, BPV,
Lamda, Mu, M13), Cosmids and Phosmids, YAC’s, BACs and PACs.
Cloning strategies (Prokaryotic and Eukaryotic); selection and
characterizations of recombinant molecules, verifications and
amplifications of desired genes, Construction and analysis of DNA
29
libraries, Maximizing the cloned expression, site directed mutagenesis,
DNA sequencing techniques, Applications of genetic engineering in
medicine, agriculture and environment.

Lab Contents
Isolation of plasmid and chromosomal DNA from bacteria and yeast,
Screening of bacteria from plasmid by electrophoresis of total cell lysate,
Gel electrophoresis of plasmid DNA (supercoiled, linear and digested with
restriction enzyme) and chromosomal DNA, Plasmid transformation of E.
coli, comparing plasmids of different molecular weights using molecular
weight markers, DNA amplification by PCR, Numerical problems related
to recombinant DNA.

Recommended Books
Latest editions of following books
1. Brown T. A, “Gene Cloning and DNA analysis: An introduction”,
Wiley-Blackwell.
2. Desmond S.T. Nicholl, “An Introduction to genetic engineering”,
Cambridge University Press.
3. Hodge R and N Rosenthal, “Genetic Engineering: Manipulating the
mechanism of life (Genetics and Evolution)” Facts on File.
4. Old R. W. and S. B. Primrose, “Principles of Gene manipulation, an
introduction to Genetics engineering”, Blackwell Scientific
Publications.

CS-302 Database Management Systems 3+1

Prerequisite: None
Specific objectives of the course
The course aims to introduce basic database concepts, different data
models, storage and retrieval techniques, database design techniques.

Course Outline
Basic database concepts, conceptual modeling, hierarchical, network and
relational data models, relational theory and languages, databases
design, database security and integrity, query languages, relational
calculus, relational algebra, SQL, query processing and optimization,
normalization, concurrency and recovery, front-end and back-end
databases.

Lab Outline
Structured query language commands, creating and populating tables,
design of simple databases, database normalization techniques, query
optimization, indexing techniques, partial and full recovery techniques,

30
developing GUI techniques, implementation of database security
mechanisms, MySQL.

Recommended Books
Latest editions of following books
1. Thomas Connolly and Steven Morris, “Database Systems: Design,
Implementation & Management”, Cengage Learning.
2. Jeffrey A. Hoffer, Ramesh Venkataraman and Heikki Topi, “Modern
database management”, Prentice Hall.
3. Abraham Silberschatz, Henry Korth and S. Sudarshan, “Database
system concepts”, McGraw-Hill Science.
4. Jeffrey A. Hoffer, Ramesh Venkataraman and Heikki Topi, “Modern
database management”, Prentice Hall.

BI-202 Ethical & Legal Issues in Bioinformatics 2+0

Prerequisite (s): None

Specific objectives of the course
This course introduces the ethical and legal aspects related to
bioinformatics practices and products.

Course Outline
Social context of computing and biology, Intellectual property, Privacy and
civil liberties, Economic issues in bioinformatics, monopolies and their
economic implications, effect of skilled labor supply and demand on the
quality of bioinformatics products, pricing strategies in the bioinformatics
domain, differences in access to bioinformatics resources and the possible
effects thereof. Health, psychological and legal issues in GMOs, biosafety
and bio-security issues

Recommended Book
Latest editions of following books
1. Katina Strauch and Bruce Strauch, “Legal and Ethical Issues in
Acquisitions”, Routledge.
2. Tom Forester and Perry Morrison, “Computer Ethics: Cautionary
Tales and Ethical Dilemmas in Computing”, The MIT Press.
3. Bruce A Rocheleau, “Public Management Information Systems”,
Idea Group Publishing.
4. Charles P. Pfleeger, Shari Lawrence Pfleeger and Jonathan
Margulies, “Security in Computing”, Prentice Hall.

31
BI-301 Bioinformatics II 3+1

Prerequisite (s): Bioinformatics I

Specific objectives of the course

This course is designed to develop understanding of gene and protein at
structural level using computational tools.

Course Outline
Introduction to genome, gene prediction in prokaryotes and eukaryotes,
ORF, TFBS, codon usage table, EST and SNP databases, primer
designing, restriction enzyme databases, RNA structure prediction,
computational secondary and tertiary protein structure prediction
methods, structure optimization and refinement methods, hydrogen
bonding, PTMs of proteins, Chou Fasman, PHD and PSIPred, neural
network, X-ray crystallography, NMR, ab initio, threading and homology
modeling methods, protein fold identification using Pfam (A & B) and other
tools.

Lab Contents
Online tools: Gene finder, ORF finder, EST database, SNP data, Primer
3, protein structure prediction using online server, protein structure
visualizing using visualization programs, Secondary structure prediction,
using pfam database.

Recommended Books
Latest editions of following books
1. David Mount, “Bioinformatics: Sequence and Genome analysis”,
Cold Spring Harbour Laboratories.
2. P. Rastogi and N. Mendiritta, “Bioinformatics: Methods and
Applications: Genomics, Proteomics and Drug Discovery”, Prentice-
Hall of India Pvt.Ltd.
3. Richard S. Larson, “Bioinformatics and drug discovery”, Humana
Press.

Bio-302 Genomics 3+0

Prerequisite: Biochemistry I/Molecular Biology

Specific objectives of the course

32
Students will be trained to grasp knowledge about structural and functional
genomics and their applications.

Course Outline
Introduction , types of genome, genome evolution, genome organization
and structure , global expression profiling, microarray data analysis,
genome mapping, DNA markers, linkage analysis, genome-wide
screening, mutation, type of mutations, mutation identification, DNA
repeats, QTL, Human Genome Project, Genevestigator, Non-coding
RNAs and their regulation, siRNA, completed genomes, applications of
genome analysis, Next generation sequencing.

Recommended Books
Latest editions of following books
1. David Mount, “Bioinformatics: Sequence and Genome analysis”,
Cold Spring Harbour Laboratories.
2. Mount, “Bioinformatics: Sequence and Genome: Analysis”, CBS
publisher & distributors New Delhi Bangalore by Spring Harbour
laboratory press.
3. Tom Strachan and Andrew Read, “Human Molecular Genetics”,
Garland Science.
4. T.A. Brown, “Genome”, Garland Science.
5. Arthur M. Lesk, “Introduction to Genomics”, Oxford University Press
6. Lewin, “Gene”, Jones & Bartlett Learning.

Semester-VI

BI-302 Bioinformatics Computing-I 3+1

Prerequisite: Programming Fundamentals

Specific objectives of the course

This course aims to introduce the concepts of data representation,
searching, security and ownership. Develop techniques for pattern
matching, recognition and their applications in bioinformatics.

Course Outline
Databases: Data management, networks, geographical scope,
communications models, transmissions technology, protocols, bandwidth,
topology, hardware, contents, security, ownership, implementation,
Search engines. search process, search engine technology, searching
and information theory, computational methods, knowledge management,
sequence and structure visualization, data mining methods and
technology, pattern recognition and discovery, pattern matching, dot
matrix analysis, substitution matrices, dynamic programming, Scripting

33
Lab Outline
Simulation of various bioinformatics entities, application of various
bioinformatics methods, scripting languages Python, Perl and PHP, and
their applications in Bioinformatics

Recommended Books
Latest editions of following books
1. Bryan Borgeron, “Bioinformatics Computing”, Prentice Hall.
2. Vyas S.P. and Kohli D.V, “Methods in Biotechnology and
Bioengineering”, CBS Publisher.

CS-303 Modeling & Simulation 2+1

Prerequisite: Programming Fundamentals, Probability and Biostatistics

Specific objectives of the course

This course emphasizes the development of modeling and simulation
concepts and analytical skills necessary to design, program and
implement various biological models. .

Course Outline
Performance modeling and evaluation, bench marking, performance
evaluation of high parallel systems architecture, application of
performance evaluation, measurement techniques, hardware monitoring,
software monitoring, hybrid monitoring, fundamentals of queuing models,
structure and performance parameters, operational analysis of queuing
models, general features of queuing models, birth and death processes,
m/m/i and m/g/1 systems, dependability modeling, analysis of reliable,
available and high assurance systems, fault-tolerant techniques, software
reliability modeling, adaptive modeling, agent based modeling, Types of
simulations, applications of simulations

Lab Outline
Introduction to modeling techniques using simulation tools like MATLAB
toolbox for various performance modeling and evaluation of high parallel
systems.

Recommended Books
Latest editions of following books
1. Willem van Meurs, “Modeling and Simulation in Biomedical
Engineering: Applications in Cardiorespiratory Physiology”, The
McGraw-Hill Companies.
2. John A. Sokolowski, “Principles of Modeling and Simulation: A
Multidisciplinary Approach”, John Wiley 7 Sons.
3. Jerry Banks, “Discrete-Event System Simulation”, Prentice Hall.

34
4. Frank C. Hoppensteadt, “Modeling and Simulation in Medicine and
the Life Sciences”, Springer.
5. John A. Sokolowski, “Modeling and Simulation in the Medical and
Health Sciences”, John Wiley & Sons.

Bio-303 Proteomics 3+0

Prerequisite: Biochemistry I/Molecular Biology

Specific objectives of the course

This course intends to provide basic concepts regarding proteome and
protein chemistry with special focus on protein identification techniques.

Course Outline
Introduction, techniques in proteomics, amino acids structures, properties
and function, one dimensional and two dimensional PAGE and analysis,
Mass spectrometry and its types. Protein-protein interaction,
Bioinformatics tools for analysis of proteomics data, proteomics
databases, MS data analysis, peptide mass and fragment fingerprinting,
protein identification, post-translational modification, applications of
proteomics, protein microarrays.

Recommended Books
Latest editions of following books
1. Richard T., “Principles of Proteomics”, Garland Science.
2. Rigden D. J., “From protein structure to function with bioinformatics”,
Springer.
3. Hubbard S. J., “Proteome Bioinformatics”, Humana Press.
4. Rastogi et al., “Bioinformatics methods and applications. Genomics,
Proteomics and Drug discovery”, Prentice Hall of India Pvt. Limited.
5. Richerd Simpson J., “Purifying Proteins for Proteomics (a laboratory
manual)”, Cord Spring Harbor Laboratory Press.

CS-304 Graphics and Visualization 3+1

Prerequisite: Programming Fundamentals

Specific objectives of the course

This course introduces algorithms and tools for data visualization and its
applications to data manipulation.

Course Outline
Introduction, Graphics hardware, fundamental algorithms, applications of
graphics, interactive graphics programming, graph plotting, windows,
clipping and segmentation, programming raster display systems, panning

35
and zooming, raster algorithms and software, scan-converting lines,
characters and circles, region filling, two and three dimensional imaging
geometry and transformations, curve and surface design, rendering,
shading, colour and animation.

Lab Outline
Line drawing techniques, clipping effects, 2D and 3D representations and
transformations using open GL, development of graphical user interface
with various blocks and modules, elliptical and curve creation exercises.

Recommended Books
Latest editions of following books
1. Donald Hearn, “Computer Graphics, C Version”, Prentice Hall.
2. F. S. Hill and Stephen M. Kelly, “Computer graphics: Using Open
GL”, Pearson Prentice Hall.
3. T. Theoharis et al., “Graphics and Visualization-principles and
algorithms”, CRC Press.

BIO-304 Systems Biology 3+0

Prerequisite
Probability & Statistics, Linear Algebra & Differential Equations, Genomics

Specific objectives of the course

The purpose of the course is to introduce the students to the field of
systems biology and to provide an understanding of the cell at systems
level.

Course Outline
Introduction to systems biology; modeling of biochemical systems; kinetic
modeling of enzymatic reactions; law of mass action; Michaelis-Menten
Kinetics; rate equation; model systems: lac operon, phages, plasmids and
chemotaxis; analysis of high throughput data; gene expression models;
stochastic modeling of biological systems; chemical master equation.
stochastic simulation, fluctuations in gene expression; biological networks;
network structure, network dynamics and function; network motifs,
network modularity

Recommended Books
Latest editions of following books
1. Klipp, E., Wolfram L., Christoph W., Axel K., Hans L., and Ralf H.,
“Systems biology”, Wiley.
2. Ullah, M., and Olaf W., “Stochastic approaches in systems biology”,
Springer.
3. Newman M., “Networks: An Introduction”, Oxford University Press,
USA.
36
4. Alon U., “An introduction to systems biology: design principles of
biological circuits. Boca Raton”, Chapman & Hall/CRC.

Semester-VII

CS-402 Artificial Intelligence 3+0

Prerequisite
Programming Fundamentals, Data Structures and Algorithms

Course objectives
Presentation of artificial intelligence as a coherent body of ideas and
methods to acquaint the student with basic programs in the field and their
underlying theory.

Course Contents
Basic definition of AI and its potential applications, different types of AI
agents, Searching as a problem-solving technique: Heuristic functions and
their effect on performance of search algorithms, Introduction to genetic
algorithms. Knowledge-based agents and logical problem solving,
Knowledge engineering: Building knowledge bases and automated
theorems, Production systems as an example of logical problem solving,
Introduction to truth-maintenance systems and default reasoning.
Planning agents: representation of states, goals and actions, Decision
trees and the ID3 algorithm, Neural Network concepts: Introduction &
Simple neuron model, Type of Learning Methods: Back propagation, Least
Square, Steepest descent, Type of Neural Network: Perceptron, Linear
networks, Multi layer perceptron, Self-organizing maps, Introduction to
Fuzzy Sets.

Recommended Books
Latest editions of following books
1. Stuard Russell and Peter Norvig, “Artificial Intelligence: A Modern
Approach”, Prentice Hall Inc.
2. George F. Luger, and William A. Stubblefield, “Artificial Intelligence:
Structures and Strategies for Complex Problem Solving”, Addison -
Wesley.
3. Edward A. Bender, “Mathematical Methods in Artificial Intelligence”,
Wiley IEEE Computer Society Press.
4. David W. Rolston, “Principals of Artificial Intelligence and Expert
Systems Development”, Mcgraw Hill.
5. Robin R. Murphy, “Introduction to AI and Robotics”, A Bradford
Book.
6. Winston and Horn, “LISP”, Addison Wesley.

37
Bio-406 Bioinformatics Software Engineering 2+1

Prerequisite
Specific objectives of the course
This course introduces the software engineering principles and
methodologies with the goal of developing bioinformatics applications.

Course Outline
System analysis and design, UML, software development methodology,
waterfall model, iterative model, rapid application development,
prototyping, software life cycle, development of software projects for
bioinformatics problems, overview of software architecture, web-based
applications, architecture, developing front end applications, database
connectivity, software testing and validation, software robustness,
software quality assurance.

Lab Outline
Introduction to software development techniques, developing use cases,
implementation of various software models using simple case studies,
introduction to HTML, XML, use of front end application tool. Designing
database driven applications

Recommended Books
Latest editions of following books
1. Pressman R. S., “Software engineering: A practitioner’s approach”,
McGraw Hill.
2. Sommerville, “Software Engineering”, Addison Wesley.
3. Larman C., “Applying UML and patterns”, Prentice Hall.
4. Weston P., “Bioinformatics Software Engineering: Delivering
effective applications”, Wiley.

BI-407 Special Topics in Bioinformatics 3+0

Prerequisite: Bioinformatics-I
Specific objectives of the course
This course intends to introduce recent advances in bioinformatics.

Course Outline
The course will review the major advances in bioinformatics and the topics
will be selected by the faculty members / Coordinator conducting
Bioinformatics Program.

38
*** Elective-I 3+0
Prerequisite: None

Course Outline
To be chosen from the list of electives

*** Elective-II 3+0

Prerequisite: None

Course Outline
To be chosen from the list of electives

*** Research Project 0+3

Prerequisite: None

Course Outline
An independent research project and directed by the student and directed
by a full time faculty member of the department.

Semester-VIII

BI-401 Bioinformatics Computing-II 3+0

Prerequisite: Bioinformatics Computing- I
Specific objectives of the course
This course introduces advanced concepts of neural networks and pattern
recognition for solving bioinformatics problems.

Course Outline
This course is emphasized on cellular, tissue, organ and system modeling,
simulation, analysis, Bio-inspired computation, evolutionary algorithms,
Swarm Intelligence, neural networks, application of neural networks to
Bioinformatics, neural computation, approximate matching algorithm and
their applications for DNA Matching.

Lab Outline
Simulation and application of neural network related techniques for
bioinformatics, implementation of approximate matching algorithms, DNA
matching algorithms and applications.

Recommended Books
Latest editions of following books
1. SC Rastogi, Namita M, P Rastogi, “Bioinformatics: Concepts, Skills
and Applications”, CSB Publishers.

39
2. Lacroix Zor, Terence Critchlow, “Bioinformatics: Managing Scientific
Data”, Morgan Kaufmann.

*** Elective-III 3+0

Prerequisite: None

Course Outline
To be chosen from the list of electives.

*** Elective-IV 3+0

Prerequisite: None

Course Outline
To be chosen from the list of electives.

*** Research Project 0+3

Prerequisite: None

Course Outline
An independent research project and directed by a full time faculty
member of the department.

List of Electives

1. Enzyme Kinetics
2. Functional genomics
3. Human Computer Interaction
4. Nanotechnology
5. Environmental Biotechnology
6. Special Topics in Biochemistry
7. Immuno-Informatics
8. Microbial genomics and proteomics
9. Network Biology
10. Biophysics
11. Modern programming languages
12. Methods in protein modeling
13. Pharmacoinformatics
14. Statistical methods in bioinformatics
15. Design and analysis of algorithms
16. Epigenetics and gene regulation
17. Protein chemistry
18. Microbial genetics
19. Molecular oncology
20. Immunology
40
Note
In addition to the above, the universities can offer any elective which they
feel necessary subject to the availability of resources.

RECOMMENDED BOOKS
The latest editions of

Cell and Molecular Biology: Concepts and Experiments

Gerald Karp
John Wiley and Sons

Introduction to Computational Molecular Biology

Setubal, Meidanis
Brooks/Cole

Principles and Techniques of Biochemistry and Molecular Biology

Keith Wilson, John Walker
Cambridge University Press

Instant Notes: Biochemistry

B D Hames
Viva Books Pvt. Ltd.

Basics of Theoretical and Computational Chemistry

BM Rode
John Willey and Sons

Instant Notes: Genetics

P C Winter
Viva Books Pvt. Ltd.

Instant Notes: Molecular Biology

P C Turner
Viva Books Pvt. Ltd.

Molecular Cloning: A laboratory manual

Sambrook
Cold Spring Harbor, Laboratory Press.

Instant Notes: Bioinformatics

David R. Westhead, J. Howard Parish and Richard M. Twyman
Viva Books Pvt. Ltd.

Bioinformatics for Dummies

Jean-Michel Claverie,Cedric Notredame
Wiley Publishing, Inc.
41
Essential Bioinformatics
Jin Xiong
Cambridge University Press.

Bioinformatics
Bal
Tata McGraw-Hill.

Bioinformatics
Andrzej Polański, Marek Kimmel
Springer.

Bioinformatics: An Introduction
Jeremy Ramsden
Springer.

Bioinformatics: A Concept-based Introduction

Venkatarajan Subramanian Mathura, Pandjassarame Kangueane
Springer.

Bioinformatics: Tools and Applications

David Edwards, Jason Eric Stajich, David Hansen
Springer.

Bioinformatics: Principles and Basic Internet Applications

Hassan A. Sadek
Trafford Publishing, Canada.

Bioinformatics: Applications in Life and Environmental Sciences

M. H. Fulekar
Springer.

Bioinformatics: A Practical Approach

Shui Qing Ye
Chapman & Hall / CRC.

Applied Bioinformatics: An Introduction

Paul M. Selzer, Richard J. Marhöfer, Andreas Rohwer
Springer.

Bioinformatics: A Practical Guide to the Analysis of Genes and

Proteins
Andreas D. Baxevanis, B. F. Francis Ouellette
John Wiley and Sons, USA.

42
Bioinformatics: a Swiss perspective
Ron D. Appel, Ernest Feytmans
World Scientific, Singapore.

Bioinformatics: Genomics and Post-genomics

Frédéric Dardel, François Képès, Translated by Noah Hardy
John Wiley and Sons, France.

Bioinformatics: Methods and Applications: Genomics, Proteomics

and Drug Discovery
S. C. Rastogi, Namita Mendiratta, Parag Rastogi
PHI Learning Pvt. Ltd.

Bioinformatics and drug discovery

Richard S. Larson
Humana Press.

Computational molecular biology: an algorithmic approach

Pavel Pevzner
MIT Press.

Bioinformatics algorithms: techniques and applications

Ion Măndoiu, Alexander Zelikovsky
Wiley-Interscience.

Bioinformatics: problem solving paradigms

Volker Sperschneider, Jana Sperschneider, Lena Scheubert
Springer.

Parallel computing for bioinformatics and computational biology

Zomaya A. Y.
John Wiley & Sons, Inc.

Research and trends in data mining technologies and applications

David Taniar
Idea Group Inc (IGI).

Machine learning in bioinformatics

Yan-Qing Zhang, Jagath Chandana Rajapakse
John Wiley and Sons.

Computational Intelligence in Bioinformatics

Árpád Kelemen, Ajith Abraham, Yuehui Chen
Springer.

43
Bioinformatics and the Cell: Modern Computational Approaches in
Genomics, Proteomics and Transcriptomics
Xuhua Xia
Springer.

Bioinformatics for Dummies

Jean-Michel Claverie and Cerdric Notredame

Bioinformatics-Sequence and Genome Analysis

David W. Mount.

Introduction to Bioinformatics
T K Attwood and D J Parry-Smith.

Bioinformatics-Gene, Proteins and Computers

C. A. Orengo, D. T. Jones and J. M. Thornton.

44
 MASTER OF SCIENCE (MS) in
Bioinformatics

Introduction
The purpose of MS degree program in bioinformatics is to provide the
students with an advanced knowledge and practices that will train them to
decipher the biological processes with the help of computational tools and
to prepare them for further research and/or industry.

Program objectives

At the end of MS program, the graduates should be able to:

1. Develop innovative computer applications to solve biological

problems
2. Facilitate other researchers using bioinformatics tools and
databases
3. Undertake problem-based research
4. Tackle research based problems in various industries such as
pharmaceutical, biotechnology, software industry etc

Learning Outcomes

After completion of MS program in bioinformatics, the graduates will be

able to:
● Answer questions about molecular evolution, biological functions
and control of biological systems
● Use bioinformatics skills to predict functions from structures,
networks, complexes, transcriptome and proteome data
● Develop advanced computational applications related to
bioinformatics

Admission Requirements

Eligibility
1. BS in Bioinformatics/Biological Sciences/Computer Sciences/
Biotechnology or equivalent in relevant disciplines (deficiency
courses to be completed if needed).
2. Any other criteria set by the University.

Duration
2 years (course work may be completed in two semesters and one year
for research work).
Total Credit Hrs
30 (24 credit hours course work + 6 credit hours thesis)
45
 Scheme of Studies for MS Program in Bioinformatics

Semester I and II

Note:
Students coming from computer and physical sciences background must
take 1-2 courses from group A and may take at most one course from
group B. Similarly, students coming from biological sciences background
must take 1-2 courses from group B and may take at most one course
from group A.

Students coming from bioinformatics background may take at most 1

course each from groups A and B.

Remaining credit hours for all students must be completed from

group C.

Group A- Biological Sciences

1. Molecular Biology
2. Cell Biology
3. Genomics
4. Proteomics
5. Metabolomics
6. Microbial Genetics
7. Biochemistry
8. Gene Manipulation
9. Enzymology
10. Epigenetics
11. Biotechnology
12. Immunology
13. Biostatistics

Group B- Computer Sciences

1. Fundamentals of Programming
2. Object Oriented Programming
3. Data structure
4. Algorithm development
5. Database design
6. Software engineering
7. Graphics and visualization
8. Probability

Group C- Bioinformatics
1. Genome Informatics/Computational Genomics

46
2. Advanced Bioinformatics/Computational Biology
3. Systems Biology
4. Protein Informatics/Computational Proteomics
5. Computational Drug Design
6. Computational Molecular Evolution
7. Biophysics
8. Molecular Modelling and Simulation
9. Mathematical Models in Biology
10. Machine Learning
11. Metagenomics
12. Data Mining
13. Stochastic Processes
14. Computational Neuroscience
15. Synthetic Biology
16. Functional genomics
17. Cheminformatics
18. Health informatics
19. Big data analysis and management
Note
In addition to the above, the universities can offer any other course in the
respective groups according to their specialization.

Semester III and IV

Research Thesis (6 Credit Hours)

Research Project
1. Duration of the research project will be at least two regular
semesters. An independent research topic chosen by the student
and supervised by a full-time faculty member of the department is
required for all students in M.S Bioinformatics.
2. The research work of each student will be reviewed periodically
by the supervisor/head of department to ensure the objectives laid
down for study are being met.
3. All students must present and defend their research work before
the panel of examiners as per the rules of the university.

Recommended Textbooks for MS Bioinformatics Program

DW Mount, Bioinformatics: Sequence and Genome Analysis
1. AD Baxevnis & BF Francis Ouellet, Bioinformatics: A practice
Guide to Analysis of Gene and Proteins, Wiley
2. C Gibas & P Jambeck, Developing Bioinformatics Computer
Skills, O’Reilly Media
3. AM Campbell & LJ Heyer, Discovering Genomics, Proteins and
Bioinformatics, Benjamin Cummings
47
4. D Stekel, Microarray Bioinformatics, Cambridge University Press
5. AM Lesk, Introduction to Bioinformatics, Oxford University Press
6. BP Bergeron, Bioinformatics Computing, Prentice Hall
7. G Gibson, A Primer of Genome Science, Sinauer Associates
8. HJ Parish, Instant Notes on Bioinformatics
9. D Marshall & J Persner, Bioinformatics and functional Genomics
10. P Baldi and S Brunak, Bioinformatics: The Machine Learning
Approach, A Bradford Book
11. NC Jones & PA Persner, An Introduction to Bioinformatics
Algorithms
12. CW Sensen, Essentials of Genomics and Bioinformatics
13. M Moorhouse & P Berry, Bioinformatics, Biocomputing and Perl:
An introduction to Bioinformatics Computing Skills and Practice,
Wiley
14. W Ewens & G Grant, Statistical Methods in Bioinformatics
15. IS Kohane, A Kho & AJ Butte, Microarrays for An Integrative
Genomics
16. D Higgins & W Taylor, Bioinformatics; Sequence and Databanks:
A Practical Approach
17. RA Dwyer, Genomic Perl: From Bioinformatics Basic To Working
Code
18. T Lengauer, Bioinformatics: From Genomes To Drugs, Wiley
19. T Atwood and D Perry-Smith, Introduction To Bioinformatics,
Benjamin Cummings
20. P Bourne and H Weissig, Structured Bioinformatics
21. S Misener and S Krawetz, Bioinformatics Methods and Protocols
22. A Tozeren and SW Byers, New Biology for Engineers and
scientists
23. P Clote & R Backofen, Computational Molecular Biology: An
Introduction
24. J Augen, Bioinformatics in Post-Genomic Era: Genomic
Transcription, Proteome and Information Based Medicine
25. U Seiffert, LC Jain & Pschwetzer, Bioinformatics: Using
Computational Intelligence Paradigms
26. S Krawetz & D Womble, Introduction To Bioinformatics: a
theoretical and Practical Approach
27. MR Barens & IC Gray, Bioinformatics for Geneticists
28. LO Nielsen, Immunological Bioinformatics
29. H Rashidi, Lukas Buehler, Bioinformatics Basics.
30. C Orengo, D Jones & J Thornton, Bioinformatics: Genes, Proteins
and Computers.
31. PG Higgs, Bioinformatics and Molecular Evolution
32. A Umar, I Kapetanovic & J Khan, The Application of Bioinformatics
in Cancer Detection
33. R Hofestadt, Bioinformatics

48
34. AF Batiza, B Schacter & K Mullis, Bioinformatics, Genomics and
Proteomics: Getting the Big Picture
35. I Jerisca, Dennis Wigle, Knowledge Discovery in Proteomics
36. G Waksman, Proteomics and Protein-Protein Introductions:
Biology, Chemistry, Bioinformatics and Drug Design
37. J Ramsden, An introduction to Bioinformatics
38. H Rashidi & L Buehler, Bioinformatics Basics: Application in
Biological Science and Medicine
39. LB Jorde, JC Carey, M Bamshad & RL White, Medical Genetics
40. WS Klug & MR Cummings, Essential of Genetics
41. RI Nussbaum, RR Mclnnes & HF Willard, Genetics in Medicine,
Thompson & Thompson
42. PA Hoffe, Medical Molecular Genetics
43. SB Primrose & R Twyman, Principles of Gene Manipulation and
Genomics
44. A Emery & R Mueller, Essential of Medical Genetics.
45. B Lewin, Gene X
46. G Acquaah, Understanding Biotechnology
47. W Klug, Michael Cumming and Charlotte Spencer, Concept of
Genetics
48. B Lewin, Essential Genes
49. G Karp, Cell and Molecular Biology: Concepts and Experiments,
Wiley
50. E Nester, Denise Anderson, C. Evans Robert Jr., Microbiology; A
Human Perspective
51. BA Pierce, Genetics
52. J Hanford, Ethics from a Faith Perspective
53. J Burrley & J Harris, A companion to Genetics
54. D Mathews, Vernon Farewell, Understanding Medical Statistics
55. R Weaver, Molecular Biology
56. PC Champe, RA Harvey and DR Ferrier, Lippincott’s Biochemistry
57. M Grammer and M Rodwell, Harper’s Biochemistry
58. Nelson & Cox, Lehninger; Principles of Biochemistry
59. D Voet, Biochemistry
60. R Schalkoff, Pattern Recognition, Statistical, Structural & Neural
Approached
61. AS Pandya & RB Macy, Pattern Recognition with Neural Networks
in C++
62. Duda, Hart & Stork, Pattern Classification
63. M Pavel, Fundamentals of Pattern Recognition
64. MK Pietikainen, Texture Analysis in Machine Vision
65. SK Pal & PP Wang, Genetic Algorithms for Pattern Recognition
66. RC Gonzales, Digital Image Processing
67. RC Gonzales, Digital Image Processing using Matlab
68. JC Russ, Hand Book of Image Processing
69. JR Parker, Algorithms for Image Processing & Computer Vision
49
 ANNEXURE - A

English I (Functional English)

Objectives: Enhance language skills and develop critical thinking.

Course Contents

Basics of Grammar
Parts of speech and use of articles
Sentence structure, active and passive voice
Practice in unified sentence
Analysis of phrase, clause and sentence structure
Transitive and intransitive verbs
Punctuation and spelling

Comprehension
Answers to questions on a given text

Discussion
General topics and every-day conversation (topics for discussion to be at
the discretion of the teacher keeping in view the level of students)

Listening
To be improved by showing documentaries/films carefully selected by
subject teachers

Translation skills
Urdu to English

Paragraph writing
Topics to be chosen at the discretion of the teacher

Presentation skills
Introduction

Note: Extensive reading is required for vocabulary building

Recommended Books
1. Functional English
a) Grammar

50
 1. Practical English Grammar by A. J. Thomson and A. V.
Martinet. Exercises 1. Third edition. Oxford University Press.
1997. ISBN 0194313492
2. Practical English Grammar by A. J. Thomson and A. V.
Martinet. Exercises 2. Third edition. Oxford University Press.
1997. ISBN 0194313506
b) Writing
1. Writing. Intermediate by Marie-Christine Boutin, Suzanne
Brinand and Francoise Grellet. Oxford Supplementary Skills.
Fourth Impression 1993. ISBN 0 19 435405 7 Pages 20-27
and 35-41.

c) Reading/Comprehension
1. Reading. Upper Intermediate. Brain Tomlinson and Rod Ellis.
Oxford Supplementary Skills. Third Impression 1992. ISBN 0
19 453402 2.

d) Speaking

English II (Communication Skills)

Objectives: Enable the students to meet their real life communication

needs.

Course Contents:

Paragraph writing
Practice in writing a good, unified and coherent paragraph

Essay writing
Introduction

CV and job application

Translation skills
Urdu to English

Study skills
Skimming and scanning, intensive and extensive, and speed reading,
summary and précis writing and comprehension

Academic skills
Letter/memo writing, minutes of meetings, use of library and internet
51
Presentation skills
Personality development (emphasis on content, style and pronunciation)

Note: documentaries to be shown for discussion and review

Recommended Books
Communication Skills
a) Grammar
1. Practical English Grammar by A. J. Thomson and A. V.
Martinet. Exercises 2. Third edition. Oxford University Press
1986. ISBN 0 19 431350 6.
b) Writing
1. Writing. Intermediate by Marie-Christine Boutin, Suzanne
Brinand and Francoise Grellet. Oxford Supplementary Skills.
Fourth Impression 1993. ISBN 019 435405 7 Pages 45-53
(note taking).
2. Writing. Upper-Intermediate by Rob Nolasco. Oxford
Supplementary Skills. Fourth Impression 1992. ISBN 0 19
435406 5 (particularly good for writing memos, introduction to
presentations, descriptive and argumentative writing).

c) Reading
1. Reading. Advanced. Brian Tomlinson and Rod Ellis. Oxford
Supplementary Skills. Third Impression 1991. ISBN 0 19
453403 0.
2. Reading and Study Skills by John Langan
3. Study Skills by Richard York.

English III (Technical Writing and

Presentation Skills)

Objectives: Enhance language skills and develop critical thinking

Course Contents

Presentation skills

Essay writing
Descriptive, narrative, discursive, argumentative

Academic writing
How to write a proposal for research paper/term paper

52
How to write a research paper/term paper (emphasis on style, content,
language, form, clarity, consistency)

Technical Report writing

Progress report writing

Note: Extensive reading is required for vocabulary building

Recommended Books

Technical Writing and Presentation Skills

a) Essay Writing and Academic Writing

1. Writing. Advanced by Ron White. Oxford Supplementary
Skills. Third Impression 1992. ISBN 0 19 435407 3
(particularly suitable for discursive, descriptive, argumentative
and report writing).
2. College Writing Skills by John Langan. McGraw-Hill Higher
Education. 2004.
3. Patterns of College Writing (4th edition) by Laurie G. Kirszner
and Stephen R. Mandell. St. Martin’s Press.
b) Presentation Skills
c) Reading
The Mercury Reader. A Custom Publication. Compiled by
Northern Illinois University. General Editors: Janice Neulib;
Kathleen Shine Cain; Stephen Ruffus and Maurice Scharton.
(A reader which will give students exposure to the best of
twentieth century literature, without taxing the taste of
engineering students).

53
 ANNEXURE - B

Pakistan Studies (Compulsory)

Introduction/Objectives

 Develop vision of historical perspective, government, politics,

contemporary Pakistan, ideological background of Pakistan.
 Study the process of governance, national development, issues
arising in the modern age and posing challenges to Pakistan.
Course Outline
1. Historical Perspective
a. Ideological rationale with special reference to Sir Syed Ahmed
Khan, Allama Muhammad Iqbal and Quaid-e-Azam
Muhammad Ali Jinnah.
b. Factors leading to Muslim separatism
c. People and Land
i. Indus Civilization
ii. Muslim advent
iii. Location and geo-physical features.
2. Government and Politics in Pakistan
Political and constitutional phases:
a. 1947-58
b. 1958-71
c. 1971-77
d. 1977-88
e. 1988-99
f. 1999 onward
3. Contemporary Pakistan
a. Economic institutions and issues
b. Society and social structure
c. Ethnicity
d. Foreign policy of Pakistan and challenges
e. Futuristic outlook of Pakistan
Recommended Books
1. Burki, Shahid Javed. State & Society in Pakistan, The MacMillan
Press Ltd 1980.

54
2. Akbar, S. Zaidi. Issue in Pakistan’s Economy. Karachi: Oxford
University Press, 2000.
3. S. M. Burke and Lawrence Ziring. Pakistan’s Foreign policy: An
Historical analysis. Karachi: Oxford University Press, 1993.
4. Mehmood, Safdar. Pakistan Political Roots & Development. Lahore,
1994.
5. Wilcox, Wayne. The Emergence of Bangladesh, Washington:
American Enterprise, Institute of Public Policy Research, 1972.
6. Mehmood, Safdar. Pakistan Kayyun Toota, Lahore: Idara-e-
Saqafat-e-Islamia, Club Road, nd.
7. Amin, Tahir. Ethno - National Movement in Pakistan, Islamabad:
Institute of Policy Studies, Islamabad.
8. Ziring, Lawrence. Enigma of Political Development. Kent England:
Wm Dawson & sons Ltd, 1980.
9. Zahid, Ansar. History & Culture of Sindh. Karachi: Royal Book
Company, 1980.
10. Afzal, M. Rafique. Political Parties in Pakistan, Vol. I, II & III.
Islamabad: National Institute of Historical and cultural Research,
1998.
11. Sayeed, Khalid Bin. The Political System of Pakistan. Boston:
Houghton Mifflin, 1967.
12. Aziz, K. K. Party, Politics in Pakistan, Islamabad: National
Commission on Historical and Cultural Research, 1976.
13. Muhammad Waseem, Pakistan Under Martial Law, Lahore:
Vanguard, 1987.
14. Haq, Noor ul. Making of Pakistan: The Military Perspective.
Islamabad: National Commission on Historical and Cultural
Research, 1993.

55
 ANNEXURE - C

ISLAMIC STUDIES
(Compulsory)
Objectives

This course is aimed at:

1 To provide Basic information about Islamic Studies
2 To enhance understanding of the students regarding Islamic
Civilization
3 To improve Students skill to perform prayers and other worships
4 To enhance the skill of the students for understanding of issues
related to faith and religious life.

Detail of Courses
Introduction to Quranic Studies
1. Basic Concepts of Quran
2. History of Quran
3. Uloom-ul-Quran
Study of Selected Text of Holly Quran

1. Verses of Surah Al-Baqara Related to Faith(Verse No-284-286)

2. Verses of Surah Al-Hujrat Related to Adab Al-Nabi (Verse No-1-18)
3. Verses of Surah Al-Mumanoon Related to Characteristics of faithful
(Verse No-1-11)
4. Verses of Surah al-Furqan Related to Social Ethics (Verse No.63-
77)
5. Verses of Surah Al-Inam Related to Ihkam (Verse No-152-154)
Study of Selected Text of Holly Quran

1. Verses of Surah Al-Ihzab Related to Adab al-Nabi (Verse No.6, 21,

40, 56, 57, 58.)
2. Verses of Surah Al-Hashar (18,19,20) Related to thinking, Day of
Judgment
3. Verses of Surah Al-Saf Related to Tafakar, Tadabar (Verse No-
1,14)
Seerat of Holy Prophet (S.A.W) I

1. Life of Muhammad Bin Abdullah ( Before Prophet Hood)

2. Life of Holy Prophet (S.A.W) in Makkah
3. Important Lessons Derived from the life of Holy Prophet in Makkah

56
Seerat of Holy Prophet (S.A.W) II
1. Life of Holy Prophet (S.A.W) in Madina
2. Important Events of Life Holy Prophet in Madina
3. Important Lessons Derived from the life of Holy Prophet in Madina
Introduction to Sunnah
1. Basic Concepts of Hadith
2. History of Hadith
3. Kinds of Hadith
4. Uloom –ul-Hadith
5. Sunnah & Hadith
6. Legal Position of Sunnah
Selected Study from Text of Hadith

Introduction to Islamic Law & Jurisprudence

1. Basic Concepts of Islamic Law & Jurisprudence
2. History & Importance of Islamic Law & Jurisprudence
3. Sources of Islamic Law & Jurisprudence
4. Nature of Differences in Islamic Law
5. Islam and Sectarianism
Islamic Culture & Civilization
1. Basic Concepts of Islamic Culture & Civilization
2. Historical Development of Islamic Culture & Civilization
3. Characteristics of Islamic Culture & Civilization
4. Islamic Culture & Civilization and Contemporary Issues
Islam & Science
1. Basic Concepts of Islam & Science
2. Contributions of Muslims in the Development of Science
3. Quran & Science
Islamic Economic System
1. Basic Concepts of Islamic Economic System
2. Means of Distribution of wealth in Islamic Economics
3. Islamic Concept of Riba
4. Islamic Ways of Trade & Commerce
Political System of Islam
1. Basic Concepts of Islamic Political System
2. Islamic Concept of Sovereignty
3. Basic Institutions of Govt. in Islam
Islamic History
1. Period of Khlaft-E-Rashida
2. Period of Ummayyads
57
3. Period of Abbasids
Social System of Islam
1. Basic Concepts of Social System of Islam
2. Elements of Family
3. Ethical Values of Islam
Reference Books
1. Hameed ullah Muhammad, “Emergence of Islam” , IRI,
Islamabad
2 Hameed ullah Muhammad, “Muslim Conduct of State”
3 Hameed ullah Muhammad, ‘Introduction to Islam
4. Mulana Muhammad Yousaf Islahi,”
5 Hussain Hamid Hassan, “An Introduction to the Study of Islamic
Law” leaf Publication Islamabad, Pakistan.
6 Ahmad Hasan, “Principles of Islamic Jurisprudence” Islamic
Research
Institute, International Islamic University, Islamabad (1993)
7 Mir Waliullah, “Muslim Jurisprudence and the Quranic Law of
Crimes”
Islamic Book Service (1982)
8 H. S. Bhatia, “Studies in Islamic Law, Religion and Society” Deep &
Deep
Publications New Delhi (1989)
9 Dr. Muhammad Zia-ul-Haq, “Introduction to Al Sharia Al Islamia”
Allama
Iqbal Open University, Islamabad (2001)

58
 Annexure - D

Note: One course will be selected from the following six courses of
Mathematics.

COMPULSORY MATHEMATICS
COURSES FOR BS (4 YEAR)

(FOR STUDENTS NOT MAJORING IN

MATHEMATICS)

1. MATHEMATICS I (ALGEBRA)

Prerequisite(s): Mathematics at secondary level

Credit Hours: 3+0

Specific Objectives of the Course: To prepare the students, not

majoring in mathematics, with the essential tools of algebra to apply the
concepts and the techniques in their respective disciplines.

Course Outline:

Preliminaries: Real-number system, complex numbers, introduction to

sets, set operations, functions, types of functions. Matrices: Introduction to
matrices, types, matrix inverse, determinants, system of linear equations,
Cramer’s rule.

Quadratic Equations: Solution of quadratic equations, qualitative analysis

of roots of a quadratic equations, equations reducible to quadratic
equations, cube roots of unity, relation between roots and coefficients of
quadratic equations.

Sequences and Series: Arithmetic progression, geometric progression,

harmonic progression. Binomial Theorem: Introduction to mathematical
induction, binomial theorem with rational and irrational indices.
Trigonometry: Fundamentals of trigonometry, trigonometric identities.

Recommended Books

1. Dolciani MP, Wooton W, Beckenback EF, Sharron S, Algebra 2 and

Trigonometry, 1978, Houghton & Mifflin, Boston (suggested text)

59
2. Kaufmann JE, College Algebra and Trigonometry, 1987, PWS-Kent
Company, Boston
3. Swokowski EW, Fundamentals of Algebra and Trigonometry (6th
edition), 1986, PWS-Kent Company, Boston

2. MATHEMATICS II (CALCULUS)

Prerequisite(s): Mathematics I (Algebra)

Credit Hours: 3+0

Specific Objectives of the Course: To prepare the students, not

majoring in mathematics, with the essential tools of calculus to apply the
concepts and the techniques in their respective disciplines.

Course Outline:
Preliminaries: Real-number line, functions and their graphs, solution of
equations involving absolute values, inequalities. Limits and Continuity: Limit
of a function, left-hand and right-hand limits, continuity, continuous functions.
Derivatives and their Applications: Differentiable functions, differentiation
of polynomial, rational and transcendental functions, derivatives.
Integration and Definite Integrals: Techniques of evaluating indefinite
integrals, integration by substitution, integration by parts, change of
variables in indefinite integrals.

Recommended Books
1. Anton H, Bevens I, Davis S, Calculus: A New Horizon (8th edition),
2005, John Wiley, New York
2. Stewart J, Calculus (3rd edition), 1995, Brooks/Cole (suggested text)
3. Swokowski EW, Calculus and Analytic Geometry, 1983, PWS-Kent
Company, Boston
4. Thomas GB, Finney AR, Calculus (11th edition), 2005, Addison-
Wesley, Reading, Ma, USA

3. MATHEMATICS III (GEOMETRY)

Prerequisite(s): Mathematics II (Calculus)

Credit Hours: 3+0
Specific Objectives of the Course: To prepare the students, not
majoring in mathematics, with the essential tools of geometry to apply the
concepts and the techniques in their respective disciplines.
60
Course Outline
Geometry in Two Dimensions: Cartesian-coördinate mesh, slope of a line,
equation of a line, parallel and perpendicular lines, various forms of
equation of a line, intersection of two lines, angle between two lines,
distance between two points, distance between a point and a line.

Circle: Equation of a circle, circles determined by various conditions,

intersection of lines and circles, locus of a point in various conditions.
Conic Sections: Parabola, ellipse, hyperbola, the general-second-degree equation

Recommended Books
1. Abraham S, Analytic Geometry, Scott, Freshman and Company,
1969
2. Kaufmann JE, College Algebra and Trigonometry, 1987, PWS-Kent
Company, Boston
3. Swokowski EW, Fundamentals of Algebra and Trigonometry (6th
edition), 1986, PWS-Kent Company, Boston
4. COURSE FOR NON-MATHEMATICS MAJORS IN SOCIAL
SCIENCES
Title of subject: MATHEMATICS
Discipline : BS (Social Sciences).
Pre-requisites : SSC (Metric) level Mathematics
Credit Hours : 03 + 00
Minimum Contact Hours: 40
Assessment : written examination;
Effective : 2008 and onward

Aims : To give the basic knowledge of Mathematics and

prepare the students not majoring in mathematics.

Objectives :After completion of this course the student should be

able to:
 Understand the use of the essential tools of basic mathematics;
 Apply the concepts and the techniques in their respective
disciplines;
 Model the effects non-isothermal problems through different
domains;
Contents :
1. Algebra

61
 Preliminaries: Real and complex numbers, Introduction to sets, set
operations, functions, types of functions. Matrices: Introduction to
matrices, types of matrices, inverse of matrices, determinants,
system of linear equations, Cramer’s rule. Quadratic equations:
Solution of quadratic equations, nature of roots of quadratic
equations, equations reducible to quadratic equations. Sequence
and Series: Arithmetic, geometric and harmonic progressions.
Permutation and combinations: Introduction to permutation and
combinations, Binomial Theorem: Introduction to binomial theorem.
Trigonometry: Fundamentals of trigonometry, trigonometric
identities. Graphs: Graph of straight line, circle and trigonometric
functions.
2. Statistics
Introduction: Meaning and definition of statistics, relationship of
statistics with social science, characteristics of statistics, limitations
of statistics and main division of statistics. Frequency distribution:
Organisation of data, array, ungrouped and grouped data, types of
frequency series, individual, discrete and continuous series, tally
sheet method, graphic presentation of the frequency distribution, bar
frequency diagram histogram, frequency polygon, cumulative
frequency curve. Measures of central tendency: Mean medium and
modes, quartiles, deciles and percentiles. Measures of dispersion:
Range, inter quartile deviation mean deviation, standard deviation,
variance, moments, skewness and kurtosis.

Recommended Books
1. Swokowski. E. W., ‘Fundamentals of Algebra and Trigonometry’,
Latest Edition.
2. Kaufmann. J. E., ‘College Algebra and Trigonometry’, PWS-
Kent Company, Boston, Latest Edition.
3. Walpole, R. E., ‘Introduction of Statistics’, Prentice Hall, Latest
Edition.
4. Wilcox, R. R., ‘Statistics for The Social Sciences’,

5. MATHEMATICS FOR CHEMISTRY

Credit Hours: 3

Prerequisites: Mathematics at Secondary level

62
Specific Objectives of Course:
To prepare the students not majoring in mathematics with the essential
tools of Calculus to apply the concepts and the techniques in their
respective disciplines.

Course Outline
Preliminaries: Real Numbers and the Real Line, Functions and their
graphs: Polynomial Functions, Rational Functions, Trigonometric
Functions, and Transcendental Functions. Slope of a Line, Equation of a
Line, Solution of equations involving absolute values, Inequalities. Limits
and Continuity: Limit of a Function, Left Hand and Right Hand Limits,
Continuity, Continuous Functions. Derivatives and its Applications:
Differentiation of Polynomial, Rational and Transcendental Functions,
Extreme Values of Functions. Integration and Indefinite Integrals:
Integration by Substitution, Integration by Parts, Change of Variables in
Indefinite Integrals. Least-Squares Line.
Recommended Books
1. Thomas, Calculus, 11th Edition. Addison Wesley publishing
company, 2005.
2. H. Anton, I. Bevens, S. Davis, Calculus, 8th edition, John Willey &
Sons, Inc. 2005.
3. Hughes-Hallett, Gleason, McCallum, et al, Calculus Single and
Multivariable, 3rd Edition. John Wiley & Sons, Inc. 2002.
4. Frank A. Jr, Elliott Mendelsohn, Calculus, Schaum’s Outline Series,
4th edition, 1999.
5. E. W. Swokowski, Calculus and Analytic Geometry PWS Publishers,
Boston, 1983.
6. John H. Mathews, Numerical Methods for Mathematics Science and
Engineering, Prentice-Hall, Second Edition 1992.
6. MATHEMATICS FOR PHYSICS

Contents

1. Preliminary calculus.

 Differentiation
Differentiation from first principles; products; the chain rule;
quotients; implicit differentiation; logarithmic differentiation; Leibnitz’
theorem; special points of a function; theorems of differentiation.
 Integration

63
 Integration from first principles; the inverse of differentiation;
integration by inspection; sinusoidal function; logarithmic
integration; integration using partial fractions; substitution method;
integration by parts; reduction formulae; infinite and improper
integrals; plane polar coordinates; integral inequalities; applications
of integration.

2. Complex numbers and hyperbolic functions

 The need for complex numbers

 Manipulation of complex numbers
Additions and subtraction; modulus and argument; multiplication;
complex conjugate; division
 Polar representation of complex numbers Multiplication and division
in polar form
 de Moivre’s theorem
Trigonometrical identities; finding the nth roots of unity; solving
polynomial equations
 Complex logarithms and complex powers
 Applications to differentiation and integration
 Hyperbolic functions
Definitions; hyperbolic-trigonometric analogies; identities of
hyperbolic functions; solving hyperbolic equations; inverses of
hyperbolic functions; calculus of hyperbolic functions

3. Series and limits

 Series
 Summation of series
Arithmetic series; geometric series; arithmetico-geometric series;
the difference method; series involving natural numbers;
transformation of series
 Convergence of infinite series
Absolute and conditional convergence; convergence of a series
containing only real positive terms; alternating series test
 Operations with series
 Power series
Convergence of power series; operations with power series
 Taylor series
Taylor’s theorem; approximation errors in Taylor series; standard
McLaurin series
 Evaluation of limits

64
4. Partial differentiation

 Definition of the partial derivative

 The total differential and total derivative
 Exact and inexact differentials
 Useful theorems of partial differentiation
 The chain rule
 Change of variables
 Taylor’s theorem for many-variable functions
 Stationary values of many-variable functions
 Stationary values under constraints
5. Multiple integrals

 Double integrals
 Triple integrals
 Applications of multiple integrals
Areas and volumes; masses, centers of mass and centroids;
Pappus’ theorems; moments of inertia; mean values of functions
 Change of variables in multiple integrals
Change of variables in double integrals;

6. Vector algebra

 Scalars and vectors

 Addition and subtraction of vectors
 Multiplication by a scalar
 Basis vectors and components
 Magnitude of a vectors
 Multiplication of vectors
Scalar product; vector product; scalar triple product; vector triple
product
 Equations of lines and planes
Equation of a line; equation of a plane
 Using vectors to find distances
Point to line; point to plane; line to line; line to plane
 Reciprocal vectors
7. Matrices and vector spaces

 Vectors spaces Basic vectors; the inner product; some useful

inequalities
 Matrices
 The complex and Hermitian conjugates of a matrix
 The determinant of a matrix
65
 Properties of determinants
 The inverse of a matrix
 The rank of a matrix
 Simultaneous linear equations
N simultaneous linear equations in N unknowns
 Special square matrices
Diagonal; symmetric and antisymmetric; orthogonal; Hermitian;
unitary normal
 Eigen vectors and eigen values
Of a normal matrix; of Hermitian and anti-Hermitian matrices; of a
unitary matrix; of a general square matrix
 Determination of eigen values and eigen vectors Degenerate eigen
values
8. Vector calculus
 Differentiation of vectors Composite vector expressions; differential
of a vector
 Integration of vectors
 Space curves
 Vector functions of several arguments
 Surfaces
 Scalar and vector fields
 Vector operators
 Gradient of a scalar field; divergence of a vector field; curl of a vector
field
 Vector operator formulae
 Vector operators acting on sums and products; combinations of
grad, div and curl
 Cylindrical and spherical polar coordinates
 Cylindrical polar coordinates; spherical polar coordinates.

66
 Annexure - E

Statistics-I Credit 3 (2-1)

Definition and importance of Statistics in Agriculture, Data Different types
of data and variables

Classification and Tabulation of data, Frequency distribution, stem-and-

Leaf diagram, Graphical representation of data Histogram, frequency
polygon, frequency curve.

Measure of Central tendency, Definition and calculation of Arithmetic

mean, Geometric mean, Harmonic mean, Median quantiles and Mode in
grouped and un-grouped data.

Measure of Dispersion, Definition and Calculation of Range, quartile

deviation, Mean deviation, Standard deviation and variance, coefficient of
variation.

Practical
a. Frequency Distribution
b. Stem-and-Leaf diagram
c. Various types of Graphs
d. Mean, Geometric mean Harmonic Mean,
e. Median, Quartiles Deviation, mean Deviation.
f. Standard Deviation, Variance, Coefficient of variation,
g. Skewness and kenosis

Recommended Books
1. Introduction to Statistical Theory Part- I by Sher Muhammad and Dr.
Shahid Kamal (Latest Edition)
2. Statistical Methods and Data Analysis by Dr. Faquir Muhammad
3. A. Concise Course in A. Level Statistic with world examples by J.
Crashaw and J. Chambers (1994)
4. Basic Statistics an Inferential Approach 2 nd Ed. (1986) Fran II.
Dietrich-II and Thomas J. Keans
Statistics-II Credit 3 (2-1)

Sampling Probability and non-Probability Sampling, Simple random

sampling stratified random sampling Systematic sampling error, Sampling
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distribution of mean and difference between two means. Interference
Theory: Estimation and testing of hypothesis, Type—I and type-II error,
Testing of hypothesis about mean and difference between two means
using Z-test and t-test, Paired t-test, Test of association of attributes using
X2 (chi-square) Testing hypothesis about variance.
Practical
a. Sampling random sampling
b. Stratified random sampling.
c. Sampling distribution of mean
d. Testing of hypotheses regarding population mean
e. Testing of hypotheses about the difference between population
means
f. Chi-square test
g. Testing of Correlation Coefficient
h. Fitting of simple linear regression
i. One-way ANOVA
j. Two-way ANOVA
Recommended Books
1. Introduction to Statistical Theory Part-II by Sher Muhammad and
Dr. Shahid Kamal (Latest Edition)
2. Statistical Methods and Data Analysis by Dr. Faquir Muhammad
3. Principles and Procedures of Statistics A Bio-material approach,
2nd Edition, 1980 by R. G. D Steal and James H. Tarric
4. Statistical Procedures for Agricultural Research 2 nd Edition (1980)
by K. A. Gomez and A. A. Gomez

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 ANNEXURE - F
Introduction to Information and Communication Technologies

Course Structure: Lectures: 2 Labs: 1 Credit Hours: 3

Pre-requisite: None Semester: 1

Course Description

This is an introductory course on Information and Communication

Technologies. Topics include ICT terminologies, hardware and software
components, the internet and World Wide Web, and ICT based
applications.
After completing this course, a student will be able to:
 Understand different terms associated with ICT
 Identify various components of a computer system
 Identify the various categories of software and their usage
 Define the basic terms associated with communications and
networking
 Understand different terms associated with the Internet and World
Wide Web.
 Use various web tools including Web Browsers, E-mail clients and
search utilities.
 Use text processing, spreadsheets and presentation tools
 Understand the enabling/pervasive features of ICT
Course Contents

Basic Definitions & Concepts

Hardware: Computer Systems & Components
Storage Devices, Number Systems
Software: Operating Systems, Programming and Application Software
Introduction to Programming, Databases and Information Systems
Networks
Data Communication
The Internet, Browsers and Search Engines
The Internet: Email, Collaborative Computing and Social Networking
The Internet: E-Commerce
IT Security and other issues
Project Week
Review Week

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Text Books/Reference Books
1. Introduction to Computers by Peter Norton, 6th International
Edition, McGraw-Hill
2. Using Information Technology: A Practical Introduction to Computer
& Communications by Williams Sawyer, 6th Edition, McGraw-Hill
3. Computers, Communications & information: A user's introduction by
Sarah E. Hutchinson, Stacey C. Swayer
4. Fundamentals of Information Technology by Alexis Leon, Mathews
Leon, Leon Press.

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 RECOMMENDATIONS
1. There is a need to encourage public and private
universities/institutes to develop expertise in bioinformatics at
their respective campuses.
2. HEC should provide sufficient funds and grants on priority basis
in this field. More emphasis should be given to
universities/institutes located in developing areas of Pakistan.
3. Both undergraduate and postgraduate courses in bioinformatics
should be included in teaching curriculum of relevant disciplines
of public and private sector universities and degree awarding
institutes.
4. Future emphasis should be on graduate degree program in
bioinformatics instead of undergraduate.
5. The option for computer sciences and biology should not be there
at matric level. Instead both subjects should be compulsory for
science students.
6. At intermediate level, the distinction between pre-medical and pre-
engineering groups should be strongly discouraged.
7. HEC should facilitate a survey to identify the opportunities
available to and challenges faced by bioinformatics graduates.
8. To promote awareness among students, scientific community and
industry, series of seminars and workshops should be organized
on regular basis.
9. There should be a strong link between academia and industry for
the absorption of bioinformatics graduates.

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