bioinformatics bs (hons) - Higher Education Commission

earthsomberΒιοτεχνολογία

29 Σεπ 2013 (πριν από 3 χρόνια και 9 μήνες)

245 εμφανίσεις


1
H
I
G
H
E
R

E
D
U
C
A
T
I
O
N
C
O
M
M
I
S
S
I
O
N


CURRICULUM

OF

BIOINFORMATICS
BS (HONS)
MS (HONS)



(Revised 2006)









HIGHER EDUCATION COMMISSION
ISLAMABAD




2

CURRICULUM DIVISION, HEC


Prof. Dr. Altaf Ali G. Shaikh Adviser (Acad/R&D)
Malik Ghulam Abbas Deputy Director
Miss Ghayyur Fatima Deputy Director (Curri)
Mr. M. Tahir Ali Shah Assistant Director
Mr. Shafiullah Khan Assistant Director























Composed by Mr. Zulfiqar Ali, HEC Islamabad


3


CONTENTS


1. Introduction 7

2. Curriculum for BS (Hons)
i) Scheme of Studies 10
ii) Details of Courses 11

3. Curriculum for MS (Hons)
i) Scheme of Studies 32
ii) Details of Courses 33

4. Recommendations 42






















4
PREFACE

Curriculum of a subject is said to be the throbbing pulse of a nation. By
looking at the curriculum one can judge the state of intellectual
development and the state of progress of the nation. The world has
turned into a global village; new ideas and information are pouring in
like a stream. It is, therefore, imperative to update our curricula regularly
by introducing the recent developments in the relevant fields of
knowledge.

In exercise of the powers conferred by sub-section (1) of section 3 of
the Federal Supervision of Curricula Textbooks and Maintenance of
Standards of Education Act 1976, the Federal Government vide
notification no. D773/76-JEA (Cur.), dated December 4, 1976,
appointed University Grants Commission as the competent authority to
look after the curriculum revision work beyond class XII at bachelor
level and onwards to all degrees, certificates and diplomas awarded by
degree colleges, universities and other institutions of higher education.

In pursuance of the above decisions and directives, the Higher
Education Commission (HEC) is continually performing curriculum
revision in collaboration with universities. According to the decision of
the special meeting of Vice-Chancellors’ Committee, curriculum of a
subject must be reviewed after every 3 years. For the purpose, various
committees are constituted at the national level comprising senior
teachers nominated by universities. Teachers from local degree
colleges and experts from user organizations, where required, are also
included in these committees. The National Curriculum Revision
Committee for Bio-Informatics in its meeting held in July 3-5, 2006 at
the HEC Regional Centre, Lahore revised the curriculum after due
consideration of the comments and suggestions received from
universities and colleges where the subject under consideration is
taught. The final draft prepared by the National Curriculum Revision
Committee duly approved by the Competent Authority is being
circulated for implementation by the institutions.


Prof. Dr.Altaf Ali G. Shaikh
Adviser (Acad/R&D)
August 2006




5
CURRICULUM DEVELOPMENT






STAGE-I
STAGE-II
STAGE-III
STAGE-IV
CURRI. UNDER
CONSIDERATION
CURRI. IN DRAFT
STAGE
FINAL STAGE
FOLLOW UP
STUDY
COLLECTION OF
REC
APPRAISAL OF 1
ST

DRAFT BY EXP. OF
COL./UNIV
PREP. OF FINAL
CURRI.
QUESTIONNAIRE
CONS. OF CRC.
FINALIZATION OF
DRAFT BY CRC
INCORPORATION
OF REC. OF V.C.C.
COMMENTS
PREP. OF DRAFT
BY CRC
APPROVAL OF
CURRI. BY V.C.C.
PRINTING OF
CURRI.
REVIEW
IMPLE. OF
CURRI.
BACK TO
STAGE-I
ORIENTATION
COURSES
Abbreviations Used:
CRC. Curriculum Revision Committee
VCC. Vice-Chancellor’s Committee
EXP. Experts
COL. Colleges
UNI. Universities
PREP. Preparation
REC. Recommendations

6











































7
INTRODUCTION

The preliminary meeting of the National Curriculum Revision
Committee in Bio-Informatics was held from on July 3-5, 2006 at HEC,
Regional Centre, Lahore to devise the curriculum for BS (4 year) and MS in
the discipline of Bio-informatics. Following experts attended the meeting.

1. Prof. Dr. Gulzar Ahmed Naizi Convener
HEC Foreign Professor,
Centre of Excellence in Microbiology,
78 West Canal Bank Road,
Thokar Niazbaig, Lahore.

2. Prof. Dr. Nazeer Ahmed, Member
Faculty of Engg. Tech.,
Hamdard University,
Muhammad Bin Qasim Avenue,
Main Campus, Karachi

3. Dr. S.M. Saqlan Naqvi, Member
Associate Professor,
Department of Bio-Chemistry,
University of Arid Agriculture,
Murree Road, Rawalpindi

4. Prof. Dr. Shahida Hasnain, Member
Dean (Life Sciences) & Chairperson,
Deptt. of Microbiology & Molecular Genetic,
University of the Punjab. Lahore

5. Prof. Dr. Shahid Masihuddin Khan, Member
Professor,
Centre of Excellence in Molecular Biology,
University of the Punjab, Lahore

6. Prof. Dr. Hidayat-ur-Rahman, Member
Chairman,
Department of Plant Breeding & Genetics,
NWFP Agricultural University,
Peshawar

7. Dr. Muhammad Inayatullah Khan, Member
Chairman,
Department of Computer Science & Information Technology,
NWFP University of Engineering & Technology,
Peshawar


8
8. Dr. Romana Tabassum Member
Principal Scientist,
National Institute of Biotechnology & Genetic Engineering
(NIBGE)P.O. Box 577, Jhang Road, Faisalabad

9. Dr. Syed Ali Bokhari, Member
Associate Professor,
COMSAT Institute of Information Technology,
Chak Shahzad Campus , Islamabad

10. Prof. Dr. Syed Afaq Hussain, Member
Head, Department of Electronic Engineering,
International Islamic University,
Chak Shahzad Campus, Islamabad

11. Dr. Mian Wajahat Hussain, Member
Professor,
Forman Christian College,
Gulberg, Lahore

12. Mr. Abrar Hussain, Member
Lecturer,
Balochistan University of Information Tech. &
Management Sciences, Samungli Road, Quetta

13. Mr. Bilal Hussain, Member
Lecturer,
Department of Bio Informatics,
GC University Faisalabad

Meeting started with recitation from the Holy Quran.

Mr. Muhammad Tahir Ali Shah, Assistant Director (Curriculum) HEC,
Islamabad welcomed the participants on behalf of Chairman, HEC. He briefly
described the procedure of curriculum development and informed the
Committee that the main objective of curriculum is to give a minimum
baseline of curriculum for the graduates of a certain subject so that uniformity
and standardization of curriculum may be maintained and to bring it at par
with International standards.

The Assistant Director assured the committee of full cooperation and
assistance.
Then the session was declared open for general discussion.
Prof. Dr. Gulzar Ahmed Naizi, HEC Foreign faculty expert, Centre of
Excellence in Molecular Biology, University of the Punjab, Lahore acted as
convener of the meeting.


9
After three days deliberations the NCRC prepared the curriculum for 4 year
BS and framework for 2 year MS in Bio-Informatics

Admission Requirements:


Eligibility:
Higher Secondary school or equivalent (2
nd
Division with at least 50%
marks)

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

Course and Credit Requirements:
Minimum of 130 credits are required to complete Bachelor of Science
in Bio-informatics.

Evaluation:
For the uniformity in the evaluation system, NCRC recommends that
the minimum CGPA required to pass a semester is 2.0 out of 4.0 at
undergraduate level subject to meeting the requirement of the
university.


10

Scheme of Studies BS(Bioinformatics)

Semester 1 Hours/Week
Semester 2 Hours/Week
Course
Code
Courses Lectures Lab
Course
Code
Course Lectures Lab
BSI-193 English Comprehension 3 0 BSI-195 Technical Report Writing 3 0
BSI-101 Islamic Study/ Pak Studies 4 0 Bio-103 Cellular Biology 2 1
Bio-101 Basic I (Mathematics / /Biology) 3 1 CS-102
Introduction to Computer
Programming
3 1
Bio-102
Basic II (Chemistry/ Introduction
to computer)
3 1 BSI-191 Multivariable Calculus 3 0
Bio-104 Biochemistry-I 3 1
Total Credit Hours 13 2 Total Credit Hours 14 3

Semester 3 Hours/Week
Semester 4 Hours/Week
Course
Code
Courses Lectures Lab
Course
Code
Courses Lectures Lab
BSI-194 Communication skills 3 0 IT-405
Ethical & Legal Issues in
Computing
3 0
BSI-192
Linear Algebra & Differential
Equation
3 0 Bio-203 Biostatistics 2 1
Bio-201 Essentials of Genetics 2 1 Bio-204 Biochemistry II 3 1
Bio-202 Molecular Biology 3 1 Bio-205 Introduction to Bioinformatics 2 1
CS-103 Data Structure & Algorithms-I 3 1 CS-201 Object Oriented Programming 3 1
Total Credit Hours 14 3 Total Credit Hours 13 4

Semester 5 Hours/Week
Semester 6 Hours/Week
Course
Code
Courses Lectures Lab
Course
Code
Courses Lectures Lab
BSI-197 Computational Mathematics 3 0 Bio-304 Bioinformatics Methods 2 1
Bio-301 Microbial Genetics 2 1 CS-309 Modeling & Simulation 2 1
CS-204 Database System-I 3 1 Bio-305 Proteomics 3 0
Bio-302 Molecular Methods 0 3 CS-303
Introduction to Computer
Graphics
3 1
Bio-303 Genomics 3 0 Bio-306 Elective I 3 1
Total Credit Hours 11 5 Total Credit Hours 13 4

Semester 7 Hours/Week
Semester 8 Hours/Week
Course
Code
Courses Lectures Lab
Course
Code
Courses Lectures Lab
Bio-401 Applied Bioinformatics 3 1 Bio-406
Bioinformatics Software
Development
2 1
Bio-402 Bio Ethics & Safety 3 0 Bio-407
Special Topics in
Bioinformatics
3 0
Bio-403 Elective II 3 1 Bio-408 Elective IV 3 1
Bio-404 Elective III 3 1 Bio-400 Research Project 0 3
Bio-400 Research Project 0 3
Total Credit Hours 12 6 Total Credit Hours 8 5


Grand Total Credit Hours
98
32







11
DETAILS OF COURSES

Semester-I
BSI-193
English Comprehension
2+0
Prerequisite:
None

Course Outline:
Using the dictionary and reading for general meaning, pronunciation:
reading for main idea: locating main Ideas and topic sentence contextual
references, reading: references, connectives and transitional words,
synonyms and antonyms, word formation, organizing conformation, word
forms, contextual references and organization, making inferences,
assessing the text: distinguishing facts from opinions, assessing texts,
imaginative texts, evaluating texts: interpreting visual data, writer's tone
and intention, close for comprehension, skimming and scanning for overall
information, scanning and language functions, classifying, cause and
effect relationships, presenting information graphically: flow charts,
sentence types, effective word choice, punctuation: comma and
apostrophe, paragraphs: structural parts: essay writing, ways of organizing
texts, paraphrasing, grammar and usage.
Recommended Books:
1. Core Skills in English Bk.3 by Folens Limited
2. Teacher’s Guide by Nelson
3. Practical Guide to Primary English by Diana Bentley


BSI-101
Islamic Study & Pakistan
Studies
4+0
Prerequisite (s) :
Course Outline:
Fundamentals of Islam. (Aqaid, Ibadat, Islamic Dawah etc.); ethical values
of Islam; Ser ah of the Holy Prophet (PBUH); Islamic Civilization and its
affects on humanity. Study of other prominent world religions and ethical
systems in comparison with Islamic viewpoint. Multicultural societies.
historical background of Pakistan: Muslim society in Indo-Pakistan, the
movement led by the societies, The downfall of Islamic society, The
establishment of British Raj- causes and consequences. Political evolution
of Muslims in the twentieth century: Sir Syed Ahmed Khan; Muslim
League; Nehru; Allama Iqbal: independence movement; Lahore resolution;
Pakistan culture and society, constitutional and administrative issues,
Pakistan and its geo-political dimension, Pakistan and international affairs,
Pakistan and the challenges ahead.
Recommended Book:

Chaudary M. Al: The Emergence of Pakistan, 1967.

K. K. Aziz: The Making of Pakistan, 1976.




12


Bio-101
Basic Mathematics I
3+1
Prerequisite:
None

Course Outline:
This course is

designed for those students who lack sufficient skill in basic
mathematics. The topics include: linear algebra, trigonometry, basic
calculus etc.

Bio-101
Basic Biology
3+1
Prerequisite:
None

Course Outline:
This course is for non-biology students and considers basic concepts of
the life science, with special emphasis on the diversity of life, the physical
and chemical nature of living matter, the form and function of the cells and
organism, and the ecological relationships among living organism.
Selected topics in structural, functional, developmental,

environmental and
systemic biology will be taught laboratory to accompany this Biology
course.
Lab Outline:
Culture and staining of microorganisms, study of mitosis and meiosis,
study of cell structure using compound microscope, tests for
carbohydrates, protein and lipid, study of some common flower, field trips
to study pollution caused by industrial waste

Recommended Books:
• Campbell and Mitchell 2000. Biology. Concepts and connections.
3
rd
Ed. Wesley Longman Inc. New York.
• Star C. 1999.Biology Concepts and Applications 4
th
Ed.
• Fogiel M. The Biology Problem Solver. Published by Research And
Education Association.



Bio-102
Basic Chemistry
3+1
Prerequisite:
None

Course Outline:
This is a foundation course. The course will describe the periodic table
nature of chemical bonding; state of matter; properties of solutions;
chemical reactivity; acid, bases; oxidation-reduction reactions, chemical
kinetics and hydrocarbons; organic chemicals and polymers; the chemistry
of life.

Lab Outline:
Preparation of molar and normal solutions, use of pH meter to determine

13
pH of various solutions, acid base titration, use of spectrophotometer to
determine the absorbance, determination of melting point and boiling point
.
Recommended Books:
• Brown et al. 2006. Chemistry the central Science Pearson Printing
Hall.
• Raymond Chang. 2005. Chemistry. 8
th
Ed. McGraw Hill.
• Christopher J Crammer. 2004. Computational Chemistry Theories
and Models. John Willey & Sons.
• Philips / Meathews.2003. Advanced Chemistry. Physical and
Industrial. Cambridge University Press.


CS-101
Introduction to Computers
3+1
Prerequisite:
Course Outline:
Brief history of computers and their applications. Major components of a
computer. Application software and system software. Computers in offices,
industry, and education. Office automation tools: Word-processing,
graphics packages, databases and spreadsheets. Introduction to Microsoft
Windows, and Linux Operating System. Using Internet: Introduction to
WWW (Web Server, Web Client, HTML, and HTTP). Computer and
Society. The social impact of computer age. Current trends, research and
future prospects. Legal and moral aspects of computer science.

Lab Outline:
Observe the major components of a Desktop PC, especially CPU.
Installation of different types of application software. Installation of different
Microsoft Windows Operating Systems. Installation of Linux Operating
System and applying its basic commands. Implementing some basic
HTML tags to construct a simple static web page. Installation of Microsoft
IIS (Internet Information Server) and Microsoft IE (Internet Explorer).
Submitting a report describing the impact of computer on human society
and the social issues of IT.
Recommended Books:

Glenn Brooks Hear, Computer Science – An Overview, 3
rd
Edition.

PK Sinha, Introduction to Computer Science








14
Semester-II

BSI-195
Technical Report Writing
2+0
Prerequisite:
English Comprehension

Course Outline:
Technical writing, definition, purpose & characteristics, types of
documents, types of skills, technical reading process, and technical writing
process: before, during & after
defining audience, technical writing techniques, researching, summarizing,
formatting, technical writing application, writing letters, writing
memorandums, meeting minutes, proposals, feasibility reports, writing long
technical reports, progress report, Manuals, An oral Presentation, letters,
interviewing
Recommended Books:
• Technical Report Writing Today ---Houghton Mifflin --- 4
th
Edition

Bio-103
Cellular Biology
2+1
Prerequisite:
None

Course Outline:
An introduction to cellular structure and function. Examination of the role of
biological membranes in cellular activity and forming functional
compartments within organelles. The function of other cellular and extra
cellular structure such as cytoskeleton and extra cellular matrix. Additional
topics include vector structure and function, cellular signaling,
differentiation and mortality
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, extraction and estimation of carbohydrate,
protein, RNA and DNA from plant sources, blood group test , TLC, DLC
etc

Recommended Books:
• David M. P. Academic Press London Methods in Cell Biology
Volume XVI
• Lowery Sekivetz. Cell Structure and Function. 3
rd
Ed. John Willey
and Sons Publication.
• Gerald Carp. Cell Biology 2
nd
Ed.
• Lodish H. Molecular Cell Biology 2000. 4
th
Ed .Media Connected



15
CS-102
Introduction to Computer
Programming

3+1
Prerequisite:
Course Outline:
Programming and problem analysis. Development of basic algorithms.
Translation of algorithms into programs. Putting different constructs of C++
to help in solving problems of moderate complexity. Standard data types.
Basic control structures. Functions. Structured data types; arrays,
structures, pointers and dynamic memory allocation. I/O streams and files.
Introduction to classes in C++. Debugging and testing programs.

Lab Outline:
Applying the problem solving steps to different case studies. Solving
arithmetic problems using C++. Solving problems involving decision
structures and loops. Designing and implementing Functions in C++ from a
problem specification. Development of a simple information system using
C++ Arrays, Structures, and Files. Implementing the same information
system using C++ Classes instead of Structures.

Recommended Books:


Deitel and Deitel, C++: How to Program, Prentice-Hall.

Gott Fried, Programming with C/C++ (Schaum’s Series), McGraw-
Hill.

Ammeraal, C++ for Programmers: John Willey.

BSI-191
Multivariable Calculus
3+0
Prerequisite (s) :
Course Outline:
Functions of several variables and partial differentiation, multiple integrals,
line and surface integrals. Green’s and Stoke’s Theorem. Fourier Series:
Periodic functions, functions of any period P-2L, even & odd functions, half
range expansions, fourier transform. Laplace transform, Z-transform.

Recommended Book:
• Calculus by Thomas and Finney, Addison-Wesley Publishing Co.

Advance Engineering Mathematics, by Erwin Kreyszig. John Willey



Bio-104
Biochemistry-I
3+1
Prerequisite:
None

Course Outline:
This course will include comprehensive study of various biomolecules,
enzymes and buffer system. Topic include: Water, pH and buffer systems,
structure and function of protein, carbohydrates, lipids of physiologic
importance with special reference to structure, assembly and functions of

16
plasma membrane, structure and function of informational
macromolecules, enzymes.
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 and Kjeldahl methods; titration curves of amino acids.
Preparation and assay of peroxidase; effect of pH, temperature and
substrate concentration on activity.
Distinction between pentoses and hexoses, reducing and non-reducing
sugars, mono-, di- and polysaccharides; estimation of glucose in a mixture
of monosaccharides; estimation of sucrose by polarimeter; paper
chromatography of sugars; extraction of glycogen from liver; acid and
enzymic hydrolysis of glycogen. Lipid separation from brain tissue and
fractionation by TLC; tests for fats, sterols and phospholipids; estimation of
cholesterol; acid, saponification and iodine values of fat.
Estimation of vitamins A and C in food materials.

Recommended Books:
• Nelson and Michel. 2005 LEHNINGER Principles of Biochemistry.
4
th
Ed. Pub Freeman and Company.
• Conn and Stumpf. 2002. Outlines of Biochemistry. John Willey and
Son Pub.
• Devlin and Thomas. 2002. Text book of Biochemistry with Clinical
Correlations. 5
th
Ed.
• Campbell M and Shawn F. 2003. Biochemistry. 4
th
Ed. Thomas
Book Pub.

Semester-III
BSI-194
Communication Skills
2+0
Prerequisite:
English Comprehension

Course Outline:
To develop good English writing, language usage and reading skills, to
appreciate the importance of business communication and to develop
understanding of communication concepts, principles, theories and
problems, to develop good oral communication and presentation skills.
Principles of writing good English, understanding the composition process:
writing clearly; words sentence and paragraphs, comprehension and
expression, Use of grammar and punctuation, Process of writing,
observing, audience collecting, composing, drafting and revising,
persuasive writing, reading skills, listening skills and comprehension, skills
for taking notes in class, skill for exams, Business communications;
planning messages, writing concise but with impact. Letter formats,


17
Mechanics of business, letter writing, letters, memo and applications,
summaries, proposals, writing resumes, styles and formats, oral
communications, verbal and nonverbal communication, conducting
meetings, small group communication, taking minutes. Presentation skills;
presentation strategies, defining the objectives, scope and audience of the
presentation, material gathering material organization strategies, time
management, opening and concluding, use of audio-visual aids, delivery
and presentation. oral expression is encouraged through group discussion
and the sharing of individual written assignments. Emphasis will be on how
to write Business letters and reports, Technical Report writing.
Recommended Books:
• Business Communication --- Murphy Hurta (1998) Latest Edition,
M.G. Hill
• Effective Business Communication --- Murphy Rickard (1998)
M.G. Hill

BSI-192
Linear Algebra and Differential
Equations
3+0
Prerequisite:


Course Outline:
Introduction to matrices, elementary row operations and vector spaces:
Brief introduction to matrices. Symmetric and Hermitian matrices,
Introduction to elementary row operations, Echelon form and reduced
echelon form. Rank of a matrix. Inverse of a matrix by using elementary
row operations. Vector spaces. Vector subspaces. Linear combination,
Linear dependence and basis, linear transformation. System of Linear
equations: System of non-homogeneous and homogeneous linear
equations, Gaussian elimination method, Gauss Jardon method,
Consistency criterion for solution of homogeneous and nonhomogeneous
system of linear equations. Applications of system of linear equations.
Determinants: introduction to determinants, properties of determinants of
order n, axiomatic definition of a determinant. Applications of determinants
(Cramer’s Rule). Multiple integrals: definition, double integral as volume,
evaluation of double integral, change of order of integration, application of
double integrals, area, mass of an element, moment of inertia, and center
of gravity. Triple integrals, evaluation of triple integrals, application of triple
integrals, volume, mass of an element, center of gravity, moment of inertia
by triple integrals, triple integration in cylindrical and spherical coordinates.
Differential equations of first order: differential equations and their
classification, formation of differential equations, solution of differential
equations, initial and boundary conditions, methods of solution of
differential equation of first order and first-degree: separable equations,
homogeneous equations, equations reducible to homogeneous, exact

18
differential equations, integrating factor, linear equations, Bernoulli
equations, orthogonal trajectories in Cartesian and polar coordinates,
applications of first order differential equations. non linear first order
differential equations. non linear first order differential equations: equations
solvable for p, for y and for x, Clairauts equations. Higher order linear
differential equations: Homogeneous linear equations of order n with
constant coefficients, auxiliary/ characteristics equations. Solution of
higher order differential equation according to the

roots of auxiliary equation. (Real and distinct, Real and repeated, and
Complex). Non-homogeneous linear equations. Working rules for finding
particular integral. Cauchy Euler equation.
Recommended Books:
• Linear Algebra, David C Lay, Pearson Addison Wesley, 1999, ISBN:
0201660369
• Advanced Engineering Mathematics, Michael Greenberg, ISBN:
0133214311.
• Advanced Engineering Mathematics,7/e, Erwin Kreyszig. John Wiley
& Sons 1992
ISBN: 0471553808.


Bio-201
Essentials of Genetics
2+1
Prerequisite:
None

Course Outline:
Topics include:- Genetics; definition, classification and concept, heredity
and variations, chromosome theory of heredity, Mendelian laws of
genetics, fine structure of chromosome, monohybrid, dihybrid and modified
phenotypic and genotypic ratios, multiple alleles, use of binomial theorem,
linkage analysis, gene and chromosomal mutation, single gene defect and
multifactor disorders and cancer genetics.
Lab Contents:
Drosophila culture techniques, Problems related to Mendelian inheritance,
Gene interaction, Gene mapping. Preparation of culture medium and
maintenance of Drosophila cultures in lab. Study of morphological
characters and setting crosses of Drosophila. Verification of Monohybird
and dihybird F2 ratios. Identification of first and second division
segregations in Neurespora or Sordria asci. Problems involving various
type of alleles, gene interaction, linkage, crossing over, gene mapping sex
linked inheritance, extra nuclear inheritance and complementation.

Recommended Books:
• William S. Klug, Michael Cummings. Essentials of Genetics 5
th
d
2005. Pearson /Prentice Hall
• Ricky Lewis: Human Genetics. McGraw Hill sixth ed 2005




19
Bio-202
Molecular Biology
3+1
Prerequisite:
None

Course Outline:
The student will learn basic concepts about DNA, RNA and proteins, which
make the basis of understanding sequence and structural information.
With special emphasis on nature of hereditary material, genetic material
and its organization in viruses, prokaryotes and eukaryotes, chemistry of
DNA, RNA and protein, DNA replication, recombination, mutations and
repair, transcription, regulatory elements, initiation, elongation and
termination, RNA processing, splicing and editing, translation and post-
translational modifications, control of gene expression in prokaryotes and
eukaryotes. Plasmids and vectors

Lab Outline:
Isolation of plasmid and chromosomal DNA from bacteria and yeast.
Screening of bacteria for plasmid by electrophoresis of total cell lysate.
Gel electrophoresis of plasmid DNA chromosomal DNA & RNA. Plasmid
transformation in E. coli. . Comparing plasmids of different molecular
weights using molecular weight markers.

Recommended Books:
• Robert Weaver. Molecular Biology. 3rd Ed; 2005Graw Hill
• Benjamin Lewin. Genes VIII. 2005 Pearson/ Prentice Hall
• Gerald Carp. Cell and Molecular Biology concepts and Experiments.
John Willey and Sons Publications.
• Gerald Carp. Cell and Molecular Biology. 4
th
Ed. Jhon Willey and
Sons Publications.
• Brown T. A. 1998. Molecular Biology Lab .FEX. 2
nd
Ed. Academic
Press Publication.

CS-103

Data Structure & Algorithms I
3+1
Prerequisite:
Introduction to Programming

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 simple and their application,
priority queues store, retrieve and search functionalities in stacks and
queues linked list, simple a linked list, finding and deleting specific dinks,
double ended links, linked list efficiency, sorted list, doubly linked list.
Recursion application, Triangular Numbers, Factorials. Merge Sort
.
Lab Outline:

Implementation of Basic Arrays


20

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.


Recommended Books:
• Data Structures and Algorithms By Robert Lafore, 2
nd
Edition
• An introduction to Bioinformatics Algorithims. Neil C.Jones, Pavel
Persner
• Gary Benson and Rodric Page. 2004. Algorithims in Bioinformatics
Singapur New York.

Semester-IV

IT-405
Ethical & Legal Issues in
Computing
3+0
Prerequisite (s):
Course Outline:
Social context of computing: Introduction to the social implications of
computing, Social implications of networked communication, growth of,
control of, and access to the Internet, Gender-related issues, International
issues, Risks and liabilities of computer-based systems: Historical
examples of software risks (such as the Therac-25 case), implications of
software complexity, risk assessment and management, Intellectual
property: Foundations of intellectual property, copyrights, patents, and
trade secrets, software piracy, software patents, transnational issues
concerning intellectual property, Privacy and civil liberties: Ethical and
legal basis for privacy protection, privacy implications of massive database
systems, technological strategies for privacy protection, freedom of
expression in cyberspace, International and intercultural implications,
Computer crime: History and examples of computer crime, "Cracking"
("hacking") and its effects, viruses, worms, and Trojan horses, crime
prevention strategies, Economic issues in computing, monopolies and
their economic implications, effect of skilled labor supply and demand on
the quality of computing products, pricing strategies in the computing
domain, differences in access to computing resources and the possible
effects thereof

21
Recommended Book:
• Legal and Ethical Issues in Acquisitions. Edited by Katina Strauch, A
Bruce Strauch
• Computer Ethics: Cautionary Tales and Ethical Dilemmas in
Computing By Tom Forester, Perry Morrison.
• Public Management Information Systems. By Bruce A Rocheleau
• Security in Computing. By Willis H Ware, Charles P Pfleeger, Shari
Lawrence Pfleeger
• Computer Ethics: Cautionary Tales and Ethical Dilemmas in
Computing By Tom Forester, Perry Morrison


Bio-203
Bio-statistics
2+1
Prerequisite:
None

Course Outline:
Non calculus based course includes introduction and scope; 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 software
Lab Outline:
Collection of Data, Acquisition of random samples, graphical/tabular
representation of data, 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
Problems of gene and genotype frequencies, Problems related to
polygenic inheritance.

Recommended Books:
• Gravetter Frederick J. 2000. Statistic for Behavioral Sciences 4
th
Ed.
• Mead R Curnow R.N. Statistical Method in Agriculture and
Experimental Biology. Chairman and Hall.
• Mathews and Farewell: Using and understanding Medical Statistics.
Krager New York









22
Bio-204
Biochemistry II
3+1
Prerequisite:
None

Course Outline:
This course will include the study of bioenergetics, metabolism of
biomolecules, such as proteins, carbohydrates, lipids, nucleic acids and
xenobiotics.

Lab Outline:
Estimation of normal and abnormal constituents in urine including glucose,
albumin, uric acid, chloride and phosphate. Blood analysis for hemoglobin,
ESR, platelets, TLC, DLC, etc. identification of blood groups; bleeding and
clotting time; estimation of inorganic constituents like calcium, iron and
organic constituents such as urea and bilirubin. glucose tolerance and
creatinine clearance tests. Use of ultracentrifugation and density gradient
centrifugation for the fractionation of biological compounds and molecular
weight determination. dialysis, ultrafiltration and preservation of proteins by
lyophilization; fractionation of
proteins using gel filtration, ion exchange chromatography and other
chromatographic techniques; molecular weight determination of proteins
by gel filtration; fractionation of proteins using native and SDS gel
electrophoresis; molecular weight determination of proteins by SDS-
PAGE; isoelectric focusing of proteins.

Recommended Books:
• Nelson and Michel. 2005 LEHINGER Principles of Biochemistry. 4
th

Ed. Pub Freedman and Company.
• Conn and Stumpf. 2002. Outlines of Biochemistry. John Willey and
Son Pub.
• Devlin and Thomas. 2002. Text book of Biochemistry with Clinical
Correlations. 5
th
Ed.
• Campbell M and Shawn F. 2003. Biochemistry. 4
th
Ed. Thomas
Book Pub.

Bio-205
Introduction to Bioinformatics
2+1
Prerequisite:
None

Course Outline:
Students will learn about the application of computer sciences in solving
biological problems. The course will focus on: Introduction, scope, history,
limitations and applications of Bioinformatics, Bioinformatics alignment
tools such as BLAST and FASTA will be covered, an insight into the future
challenges in Bioinformatics will be provided.
Lab Outline:
Determination of gene promoters termination and gene sequences,
determination of primary secondary and tertiary structure of protein by

23
computer programming, sequence comparison and determination of
conserved regions and Macromolecules.

Recommended Books:
• Arthur M. Lesk 2002. Introduction to Bioinformatics Oxford University
Press.
• Ignacimuthu SJ 2005. Basic Bioinformatics Narosa Publishing
House.
• Yadav Neelam. 2004. A Hand Book of Bioinformatics. Anmal
Publications Pvt.Ltd.
• Krawetz. Stephen A 2003. Introduction to Bioinformatics: A
Theoretical and Practical Approach, Humana Press.

CS-201
Object Oriented Programming
3+1
Prerequisite (s):
Course Outline:
Concept of object oriented programming, characteristics of oop,
polymorphism, encapsulation, data hiding. Java introduction, byte Code,
JVM, java architectural neutral language, the creation of simple java
program, compiling and execution of a program. dynamic initializing, scope
and lifetime of variables, type conversion and casting, the type promotion
rules, arrays, one dimensional array, multidimensional array, string data
type. operators, arithmetic operators, Bit wise operators, relational
operator. Boolean logical operators. Introducing classes, general form of
the class, declaring objects, object reference, control access specified
public, private, static data member and methods. Creating packages,
constructors, function overloading, constructor overloading, method, this
reference, finalize, static class member super class, sub class, protected
members, inheritance, polymorphism, dynamic, method binding, and 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. Defining a package, access protection, importing
packages, interfaces, exception handling fundamentals, exception types,
using Try and Catch, Java built-in exceptions, class libraries, object
oriented software development and course revision.

Lab Outline:
Programs formulation according to the Course outlines.
Recommended Book:
• Complete Reference Java 2 5th edition by “Herbert Schildt”
• Object Oriented Programming by “Robert Lafore”, JAVA How To
Program Third edition by Deitel & Deitel.




24
Semester-IV

BSI-197
Computational Mathematics
3+0
Prerequisite:
None

Course Outline:
Mathematical preliminaries, solution of equation in one variable,
interpolation and polynomial approximations, initial values problems for
ordinary differential equations, direct methods for solving linear systems,
iterative

techniques in matrix algebra and solution of nonlinear equations,
approximations theory, eigen values and eigen vectors computation.

Bio-301
Microbial Genetics
2+1
Prerequisite:
None

Course Outline:
Introduction to microbial genetic, morphology and life cycles of bacteria
and viruses, genetic manipulation in bacteria
.
Bacterial and viral
chromosomes, mechanism of genetic exchange among prokaryotes,
mutation transformation transduction,conjugation, bacteriophages, virulent
and avirulent phages, transposons and integrons. Host-Pathogen
interactions, immune response.
Lab Outline:
Growth curve of bacteria, induction of lytic cycle by U.V. Oligody. namic
action of metals on bacteria and yeast. Detection of R-plasmids in
bacterial strains. Detection of transposons in bacterial strains Curing of
bacterial plasmids Detection of mutants using replica plating techniques
Transfer of genetic markers through conjugation Gene mapping by
interrupted mating in bacteria Detection of mutagenic activity by Ames
test/yeast system.
Recommended Books:
• James M. and David V. 1997. The Book of Genetics. 2
nd
Ed.Ser.
ELDs Pub.
• Tortora et al. 2001. Microbiology an introduction. 7
th
Ed. Benjanium
Lumming.

CS-204
Database System-I
3+1
Prerequisite:
None

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

25
Lab Outline:
Structures Query Language commands, SQL commands, creating and
populating tables, design of simple databases, database normalization
process techniques, query optimization, indexing techniques, partial and
full recovery techniques, developing GUI techniques, implementation of
database security mechanisms.

Recommended Books:
• Data Structures and Algorithms By Robert Lafore, 2
nd
Edition
• An introduction to Bioinformatics Algorithims. Neil C.Jones, Pavel
A.Persner

Gary Benson and Rodric Page. 2004. Algorithims in Bioinformatics
Singapur, New York.



Bio-302
Molecular Methods
0+3
Prerequisite:
None

Course Outline:
This is a Lab bases course that involve DNA isolation; plasmid and
genomic DNA; gene cloning and sequencing, restriction digestion, RFLP,
polymerase chain reaction (PCR), protein purification; gel filtration, ion
exchange and affinity chromatography, GLC, HPLC and FPLC,
DNA/protein sequencing, DNA and protein electrophoresis,
centrifugation/ultracentrifugation, spectrophotometry, microarray analysis
of DNA and proteins.
Recommended Books:

Vyas SP and Kohli DV 20004. Methods in Biotechnology and
Bioengineering. CSB Publishers.


Michael et al. PCR Protocols. A Guide to Methods and Applications.
Academic Press


Bio-303
Genomics
3+0
Prerequisite:
None

Course Outline:
This course combines information from most recent genomic projects with
traditional genetic research methods to provide novel understanding of the
role of the genome as the blueprint of life. Emphasis is placed on exploring
the expression of genes in the context of activity and function of the whole
genome. Topics include genome anatomy, regulation of the activity of
genome, genome evolution, Genome mapping, Protein-protein interaction
etc.
Recommended Books:
• David M.W. Bioinformatics Sequences and Genome Analysis. 2
nd

Ed. CSB publishers and distributors.

26
Bioinfomatic: Sequence and Genome: Analysis 2
nd
edition, CBS
publisher & distributors New Delhi Bangalore by Spring Harbor
laboratory press.

Semester-VI

Bio-304
Bioinformatics Methods
2+1
Prerequisite:
None

Course Outline:
Students will develop custom based programs by using programming
languages such as C, C++ etc to simulate and solve Bioinformatics
problems. This course will explore the role of computational approaches in
health, agricultural and pharmaceutical sectors. Student will learn the use
of various bioinformatics related platforms, programming languages and
tools.
Lab Outline:
Implementation and design of simple programs related to bioinformatics,
simulation various bioinformatics entities, field visit for various
bioinformatics related sectors.

Recommended Books:

Borgeron Bryan. 2003. Bioinformatics Computing Pearson
Education.


Meenakshi. M and Sopory. S. K 2004.Biotechnology. Application
and Carriers. Viva Book Private Limited. New Delhi.


Vyas.S.P and Kohli D.V 20004. Methods in Biotechnology and
Bioengineering. CSB Publishers.


Adolph Kenneth W.1996. Viral Genome methods. CRC Press.



CS-301
Modeling & Simulation
2+1
Prerequisite:
None

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, Matlab Bioinformatics toolbox would be used for modeling and
simulation.


27
Lab Outline:
Introduction to modeling techniques and tools, using simulation tools,
using 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:
• Complete Reference Java 2 fifth edition by “Herbert Schildt”
• Object Oriented Programming by “Robert Lafore”, JAVA How to
Program Third edition by Deitel & Deitel.
• Computer Graphics (C Version), by Donald Hearn and M. Pauline
Baker (Prentice Hall, 1997)

Flash Professional 8, by M Waqar Aziz (2006)


Bio-305
Proteomics
3+0
Prerequisite:
None

Course Outline:
Proteomics identifies and analyzes the protein in a cell. In this course the
student will review protein chemistry and learn about proteomics
technology such as expression analysis, sorting, protein-protein
interaction. Primary, secondary and tertiary structure prediction, proteome
analysis of an organelle: the nucleolus.
Recommended Books:
• Richerd Simpson J. Purifying Proteins for Proteomics ( a laboratory
manual) Cord Spring Harbor Laboratory Press.
• Rastogi et al. 2004. Bioinformatics methods and applications.
Genomics, Proteomics and Drug discovery

CS-303
Introduction to Computer Graphics
3+1
Prerequisite:

Familiarity with any computer language

Course Outline:
Introduction to computer graphics, graphics systems and devices, line
drawing techniques, circle drawing techniques, ellipses and curves, filled
area primitives, 2D-transformation, Clipping, 3 D-Transformation,
projection, shading, viewing, animation.
Lab Outline:

Flash: introduction, interface, tools, symbols, importing bitmaps, tweening,
library movie clips, buttons. publishing in Flash
Recommended Books:

• Computer Graphics (C Version), by Donald Hearn and M. Pauline
Baker (Prentice Hall, 1997)

Flash Professional 8, by M.Waqar Aziz (2006)



28
Bio-306
Elective-I
3+1
Prerequisite:


Course Outline:
To be chosen from the list of electives

Semester-VII

Bio-401
Applied Bioinformatics
3+1
Prerequisite:
None

Course Outline:
This course emphasizes on cellular, tissue, organ and system modeling,
simulation, analysis using an object oriented programming language.
Biologically inspired computation, evolutionary algorithms, swarm
intelligence, neural computation, artificial life, approximate matching
algorithms,
Recommended Books:
• Namita M . 2003. Bioinformatics concepts, skills and applications.
CSB publishers and distributors.
• Lacroix Zor. 2003. Bioinformatics managing scientific data, Morgan
Kaufmann publishers.
• Higgs Paul .G. 2005. Bioinformatics and Molecular Evolution. Black
Well Scientific Publishing.

Bio-403
Bioethics & Safety
3+0
Prerequisite:
None

Course Outline:
Development of biotechnology has raised many ethical issues and the
public perception about the abuse of genetic engineering is of major
concern. In this course, the students will learn to distinguish between
ethics, morals and values, their impact on the development and application
of biotechnology; public acceptance of biotechnology.


Bio-404
Elective-II
3+1
Prerequisite:


Course Outline:
To b e chosen from the list of electives

Bio-405
Elective-III
3+1
Prerequisite:
None

Course Outline:
To be chosen from the list of electives

29

Bio-400
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
Development
2+1
Prerequisite:


Course Outline:
Software development methodology including waterfall model, iterative
model, rapid application development, prototyping, software life cycle.
Development of software projects for bioinformatics problems. HTML,
XML, overview of software architecture, Web based applications
architecture. Developing front end applications; front End development
tools.
Lab Outline:
Introduction to software development techniques, study of various software
models including water fall model, using simple case studies to develop
software for various software process models, introduction to XML , use of
front end application tool.


Bio-407
Special Topics in
Bioinformatics
3+0
Prerequisite:


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 Program.
Recommended Books:
• Namita M . 2003. Bioinformatics concepts, skills and applications.
CSB publishers and distributors.
• Lacroix Zor. 2003. Bioinformatics managing scientific data, Morgan
Kaufmann publishers.
• Higgs Paul .G. 2005. Bioinformatics and Molecular evolution. Black
well Publishing.
• Schulze. S Kremer. Advances in molecular Bioinformatics.
Netherland Printing.



30
Bio-408
Elective-IV
3+1
Prerequisite:
None

Course Outline:
To be chosen from the list of electives


Bio-400
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.

List of Electives

1. Enzyme Kinetics
2. Biomedical instrumentation
3. Microbial diversity
4. Biological Database Management System
5. Microarray Data Analysis
6. Artificial Intelligence
7. Nano Technology
8. Environmental Health
9. Environmental Biotechnology
10. Special Topics in Biochemistry
11. Virology
12. Bacteriology
13. Immunology
14. Microbiology
15. Mycology
16. Cytoplasmic Genomes
17. Digital Image Processing
18. Gene Mining
19. Pattern reorganization and matching
20. Platform Independent Programming
21. Operating Systems
22. Bio Physics
23. Medical Imaging

*
Subject to availability of minimum number of 5 students for registration for
courses.




31
MASTER OF SCIENCE (MS) IN
BIOINFORMATICS

The purpose of this MS degree program in bioinformatics is to provide
the students with an advanced knowledge and training that will help them to
decipher the biological processes. The expansive nature of biological data
can only be translated effectively into knowledge by the use of information
technology, as has recently been demonstrated by solving some of the
mysteries of gene sequence analysis and decoding the human genome. The
students should have thorough knowledge about the data storage and
retrieval systems; the types and sources of databases used in biotechnology
and how to retrieve data from genetic databases.

Admission Requirements:

Eligibility:
1. BS Bioinformatics
2. BS in biological sciences/ Computer sciences/ Biotechnology or
equivalent.
3. 2
nd
Division class or GPA 2.50 or above.
4. Subject GRE/ NTS or in-house written test
5. Interview

Duration:
2 years (4 semesters: course work should be completed in two
semesters; one year for research )

Total Credit Hrs:
30 (24 CH course work + 6 CH thesis)

32
Scheme of Studies for MS Program


Semester I Credit Hrs.
Advanced Molecular Biology 3
Advanced Bioinformatics 3
Information Retrieval Processing 3
Applied Biotechnology 3
Semester II Credit Hrs.
Specialization-1 3
Specialization-II 3
Elective-1 3
Elective-II 3

12 12
Total CH: 24

Specialization Track Courses
Computational Science Biological Science
Data Mining Modern Technique in Molecular
Biology
Machine Learning Metabolonomics
Artificial Intelligence Molecular Evolution
Advanced Computational Algorithms Proteomics & genomics
Pattern Recognition Theory & Applications of
Bioinformatics
Advanced Software Engineering Statistical Methods for
Computational Biology

























33
DETAILS OF COURSES



Advance Molecular Biology

Prerequisite:
None

Course Outline:
Transcription, Translation, DNA & protein modification and repairing
mechanism, gene expression models (prokaryotes & eukaryotes),
regulation, mutagenesis, plasmid construction, RNA interference,
sequencing methods, gene mapping, genetic interactions; application of
recombinant DNA techniques to genetic analysis

Recommended Books:
Wisden and Richered. 2003. Advanced Molecular Biology. Viva Book
Private Ltd.
Benjamin Lewin: GENES VIII. Pearson/Prentice Hall 2005
Robert Weaver. Molecular Biology 3
rd
Edition 2005 McGraw Hill


Advance Bioinformatics

Prerequisite:


Course Outline:
This course aims to provide an introduction to bioinformatics with three
main themes: Genomics (including mapping, sequencing & assembly,
coding region identification, genome projects & model genomes, disease
genes, applications in therapy, etc. ); analysis of protein sequences
(including an introduction to databases, information networks, the World
Wide Web, sequence alignment, structural and/or functional motif
recognition, estimation of significance, etc.); analysis of protein structure
(including structure comparison, fold classification, structure prediction,
phylogenetic analysis)
Lab Contents:

Recommended Books:
• Schulze S. Kremer. Latest Ed. Advances in Molecular
Bioinformatics. Netherland Printing.
• Rastogi et al. 2004. Bioinformatics methods and applications.
Genomics, Proteomics and Drug discovery.







34

Information Retrieval &
Processing

Prerequisite:


Course Outline:
Information organization & retrieval, image databases, biological
databases, advanced query languages, searching strategies, matching
techniques (exact & approximate), information processing, content based
image retrieval.
Lab Contents:


Applied Biotechnology

Prerequisite:


Course Outline:
This course aims to address the use of biotechnology in health,
agricultural, environmental and industrial area issues. The broad
perspective of genetic engineering technology to cater the requirement in
above mentioned sectors such as vaccine development, drug discovery,
development of crop cultivars with improved attributes, production of
industrial enzymes, bioremediation, transgenic organism.
Lab Contents:
Recommended Books:


George Acquaah. Understanding Biotechnology. Pearson / Prentice
Hall 2005

• Glick, pasternnak. 2003. Molecular biotechnology principles and
application of recombinant DNA publisher ASM 3
rd
edition.
• Sosh T.K Dr.Chokra barite. 2005. Biotechnology in invirmental
management Vol 1 & 2 published by A.P.H


Specialization Track Course

(Computational Sciences) Courses



Data Mining

Prerequisite:


Course Outline:
Data mining & advanced retrieval capabilities, rules of inductive inference,
classification, clustering, machine learning techniques, advanced
searching and matching techniques.
Lab Contents:


35

Machine Learning

Prerequisite:


Course Outline:
Basic concepts, generalization, specialization, Winsten approach, Hayes-
Roth Sprouter approach, AQ, ID3, CN2, incremental concept formation,
evolutionary computing, genetic algorithms & computing, neural networks
and neural computing.
Lab Contents:



Artificial Intelligence

Prerequisite:


Course Outline:
Hebbian Learning, Perceptron Learning, Adaline, Pattern Association,
Hetero-associative, Auto-associative, competition based Neural networks,
Kohonen, SONN, LVQ. Predicate logic, searching techniques, rule-based
systems, knowledge based systems, fuzzy logic
Lab Contents:


Advance Computational
Algorithms

Prerequisite:


Course Outline:
Graph algorithms, strongly connected components, dominators in acyclic
graphs, network flow, bi-partite matching,theory of NP completeness,
design and analysis of approximation algorithms for NP complete
problems.

Lab Contents:


Pattern Recognition

Prerequisite:


Course Outline:
Introduction, description of textures/patterns, patterns & features,
classifiers & discriminant functions, training & learning, statistical pattern
recognition, syntactical & structural pattern recognition, Neural-
approaches, reason driven/ expert system based approaches.
Lab Contents:



36

Advance Software Engineering

Prerequisite:


Course Outline:
Advanced object oriented design techniques, graphical user interface
design and interface implementation, animation, simple line and filled
graphics, thread based programming, thread creation and interaction,
shared variables, synchronization, software testing, quality assurance,
deployment technique
Lab Contents:

(Biological Sciences) Courses


Metabolobonomics

Prerequisite:


Course Outline:
Topics discussed will be principles of metabolic control, membrane signal
transduction and mechanisms of hormonal control of metabolism, growth
and differentiation, mechanisms of metabolic diseases: diabetes,
cardiovascular diseases, osteoporosis, obesity, disorders of lipid
metabolism.
Lab Contents:



Modern Techniques in
Molecular Biology

Prerequisite:


Course Outline:

Buffer, Paper and thin layer chromatography.
Fractionation, Centrifugation.
Ion-Exchange Chromatography.
Gel – Filtration Chromatography.
Electrophoresis – PAGE, GEL
ELISA, RIA – Radio Immune Assay Technique
Enzyme Linked

Lab Contents:


Molecular Evolution

Prerequisite:


Course Outline:

Lab Contents:

37


Geonomics & Proteomics

Prerequisite:


Course Outline:
This detailed course combines information from most recent genomic
projects and protein databanks with traditional genetic research methods
to provide understanding of the role of the genome as the blueprint of life.
Emphasis is placed on exploring the expression of genes and the
interaction of their products. Topics include effects of mutations on the
structure of proteins, mitochondrial genomes and mitochondrial disorders,
DNA microarrays, regulation of the activity of genome,
Lab Contents:
Recommended Books:
• Richerd Simpson J. Purifying Proteins for Proteomics ( a alaboratory
manual) Cord Spring Harbor Laboratory Press.
• Rastogi et al. 2004. Bioinformatics methods and applications.
Genomics, Proteomics and Drug discovery.
• David M.W. Bioinformatics Sequences and Genome Analysis. 2
nd

Ed. CSB publishers and distributors.
• Bioinfomatics sequence and genome. Analyeis 2
nd
edition, CBS
publisher


Theory & Application of
Bioinformatics

Prerequisite:


Course Outline:
The course aims to expose students to a selection of the algorithms used
in Bioinformatics applications, and to some of the underlying theories. This
should enable the students to perform experiments, especially in sequence
analysis, or read research papers, in an informed manner The topics
include: Introduction to probability theory, introduction to algorithms and
complexity, traditional alignment algorithms, refinements, Markov chains,
Hidden Markov models, traditional phylogeny, probabilistic phylogeny
Lab Contents:
Recommended Books:
• Rastogi et al. 2004. Bioinformatics methods and applications.
Genomics, Proteomics and Drug discovery.
• Namita M . 2003. Bioinformatics concepts, skills and applications.
CSB publishers and distributors.
• Lacroix Zor. 2003. Bioinformatics managing scientific data, Morgan
Kaufmann publishers.



38

Statistical Methods for
Computational Biology

Prerequisite:


Course Outline:
Biological science generates immense data sets from today’s genome
projects. Examples include DNA and protein sequence data, and recently
produced DNA microarray data. There is a strong motivation for
developing computational methods that can infer biological information
from these data sets. This course is about the many problems in
computational biology that are essentially statistical. Statistical methods in
biological sequence analysis and introduction to DNA microarray data sets
and some associated topics on their analyses will be discussed: detailed
use of SPSS Package
Lab Contents:

LIST OF ELECTIVES

Advance software Engineering
Scientific Database
Advance biochemistry
DNA microarrays and integrative genetics
Immunological bioinformatics
Biomechanics
High performance and parallel computing
Epidemiology
Advance topics in information system
Advance Intelligent Agents
Research Method in Biological Sciences
Graph theory and application
Advance data structure
Nanotechnology
Population Genetics
Immunogenetics

*
Student must select the elective (s) from the above list and is subject to
the offering by the concerned department.


Research Thesis (6 Credit Hrs.):
Research Project:
1. Duration of the research project will be at least one full year. An
independent research topic chosen by the student and directed by a
full time faculty member of the department is required of all students in
M.S Bioinformatics.
2. The research project plays an important role for the students in
developing a deeper understanding of the subject involved and build

39
skills necessary to work independently and communicate the results of
the work to other scientists.
3. 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.
4. All students must present and defend their research work before the
panel of examiners as per the rules of the university.

Recommended Text Books For
Bioinformatics Program
S# Title Author

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

40
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
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 Picture
Ann 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

41
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.EvansRobert 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
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






42
RECOMMENDATIONS

• Both under-graduate and graduate courses in Bioinformatics should be
included in the teaching curriculum of the public, private sector
universities and degree awarding institutes.

• HEC should facilitate and provide the infrastructure, funds for
equipment and human resources development in Bioinformatics in
universities and teaching institutes.

• HEC should facilitate and arrange short- and long term training
program for faculty development in Bioinformatics.

• Job opportunities should be created for Bioinformatics graduates in
public and private sectors.

• At secondary school level the courses in biology and computer science
should be taught to all science students.

• At higher secondary school level both biology and mathematics should
be compulsory subjects for all science students.