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CURRICULUM DRAFT

BIOINFORMATICS

BS (4-YEAR)

National Centre for Bioinformatics

Faculty of Biological Sciences

Quaid-i-Azam University, Islamabad

LAYOUT FOR BS Bioinformatics

(4 YEAR PROGRAM)

Total numbers of Credit hours 135

Duration 4 years

Semester duration 15-18 weeks

Semesters 8

Course Load per Semester 15-18 credit hours

Number of courses per semester 5- 6

LAYOUT

Compulsory Courses (student has no choice)		General Courses to be chosen from other departments		Discipline Specific Foundation Courses		Major Courses including research project/ internship		Elective Courses within the Major
9 Courses	Cr. hr.	7-8 Courses	Cr. hr.	9-10 Courses	Cr. hr.	11-13 Courses	Cr. hr.	4 Courses	Cr. hr.
1. English I 2. English II 3. English III 4. Pak Studies 5. Islamic Studies/Ethics 6. Mathematics I 7. Introduction to Computer 8. Mathematics II 9 Physical Chemistry	3 3 3 2 2 3 3 3 3	1. Data Structure and Algorithms 2. Object oriented programming 3. Programming Fundamentals 4. Discrete Structures 5. Database Management Systems 6. Social Sciences Subject 7. Ethical and legal issues in Bioinformatics	3 3 4 4 3 3 3	1. Linear Algebra and Differential Equations 2. Essentials of Genetics 3. Basic Cell Biology 4. Bioinformatics I 5. Bioinformatics II 6. Introductory Biochemistry 7. Biochemistry 8. Molecular Biology 9. Recombinant DN A Ttechnology	3 4 3 4 3 4 3 4 4	1. Bioinformatics Computing I 2. Genomics 3. Proteomics 4. Graphics and Visualization 5. Bioinformatics Computing II 6. Artificial Intelligence 7. Bioinformatics Software Engineering 8. Special topics in Bioinformatics 9. Research Project Paper-I 10. Research Project Paper-II 11. Systems Biology 12. Modeling and Simulation 13. Probability and Biostatistics	4 3 3 4 3 3 3 3 3 3 4 4 3	1. Elective I 2. Elective II 3. Elective III 4. Elective IV	3 3 3 3
Credit Hours in each Category	25		23		32		43		12

BS (4 YEARS) Bioinformatics

PROGRAM

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

STRUCTURE

Sr.	Categories	No. of courses	Credit Hours
1.	Compulsory Requirement (No Choice)	09	25
2.	General Courses to be chosen from other departments	07	23
3.	Discipline Specific Foundation Courses	09	32
4.	Major Courses including research project/Internship	13	43
5.	Electives within the major	04	12
	Total	42	135

Scheme of Studies for BS (Bioinformatics)

Year-1: In 1^st year, course catalogue consists of semester 1 and 2.

Semester-1

	Semester 1		Credit hours
Course Categories	Course Code	Courses Title	Lectures
Compulsory-I	ENG-101	English 1	3(3+0)
Compulsory-II	PST-101	Pakistan Studies	2(2+0)
Compulsory-III	MTH-101	Mathematics I	3(3+0)
Compulsory-IV	CS-201	Computer Fundamentals	3(2+1)
Compulsory-V	CHE-201	Physical Chemistry	3(2+1)
Foundation I	BIF-201	Basic Cell Biology	3(2+1)
Total Credit Hours			17

Semester-2

	Semester 2		Credit hours
Course Categories	Course Code	Courses title	Lectures
Compulsory-VI	ENG-102	English II	3(3+0)
Compulsory-VII	ISM-101	Islamic Studies/Ethics	2(2+0)
Compulsory-VIII	MTH-102	Mathematics II	3(3+0)
Foundation II	BCH-101	Introductory Biochemistry	4(3+1)
General-I	BIF -202	Programming Fundamentals	4(3+1)
Total Credit Hours			16

Year-2: In 2^nd year, course catalogue consists of semester 3 and 4.

Semester-3

	Semester 3		Credit hours
Course Categories	Course Code	Courses title	Lectures
Compulsory-IX	ENG-201	English III (Writing & Comm)	3(3+0)
Foundation-III	BIF-204	Essential of Genetics	4(3+1)
General-II	CS-202	Object Oriented Programming	3(2+1)
Foundation-IV	BCH-334	Molecular Biology	4(3+1)
Foundation-V	MTH-201	Linear Algebra and Differential Equations	3(3+0)
Total Credit Hours			17

Semester-4

	Semester 4		Credit hours
Course Categories	Course Code	Courses title	Lectures
General-III	SOC-101	Sociology	3(3+0)
General-IV	BIF-208	Database Management Systems	3(2+1)
Foundation-VI	BIF-206	Biochemistry	3(3+0)
Foundation-VII	BIF-205	Bioinformatics I	4(3+1)
Foundation-VIII	BIF-219	Recombinant DNA technology	4(3+1)
Total Credit Hours			17

Year-3: In 3^rd year, course catalogue consists of semester 5 and 6.

Semester-5

	Semester 5		Credit hours
Course Categories	Course Code	Courses title	Lectures
General-V	BIF-209	Ethical and Legal Issues in Bioinformatics	3(3+0)
Major-I	BIF-200	Probability and Biostatistics	3(2+1)
Major-II	BIF-212	Bioinformatics Computing 1	4(3+1)
General-VI	CS-203	Data Structure and Algorithms	4(3+1)
Major-III	BIF-211	Genomics	3(3+0)
Total Credit Hours			17

Semester-6

	Semester 6		Credit hours
Categories	Course Code	Courses	Lectures
Foundation-IX	BIF-210	Bioinformatics II	3(3+0)
Major-IV	BIF-214	Proteomics	3(3+0)
Major-V	BIF-213	Modeling and Simulation	4(3+1)
Major-VI	BIF-215	Systems Biology	4(3+1)
General-VII	BIF-207	Discrete Structures	3(3+0)
Total Credit Hours			17

Year-4: In 4^th year, course catalogue consists of semester 7 and 8.

Semester-7

	Semester 7		Credit hours
Course Categories	Course Code	Courses title	Lectures
Major-VII	BIF-216	Bioinformatics Software Engineering	3(2+1)
Major-VIII	CS-401	Artificial Intelligence	3(3+0)
Major-IX	BIF-218	Bioinformatics Computing II	3(2+1)
Elective	BIF-	Elective-I	3(3+0)
Elective	BIF-	Elective-II	3(3+0)
Major-X	BIF-222	Research Project	3(0+3)
Total Credit Hours			18

Semester-8

	Semester 8		Credit hours
Course Categories	Course Code	Courses title	Lectures
Major-XI	BIF-217	Special topics in Bioinformatics	3(3+0)
Major-XII	CS-304	Graphics and Visualization	4(3+1)
Elective	BIF-	Elective-III	3(3+0)
Elective	BIF-	Elective-IV	3(3+0)
Major-XIII	BIF-222	Research Project	3(0+3)
Total Credit Hours			16

Credit hours distribution in each semester

Credit hours distribution/semester
Sem I	Sem II	Sem III	Sem IV	Sem V	Sem VI	Sem VII	Sem VIII	Total
17	16	17	17	17	17	18	16	135

DETAIL OF COURSES

Semester-I

	Semester 1		Credit hours	Shifting Order
Course Categories	Course Code	Courses Title	Lectures
Compulsory-I	ENG-101	English 1	3(3+0)
Compulsory-II	PST-101	Pakistan Studies	2(2+0)
Compulsory-III	MTH-101	Mathematics I	3(3+0)
Compulsory-IV	CS-201	Computer Fundamentals	3(2+1)
Compulsory-V	CHE-201	Physical Chemistry	3(2+1)
Foundation I	BIF-201	Basic Cell Biology	3(2+1)	II I
Total Credit Hours			17

ENG-101 English I 3(3+0)

Prerequisite: None

Specific objectives of the course:

Enhance language skills through grammar, phrases and sentence making. Develop skills for English writing and translation. Enhance listening and speaking skills for wider use.

Course Outline:

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 verb, Punctuation and spelling Answers to questions on a given text. General topics and every-day conversation (topics for discussion to be at the discretion of the teacher keeping in view the level of students) to be improved by showing documentaries/films carefully selected by subject teachers, Urdu to English, Topics to be chosen at the discretion of the teacher, Introduction to presentations and deliberations.

Recommended Books:

Latest editions of following books

1. Thomson, A.J., Martinet, A.V. 1997. Practical English Grammar and Exercises 3rd Ed. Oxford University Press.

2. Boutin, M-C., Brinand, S., Grellet, F. 1993. Writing. Intermediate and Supplementary Skills. Oxford Fourth Impression

3. Tomlinson, B., Ellis, R. 1992. Reading. Upper Intermediate. Oxford Supplementary Skills. Third Impression.

PST-101 Pakistan Studies 2(2+0)

Prerequisite: None

Specific objectives of the course:

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:

Ideological rationale with special reference to Sir Syed Ahmed Khan, Allama Muhammad Iqbal and Quaid-i-Azam Muhammad Ali Jinnah; Factors leading to Muslim separatism; People and Land: Indus Civilization, Muslim advent, Location and geo-physical features. Political and constitutional phases:s 1947-58; 1958-71; 1971-77; 1977-88; 1988-99; 1999 onward. Economic institutions and issues, Society and social structure, Ethnicity, Foreign policy of Pakistan and challenges, Futuristic outlook of Pakistan.

Recommended Books:

Latest editions of following books

1. Zaidi A.S. 2000. Issue in Pakistan’s Economy. Karachi: Oxford University Press.

2. Rafique A. M. 1998. Political Parties in Pakistan, Vol. I, II & III. Islamabad: National Institute of Historical and cultural Research.

3. Safdar, M. 1994. Pakistan Political Roots & Development. Lahore.

4. Burke, S.M., Ziring L. 1993. Pakistan’s Foreign policy: An Historical analysis. Karachi: Oxford University Press.

5. Noor ul Haq. 1993. Making of Pakistan: The Military Perspective. Islamabad: National Commission on Historical and Cultural Research.

6. Waseem, M. 1987. Pakistan Under Martial Law, Lahore: Vanguard.

7. Javed, B. S. 1980. State and Society in Pakistan.The Macmillan Press Ltd.

8. Lawrence, Z. 1980. Enigma of Political Development. Kent England: WmDawson & sons Ltd.

9. Ansar, Z. 1980. History & Culture of Sindh. Karachi: Royal Book Company.

10. Aziz, K.K. 1976. Party, Politics in Pakistan, Islamabad: National Commission on Historical and Cultural Research.

11. Wayne, W. 1972. The Emergence of Banglades., Washington: American Enterprise, Institute of Public Policy Research.

12. Khalid Bin Sayeed. 1967. The Political System of Pakistan. Boston: Houghton Mifflin.

13. Safdar, M. Pakistan Kayyun Toota, Lahore: Idara-e-Saqafat-e-Islamia, Club Road, nd.

14. Tahir, A. Ethno - National Movement in Pakistan, Islamabad: Institute of Policy Studies, Islamabad.

MTH-101 Mathematics I 3(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. Hebeorn and Littlewood,“Modular Math”, Heinemann, 1990

2. Keith Pledger, “Core Mathematics”,Edexcel 4; 2001

CS-201 Computer Fundamentals 3(2+1)

Prerequisite: None

Specific objectives of the course:

Course Outline:

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

Lab Outline:

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

Books Recommended:

Introduction to Computer Networks /4, A. S. Tanenbaum, Prentice Hall 2003
Computer Networks and Internets, 5/E, 2008
Douglas E. Comer, Purdue University ISBN-10: 0136061273 ISBN-13: 9780136061274 Publisher: Prentice Hall
Data and Computer Communications by William Stallings Published by Macmillan Pub. Co., 8th Edition 2006

BIF-201 Basic Cell Biology 3(2+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 membrane, structure and transport properties, fluid mosaic model, organelles: mitochondria, endoplasmic reticulum, golgi bodies, plastids, lysosomes, peroxisomes, cell internal structure, cytoskeleton, microtubules, microfilaments, intermediate filaments, structure of chromosomes, cell division and cell cycle.

Lab Outline:

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

Recommended Books:

Latest editions of following books

1. David M. P., “Methods in Cell Biology”, Academic Press London.; 3 edition (October 7, 2011)

2. Lowery Sekivetz. “Cell Structure and Function”, John Willey and Sons Publication; 1 edition (August 4, 2008)

3. Gerald Karp. “Cell Biology”, Wiley: 6th Edition International Student Version edition (January 26, 2010)

4. Lodish H. “Molecular Cell Biology”, Media Connected; Seventh Edition edition (May 2, 2012)

5. Lewin B. “Genes X”, Pearson/Prentice Hall; 10 edition (November 27, 2009)

6. De Robertis, “Cell and Molecular Biology”, Lippincott Williams &Wikins: 8^th (edition 2010)

7. Sadava D. et al., “Life, The Science of Biology”, WH Freeman: 10^th, Edition edition (December 10, 2012)

8. Bruce Alberts et al., “Molecular Biology of Cell”, Garland Science: 6^th, edition (November 18, 2014)

CHE-201 Physical Chemistry 3(2+1)

Prerequisite: None

Specific objectives of the course:

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

Course Outline:

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

Lab Outline:

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

Recommended Books:

Latest editions of following books

1. Brown et al.,“Chemistry:The central Science”, Pearson Printing Hall; 13 edition (January 11, 2014)

2. Raymond Chang,“Chemistry”, McGraw Hill.10 (edition 2010)

3. Christopher J. Crammer,“Computational Chemistry: Theories and Models”, John Willey & Sons. 2 edition (October 29, 2004)

4. Philips / Mathews,“Advanced Chemistry: Physical and Industrial”, Cambridge University Press.(12 Dec. 1991)

Semester-II

	Semester 2		Credit hours	Shifting Order
Course Categories	Course Code	Courses title	Lectures
Compulsory-VI	ENG-102	English II	3(3+0)
Compulsory-VII	ISM-101	Islamic Studies/Ethics	2(2+0)
Compulsory-VIII	MTH-102	Mathematics II	3(3+0)
Foundation II	BCH-101	Introductory Biochemistry	4(3+1)
General-I	BIF -202	Programming Fundamentals	4(3+1)	I II
Total Credit Hours			16

ENG-102 English II 3(3+0)

Objectives:

The course aims to:

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

Books Recommended:

Boutin, Marie-Chrisitine, Brinandm, S., Grellet, F. 1993. Writing: Intermediate. Oxford Supplementary Skills. Fourth Impression.

Nolasco, R. 1992. Writing: Upper-Intermediate. Oxford Supplementary Skills. Fourth Impression. (particularly good for writing memos, introduction to presentations, descriptive and argumentative writing).

Tomlinson, B., Ellis, R. 1991. Reading. Advanced. Oxford Supplementary Skills. Third Impression.

Thomson, A.J., Martinet, A.V. 1986. Practical English Grammar Exercises 2. 3^rd Ed. Oxford University Press.

ISM-101 ISLAMIC STUDIES/ETHICS 2(2+0)

Objectives:

This course is aimed at:

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

Course Contents:

Introduction to Quranic Studies: Basic Concepts of Quran: History of Quran; Uloom-ul -Quran

Study of Selected Text of Holly Quran: Verses of Surah Al-Baqra Related to Faith (Verse No-284-286), Verses of Surah Al-Hujrat Related to Adab Al-Nabi

(Verse No-1-18), Verses of Surah Al-Mumanoon Related to Characteristics of faithful (Verse No-1-11), Verses of Surah al-Furqan Related to Social Ethics (Verse No.63-77), Verses of Surah Al-Inam Related to Ihkam(Verse No-152-154)

Study of Sellected Text of Holly Quran: Verses of Surah Al-Ihzab Related to Adab al-Nabi (Verse No.6,21,40,56,57,58.), Verses of Surah Al-Hashar (18,19,20) Related to thinking, Day of Judgment, Verses of Surah Al-Saf Related to Tafakar, Tadabar (Verse No-1,14)

Seerat of Holy Prophet (S.A.W) I: Life of Muhammad Bin Abdullah (Before Prophet Hood); Life of Holy Prophet (S.A.W) in Makkah; Important Lessons Derived from the life of Holy Prophet in Makkah

Seerat of Holy Prophet (S.A.W) II: Life of Holy Prophet (S.A.W) in Madina: Important Events of Life Holy Prophet in Madina; Important Lessons Derived from the life of Holy Prophet in Madina

Introduction to Sunnah: Basic Concepts of Hadith; History of Hadith; Kinds of Hadith; Uloom –ul-Hadith; Sunnah & Hadith; Legal Position of Sunnah

Selected Study from Text of Hadith

Introduction to Islamic Law & Jurisprudence: Basic Concepts of Islamic Law & Jurisprudence; History & Importance of Islamic Law & Jurisprudence; Sources of Islamic Law & Jurisprudence; Nature of Differences in Islamic Law; Islam and Sectarianism

Islamic Culture & Civilization: Basic Concepts of Islamic Culture & Civilization; Historical Development of Islamic Culture & Civilization; Characteristics of Islamic Culture & Civilization; Islamic Culture & Civilization and Contemporary Issues

Islam & Science: Basic Concepts of Islam & Science; Contributions of Muslims in the Development of Science; Quranic & Science

Islamic Economic System: Basic Concepts of Islamic Economic System; Means of Distribution of wealth in Islamic Economics; Islamic Concept of Riba; Islamic Ways of Trade & Commerce

Political System of Islam; Basic Concepts of Islamic Political System; Islamic Concept of Sovereignty; Basic Institutions of Govt. in Islam

Islamic History: Period of Khlaft-E-Rashida; Period of Ummayyads; Period of Abbasids

Social System of Islam; Basic Concepts of Social System of Islam; Elements of Family;Ethical Values of Islam.

Books Recommended:

1. Hameed ullah M, “Emergence of Islam”, IRI,Islamabad

2) Hameed ullah M, “Muslim Conduct of State”

3) Hameed ullah M. ‘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) Hasan A.1993. Principles of Islamic Jurisprudence. Islamic Research Institute, International Islamic University, Islamabad.

7) Waliullah, M.1982. Muslim Jurisprudence and the Quranic Law of Crimes. Islamic Book Service.

8) Bhatia, H.S.1989. Studies in Islamic Law, Religion and Society. Deep & Deep Publications New Delhi

9) Zia-ul-Haq M.2001. Introduction to Al Sharia Al Islamia” Allama Iqbal Open University, Islamabad.

MTH-102 MATHEMATICS-II 3(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.

Recommended Books:

Latest editions of following books

1. Thomas Finney, “Calculus”,Penguin; 12 edition (September 12, 2009)

2. Doniel D. Benice, “Brief Calculus and its applications”, Houghton Mifflin College Division: 13 edition (February 9, 2013)

3. Raymond A. Barnett, “Applied Calculus”,Prentice Hall; 5 edition (November 4, 2013)

4. Gerald L. Bradley, “Calculus”, Hoffman, McGraw Hill: (October 1, 2000)

5. Earl W. Swokowski, Michael Olinick, “Calculus 6ed (1996)

6. James Stewart, “Calculus” 7^th edition

BCH-102 INTRODUCTORY BIOCHEMISTRY 3(3+1)

Prerequisite: None

Specific objectives of the course:

The course will provide fundamental knowledge about chemistry of biomolecules.

Course Outline:

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

Lab Outline:

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

Recommended Books:

Latest editions of the following books

1.Nelson and Michel, “Lehninger:Principles of Biochemistry”, Freeman and Company.

6th edition edition (13 Feb. 2013)

2.Devlin and Thomas,“Text book of Biochemistry with Clinical Correlations”, John Willey and Sons. 7 edition (January 19, 2010)

3.Campbell M. and Shawn F,“Biochemistry”, Cengage Learning. 7 edition (January 1, 2011)

4.Voet and Voet, “Biochemistry”, John Wiley and Sons, 3 edition (March 9, 2004)

5. Jeremy M. Berg, John L., T, STRYER L,“Biochemistry”, WH Freeman & Co: 1, edition (January 9, 2009)

BIF-202 Programming Fundamentals 4(3+1)

Prerequisite: Basic Math

Specific objectives of the course:

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

Course Outline:

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

Lab Outline:

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

Recommended Books:

Latest editions of following books

1.R. P. Halpern, “C for Yourself – Learning C Using Experiments”, OxfordUniversity Press: 1 edition (February 20, 1997)

2.Yashwant Kanetkar, “Let us C”, Jones & Bartlett Learning ; 8 edition (March 21, 2008)

3.Robert Lafore, “Turbo C. Programming for PC”, Prentice Hall; Rev Sub edition (November 1, 1988)

Semester-III

	Semester 3		Credit hours	Shifting Order
Course Categories	Course Code	Courses title	Lectures
Compulsory-IX	ENG-201	English III (Writing & Comm)	3(3+0)
Foundation-III	BIF-204	Essential of Genetics	4(3+1)	IV III
General-II	CS-202	Object Oriented Programming	3(2+1)	II III
Foundation-IV	BCH-334	Molecular Biology	4(3+1)	V II
Foundation-V	MTH-201	Linear Algebra and Differential Equations	3(3+0)
Total Credit Hours			17

ENG-201 English III (Writing and Communication) 3(3+0)

Objectives:

The course aims to:

Enhance language skills
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

Books Recommended:

Langan, J. 2004. College Writing Skills McGraw-Hill Higher Education.

Kirszner. L.G., Mandell, S. R. Patterns of College Writing. 4th Ed. by St. Martin’s Press.

White, R. 1992. Advanced Writing. Oxford Supplementary Skills. Third Impression (particularly suitable for discursive, descriptive, argumentative and report writing).

Presentation Skills.

Neulib, J., Cain, K. S., Ruffus, S., Scharton, M. (Editors). Reading. The Mercury Reader. A Custom Publication. Compiled by Northern Illinois University. (A reader which will give students exposure to the best of twentieth century literature, without taxing the taste of engineering students).

BIF-204 Essentials of Genetics 3+1

Prerequisite: Biochemistry 1

Specific objectives of the course:

This course provides the basic principles of inheritance and students will gain experience in variety of techniques used in gene analysis.

Course Outline:

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

Lab Contents:

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

Recommended Books:

Latest editions of following books

1.Strickburger, “Genetics”, Mac Millan; 5 edition (January 10, 2014)

2.Gardner, “Principles of Genetics”, John Wiley and Sons. , 5 edition (December 22, 2008)

3.Griffith et al., “An Introduction to Genetics analysis”, W. H. Freeman. , 11 Edition edition (January 12, 2015)

4.William S. Klug, Michael Cummings,“Essentials of Genetics”, Pearson/Prentice Hall. 8 edition (October 22, 2012)

5.Ricky Lewis,“Human Genetics”, McGraw Hill. 11 edition (September 10, 2014)

BCH-334 Molecular Biology 4(3+1)

Prerequisite: Biochemistry 1

Specific objectives of the course:

This course is designed to teach the students about organization of genetic material, regulation of gene expression and translation.

Course Outline:

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

Lab Outline:

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

Recommended Books:

Latest editions of following books

1.Robert Weaver,“Molecular Biology”, McGraw Hill.4 edition January 27, 2007

2.Benjamin Lewin,“Genes XI”, Pearson/Prentice Hall. 11 edition (December 31, 2012)

3.Gerald Karp,“Cell and Molecular Biology concepts and Experiments”, John Willey and Sons. 7 edition (January 22, 2013)

4.Brown T. A.,“Molecular Biology Lab .FEX”, Academic Press Publication.

5.Lodish H. et al., “Molecular Cell Biology”, W.H. Freeman. 7 edition (May 2, 2012)

6.Bruce Alberts et al., “Molecular Biology of Cell”, Garland Science. 6 edition (November 18, 2014)

7.Reece et al., “Campbell Biology”, Pearson. 10 edition (November 10, 2013)

8.David Clark,“Molecular Biology”, Elsevier. 2 edition (February 27, 2012)

CS-202 Object Oriented Programming 3(2+1)

Prerequisite (s): Programming Fundamentals

Specific objectives of the course:

The course focuses on object-oriented concepts, analysis and software development.

Course Outline:

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

Lab Outline: Programs formulation according to the Course outlines.

Recommended Book:

Latest editions of following books:

1.Ivor Horton, “Beginning Java”,Wrox; 7 Edition edition (September 27, 2011)

2. Herbert Schildt, “Java: The Complete Reference”, Mcgraw-HillOsborne Media.; 9 edition (April 1, 2014)

3. Robert Lafore, “Object Oriented Programming in C++”, Sams Publishing; 4 edition (December 29, 2001)

4. Deitel&Deitel, “JAVA: How To Program”,Prentice Hall; ; 10 edition (March 6, 2014)

MTH-201 Linear Algebra and Differential Equations 3(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, systems of non-homogeneous and homogeneous linear equations, determinants, properties of determinants of order, axiomatic definition of a determinant, ordinary differential equations of first order, initial and boundary conditions, methods of solution of non-homogeneous and homogeneous differential equations, separable equation, linear differential equations, Bernoulli equations, applications of first order differential equations, Higher order linear differential equations, homogeneous linear differential equations, solution of higher order differential equations.

Recommended Books:

Latest editions of following books

1.David C. Lay, “Linear Algebra and its applications”, Pearson Addison Wesley; ; 5 edition (January 3, 2015)

2.Michael Greenberg, “Advanced Engineering Mathematics”, Pearson: 2 edition (January 18, 1998)

3.Erwin Kreyszig, “Advanced Engineering Mathematics”, John Wiley & Sons: 10 edition (August 16, 2011)

4. Dennis Zill “Differential Equations” 3^rd edition.

Semester-IV

	Semester 4		Credit hours	Shifting Order
Course Categories	Course Code	Courses title	Lectures
General-III	SOC-101	Sociology	3(3+0)	III IV
General-IV	BIF-208	Database Management Systems	3(2+1)	III IV
Foundation-VI	BIF-206	Biochemistry	3(3+0)	III IV
Foundation-VII	BIF-205	Bioinformatics I	4(3+1)
Foundation-VIII	BIF-219	Recombinant DNA technology	4(3+1)	V IV
Total Credit Hours			17

SOC-101 Sociology 3(3+0)

Course Outline:

Social Groups – Definition and functions, Types of social groups; Social Institutions – Definition, Structure and function of social institutions, Inter-relationships among various social institutions; Culture and related concepts – Definition and aspects of culture, Elements of culture, Organization of culture, other concepts, cultural relativism, sub cultures, ethnocentrism, cultural lag; Socialization and Personality – Role and status, Socialization, Culture and personality; Deviance and Social Control – Definition and types of deviance, Juvenile delinquency, Formal and informal methods of social control ; Social Stratification – Approach to study social stratification, Caste class and race as basics of social stratification; Social Movement – Theories of social movement, Social and cultural change, Collective behavior, Social movements, Mob and crowd behavior; Social and Cultural Change – Definition of social change, Dynamics of social change, Impact of globalization on society and culture, Resistance to change.

Books Recommended:

Latest editions of following books

1. Giddens, Anthony. (2006). Sociology. Polity Press: Cambridge.

2. Macionis, John J. (2009). Society: The Basics. Prentice Hall.

3. Berger, Peter L. 1963. Invitation to Sociology: A Humanistic Perspective.

4. Tischler, Henry L. 2010. Introduction to Sociology. Wadsworth, Cengage Learning.

5. Anderson, Margaret L. &Taylor, Howard F. 2010. Sociology: The Essentials.

BIF-208 Database Management Systems 3(2+1)

Prerequisite: None

Specific objectives of the course:

The course aims to introduce basic database concepts, different data models, storage and retrieval techniques, database design techniques.

Course Outline:

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

Lab Outline:

Structured query language commands, creating and populating tables, design of simple databases, database normalization techniques, query optimization, indexing techniques, partial and full recovery techniques, developing GUI techniques, implementation of database security mechanisms, MySQL.

Recommended Books:

Latest editions of following books

1. Thomas Connolly and Steven Morris, “Database Systems: Design, Implementation& Management”, Cengage Learning; ; 11 edition (February 4, 2014)

2. Jeffrey A. Hoffer, RameshVenkataraman and HeikkiTopi, “Modern database management”, Prentice Hall; 11 edition (July 26, 2012)

3. Abraham Silberschatz, Henry Korth and S. Sudarshan, “Database system concepts”, McGraw-Hill Science; 5 edition (May 17, 2005)

4. Jeffrey A. Hoffer, Ramesh Venkataraman and HeikkiTopi, “Modern database management”, Prentice Hall; 11 edition (July 26, 2012)

Recommended Books:

Latest editions of following books

1.P.K Sinha,“Introduction to Computer Science”, (30 November 2004)

2.Glenn Brookshear, “Computer Science- An Overview”,Prentice Hall ; 12 edition (April 11, 2014)

BIF-206 Biochemistry 3(3+0)

Prerequisite: Biochemistry I

Specific objectives of the course:

This course focuses on macromolecules and their metabolisms with emphasis on various cellular pathways.

Course Outline:

Study of bioenergetics, introduction to metabolic pathways, metabolism of carbohydrates, Glycolysis, Citric acid cycle, Pentose pathway, electron transport chain, and oxidative phosphorylation, lipid metabolism, β-oxidation, ketone bodies formation and biosynthesis of triglyceride, protein metabolism, oxidative deamination and decarboxylation, transamination, amino acids metabolism, urea cycle, nucleic acid metabolism, break down and synthesis of purine and pyramidine bases

Recommended Books:

Latest editions of following books

1.Nelson and Michel,“Lehinger Principles of Biochemistry”, Freedman and Company. Sixth Edition edition (November 21, 2012)

2.Conn and Stumpf,“Outlines of Biochemistry”, John Willey and Sons. 2006

3.Devlin and Thomas,“Text book of Biochemistry with Clinical Correlations”, Wiley. 7 edition (January 19, 2010)

4.Campbell M and Shawn F,“Biochemistry”, Thomas Book Pub. 7 edition (January 1, 2011)

5. Voet and Voet,“Biochemistry”, John Wiley and Sons. 4th edition (December 1, 2010)

6. Jeremy M Berg, John L T, Stryer L, “Biochemistry”, MacMillan. 8 editions (April 8, 2015

BIF-205 Bioinformatics I 3(2+1)

Prerequisite: Computer science

Specific objectives of the course:

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

Course Outline:

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

Lab Outline:

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

Recommended Books:

Latest editions of following books

1.Arthur M. Lesk, “Introduction to Bioinformatics”, Oxford University Press. 4 edition (January 1, 2014)

2.Ignacimuthu SJ,“Basic Bioinformatics”,Narosa Publishing House. December 2004

3.YadavNeelam, “A Hand Book of Bioinformatics”,Anmal Publications Pvt.Ltd. December 1, 2004

4.Krawetz. Stephen A.,“Introduction to Bioinformatics: A Theoretical and Practical Approach”, Humana

Press. 200

BIF-219 Recombinant DNA technology 4(3+1)

Prerequisite: None

Specific objectives of the course:

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

Course Outline:

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

Lab Contents:

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

Recommended Books:

Latest editions of following books

1. Brown T. A, “Gene Cloning and DNA analysis: An introduction”, Wiley-Blackwell. 7^th edition (January

11, 2016)

2. Desmond S.T. Nicholl, “An Introduction to genetic engineering”, Cambridge University Press. 3rd Edition (December 23, 2008)

3. Hodge R and N Rosenthal, “Genetic Engineering: Manipulating the mechanism of life (Genetics and Evolution)” Facts on File.

4. Old R. W. and S. B. Primrose, “Principles of Gene manipulation, an introduction to Genetics

engineering”, Blackwell Scientific Publications. 6 edition (February 8, 2002)

Semester V

	Semester 5		Credit hours	Shifting Order
Course Categories	Course Code	Courses title	Lectures
General-V	BIF-209	Ethical and Legal Issues in Bioinformatics	3(3+0)
Major-I	BIF-200	Probability and Biostatistics	3(2+1)	IV V
Major-II	BIF-212	Bioinformatics Computing 1	4(3+1)	IV V
General-VI	CS-203	Data Structure and Algorithms	4(3+1)	VIII V
Major-III	BIF-211	Genomics	3(3+0)
Total Credit Hours			17

BIF-209 Ethical & Legal Issues in Bioinformatics 3(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. Katina Strauch and Bruce Strauch, “Legal and Ethical Issues in Acquisitions”, Routledge.

2. Tom Forester and Perry Morrison, “Computer Ethics: Cautionary Tales and Ethical Dilemmas in Computing”, The MIT Press. 2 edition (December 16, 1993)

3. Bruce A Rocheleau, “Public Management Information Systems”, Idea Group Publishing. December 13, 2005

4. Charles P. Pfleeger, Shari Lawrence Pfleeger and Jonathan Margulies, “Security in Computing”, Prentice Hall. 5 edition (February 5, 2015)

BIF-200 Probability and Biostatistics 3(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, Elementary probability theory, Laws of Probability, Conditional Probability, Introduction to Bayes Theorem Introduction to Random Variable and Probability Distributions, Binomial Distribution, Properties of binomial distribution, Poisson distribution, Normal distribution area under the normal curves, Introduction to sampling and various sampling design, Applications of Normal distributions and tests of significance,. Test of independence or association, method related to one and two means, variance and covariance, heritability and its uses, analysis of variance (ANOVA), regression analysis, Pedcheck and merlin for LOD score calculation.

Lab Outline:

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

Recommended Books:

Latest editions of following books

1.Gravetter Frederick J.,“Statistics for Behavioral Sciences”, Wadsworth publishing. 9, edition (2012)

2.Mead R Curnow R. N.,“Statistical Methods in Agriculture and Experimental Biology”. Chairman and Hall. 3 edition (August 28, 2002)

3.Mathews and Farewell,“Using and understanding Medical Statistics”, Krager New York.

5th, (July 1, 2015)

4.Ross, S.,“Introduction to Probability Models”, Elsevier. 9 edition (December 5, 2006)

5.Bernard Rosner, “Fundamentals of Biostatistics”,Cengage Learning.7 edition (August 19, 2010)

6.Wayne W. Daniel, “Biostatistics: A Foundation for Analysis in the Health Sciences”,Wiley: 10 edition (January 9, 2013)

7.Ronald E. Walpole, “Probability and Statistics for Engineering and the Sciences”, Pearson. 9 edition (January 6, 2011)

8.Steel and Torrie, “Principles and procedures of Statistics: a biometrical approach”, McGraw-Hill.

3 Sub edition (May 1, 1996)

BIF-212 Bioinformatics Computing-I 3+1

Prerequisite: Programming Fundamentals

Specific objectives of the course:

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

Course Outline:

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

Lab Outline:

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

Recommended Books:

Latest editions of following books

1.Bryan Borgeron, “Bioinformatics Computing”, Prentice Hall. 1 edition (November 29, 2002)

2.Vyas S.P. and Kohli D.V, “Methods in Biotechnology and Bioengineering”, CBS Publisher. 1st edition (June 15, 2003)

CS-203 Data Structure and Algorithms 4(3+1)

Prerequisite: Programming Fundamentals

Specific objectives of the course:

It describes data structures and explains some common data structures and their implementation.

Course Outline:

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

Lab Outline:

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

Recommended Books:

Latest editions of following books

1.Neil C. Jones, PavelPevzner, “An introduction to Bioinformatics Algorithms”,The MIT Press

edition (August 6, 2004)

2.Gary Benson and Roderic Page,“Algorithms in Bioinformatics”: (2003)

.R. Sedgewick, “Algorithms in C”, Addison-Wesley; 3 edition (September 10, 2001)

3.S. Lipschutz, “Data structures with C”,Schaum Series; 1^st edition (2010)

BIF-211 Genomics 3(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, types of genome, genome evolution, genome organization and structure , global expression profiling, microarray data analysis, genome mapping, DNA markers, linkage analysis, genome-wide screening, mutation, type of mutations, mutation identification, DNA repeats, QTL, Human Genome Project, Genevestigator, Non-coding RNAs and their regulation, siRNA, completed genomes, applications of genome analysis, Next generation sequencing.

Recommended Books:

Latest editions of following books

1. David Mount, “Bioinformatics: Sequence and Genome analysis”, Cold Spring Harbour Laboratories ; 2 edition (August 16, 2004)

2. Mount, “Bioinformatics: Sequence and Genome: Analysis”, CBS publisher & distributors New Delhi Bangalore by Spring Harbour laboratory press ; 2 edition (August 16, 2004)

3. Tom Strachan and Andrew Read, “Human Molecular Genetics”, Garland Science; 4 edition (April 2, 2010)

4. T.A. Brown, “Genome”, Garland Science ; 3 edition (May 3, 2006)

5. Arthur M. Lesk, “Introduction to Genomics”, Oxford University Press ; 2 edition (April 26, 2012)

6. Lewin, “Gene”, Jones & Bartlett Learning; 9 edition (March 6, 2007)

Semester-VI

	Semester 6		Credit hours	Shifting Order
Categories	Course Code	Courses	Lectures
Foundation-IX	BIF-210	Bioinformatics II	3(3+0)	V VI
Major-IV	BIF-214	Proteomics	3(3+0)
Major-V	BIF-213	Modeling and Simulation	4(3+1)
Major-VI	BIF-215	Systems Biology	4(3+1)
General-VII	BIF-207	Discrete Structures	3(3+0)	IV VI
Total Credit Hours			17

BIF-210 Bioinformatics II 3(3+0)

Prerequisite (s): Bioinformatics I

Specific objectives of the course:

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

Course Outline:

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

Lab Contents:

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

Recommended Books:

Latest editions of following books

1. David Mount, “Bioinformatics: Sequence and Genome analysis”, Cold Spring Harbour Laboratories. 2 edition (August 16, 2004)

2. P. Rastogi and N. Mendiritta, “Bioinformatics: Methods and Applications: Genomics, Proteomics and Drug Discovery”, Prentice-Hall of India Pvt.Ltd. 4 Revised edition edition (July 30, 2013)

3. Richard S. Larson, “Bioinformatics and drug discovery”, Humana Press. 2nd ed. 2012 edition (July 21, 2012)

BIF-214 Proteomics 3(3+0)

Prerequisite: Biochemistry I/Molecular Biology

Specific objectives of the course:

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

Course Outline:

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

Recommended Books:

Latest editions of following books

1.Richard T., “Principles of Proteomics”, Garland Science. 2 edition (September 16, 2013)

2.Rigden D. J., “From protein structure to function with bioinformatics”, Springer. 2009 edition (February 13, 2009)

3.Hubbard S. J.,“Proteome Bioinformatics”, Humana Press. 2010 edition (May 3, 2012)

4. Rastogiet al.,“Bioinformatics methods and applications. Genomics, Proteomics and Drug discovery”, Prentice Hall of India Pvt. Limited. 4th Revised edition edition (July 30, 2013)

5.Richerd Simpson J., “Purifying Proteins for Proteomics (a laboratory manual)”, Cord Spring Harbor Laboratory Press. 1 edition (January 2004)

BIF-213 Modeling & Simulation 4(3+1)

Prerequisite: Programming Fundamentals, Probability and Biostatistics

Specific objectives of the course:

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

Course Outline:

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

Lab Outline:

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

Recommended Books:

Latest editions of following books

1. Willem van Meurs, “Modeling and Simulation in Biomedical Engineering: Applications in Cardiorespiratory Physiology”, The McGraw-Hill Companies. 1 edition (August 4, 2011)

2. John A. Sokolowski, “Principles of Modeling and Simulation: A Multidisciplinary Approach”, John Wiley 7 Sons. 1 edition (February 9, 2009)

3. Jerry Banks, “Discrete-Event System Simulation”, Prentice Hall. 5 edition (July 6, 2009)

4. Frank C. Hoppensteadt, “Modeling and Simulation in Medicine and the Life Sciences”, Springer. 2nd edition (January 16, 2004)

5. John A. Sokolowski, “Modeling and Simulation in the Medical and Health Sciences”, John Wiley& Sons. 1 edition (June 7, 2011)

BIF-215 Systems Biology 4(3+1)

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

Specific objectives of the course:

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

Course Outline

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

Recommended Books

Latest editions of following books

1. Klipp, E., Wolfram L., Christoph W., Axel K., Hans L., and Ralf H.,“Systems biology”, Wiley; ; 1 edition (24 Jun. 2009)

2. Ullah, M., and Olaf W.,“Stochastic approaches in systems biology”,Springer; ; 2011 edition (July 15, 2011)

3. Newman M.,“Networks: An Introduction”, Oxford University Press, USA; ; 1 edition (May 20, 2010)

4. Alon U.,“An introduction to systems biology: design principles of biological circuits. Boca Raton”, Chapman & Hall/CRC; ; 1 edition (July 7, 2006)

BIF-207 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:

Latest editions of following books

1. Kenneth H. Rosen, “Discrete Mathematics and Its Applications”, McGraw Hill Book Co. 7 edition

(June 14, 2011)

2. Richard Johnsonbaugh, “Discrete Mathematics”, Prentice Hall Publishers. 7 edition (December 29,

2007)

3. Kolman, Busby and Ross, “Discrete Mathematical Structures”, Prentice-Hall Publishers. 6 edition

(July 24, 2008)

4. Ralph P. Grimaldi, “Discrete and Combinatorial Mathematics: An Applied Introduction”, Pearson. 5

edition (July 27, 2003)

5. Prather R, “Elements of Discrete mathematics”, Houghton Mifflin. (March 1986)

Semester-VII

	Semester 7		Credit hours	Shifting Order
Course Categories	Course Code	Courses title	Lectures
Major-VII	BIF-216	Bioinformatics Software Engineering	3(2+1)
Major-VIII	CS-401	Artificial Intelligence	3(3+0)	VI VII
Major-IX	BIF-218	Bioinformatics Computing II	3(2+1)	VIII VII
Elective	BIF-	Elective-I	3(3+0)
Elective	BIF-	Elective-II	3(3+0)
Major-X	BIF-222	Research Project	3(0+3)
Total Credit Hours			18

BIF-216 Bioinformatics Software Engineering 2+1

Prerequisite:

Specific objectives of the course:

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

Course Outline:

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

Lab Outline:

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

Recommended Books:

Latest editions of following books

1. Pressman R. S., “Software engineering: A practitioner’s approach”, McGraw Hill. 8 edition (January 23, 2014)

2. Sommerville, “Software Engineering”, Addison Wesley. 10 edition (April 3, 2015)

3. Larman C., “Applying UML and patterns”, Prentice Hall. December 1, 2008

4. Weston P., “Bioinformatics Software Engineering: Delivering effective applications”, Wiley.

December 6, 2004

CS-401 Artificial Intelligence 3( 3+0)

Prerequisite: Programming Fundamentals, Data Structures and Algorithms

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

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

Text/ Reference books:

Latest editions of following books

1. Stuard Russell and Peter Norvig, “Artificial Intelligence: A Modern Approach”, Prentice HallInc; ; 3 edition (December 11, 2009)

2. George F. Luger, and William A. Stubblefield, “Artificial Intelligence: Structures and Strategies for Complex Problem Solving”, Addison – Wesley; 3 edition (October 1997)

3. Edward A. Bender, “Mathematical Methods in Artificial Intelligence”, Wiley IEEE Computer Society Press; ; 1 edition (February 10, 1996)

4. David W. Rolston, “Principals of Artificial Intelligence and Expert Systems Development”, Mcgraw Hill; (January 1988)

5. Robin R. Murphy, “Introduction to AI and Robotics”, A Bradford Book; 1 edition (November 13, 2000)

6. Winston and Horn,“LISP”, Addison Wesley; (October 19, 2014)

BIF-218 Bioinformatics Computing-II 3+0

Prerequisite: Bioinformatics Computing- I

Specific objectives of the course:

This course introduces advanced concepts of neural networks and pattern recognition for solving bioinformatics problems.

Course Outline:

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

Lab Outline:

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

Recommended Books:

Latest editions of following books

1.SC Rastogi, Namita M, P Rastogi, “Bioinformatics: Concepts, Skills and Applications”, CSB Publishers. 2 edition (December 1, 2009)

2.LacroixZor, Terence Critchlow, “Bioinformatics: Managing Scientific Data”, Morgan Kaufmann. 2007

Elect -I

3(3+0)

Prerequisite: None

Specific objectives of the course:

Course Outline:

Lab Outline:

Recommended Books:

Elect -II

3(3+0)

Prerequisite: None

Specific objectives of the course:

Course Outline:

Lab Outline:

Recommended Books:

BIF-222 Research Project part-I 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

	Semester 8		Credit hours	Shifting Order
Course Categories	Course Code	Courses title	Lectures
Major-XI	BIF-217	Special topics in Bioinformatics	3(3+0)	VII VIII
Major-XII	CS-304	Graphics and Visualization	4(3+1)	VI VIII
Elective	BIF-	Elective-III	3(3+0)
Elective	BIF-	Elective-IV	3(3+0)
Major-XIII	BIF-222	Research Project	3(0+3)
Total Credit Hours			16

BIF-217 Special Topics in Bioinformatics 3+0

Prerequisite: Bioinformatics-I

Specific objectives of the course:

This course intends to introduce recent advances in bioinformatics.

Course Outline:

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

CS-304 Graphics and Visualization 4(3+1)

Prerequisite: Programming Fundamentals

Specific objectives of the course:

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

Course Outline:

Introduction, Graphics hardware, fundamental algorithms, applications of graphics, interactive graphics programming, graph plotting, windows, clipping and segmentation, programming raster display systems, panning and zooming, raster algorithms and software, scan-converting lines, characters and circles, region filling, two and three dimensional imaging geometry and transformations, curve and surface design, rendering, shading, colour and animation.

Lab Outline:

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

Recommended Books:

Latest editions of following books

1.Donald Hearn, “Computer Graphics, C Version”, Prentice Hall; 2 Sub edition (May 24, 1996)

2.F. S. Hill and Stephen M. Kelly, “Computer graphics:Using Open GL”, Pearson Prentice Hall ; 2 edition (May 15, 2000)

3.T. Theoharis et al., “Graphics and Visualization-principles and algorithms”,CRC Press; October 10, 2007)

*** Elective-III 3+0

Prerequisite: None

Course Outline:

To be chosen from the list of electives

*** Elective-IV 3+0

Prerequisite: None

Course Outline:

To be chosen from the list of electives

BIF-222 Research Project part- II 0+3

Prerequisite: None

Course Outline:

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

List of Electives

1. Enzyme Kinetics

2. Functional genomics

3. Human Computer Interaction

4. Nanotechnology

5. Environmental Biotechnology

6. Special Topics in Biochemistry

7. Immuno-Informatics

8. Microbial genomics and proteomics

9. Network Biology

10. Biophysics

11. Modern programming languages

12. Methods in protein modeling

13. Pharmacoinformatics

14. Statistical methods in bioinformatics

15. Design and analysis of algorithms

16. Epigenetics and gene regulation

17. Protein chemistry

18. Microbial genetics

19. Molecular oncology

20. Immunology

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 7 edition (January 22, 2013)

Gerald Karp John Wiley and Sons

Introduction to Computational Molecular Biology 2007

Setubal, Meidanis Brooks/Cole

Principles and Techniques of Biochemistry and Molecular Biology 7 edition (April 12, 2010)

Keith Wilson, John Walker Cambridge University Press

Instant Notes: Biochemistry

B D Hames Viva Books Pvt. Ltd.

Basics of Theoretical and Computational Chemistry 1 edition (March 12, 2007)

BM Rode John Willey and Sons

Instant Notes: Genetics 1998 edition

P C Winter Viva Books Pvt. Ltd.

Instant Notes: Molecular Biology September 2005

P C Turner Viva Books Pvt. Ltd.

Molecular Cloning: A laboratory manual 4 edition (June 15, 2012)

Sambrook Cold Spring Harbor, Laboratory Press.

Instant Notes: Bioinformatics June 2002

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

Bioinformatics for Dummies 2 edition (December 18, 2006)

Jean-Michel Claverie,CedricNotredame Wiley Publishing, Inc.

Essential Bioinformatics 1 edition (March 13, 2006)

Jin Xiong Cambridge University Press.

Bioinformatics

Bal Tata McGraw-Hill.

Bioinformatics 2007 edition (May 29, 2007)

AndrzejPolański, Marek Kimmel Springer.

Bioinformatics: An Introduction 3 ed. 2015 edition (May 20, 2015)

Jeremy Ramsden Springer.

Bioinformatics: A Concept-based Introduction 1 ed. 2009 edition (November 4, 2010)

Venkatarajan Subramanian Mathura, PandjassarameKangueane Springer.

Bioinformatics: Tools and Applications 2009 edition

David Edwards, Jason Eric Stajich, David Hansen Springer.

Bioinformatics: Principles and Basic Internet Applications July 6, 2006

Hassan A. Sadek Trafford Publishing, Canada.

Bioinformatics: Applications in Life and Environmental Sciences 1st ed. 2009 edition

M. H. Fulekar Springer.

Bioinformatics: A Practical Approach August 20, 2007

Shui Qing Ye Chapman & Hall / CRC.

Applied Bioinformatics: An Introduction 2008 edition (February 6, 2008)

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

Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins 3 edition (October 29, 2004)

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

Bioinformatics: a Swiss perspective April 24, 2009

Ron D. Appel, Ernest Feytmans World Scientific, Singapore.

Bioinformatics: Genomics and Post-genomics 1 edition (September 11, 2006)

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

Bioinformatics: Methods and Applications: Genomics, Proteomics and Drug Discovery 4 Revised edition edition (July 30, 2013)

S. C. Rastogi, NamitaMendiratta, ParagRastogi PHI Learning Pvt. Ltd.

Bioinformatics and drug discovery 2006 edition (October 1, 2005)

Richard S. Larson Humana Press.

Computational molecular biology: an algorithmic approach 2004

PavelPevzner MIT Press.

Bioinformatics algorithms: techniques and applications 1 edition (February 25, 2008)

Ion Măndoiu, Alexander Zelikovsky Wiley-Interscience.

Bioinformatics: problem solving paradigms 1 ed. 2008 edition (November 19, 2010)

Volker Sperschneider, Jana Sperschneider, Lena Scheubert Springer.

Parallel computing for bioinformatics and computational biology 1 edition (April 21, 2006)

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

Research and trends in data mining technologies and applications February 5, 2007

David Taniar Idea Group Inc (IGI).

Machine learning in bioinformatics 1 edition (December 3, 2008)

Yan-Qing Zhang, JagathChandanaRajapakse John Wiley and Sons.

Computational Intelligence in Bioinformatics 1 ed. 2008 edition (November 19, 2010)

ÁrpádKelemen, Ajith Abraham, Yuehui Chen Springer.

Bioinformatics and the Cell: Modern Computational Approaches in Genomics, Proteomics and Transcriptomics 1 ed. 2007 edition (November 4, 2010)

Xuhua Xia Springer.

Bioinformatics for Dummies 2 edition (2006)

Jean-Michel Claverie and CerdricNotredame

Bioinformatics-Sequence and Genome Analysis 2nd edition (2004)

David W. Mount.

Introduction to Bioinformatics 1 Ed. edition (2007)

T K Attwood and D J Parry-Smith.

Bioinformatics-Gene, Proteins and Computers 1 edition (2003)

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

New Courses need to be add

Course name: immunological bioinformatics

General Program:

Introduction to bioinformatics and immunology, immunoinformatics, the immune system, cellular immunity, antibody mediated immunity, virus infection, vaccine design, modeling the immune system in the genome era, information theory of the immune system, databases and web resources in immunological bioinformatics, systems biology, experimental and theoretical description of peptide-MHC binding, prediction of T-cell epitopes using neural networks, selection of epitopes using bioinformatics, prediction of proteasome processing, and TAP binding, DNA vaccines and maturation of the immune response, discovery of disease related genes using analysis of DNA array data, modeling of structural epitopes, vaccination against allergy, practical exercises in alignment, database search and prediction.

Prerequisites:
All students from DTU and other universities are welcome. Prerequisites are DTU courses 27611 or 27321 or equivalents, i.e., basic knowledge of either immunology or bioinformatics. The course is a combination of lectures and exercises, and will be conducted in English.