CURRICULUM

OF

BIOINFORMATICS
BS
MS
(Revised 2011)

HIG HER ISSION

EDUC ATIO N CO MM

HIGHER EDUCATION COMMISSION

ISLAMABAD

1
 CURRICULUM DIVISION, HEC

Prof. Dr. Syed Sohail H. Naqvi Executive Director

Prof. Dr. Altaf Ali G. Shaikh Member (Acad)

Mr. Muhammad Javed Khan Adviser (Academic)

Mr. Malik Arshad Mahmood Director (Curri)

Dr. M. Tahir Ali Shah Deputy Director (Curri)

Mr. Abdul Fatah Bhatti Asstt. Director (Curri)

Composed by: Mr. Zulfiqar Ali, HEC, Islamabad

2
 CONTENTS
I. Preface 4
II. Curriculum Development Chart 5

III. Curriculum for BS

1. Introduction 6
2. Mission Statement 8
3. Programme Objectives 8
4. Learning Outcomes 8
5. Admission requirements 8
6. Standardized Format 10
7. Layout 11
8. Scheme of Studies 12
9. Detail of Courses 14
10.List of Recommended Books 35

IV. Curriculum for MS

1. Introduction 39
2. General objectives 39
3. Learning outcomes 39
4. Admission requirements 39
5. Scheme of Studies 40
6. Detail of Courses 41
7. List of Recommended Books 44
V. Annexure A – C 47
VI. Recommendations 55

3
 PREFACE
The curriculum of subject is described as a throbbing pulse of a nation. By viewing
curriculum one can judge the stage of development and its pace of socio-economic
development of a nation. With the advent of new technology, the world has turned
into a global village. In view of tremendous research taking place world over new
ideas and information pours in like of a stream of fresh water, making it imperative
to update the curricula after regular intervals, for introducing latest development
and innovation in the relevant field of knowledge.
In exercise of the powers conferred under Section 3, Sub-Section 2 (ii) of Act of
Parliament No. X of 1976 titled “Supervision of Curricula and Textbooks and
Maintenance of Standard of Education” the erstwhile University Grants
Commission was designated as competent authority to develop review and revise
curricula beyond Class-XII. With the repeal of UGC Act, the same function was
assigned to the Higher Education Commission under its Ordinance of 2002 Section
10 Sub-Section 1 (v).
In compliance with the above provisions, the HEC undertakes revamping and
refurbishing of curricula after regular intervals in a democratic manner involving
universities/DAIs, research and development institutions and local Chamber of
Commerce and Industry. The intellectual inputs by expatriate Pakistanis working
in universities and R&D institutions of technically advanced countries are also
invited to contribute and their views are incorporated where considered appropriate
by the National Curriculum Revision Committee (NCRC).
To bring international compatibility to qualifications held from Pakistani
universities/DAIs for promotion of students mobility and job seekers around the
globe, a Committee comprising of Conveners of the National Curriculum Revision
Committee of HEC met in 2009 and developed a unified template for standardized
4-years/8-semesters BS degree programs. This unified template was aimed to
inculcate broader base of knowledge in the subjects like English, Sociology,
Philosophy, Economics etc. in addition to major discipline of study. The Bachelor
(BS) degree course requires to be completed in 4-years/8-semesters, and shall
require qualifying of 130-140 credit hours of which 77% of the curriculum will
constitute discipline specific and remaining 23% will comprise compulsory and
general courses.
In line with above, NCRC comprising senior university faculty and experts from
various stakeholders and the respective accreditation councils has finalized the
curriculum for B.S 4-years and M.S 2-years in Bioinformatics. The same is being
recommended for adoption by the universities/DAIs channelizing through relevant
statutory bodies of the universities.

MUHAMMAD JAVED KHAN

Adviser (Academics)
June, 2011

4
 CURRICULUM DEVELOPMENT
STAGE-I STAGE-II STAGE-III STAGE-IV

CURRI. UNDER CURRI. IN DRAFT FINAL STAGE FOLLOW UP

CONSIDERATION STAGE

COLLECTION OF
EXP
NOMINATION APPRAISAL OF 1ST PREP. OF FINAL QUESTIONNAIRE
UNI, R&D, DRAFT BY EXP CURRI.
INDUSTRY &
COUNCILS

CONS. OF NCRC. FINALIZATION OF COMMENTS

DRAFT BY NCRC
PRINTING OF
CURRI.

PREP. OF DRAFT REVIEW

BY NCRC
IMPLE. OF
CURRI.

Abbreviations Used: ORIENTATION BACK TO

COURSES BY
NCRC. National Curriculum Revision Committee LI, HEC STAGE-I
VCC. Vice-Chancellor’s Committee
EXP. Experts
COL. Colleges
UNI. Universities
PREP. Preparation
REC. Recommendations
LI Learning Innovation
R&D Research & Development Organization

INTRODUCTION
HECHigher Education Commission

5
INTRODUCTION

The final meeting of the National Curriculum Revision Committee in

Bioinformatics was held on May 17-19, 2011 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. Prof. Dr. Gulzar Ahmed Niazi Convener

HEC Foreign Professor,
Centre of Excellence in Molecular Biology,
78 West Canal Bank Road,
Thokar Niazbaig,
Lahore

2. Prof. Dr. Masroor Ellahi Babar Member

Director,
Institute of Biochemistry and Biotechnology
University of Veterinary and Animal Sciences,
Lahore.

3. Prof. Dr. Mohammad Inayatullah Khan Babar Member

Professor, Electrical Engineering and
Chairman, Computer Science and IT Department,
University of Engineering and Technology,
Peshawar.

4. Prof. Dr. Shamshad Zarina Member

Director,
National Center for Proteomics,
University of Karachi,
Karachi.

5. Prof. Dr. Ahmad Saeed Member

Dean,
Faculty of Biological Sciences,
University of Science and Technology,
Bannu.

6. Prof. Dr. Fida Mohammad Member

Chairman,
Department of Plant Breeding and Genetics,
University of Agricultural,
Peshawar, Khyber Pakhtunkhwa

6
7. Dr. Rani Faryal Member
Associate Professor,
Department of Biosciences,
COMSATS Institute of Information Technology (CIIT),
Islamabad.

8. Dr. Imran Sajid Member

Assistant Professor,
Department of Microbiology and Molecular Genetics,
University of the Punjab,
Lahore.

9. Dr. Nazeer Ahmed Member

Assistant Professor,
Faculty of Life Sciences & Informatics,
Balochistan University of Information Technology,
Engineering and Management Sciences, Quetta

10. Dr. Muhammad Asif Member

Senior Scientist,
National Institute for Biotechnology and
Genetic Engineering,
Faisalabad.

11. Mrs. Afshan Kaleem Member

Lecturer,
Department of Zoology,
Lahore College for Women University (LCWU),
Lahore.

12. Prof. Dr. Syed Afaq Hussain Member

Faculty of Engineering and Applied Sciences,
Ripah International University,
Islamabad.

13. Prof. Dr. Zubair A. Shaikh Member

Associate Dean,
Faculty of Computer Science,
National University of Computer and
Emerging Sciences,
Karachi.

14. Dr. Syed Sikander Azam Member

Assistant Professor,
Department of Biotechnology and Bioinformatics,
Quaid-i-Azam University, Islamabad
7
15. Dr. Muhammad Nauman Aftab Secretary
Assistant Professor,
Institute of Industrial Biotechnology,
Government College University,
Lahore.

Mission Statement:
To train the next generation professionals to gain advanced knowledge in
Bioinformatics that is required to design and implement novel methods
which can be useful to define and solve problems with emphasis on
acquisition, representation, retrieval, visualization and analysis of biological
data.

Programme Objectives:
At the end of four years BS programme, the graduates should be able to
understand:
1. Gene and protein sequence acquisition, storage, retrieval and
analysis
2. Protein structure and function relationship using computational tools
3. Development of computational applications for processing of
biological data
4. Modeling and simulation of biological systems.

Learning outcomes:
At the completion of this programme, students are expected to know
the relationship between genes and proteins and use of computers in
handling flood of biological data which started with the completion of
Human Genome project. Bioinformatics is now an established
discipline in the main stream of Biology and is a key to unlock the
information coded in genome, transcriptome and proteome. Being a
multidisciplinary field, it has diversified applications in domains like
drug designing, agriculture biotechnology and system biology.

Admission Requirements

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

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

Course and Credit Requirements:

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

Evaluation:
For uniformity in the evaluation system, NCRC recommends that the
minimum CGPA required for award of degree is 2.5 out of 4.0 at
undergraduate level subject to meet all requirements of the university.

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

Credit
No. of courses
Sr. Categories Hours
Min – Max
Min – Max
1. Compulsory Requirement (No Choice) 9–9 25 – 25
2. General Courses to be chosen from other 7–8 21 – 24
departments
3. Discipline Specific Foundation Courses 9 – 10 30 – 33
4. Major Courses including research project / 11 – 13 36 – 42
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 to be

Discipline Specific
Requirements (the student chosen from other
Foundation Courses
has no choice) departments

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 3 1. Programming 4 1. Linear Algebra and 3
Comprehension Fundamentals Differential
2. Islamic Studies 4 2. Data Structure 4 Equations
and Pak Studies and Algorithms 2. Essentials of 3
3. Basic I 4 3. Object oriented 4 Genetics
(Biology/Mathem programming 3. Biostatistics 3
atics) 4. Ethical and legal 2 4. Bioinformatics I 3
4. Basic II 4 issues in 5. Bioinformatics II 4
(Chemistry/ Bioinformatics 6. Biochemistry I 4
Computer 3 5. Discrete 3 7. Biochemistry II 4
fundamentals) Structures 8. Molecular Biology 4
5. Communication 4 6. Database System 4 9. Research
Skills 7. Modeling and 3 Methodology 2
6. Basic Cell 3 Simulation
Biology 8. Technical Report 3
7. Basic Calculus Writing
25 27 30

Major courses including research

project/internship Elective Courses 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 4
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 Engineering 3 Elective IV 4
8.Special topics in Bioinformatics 3

Research Project 6
32 14

11
 Scheme of Studies for BS (Bioinformatics)
Semester 1 Credit hours
Course Code
Courses Lectures Lab
Hum-101 English Comprehension 3 0
Hum-102 Islamic Studies and Pakistan Studies 2+2 0
Bio-101/MTH-101 Basic I (Biology/Mathematics)* 3 1
Basic II (Chemistry/ Computer
Bio-102/CS101 3 1
fundamentals)*
*Deficiency courses
Total Credit Hours 13 2

Semester 2 Credit hours

Course Code
Course Lectures Lab
Hum-103 Communication skills 3 0

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 Hours 15 3

Semester 3 Credit hours

Course Code
Courses Lectures Lab
Hum-201 Technical Report Writing 3 0
MTH-201 Linear Algebra and Differential Equations 3 0
Bio-201 Essentials of Genetics 2 1
Bio-202 Molecular Biology 3 1
CS-201 Data Structure and Algorithms 3 1
Total Credit Hours 14 3

Semester 4 Credit hours

Course Code
Courses Lectures Lab
BI-201 Bioinformatics I 2 1

Bio-203 Biostatistics 3 0
Bio-204 Biochemistry II 3 1
BI-202 Ethical and Legal Issues in Bioinformatics 2 0
CS-202 Object Oriented Programming 3 1
Total Credit Hours 13 3

12
 Semester 5 Credit hours
Course Code
Courses Lectures Lab
CS-301 Discrete Structures 3 0
Bio-301 Research Methodology 2 0
CS-302 Database Management Systems 3 1
BI-301 Bioinformatics II 3 1
Bio-302 Genomics 3 0
Total Credit Hours 14 2

Semester 6 Credit hours

Course Code
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
*** Elective I 3 0
Total Credit Hours 14 3

Semester 7 Credit hours

Course Code
Courses Lectures Lab
BI-401 Bioinformatics Computing II 3 0
CS-401 Artificial Intelligence 3 0
*** Elective II 3 1
*** Elective III 3 1
Research Project 0 3
Total Credit Hours 12 5

Semester 8 Credit hours

Course Code
Courses Lectures Lab
BI-402 Bioinformatics Software Engineering 2 1
BI-403 Special Topics in Bioinformatics 3 0
*** Elective IV 3 1
Research Project 0 3

Total Credit Hours 8 5

Grand Total Credit Hours 103 26

13
 DETAIL OF COURSES
Semester-I
Hum-101 English Comprehension 3+0

Annexure - A
Hum-102 Pakistan Studies 2+2

Annexure - B

Hum-102 Islamic Studies 2+2

Annexure - C

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.
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. “Modular Math” by Heinemann.
2. “Core Mathematics” by Keith Pledger.

Bio-101 Basic Biology 3+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 times scale, branches
of biology, prokaryotic and eukaryotic cells, viruses, structure of viruses and
14
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
3. Fogiel M. The Biology Problem Solver. Published by Research &
Education Association.

Bio-102 Chemistry 3+1

Prerequisite: None
Specific objectives of the course:
This is a deficiency course and 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.
4. Philips / Mathews. Advanced Chemistry. Physical and Industrial,
Cambridge University Press.

15
CS101 Computer Fundamentals 3+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 browser including open source browsers, Introduction to various
operating systems.

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

Semester-II
Hum-103 Communication Skills 3+0
ANNEXURE - A

Bio-103 Basic Cell Biology 3+1

Prerequisite: None
Specific objectives of the course:
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
16
membrane, structure and transport properties, fluid mosaic model
organelles, mitochondria, endoplasmic reticulum, golgi bodies, plastids,
lysosmes, peroxisomes, cell internal structure, cytoskeleton, microtubules
microfilaments, intermediate filaments, structure of chromosomes, 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. Academic Press London, Methods in Cell Biology Lowery
Sekivetz. Cell Structure and Function. John Willey and Sons
Publication.
2. Gerald Carp. Cell Biology.
3. Lodish H. Molecular Cell Biology. Media Connected
4. Lewin B. Genes VIII. Pearson/Prentice Hall.
5. Robertes, Cell and Molecular Biology.

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 computers and programming, overview of language for e.g. C
language, basics of structured and modular programming, basic algorithms
and problem solving, development of basic algorithms, analyzing problem,
designing solution, testing designed solution, fundamental programming
constructs, translation of algorithms to programs, data types, control
structures, functions, arrays, records, files, testing programs.

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.

17
Recommended Books:
Latest editions of following books
1. R. P. Halpern, “C for Yourself – Learning C Using Experiments”, Oxford
University Press.
2. “Using Information Technology”, William.
3. “Computer Organization & Architecture”, William.

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. Calculus by Thomas Finney.
2. Brief Calculus and its applications by Doniel D. Benice.
3. Applied Calculus by Raymond A. Barnett.
4. Calculus by Gerald L. Bradley.

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, nucleic acid as genetic
material, lipids, bilayers and membranes, saccharide chemistry, mono, di
and polysaccharides, amino acids the building block of proteins, levels of

18
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. Pub
Freeman and Company.
2. Conn and Stumpf. Outlines of Biochemistry. John Willey and Sons Pub.
3. Devlin and Thomas. Text book of Biochemistry with Clinical
Correlations.
4. Campbell M. and Shawn F. Biochemistry.
5. Voet and Voet Biochemistry John Wiley and Sons.

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

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, determinants,
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 equations,
homogeneous equations, equations linear equations, Bernoulli equations,
applications of first order differential equations, Higher order linear
differential equations, homogeneous linear equations, solution of higher
order differential equation.

19
Recommended Books:
Latest editions of following books
1. Linear Algebra, David C. Lay, Pearson Addison Wesley.
2. Advanced Engineering Mathematics, Michael Greenberg.
3. Advanced Engineering Mathematics,7/e, Erwin Kreyszig. John Wiley &
Sons.

Bio-201 Essentials of Genetics 2+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 molecular techniques used in gene analysis.

Course Outline:
Genetics 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, chromosomal aberrations, gene mutation, genetic
disorders; DNA polymorphism.

Lab Contents:
Chromosome staining, Problems solving related to Mendelian inheritance – DNA
extraction; PCR, Southern blotting techniques etc.

Recommended Books:
Latest editions of following books
1. Strickburger, Principles of Genetics.
2. Gardner, Principles of Genetics, UHR.
3. Griffith et al., An Introduction to Genetics analysis, W. H. Freeman.
4. William S. Klug, Michael Cummings. Essentials of Genetics 5th 2005.
Pearson/Prentice Hall.
5. Ricky Lewis: Human Genetics. McGraw Hill Sixth ed 2005.

Bio-202 Molecular Biology 3+1

Prerequisite: Biochemistry 1
Specific objectives of the course:
This course is to teach the students about organization of genetic material,
and its role in gene expression.
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,
transcription, regulatory elements, regulation of gene expression. RNA
20
processing, splicing and editing, translation and post-translational
modifications, control of gene expression in prokaryotes and eukaryotes.
Introduction about plasmids and vectors.

Lab Outline:
Isolation of plasmid and chromosomal DNA from bacteria and yeast. PCR,
gel electrophoresis, comparing plasmids of different molecular weights
using molecular weight markers, transformation in E. coli.

Recommended Books:
Latest editions of following books
1. Robert Weaver. Molecular Biology. McGraw Hill.
2. Benjamin Lewin. Genes VIII. Pearson/Prentice Hall.
3. Gerald Carp. Cell and Molecular Biology concepts and Experiments,
John Willey and Sons Publications.
4. Brown T. A. Molecular Biology Lab .FEX. Academic Press Publication.

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, definitions, overview of
algorithms, basics of array data structure, basic data structure functions,
store, retrieve and search, idea of big O notation, uses of arrays, concept of
binary search and linear search, simple sorting techniques. Stacks and
queues, overview of stacks, queues, sorting techniques, selection sort,
insertion sort and bubble sort. Comparison of sorting techniques and their
applications, 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. Merge
Sort.

Lab Outline:
Implementation of Basic Arrays, storing and Searching data in Arrays,
implementation of Linear Search, implementation of Binary Search in
Arrays, Using Bubble Sort, Selection Sort and Insertion on sample data,
comparison study of simple sorting techniques, implementing Stacks and
Queues, using priority queues for special cases, implementation of different
types of Linked Lists for various applications.

21
Recommended Books:
Latest editions of following books
1. Data Structures and Algorithms By Robert Lafore,
2. An introduction to Bioinformatics Algorithms. Neil C. Jones, Pavel
Persner
3. Gary Benson and Rodric Page. Algorithms in Bioinformatics Singapore,
New York.

Semester-IV
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, significance of scoring,
gap penalties, online tools BLAST, BLAT and FASTA.

Lab Outline:
Accessing ncbi databases, sequence databases, Genbank, EMBL, SWISS-
PROT Accessing structure database PDB, SCOP and CATH, Expasy
server, using online alignment tools for pair wise and multiple sequence
alignment, phylogenetic analysis by ClustalW, using BLAST and FASTA.

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.

22
Bio-203 Bio-statistics 2+1
Prerequisite: None
Specific objectives of the course:
This course introduces the concepts of statistical methods used in analyzing
biological data.

Course Outline:
Frequency distribution and probabilities, measure of central tendencies and
dispersion, standard distributions and tests of significance. Test of
independence or association, method related to one and two means,
variance and covariance, heritability and its uses, Bayesian statistics,
analysis of variance (ANOVA), and regression analysis, use of basic
software.

Lab Outline:
Collection of data, acquisition of random samples, graphical/tabular
representation of data, MS-Excel, SPSS, 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.
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.

Bio-204 Biochemistry II 3+1

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
transport chain, and oxidative phosphorylation, lipid metabolism, β-
oxidation, ketone bodies formation and biosynthesis of triglyceride, protein
metabolism, oxidative deamination and decarboxylation, transamination,

23
urea cycle and amino acids metabolism, nucleic acid metabolism, break
down and synthesis of pure and pyramidine bases.
Lab Outline:
Estimation of normal and abnormal constituents in urine including glucose,
albumin, uric acid, chloride and phosphate, Kidney Function test, Liver
function test.

Recommended Books:
Latest editions of following books
1. Nelson and Michel. LEHINGER Principles of Biochemistry. Pub
Freedman and Company.
2. Conn and Stumpf. Outlines of Biochemistry. John Willey and Sons Pub.
3. Devlin and Thomas. Text book of Biochemistry with Clinical
Correlations.
4. Campbell M and Shawn F. Biochemistry. Thomas Book Pub.

BI-202 Ethical & Legal Issues in Bioinformatics 3+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. Legal and Ethical Issues in Acquisitions. Edited by Katina Strauch. A
Bruce Strauch.
2. Computer Ethics: Cautionary Tales and Ethical Dilemmas in Computing
By Tom Forester, Perry Morrison.
3. Public Management Information Systems. By Bruce A Rocheleau.
4. Security in Computing. By Willis H. Ware, Charles P. Pfleeger, Shari
Lawrence Pfleeger.
5. Computer Ethics: Cautionary Tales and Ethical Dilemmas in Computing
By Tom Forester, Perry Morrison.

24
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,
polymorphism, encapsulation, data hiding. Java introduction, byte code,
architectural neutral language, simple programs, compiling and execution,
dynamic initializing, scope and lifetime of variables, type conversion and
casting, the type promotion rules, arrays, string data type, arithmetic
operators, Bit wise operators, relational operators, boolean logical
operators. 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, concatenating strings, string
constructors, string comparing, string methods, string concatenating, string
classes, string methods, Friend function, virtual functions, inline functions,
Abstract classes, Interfaces.

Lab Outline:
Programs formulation according to the Course outlines.

Recommended Book:
Latest editions of following books
1. Complete Reference Java by “Herbert Schildt”.
2. Object Oriented Programming by “Robert Lafore”, JAVA How To
Program Third edition by Deitel & Deitel.

25
 Semester-V
CS-301 Discrete Structures 3+0
Prerequisite: Basic Calculus
Specific objectives of the course:
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:
1. Kenneth H. Rosen, Discrete Mathematics and Its Applications, 6th
edition, 2006, McGraw Hill Book Co.
2. Richard Johnsonbaugh, Discrete Mathematics, 7th edition, 2008, Prentice
Hall Publishers.
3. Kolman, Busby & Ross, Discrete Mathematical Structures, 4th edition,
2000, Prentice-Hall Publishers.
4. Ralph P. Grimaldi, Discrete and Combinatorial Mathematics: An Applied
Introduction, Addison-Wesley Pub. Co., 1985.

Bio-301 Research Methodology 2+0

Prerequisite: Biochemistry 101

Specific Objectives of course:
The basic concept of this course is to provide knowledge about how to
design a research project and present it a professional manner.

Course Outline:
The main objectives of this course are: to understand the concepts of basic
and applied research and their usefulness, formulation of research
objectives, literature search, study designing, collection & compilation of
research data, biostatistical methods used in data analysis, development of
writing skills, use of reference manager software (Endnote).

Recommended Books:
Latest texts related to research methodology.

26
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, introduction to query processing and optimization,
introduction to concurrency and recovery, front-end and back-end
databases.

Lab Outline:
Structures Query Language commands, creating and populating tables,
design of simple databases, database normalization techniques, query
optimization, indexing techniques, partial and full recovery techniques,
developing GUI techniques, implementation of database security
mechanisms.

Recommended Books:
Latest editions of following books
1. Data Structures and Algorithms By Robert Lafore,
2. An introduction to Bioinformatics Algorithms. Neil C. Jones, Pavel
A.Persner
3. Gary Benson and Rodric Page, Algorithms in Bioinformatics Singapore,
New York.

BI-301 Bioinformatics-II 3+1

Prerequisite: 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,
hydrogen bonding, PTMs of proteins, Chou Fasman, PHD and PSIPred,
neural network, X-ray crystallography, NMR, ab initio, threading and
homology modeling, structure prediction evaluation, protein fold
identification using Pfam (A & B) and other tools.
27
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. Bioinformatics: Methods and Applications: Genomics, Proteomics and Drug
Discovery.PHI Learning Pvt. Ltd.
3. Bioinformatics and drug discovery Humana Press.

Bio-302 Genomics 3+0

Prerequisite: Biochemistry I/Molecular Biology
Specific objectives of the course:
Students will be trained to grasp knowledge about structural and functional
genomics and their applications.

Course Outline:
Introduction to genomics, genome anatomy, gene expression, genome
evolution, genome mapping, DNA markers, linkage analysis. QTL,
mutations, Human Genome Project, Microarray, Genevestigator, Non-
coding RNAs and their regulation, siRNA.

Recommended Books:
Latest editions of following books
1. David Mount Bioinformatics Sequences and Genome Analysis. CSB
publishers and distributors.
2. Bioinfomatics: Sequence and Genome: Analysis, CBS publisher &
distributors New Delhi Bangalore by Spring Harbour laboratory press.

28
 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, data,
sequence and structure visualization, data mining methods and technology,
pattern recognition and discovery, pattern matching, dot matrix analysis,
substitution matrices, dynamic programming, Scripting.

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. “Bioinformatics Computing” Bryan Borgeron, Pearson Education.
2. “Methods in Biotechnology and Bioengineering”, Vyas S.P. and Kohli
D.V.

CS-303 Modeling & Simulation 2+1

Prerequisite: Programming Fundamentals

Specific objectives of the course:
This course emphasizes the development of modeling and simulation concepts
and analysis skills necessary to design, program, implement, and use computers.

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
29
high assurance systems, fault-tolerant techniques, software reliability
modeling, adaptive modeling, agent based modeling.

Lab Outline:
Introduction to modeling techniques using simulation tools like MATLAB
toolbox for various performance modeling and evaluation of high parallel
systems. Using toolbox for analysis and study various faulty tolerant
techniques, study queuing techniques.

Recommended Books:
Latest editions of following books
1. Complete Reference Java 2 by “Herbert Schildt”.
2. Object Oriented Programming by “Robert Lafore”, JAVA How to
Program by Deitel & Deitel.
3. Computer Graphics (C Version), by Donald Hearn and M. Pauline
Baker (Prentice Hall).
4. Flash Professional 8, by M. Waqar Aziz.

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 to proteomics and protein chemistry, techniques in proteomics,
iso-electric focusing, one dimensional and two dimensional electrophoresis
and analysis, Mass spectrometry, bioinformatics tools for analysis of
proteomics data, proteomics databases, MS data analysis, peptide mass
and fragment fingerprinting, protein identification, post-translational
modification, protein-protein interaction, applications of proteomics.

Recommended Books:
Latest editions of following books
1. Richerd Simpson J. Purifying Proteins for Proteomics (a laboratory
manual) Cord Spring Harbor Laboratory Press.
2. Rastogi et al. Bioinformatics methods and applications. Genomics,
Proteomics and Drug discovery.

30
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:
Graphics hardware, fundamental algorithms, applications of graphics,
interactive graphics programming, graph plotting, windows, clipping and
segmentation, programming raster display systems, panning 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. “Computer Graphics”, by Donald Hearn and M. Pauline Baker, Prentice
Hall.

Elective-I 3+0

Prerequisite: None
Course Outline:
To be chosen from the list of electives.

31
 Semester-VII
BI-401 Bioinformatics Computing-II 3+1
Prerequisite: Bioinformatics Computing- I
Specific objectives of the course:
This course introduces advanced concepts of artificial intelligence, neural
networks and pattern recognition for solving bioinformatics problems.

Course Outline:
This course emphasized on cellular, tissue, organ and system modeling,
simulation, analysis using an object oriented programming languages, 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. “Bioinformatics Concepts, Skills and Applications” Namita M, CSB
Publishers.
2. “Bioinformatics Managing Scientific Data”, Lacroix Zor, Morgan
Kauffmann Publishers.

CS402 Artificial Intelligence 3+0

Prerequisite: Programming Fundamentals

Specific objectives of the course:
This course introduces the techniques of artificial intelligence for solving
advanced problems using computers.

Course Outline:
Introduction to artificial intelligence, applications, problem solving, classical
approach, generate and test, problem presentation, searching, tree and
graph terminology, searching, branch and bound, improvements in branch
and bound, common lisp. AI classical systems: general problem solver,
rules, simple search, means-ends analysis. ELIZA, pattern matching, rule
based translators, Knowledge Representation: natural language, rules,
productions, predicate logic, semantic networks, frames, objects, scripts, hill
climbing, min-max search, A* search, symbolic mathematics, solving

32
algebra problems, Logic Programming: Resolution, unification, horn-clause
logic, prolog.

Recommended Books:
1. “Artificial Intelligence” by Ela Kumar, IK International.
2. “Artificial Intelligence: A Modern Approach”, Stuart Russell and Peter
Norvig.

Elective-II 3+1
Prerequisite: None
Course Outline:
To be chosen from the list of electives

Elective-III 3+1
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
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:
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.

33
Lab Outline:
Introduction to software development techniques, implementation of various
software models using simple case studies, introduction to HTML, XML, use
of front end application tool.

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. Students are
required to make presentation of the selected topics as determined by the
faculty members / Coordinator conducting Bioinformatics Programme.

Recommended Books:
Latest editions of following books
1. Namita M. Bioinformatics concepts, skills and applications, CSB
publishers and distributors.
2. Lacroix Zor. Bioinformatics managing scientific data, Morgan Kaufmann
publishers.
3. Higgs Paul. G. Bioinformatics and Molecular evolution, Black well
Publishing.
4. Schulze. S. Kremer. Advances in molecular Bioinformatics, Netherland
Printing.

Elective-IV 3+1
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.

34
List of Electives
1. Enzyme Kinetics
2. Microarray Data Analysis
3. Human Computer Interaction
4. Nanotechnology
5. Environmental Biotechnology
6. Special Topics in Biochemistry
7. Immuno-Informatics
8. Microbial genomics and proteomics
9. Protein-protein interaction
10. Digital Image Processing
11. Gene Mining
12. Pattern recognition and matching
13. Biophysics
14. Modern programming languages
15. Medical Image processing
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.
35
Instant Notes: Molecular Biology
P C Turner
Viva Books Pvt. Ltd.

Molecular Cloning: A laboratory manual

Sambrook
Cold Dpring 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.

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.

36
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.

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.

37
Computational Intelligence in Bioinformatics
Árpád Kelemen, Ajith Abraham, Yuehui Chen
Springer.

Bioinformatics and the Cell: Modern Computational Approaches in

Genomics, Proteomics and Transcriptomics
Xuhua Xia
Springer.

Bioinformatics for Dummies 2nd Edition

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.

38
 MASTER OF SCIENCE (MS) IN
BIOINFORMATICS
Introduction:
The purpose of MS degree programme 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.
Exponential growth and complexity of biological data can be translated
effectively into knowledge by the use of computer based approaches.

General objectives
The enormous influx of biological data can only be handled with better and
faster computational approaches together with advanced knowledge in
functional genomics and proteomics. Advanced concepts, structures,
algorithms and tools are required for effective processing and analysis.
Specialized courses in molecular biology, bioinformatics and computation
are needed to achieve these objectives.

Learning Outcomes
After completion of MS program in bioinformatics, the graduates will be able
to
 answer fundamental questions about molecular evolution, biological
functions and control of biological systems.
 use bioinformatics skills predicting functions from structures,
networks, complexes, transcriptome and proteome data.
 design novel genes/proteins and small molecules with specific
functions.
 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. 2nd Division or GPA 2.50 or above.
3. Subject GRE/NTS or in-house written test.
4. Interview.

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).
39
 Scheme of Studies
for MS Programme in Bioinformatics

Semester 1 Semester 2
Course (Credit hours) Course (Credit hours)
Code Credit Code Lectures
Courses Course
hours Lab
3
BI-601 Advanced Bioinformatics Elective I 3
Advanced Molecular
Bio-601 3 Elective II 3
Biology
CS-601 Information Processing 3 Elective III 3
Advanced Computing
BI-602 3 Elective IV 3
Approaches
Total Credit Hours 12 Total Credit Hours 12
Semester 3 & 4
(Credit hours)
Research/Thesis 6
Grand Total Credit Hours 30

40
 DETAIL OF COURSES
SEMESTER-I
BI-601 Advanced Bioinformatics 3

Prerequisite: None

Specific objectives of the course:

The objective of this course is to train students to develop methods and
understanding for integration and analysis of biological data.

Course Outline:
Functional genomics, comparative genomics, DNA microarray, computer
aided drug designing (ligand and receptor based), molecular docking,
protein-protein interaction network and databases, molecular dynamics
simulation, biological networks, transcriptome, metabolomics

Recommended Books:
Latest editions of following books
1. Schulze S. Kremer. Latest Ed. Advances in Molecular Bioinformatics.
Netherland Printing.
2. S. C. Rastogi, Namita Mendiratta, Parag Rastogi Bioinformatics: Methods
and Applications: Genomics, Proteomics and Drug Discovery, PHI Learning
Pvt. Ltd.

Bio-601 Advanced Molecular Biology 3

Prerequisite: None
Specific objectives of the course:
The students will learn most recent advances in molecular biology and
molecular cloning techniques.

Course outline: Molecular nature of gene’ methods of molecular biology;

transcription in prokaryotes and eukaryotes; post transcriptional events;
translation; DNA replication, recombination and transposition; homologous;
homologous recombination. Genomics and proteomics etc.

Recommended Books:
Latest editions of following books
1. Wisden and Richered. Advanced Molecular Biology. Viva Book Private
Ltd.
2. Benjamin Lewin: GENES. Pearson/Prentice Hall.
3. Robert Weaver. Molecular Biology, McGraw Hill.

41
CS-601 Information Processing 3

Prerequisite: None
Specific objectives of the course:
To introduce the principles of data analysis, association, classification,
matching and their applications to bioinformatics.

Course Outline:
Classification, Bayesian networks, nearest neighbour and k-means
clustering, decision tree learning, clustering and data/dimensionality
reduction, sampling, feature selection and feature transformation
approaches, machine learning for user modeling, data warehousing,
advanced query processing, data mining, association analysis, sequence
mining, introduction to web mining, content, structure and usage mining.

Recommended Books:
Latest editions of following books
1. Christopher D. Manning, Prabhakar Raghavan and Hinrich Schütze.
2. “Introduction to Information Retrieval”, Cambridge University Press.
3. Ricardo Baeza-Yates and Berthier Ribeiro-Neto, “Modern Information
Retrieval” ACM Press.
4. David A. Grossman and Ophir Frieder, “Information Retrieval:
Algorithms and Heuristics”, Springer.

BI-602 Advanced Computing Approaches 3

Prerequisite: None
Specific objectives of the course:
This course provides knowledge on advanced principles and applications of
biological data analysis and processing.

Course Outline:
Introduction to microarray experiments: principles and experimental design,
biomedical image analysis (2D gel, DNA and protein chips), advanced
analysis of microarray data, exploratory data analysis and visualization,
cluster analysis: hierarchical clustering, k-means, gene shaving,
correspondence analysis, multi-dimensional scaling, neural networks,
unsupervised and supervised learning: discriminant analysis, error-rate
concepts, tree-based methods, genetic algorithms, applications to genetic
networks, genetic modeling.
Recommended Books:
Latest editions of following books
1. Image processing using Matlab, RC Gonzales.
2. Pattern classification by Huda & Hart.

42
 SEMESTER-II
In Semester-II, four subjects will be selected from the following list of
elective subjects:

LIST OF ELECTIVES
1. Computer aided drug designing
2. Advanced biotechnology
3. System biology
4. Programming for Bioinformatics
5. Data warehousing and data mining
6. Molecular dynamics simulation
7. Intelligent systems
8. DNA microarrays and integrative genetics
9. Functional genomics
10. Epidemiology
11. Advance topics in information systems
12. Neural Computing
13. Research Method in Biological Sciences
14. Advanced Algorithms
15. Current trends in bioinformatics
16. Gene regulation and expression
17. Principles and application of proteomics
18. Medical genetics
19. Epigenetics

Note: In addition to the above the universities can offer any elective course
subject to the availability of resources

SEMESTER-III and IV
Research Thesis (6 Credit Hours):
Research Project:
1. Duration of the research project will be at least one full year. 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.

43
 Recommended Text Books For
MS Bioinformatics Programme
1. Bioinformatics: sequence and Genome Analysis, David W. Mount.
2. Bioinformatics: A practice Guide to Analysis of Gene and Proteins
Andreas Baxevnis, B. F. Francis Ouellet.
3. Developing Bioinformatics Computer Skills, Cynthia Gibbs, Per
Jambeck.
4. Discovering Genomics, Proteins and Bioinformatics, A. Makom
Cambell, Laurie J. Heyer.
5. Microarray Bioinformatics, Dov Stekel, Ed Southern.
6. Introduction to Bioinformatics, Arthur M. Lesk.
7. Bioinformatics Computing, Bryan P. Bergeron.
8. A Primer of Genome Sequencing, Greg Gibson.
9. Instant Notes on Bioinformatics, Howard J. Parish.
10. Bioinformatics and functional Genomics, Donis Marshall, Jonathan
Persner.
11. Bioinformatics: The Machine learning approach, Pierre Baldi, Sren
Brunak, Soren Brunak.
12. An introduction to Bioinformatics, Algorithims Neil C. Jones, Pavel A.
Persner.
13. Essentials of Genomics and Bioinformatics, C.W Sensen.
14. Bioinformatics, Biocomputing and Perl. An introduction to
Bioinformatics Computing Skills and Practice Michael Moorhouse, Paul
Berry.
15. Statistical Methods in Bioinformatics Warren Ewens, Gregory Grant.
16. Microarray for An Integrative Genomics S. Isaac, J-Atul, Alvin Khd
17. Bioinformatics; Sequence and Databanks: A Practical Approach Des
Higgins, Willie Taylor.
18. Genomic Perl: From Basic To Workinf Code Rex A.Dwyer
19. Bioinformatics: From Genome To Drugs, Vol 1: Basic Technologies
Vol 2: Application Thomas Lengauer.
20. Biotechnology, Genomics and Bioinformatics Teresa Atwood, David
Perry-Smith
21. Introduction To Bioinformatics Teresa Atwood, David Perry-Smith
22. Structured Bioinformatics Philip Bourne, Helge Weissig
23. Bioinformatics Methods and Protocols Stephen Misener, Stephen
Krawetz.
24. New Biology for Engineers and scientists, Aydin Tozeren, Stephen
W.Byers.
25. Computational Molecular Biology: An Introduction, Peter Clote,
RlfBackofen.
26. Bioinformatics in Post-Genomic Era: Genomic Transcription, Proteome
and Information Based Medicine Jeffery Augen.
27. Bioinformatics: Using Computational Intelligence Paradims U. Seiffert,
L.C.Jain, Pschwetzer

44
28. Introduction To Bioinformatics: a theoretical and Practical Approach
Stephen Krawetz, David D.Womble.
29. Bioinformatics for Geneticsts, Michaeal R.Barens, Ian C.Gray.
30. Immunological Bioinformatics, Lund Ole Nielsen.
31. Bioinformatics Basics Hooman Rashidi, Lukas Buehler.
32. Bioinformatics: Genes, Proteins and Computers C.Orengo, D.Jones,
J.Thornton.
33. Bioinformatics and Molecular Evolution Paul G. Higgs.
34. The Application of Bioinformatics in Cancer Detection Asad Umar
35. Bioinformatics, Ralf Hofestadt.
36. Bioinformatics, Genomics and Proteomics: Getting the Bio PictureAnn
Batiza, Bernice Schacter
37. Knowledge Discovery in Proteomics Igor Jerisca, Dennis Wigle
38. Proteomics and Protein-Protein Introductions:
Biology, Chemistry, Bioinformatics and Drug Design, Gabreil Waksman
39. An introduction to Bioinformatics Jermy Ramsden.
40. Bioinformatics Basics: Application in Biological Science and Medicine
Hookman Rashidi, Lukas Buehler.
41. Medical Genetics Lynn B.Jorde, Jhon C.Carey, Micheal .Bamshad,
Raymound L. White
42. Essential of Genetics, William S.Klug, Michel R.Cummings.
43. Thompson & Thompson Genetics in Mediccine Robert I.Nussbaum,
Rodreick R.Mclnnes. Huntington F. Willard.
44. Medical Molecular Genetics, Patrick A.Hoffe.
45. Genomics, Sandy Primose, Richard Twyman
46. Essential of Medical Genetics Alan Emery, Robert Mueller.
47. Gene VIII Benjamin Lewin.
48. Understanding Biotechnology,George Acquaah.
49. Concept of Genetics, William Klug, Michael Cumming
Charlotte Spencer
50. Essential Genes, Benjamin Lewin.
51. Cell and Molecular Gerald Karp
52. Microbiology; A Human Perspective Eugene Nester, Denise
Anderson, C. Evans Robert Jr.
53. Genetics, Benjamin A. Pierce.
54. Ethics from a Faith Perspective, Jack Hanford.
55. A companion to Genetics Justine Burrley, John Harris
56. Understanding Medical Statistics David Mathews, Vernon Farewell
57. Molecular Biology, Robert Weaver.
58. Lipincot’s Biochemistry Champe; Harvey; Ferrier.
59. Harper’s; Biochemistry, Murray. Grammer, Mayes, Rodwell
60 Lehninger; Principles of Biochemistry Nelson , Cox.
61 Biochemistry Donlad Voet
62 Pattern Recognition, Statistical, Structural & Neural Approached Robert
Schalkoff
63 Pattern Recognition with neural networks in C++ Pandya/Macy
64 Pattern Classification Duda, Hart and Stork.
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65 Fundamentals of Pattern Recognition, Monique Pavel.
66 Texture Analysis in Machine Vision, M.K. Pietikainen.
67 Genetic Algorithms for Pattern Recognition, Pal/Wang.
68 Digital Image Processing R.C. Gonzales
69 Digital Image Processing using Matlab R.C. Gonzales
70 Hand Book of Image Processing John C.Russ
71 Algorithms for Image Processing & Computer Vision, J.R. Parker.

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 Annexure “A”

COMPULSORY COURSES IN ENGLISH FOR BS

(4-YEAR) IN BASIC & SOCIAL SCIENCES

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
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

47
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
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-Chrisitine 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

48
 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 Riachard 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
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. Mc-Graw-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).

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 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.
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.

50
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:
WmDawson & 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.

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 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-Baqra 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
Seerat of Holy Prophet (S.A.W) II
1) Life of Holy Prophet (S.A.W) in Madina
2) Important Events of Life of 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
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 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) Quranic & 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
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

53
 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)

54
 RECOMMENDATIONS
1. Only limited numbers of universities are offering under- and post
graduate courses in bioinformatics. There is a need to encourage
other public and private universities/institutes to develop expertise in
bioinformatics at their respective campuses.
2. HEC should allocate sufficient funds and grants on priority basis for
faculty development in this newly emerging field, especially for
universities/institutes, located in developing areas of Pakistan by
sending their faculty members for the short and long-term training
courses. This will help in elimination of shortage of specialized
manpower in bioinformatics especially at the university level.
3. HEC should facilitate and provide funds for infrastructure and
equipments for strengthening the existing program and initiating new
programs in bioinformatics.
4. HEC should implement a strict policy of monitoring and evaluation of
universities/institutes (both in public and private sectors) offering
degree courses in bioinformatics and enroll students giving them
false/deceptive information about the faculty, programs and facilities.
In this regard a special committee should be constituted comprising of
five members (02 biological sciences, 02 computational sciences, 01
HEC, taking at least one member preferably from a developing
province).
5. Both under- and post graduate courses in bioinformatics should be
included in teaching curriculum of the public and private sector of the
universities and degree awarding institutes.
6. A comprehensive course in bioinformatics should be developed for
students of other relevant disciplines.
7. To promote public awareness series of seminars and workshops
should be organized on regular basis.
8. There should be a strong link between academia and industry for the
absorption of bioinformatics graduates. This will encourage other
students to take programs in bioinformatics.

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