UNIVERSITY OF RAJASTHAN, JAIPUR
Five Year Integrated B.Sc.-M.Sc. Bioinformatics
Bioinformatics derives knowledge from computer analysis of biological data. These can consist of the information stored in the genetic code, but also experimental results from various sources, patient statistics, and scientific literature. Research in bioinformatics includes method development for storage, retrieval, and analysis of the data. Bioinformatics is a rapidly developing branch of biology and is highly interdisciplinary, using techniques and concepts from informatics, statistics, mathematics, chemistry, biochemistry, physics, and linguistics. It has many practical applications in different areas of biology and medicine.
University of Rajasthan of India is set to launch a Bioinformatics course, for the promotion, growth and prosperity of bioinformatics sciences in Rajasthan. The course has been designed for educational, R&D and development centre of bioinformatics etc. The aim and vision of the curriculum are to provide a broad-base guideline for the development of human resources for individuals, professionals, R&D Organisations, Pharmaceutical & Software companies to utilize and harness the Rajasthan's budding and aspiring bioinformatics potential. The curriculum aims not only educational and research initiative in this direction but also vouch for creating a talent pool of professionals from various fields who can contribute for the growth and prosperity of Bioinformatics/ cheminformatics / Biomedical informatics as a career .
Fields Related to Bioinformatics
Bioinformatics has various applications in research in medicine, biotechnology, agriculture etc. Following research fields has integral component of Bioinformatics
- Computational Biology: The development and application of data-analytical and theoretical methods, mathematical modelling and computational simulation techniques to the study of biological, behavioural, and social systems.
- Genomics : Genomics is any attempt to analyze or compare the entire genetic complement of a species or species (plural). It is, of course possible to compare genomes by comparing more-or-less representative subsets of genes within genomes.
- Proteomics : Proteomics is the study of proteins - their location, structure and function. It is the identification, characterization and quantification of all proteins involved in a particular pathway, organelle, cell, tissue, organ or organism that can be studied in concert to provide accurate and comprehensive data about that system.
Proteomics is the study of the function of all expressed proteins. The study of the proteome, called proteomics, now evokes not only all the proteins in any given cell, but also the set of all protein isoforms and modifications, the interactions between them, the structural description of proteins and their higher-order complexes, and for that matter almost everything 'post-genomic'. - Pharmacogenomics : Pharmacogenomics is the application of genomic approaches and technologies to the identification of drug targets. In Short, pharmacogenomics is using genetic information to predict whether a drug will help make a patient well or sick. It Studies how genes influence the response of humans to drugs, from the population to the molecular level.
- Pharmacogenetics : Pharmacogenetics is the study of how the actions of and reactions to drugs vary with the patient's genes. All individuals respond differently to drug treatments; some positively, others with little obvious change in their conditions and yet others with side effects or allergic reactions. Much of this variation is known to have a genetic basis. Pharmacogenetics is a subset of pharmacogenomics which uses genomic/bioinformatics methods to identify genomic correlates.
- Cheminformatics : The mixing of those information resources [information technology and information management to transform data into information and information into knowledge for the intended purpose of making better decisions faster in the arena of drug lead identification and optimization. Related fields of cheminformatics are chemi-informatics, chemometrics, computational chemistry, chemical informatics, chemical information management/science, and cheminformatics.
Structural genomics or structural bioinformatics refers to the analysis of macromolecular structure particularly proteins, using computational tools and theoretical frameworks. One of the goals of structural genomics is the extension of idea of genomics, to obtain accurate three-dimensional structural models for all known protein families, protein domains or protein folds. Structural alignment is a tool of structural genomics. - Comparative genomics: The study of human genetics by comparisons with model organisms such as mice, the fruit fly, and the bacterium E. coli .
- Biophysics: The British Biophysical Society defines biophysics as: "an interdisciplinary field which applies techniques from the physical sciences to understanding biological structure and function".
- Biomedical informatics / Medical informatics: Biomedical Informatics is an emerging discipline that has been defined as the study, invention, and implementation of structures and algorithms to improve communication, understanding and management of medical information.
- Mathematical Biology: Mathematical biology also tackles biological problems, but the methods it uses to tackle them need not be numerical and need not be implemented in software or hardware. It includes things of theoretical interest which are not necessarily algorithmic, not necessarily molecular in nature, and are not necessarily useful in analyzing collected data.
- Computational Chemistry: Computational chemistry is the branch of theoretical chemistry whose major goals are to create efficient computer programs that calculate the properties of molecules (such as total energy, dipole moment, vibrational frequencies) and to apply these programs to concrete chemical objects. It is also sometimes used to cover the areas of overlap between computer science and chemistry.
- Functional Genomics: Functional genomics is a field of molecular biology that is attempting to make use of the vast wealth of data produced by genome sequencing projects to describe genome function. Functional genomics uses high-through put techniques like DNA microarrays, proteomics, metabolomics and mutation analysis to describe the function and interactions of genes.
- Pharmacoinformatics: Pharmacoinformatics concentrates on the aspects of bioinformatics dealing with drug discovery
- Agroinformatics / Agricultural Informatics: Agroinformatics concentrates on the aspects of bioinformatics dealing with plant genomes.
- Systems Biology: Systems biology is the coordinated study of biological systems by investigating the components of cellular networks and their interactions, by applying experimental high-throughput and whole-genome techniques, and integrating computational methods with experimental efforts.
- There will be 10 Semesters in all
- Each paper is of 100 marks.
- Practical in each semester would be of 200 marks.
- There will be optional papers in VIII & IX Semesters.
With reference to Bio-informatics the following provision are made in the syllabus of B.Sc. and M.Sc. Bio-informatics Integrated courses:
Those students who have failed in B.Sc. Bioinformatics Integrated in 1st year shall have to appear as per revised course B.Sc. (Bioinformatics) Integrated in the session 2006-07. Such students shall also appear in Practical Examinations as per revised syllabus. Those students who have failed in II Year and III Year and due papers shall appear as per last year syllabus B.Sc. Bioinformatics (Integrated) course of the Examination, 2006.
The students of B.Sc-M.Sc. Integrated course shall not be required to appear in compulsory subjects as it is in the case of other professional courses like BBA, BCA, B. Pharma., CCT (5 -years course) run by the University. The course itself has more courses content of Environmental Technology and there is no need of repetition of the subject as compulsory papers.
First Semester Second SemesterThird Semester Fourth SemesterFifth SemesterSixth SemesterFive Year Integrated B.Sc- M.Sc. Bioinformatics
I -Semester
| PAPER CODE | PAPER TITLE | TEACHNG SCHEDULE
(Hours/Week) *for Tutorial/Seminar |
UNIVERSITY EXAM THEORY/PRACTICAL DUARATION | INTERNAL UNIVERSITY EXAM. THEORY/PRACTICAL DUARATION | TOTAL THEORY/PRACTICAL | |||
| Lecture | Practical | Hrs | Marks | Hrs | Marks | Maximum Marks | ||
| BIT-101 | Elementary Mathematics | 5+1* | 3 | 3 | 80/40 | 2 | 20/10 | 100/50 |
| BIT-102 | Computer fundamentals-I | 5+1* | 3 | 3 | 80/40 | 2 | 20/10 | 100/50 |
| BIT-103 | Programming Language Fundamentals and Applications | 5+1* | 3 | 3 | 80/40 | 2 | 20/10 | 100/50 |
| BIT-104 | Cell Biology and Genetics | 5+1* | 3 | 3 | 80/40 | 2 | 20/10 | 100/50 |
| THEORY | TOTAL | 30 | 12 | 12 | 320 | 8 | 80 | 400 |
| PRACTICAL | TOTAL | 160 | 40 | 200 | ||||
- It comprises all the practicals based on the above theory papers.
- The provision of communication skill and for proficiency in English as well as Hindi should also be made in practicals (one hour duration each on Monday and Saturday in such a manner that any exercise should begin on Monday may also assign homework to be tested on Saturday throughout the session)
- Examiner is supposed to test this and allocate 20% marks in the practical.
Five Year Integrated M.Sc. Bioinformatics
- There will be 10 Semesters in all
- Each paper is of 100 marks.
- Practical in each semester would be of 200 marks.
- There will be optional papers in VIII & IX Semesters.
YEAR I
I SEMESTER
BIT-101 Elementary Mathematics BIT-102 PC Software and Hardware Troubleshooting BIT-103 Programming Language Fundamentals and Applications BIT-104 Cell Biology and Genetics
Semester-I
BIT-101 Elementary Mathematics
Unit-I
Algebra :
Sets, Relations, functions, complex numbers, square root of a complex number and cube root of unity, sequences, AP, GP and HP series; AM, GM and HM; Exponential and Logarithmic series and their sum. Permutation and combination. Bionomial Theorem and its applications. Matrices and Determinants; Inverse of a matrix and its applications for solving linear equations in two or three variables.
Unit-II
Calculus :
Limit of a function, continuity of a function. Differentiation of a function and its physical significance. Derivative of polynomial, trigonometric exponential, logarithrmic, inverse trigonometric and implicit functions.
Integration of a function, Integration by substitution, partial fraction and their use in rational functions.
Unit-III
Definite integrals and its properties. Applications of definite integrals in finding areas bounded by a curve and area between two curves.
Order and degree of a differential equation, General and particular solutions, solution of homogenous differential equation of first order, solution of a linear differential equation.
Unit-IV
Geometry :
Two-dimensional coordinate geometry :
Cartesian system of coordinates in a plane, distance and section formulae, area of a triangle, condition of collinearity of three points in a plane, slope of a line, parallel and perpendicular lines, two point form; intercept, normal and general forms of a line, angle between two lines. Equations of circles, Parabola, Ellipse and Hyperbola; equations of their tangents.
Units-V
Three dimensional coordinate Geometry :
Coordinates of a point in three-dimensional space. Section formula. Direction ratios and cosines of a line joining two points, angle between two lines, condition for intersection of two lines, collinearity of three points, shortest distance between two lines. Equation of plane, condition of co-planarity of two lines, Angle between tow planes. Equation of a sphere - its centre and radius. Diameter form of equation of a sphere
Books :
- Binmore, "Mathematical Analysis". Cambridge University. Press.
- NCERT, New Delhi (Books related to above cited topics)
BIT-102: PC Software and Hardware Troubleshooting
Unit I: Introduction
Concept of Window, Icon, Menu, Desktop, Creating Folder and Shortcuts, Searching Files and Folders in System, Creating Files, Copying , Moving and Deleting Files, Adding programs in Start Menu, Deleting Programs from Start Menu, Using Windows Explorer utility, Introduction about System software's and Application Software's with Examples
Unit II: Word Processing Package
Introduction about MS Word, Structure of a Document, Document Creation, Editing, Saving, spell check Proofing & Reviewing, Formatting Text & Paragraphs, Introduction about all menus in MS Word, Automatic Formatting and Styles, Working with Tables, Mail Merge, AutoText and AutoShapes, Word Art & Clip art, Macros, Printing Documents.
Unit III: Spreadsheet Package
Concept of Spreadsheet, Introduction about MS Excel, Basic and Advance Features of MS Excel, Use of Mathematical, Financial and statistical Functions, Sorting and Searching Data, Filtering Data, linking Workbooks, using Formulas, Protecting and Hiding Data, Formatting a worksheet, Creating Graphic Objects, Charts (Graphs), Sharing and Importing Data, Printing Worksheets, Macros, Pivot Table and Pivot Chart Reports.
Unit IV: Presentation Package
Introduction about MS Power Point, Creating and Editing Slides, Using Objects on slides, Putting Animation and Sound effect on slides, Transition Effects on Slide, Different Views of Slides: Normal, Slide Sorter, Slide Show, and Notes Page; Printing slides, Using Macros, Comparing and Merging Presentations, Autocorrect Options, Recording Narrations, Templates, Introduction about Master Slides, Object Embedded Linking.
Unit V: Introduction of Hardware Troubleshooting
Working of a PC, Individual Components of a PC and their Functionality, Tools and Equipments such as: Screw Drivers, Crimping Tools, Multimeter etc; System Configuration, BIOS/CMOS Setting, System Resources, I/O Buses, IDE Devices, SCSI Devices, Peripheral Devices, Motherboard and its components, Architecture of Motherboard and its Troubleshooting, Different Printers Connection, Configuration and Troubleshooting; Establishing Network, Overview of Network Devices, Network Interface Cards (NIC), Creating Different Network Cables: Straight and Cross Cables; Troubleshooting Network Problems, Get Acquainted with Different Network Standards.
References:
- Introduction to Computers - Peter Norton, TMH
- Upgrading and Repairing PC - Scott Muller, QUE
- Upgrading and Repairing Network - Scott Muller, QUE
- Using MS Office 2000 - Bott - PHI
BIT 103 : Programming Language Fundamentals and Applications
Unit I
Basic concepts of programming languages: Programming domains, language evaluation criterion and language categories, evolution of the major programming languages . Describing Syntax and Semantics, formal methods of describing syntax, recursive descent parsing, attribute grammars, dynamic semantics.
Unit II
Names, Variables, Binding, Type checking, Scope and lifetime data types, array types, record types, union types, set types and pointer types, arithmetic expressions, type conversions, relational and Boolean expressions, assignment statements, mixed mode assignment. Statement level control structures, compound statements, selection statement, iterative statements, unconditional branching, guarded commands.
Unit III
Subprogram, fundamentals of subprogram, design issues, parameter passing methods, overloaded subprograms, generic subprograms, separate and independent compilation, design issues for functions, accessing nonlocal environment, user defined overloaded operators, coroutines, implementing subprograms, blocks, implementing dynamic scooping.
Programming in C:
Unit IV
Character set, variables and constants, keywords, Instructions, assignment statements, arithmetic expression, comment statements, simple input and output, Boolean expressions, Relational operators, logical operators, control structures, decision control structure, loop control structure, case control structure, functions, subroutines, scope and lifetime of identifiers, parameter passing mechanism,
Unit V
Arrays and strings, structures, array of structures, Console Input and Output functions, Disk I/O functions, Interaction with hardware, Interrupts and Interrupt Vector table, Unions of structures, operations on bits, usage of enumerated data types. Bit-fields, Pointers to Function, Function returning Pointers.
Recommended reference books:
- Robert W. Sebesta: Concepts of Programming Language, Addison Wesley, Pearson Education Asia, 1999.
- Ramon A. Mata-Toledo and Pauline K. Cushman: Introduction to Computer Science, McGraw Hill International Edition.
- D. Appleby and J J Vande Kopple: Programming Languages, Tata McGraw Hill, India.
- Deitel and Deitel: How to Program C, Addison Wesley, Pearson Education Asia, 1999.
- Bryon Gottfried, Programming with C, McGraw Hill International.
BIT 104-Cell Biology and Genetics
Unit I
- Introduction to cell: Morphology, size, shape and characteristics of Prokaryotic, Eukaryotic, Plant and animal cells; basic idea of virus and cell-theory.
- Cell membrane: Characteristics of cell membrane molecules, fluid-mosaic model of Singer and Nicolson, concept of unit membrane.
- Cell membrane transport: Passive (diffusion and osmosis facilitated (mediated) and active transport.
Unit II
- Cytoplasmic organelles:
- Structure and biogenesis of mitochondria; electron transport chain and generation of ATP molecules (chemiosmotic hypothesis of Mitchele)
- Structure and function of endoplasmic reticulum, ribosome (Prokayotic and eukaryotic) and Golgi complex.
- Structure and function of lysosome, microbodies and centrioles.
- Structure and functions of cilia, flagella, microvilli and cytoskeletal elements.
Unit III
- Nucleus :
- Structure and function of nuclear envelope, nuclear matrix and nucleolus.
- chromosomes: Morphology, chromonema, chromomeres, telomeres, primary and secondary constrictions, chromatids; prokaryotic chromosome.
- Chromosome type: Polytene and lampbrush.
- Chromosomal organization: Euchromatin, heterochromatin and folded fibre model and nucleosome concept.
- Nucleic Acids :
- DNA structure, polymorphism (A, B, Z type) and replication (semi- conservative mechanism), experiments of Messelson and Stahl: elementary idea about polymerases topoisomerase, single strand binding protein, replication forks (both unidirectional and bidirectional), leading and lagging strands, RA primers and Okazaki fragments; elementary idea about DNA repairs.
- RNA structure and type (mRNA, rRNA and tRNA) and transcription (idea about polymerase, exon and introns)
- Genetic Code and Translation, triplet code, characteristics of triplet code; protein synthesis (translation)
- Cell in Reproduction :
- Interphase nucleus and cell cycle S, G-a, G-2, M-phase.
- Mitosis : Phases and process mitosis structure and function of spindle apparatus; anaphases movement.
- Meiosis : Phase and process of meiosis, synapses and synaptonemal complex, formation and fate of chiasmata and significance of the crossing over.
Unit IV
- Mendelism : Brief history of genetic and Mendel's work; Mendelian law, their significance and current status; chromosomal theory of inheritance.
- Chromosomal mutations: Classification of chromosomal mutations, translocation, inversion deletion and duplication variation in chromosome numbers; haploidy, diploidy, polyploidy, aneuploidy, euploidy and polysomy.
Unit V
- Linkage and crossing over, elementary idea of chromosome mapping.
- Genetic interaction : supplementary genes complementary genes, duplicate genes, epistasis inhibitory and polymorphic genes multiple gene inheritance ABO blood group and Rh factor and their significance.
- Cytoplasmic inheritance.
PAPER CODE PAPER
TITLE
TEACHNG SCHEDULE
(Hours/Week)
* for Tutorial/seminar
UNIVERSITY EXAM
THEORY/PRACTICAL
DUARATION
INTERNAL UNIVERSITY EXAM.
THEORY/PRACTICAL
DUARATION
TOTAL THEORY/PRACTICAL
Lecture
Practical
Hrs
Marks
Hrs
Marks
Maximum Marks BIT-201
Immunology, Microbiology
Biotechnology
5+1*
3
3
80/40
2
20/10
100/50 BIT-202
Discrete Mathematics
5+1*
3
3
80/40
2
20/10
100/50 BIT-203
Database Management Systems
5+1*
3
3
80/40
2
20/10
100/50 BIT-204
Biological Chemistry
5+1*
3
3
80/40
2
20/10
100/50 THEORY
TOTAL
30
12
12
320
8
80
400 PRACTICAL
TOTAL 160 40
200
Practicals:
- It comprises all the practicals based on the above theory papers.
- The provision of communication skill and for proficiency in English as well as Hindi should also be made in practicals (one hour duration each on Monday and Saturday in such a manner that any exercise should begin on Monday may also assign homework to be tested on Saturday throughout the session)
- Examiner is supposed to test this and allocate 20% marks in the practical.
BIT-201.
Immunology, Microbiology & Biotechnology BIT-202.
Discrete Mathematics BIT-203
Database Management Systems BIT-204
Biological Chemistry
BIT-201: Immunology, Microbiology & Biotechnology
I SEMESTER
Semester-I
BIT-101 Elementary Mathematics
Algebra :
Sets, Relations, functions, complex numbers, square root of a complex number and cube root of unity, sequences, AP, GP and HP series; AM, GM and HM; Exponential and Logarithmic series and their sum. Permutation and combination. Bionomial Theorem and its applications. Matrices and Determinants; Inverse of a matrix and its applications for solving linear equations in two or three variables.
Unit-II
Calculus :
Limit of a function, continuity of a function. Differentiation of a function and its physical significance. Derivative of polynomial, trigonometric exponential, logarithrmic, inverse trigonometric and implicit functions.
Integration of a function, Integration by substitution, partial fraction and their use in rational functions.
Unit-III
Definite integrals and its properties. Applications of definite integrals in finding areas bounded by a curve and area between two curves.
Order and degree of a differential equation, General and particular solutions, solution of homogenous differential equation of first order, solution of a linear differential equation.
Unit-IV
Geometry :
Two-dimensional coordinate geometry :
Cartesian system of coordinates in a plane, distance and section formulae, area of a triangle, condition of collinearity of three points in a plane, slope of a line, parallel and perpendicular lines, two point form; intercept, normal and general forms of a line, angle between two lines. Equations of circles, Parabola, Ellipse and Hyperbola; equations of their tangents.
Units-V
Three dimensional coordinate Geometry :
Coordinates of a point in three-dimensional space. Section formula. Direction ratios and cosines of a line joining two points, angle between two lines, condition for intersection of two lines, collinearity of three points, shortest distance between two lines. Equation of plane, condition of co-planarity of two lines, Angle between tow planes. Equation of a sphere - its centre and radius. Diameter form of equation of a sphere
Books :
- Binmore, "Mathematical Analysis". Cambridge University. Press.
- NCERT, New Delhi (Books related to above cited topics)
BIT-102: PC Software and Hardware Troubleshooting
Unit I: IntroductionConcept of Window, Icon, Menu, Desktop, Creating Folder and Shortcuts, Searching Files and Folders in System, Creating Files, Copying , Moving and Deleting Files, Adding programs in Start Menu, Deleting Programs from Start Menu, Using Windows Explorer utility, Introduction about System software's and Application Software's with Examples
Unit II: Word Processing Package
Introduction about MS Word, Structure of a Document, Document Creation, Editing, Saving, spell check Proofing & Reviewing, Formatting Text & Paragraphs, Introduction about all menus in MS Word, Automatic Formatting and Styles, Working with Tables, Mail Merge, AutoText and AutoShapes, Word Art & Clip art, Macros, Printing Documents.
Unit III: Spreadsheet Package
Concept of Spreadsheet, Introduction about MS Excel, Basic and Advance Features of MS Excel, Use of Mathematical, Financial and statistical Functions, Sorting and Searching Data, Filtering Data, linking Workbooks, using Formulas, Protecting and Hiding Data, Formatting a worksheet, Creating Graphic Objects, Charts (Graphs), Sharing and Importing Data, Printing Worksheets, Macros, Pivot Table and Pivot Chart Reports.
Unit IV: Presentation Package
Introduction about MS Power Point, Creating and Editing Slides, Using Objects on slides, Putting Animation and Sound effect on slides, Transition Effects on Slide, Different Views of Slides: Normal, Slide Sorter, Slide Show, and Notes Page; Printing slides, Using Macros, Comparing and Merging Presentations, Autocorrect Options, Recording Narrations, Templates, Introduction about Master Slides, Object Embedded Linking.
Unit V: Introduction of Hardware Troubleshooting
Working of a PC, Individual Components of a PC and their Functionality, Tools and Equipments such as: Screw Drivers, Crimping Tools, Multimeter etc; System Configuration, BIOS/CMOS Setting, System Resources, I/O Buses, IDE Devices, SCSI Devices, Peripheral Devices, Motherboard and its components, Architecture of Motherboard and its Troubleshooting, Different Printers Connection, Configuration and Troubleshooting; Establishing Network, Overview of Network Devices, Network Interface Cards (NIC), Creating Different Network Cables: Straight and Cross Cables; Troubleshooting Network Problems, Get Acquainted with Different Network Standards.
References:
- Introduction to Computers - Peter Norton, TMH
- Upgrading and Repairing PC - Scott Muller, QUE
- Upgrading and Repairing Network - Scott Muller, QUE
- Using MS Office 2000 - Bott - PHI
BIT 103 : Programming Language Fundamentals and Applications
Unit IBasic concepts of programming languages: Programming domains, language evaluation criterion and language categories, evolution of the major programming languages . Describing Syntax and Semantics, formal methods of describing syntax, recursive descent parsing, attribute grammars, dynamic semantics.
Unit II
Names, Variables, Binding, Type checking, Scope and lifetime data types, array types, record types, union types, set types and pointer types, arithmetic expressions, type conversions, relational and Boolean expressions, assignment statements, mixed mode assignment. Statement level control structures, compound statements, selection statement, iterative statements, unconditional branching, guarded commands.
Unit III
Subprogram, fundamentals of subprogram, design issues, parameter passing methods, overloaded subprograms, generic subprograms, separate and independent compilation, design issues for functions, accessing nonlocal environment, user defined overloaded operators, coroutines, implementing subprograms, blocks, implementing dynamic scooping.
Programming in C:
Unit IV
Character set, variables and constants, keywords, Instructions, assignment statements, arithmetic expression, comment statements, simple input and output, Boolean expressions, Relational operators, logical operators, control structures, decision control structure, loop control structure, case control structure, functions, subroutines, scope and lifetime of identifiers, parameter passing mechanism,
Unit V
Arrays and strings, structures, array of structures, Console Input and Output functions, Disk I/O functions, Interaction with hardware, Interrupts and Interrupt Vector table, Unions of structures, operations on bits, usage of enumerated data types. Bit-fields, Pointers to Function, Function returning Pointers.
Recommended reference books:
- Robert W. Sebesta: Concepts of Programming Language, Addison Wesley, Pearson Education Asia, 1999.
- Ramon A. Mata-Toledo and Pauline K. Cushman: Introduction to Computer Science, McGraw Hill International Edition.
- D. Appleby and J J Vande Kopple: Programming Languages, Tata McGraw Hill, India.
- Deitel and Deitel: How to Program C, Addison Wesley, Pearson Education Asia, 1999.
- Bryon Gottfried, Programming with C, McGraw Hill International.
BIT 104-Cell Biology and Genetics
Unit I- Introduction to cell: Morphology, size, shape and characteristics of Prokaryotic, Eukaryotic, Plant and animal cells; basic idea of virus and cell-theory.
- Cell membrane: Characteristics of cell membrane molecules, fluid-mosaic model of Singer and Nicolson, concept of unit membrane.
- Cell membrane transport: Passive (diffusion and osmosis facilitated (mediated) and active transport.
- Cytoplasmic organelles:
- Structure and biogenesis of mitochondria; electron transport chain and generation of ATP molecules (chemiosmotic hypothesis of Mitchele)
- Structure and function of endoplasmic reticulum, ribosome (Prokayotic and eukaryotic) and Golgi complex.
- Structure and function of lysosome, microbodies and centrioles.
- Structure and functions of cilia, flagella, microvilli and cytoskeletal elements.
- Nucleus :
- Structure and function of nuclear envelope, nuclear matrix and nucleolus.
- chromosomes: Morphology, chromonema, chromomeres, telomeres, primary and secondary constrictions, chromatids; prokaryotic chromosome.
- Chromosome type: Polytene and lampbrush.
- Chromosomal organization: Euchromatin, heterochromatin and folded fibre model and nucleosome concept.
- Nucleic Acids :
- DNA structure, polymorphism (A, B, Z type) and replication (semi- conservative mechanism), experiments of Messelson and Stahl: elementary idea about polymerases topoisomerase, single strand binding protein, replication forks (both unidirectional and bidirectional), leading and lagging strands, RA primers and Okazaki fragments; elementary idea about DNA repairs.
- RNA structure and type (mRNA, rRNA and tRNA) and transcription (idea about polymerase, exon and introns)
- Genetic Code and Translation, triplet code, characteristics of triplet code; protein synthesis (translation)
- Cell in Reproduction :
- Interphase nucleus and cell cycle S, G-a, G-2, M-phase.
- Mitosis : Phases and process mitosis structure and function of spindle apparatus; anaphases movement.
- Meiosis : Phase and process of meiosis, synapses and synaptonemal complex, formation and fate of chiasmata and significance of the crossing over.
- Mendelism : Brief history of genetic and Mendel's work; Mendelian law, their significance and current status; chromosomal theory of inheritance.
- Chromosomal mutations: Classification of chromosomal mutations, translocation, inversion deletion and duplication variation in chromosome numbers; haploidy, diploidy, polyploidy, aneuploidy, euploidy and polysomy.
- Linkage and crossing over, elementary idea of chromosome mapping.
- Genetic interaction : supplementary genes complementary genes, duplicate genes, epistasis inhibitory and polymorphic genes multiple gene inheritance ABO blood group and Rh factor and their significance.
- Cytoplasmic inheritance.
(Hours/Week)
* for Tutorial/seminar
- Immunology : Definition, types of immunity : innate and acquired : humoral and cell mediated.
- Antigen : Antigenicity of molecules, haptens.
- Antigen : Antigenicity of molecules, haptens.
- Antigen-antibody reactions : Precipitation reaction, agglutination reaction, neutralizing reaction, complement and lytic reactions and phagocytosis.
- Cells of Immunity: Macrophages, Lymphocytes (B- and T- types) T- Helper cells. T-Killer cells, plasma cells and memory cells.
- Mechanism of humoral or antibody mediated immunity.
- Brief introduction to the history of Microbiology : work of Anatomy Van Leeuwenhoek : theory of spontaneous generation : Germ theory of fermentation and disease : Work of Louis Pasteur, John Tynadal, Rober-Koch and Jenner.
- The Prokaryota (Bacteria) :
- Structural organization :
- Size shapes and patterns of arrangement
- Structural organization :
- Slime layer (capsule) : cell envelopes : cytoplasmic membrane (inner membrane). cell wall (outer membrane) of Gram negative and Gram-positive bacteria : mesosomes : cytoplasmic organization : Cell projection : flagella dn pili.
- Genetic material of bacteria : (i) Chromosome (ii) Replication of bacterial DNA
- Reproduction in Bacteria : Asexual reproduction binary fission, budding endospore formation, exospore and cyst formation: Sexual reproduction conjugation.
- Microbial nutrition culture of bacteria
- Carbon and energy source
- Nitrogen and minerals
- organic growth factors
- Environmental factors : Temperature, hydrogen-ion concentration
- Bacteria of medical importance :
- Gram-Positive :
- Cocci : Staphylococci , Streptococci
- Bacilli: Diphtheria: Tetanus.
- Gram-Negative :
- Cocci : Gonorrhea, Meningitis
- Bacilli : Diarrhea
- Mycobacteria : Tuberculosis, Leprosy
- AIDS and hepatitis (with emphasis on B type). The causative agents. Transmission, Pathogencity, Laboratory, diagnosis, treatment and prevention.
- Concept of gene: Muton, recon and cistron : gene expression, lac operon and gene mutation.
- Eugenics and genetic counselling.
- History, scope and significance of biotechnology, Major areas of biotechnology.
- Vectors for gene transfer (plasmids and phages). Basic concepts of cell and tissue culture.
- Basic concepts of animals cell and tissue culture and hybridoma technology.
- Monoclonal antibodies and their applications.
- Protosplast fusion in prokaryotes and eukaryotes.
- Recombinant DNA technology and its application.
- Bacteria and genetic engineering (outline idea only) : benefits of genetic engineering : potential hazards and regulations of genetic engineering.
- Transgenic animals, their uses and biotechnology
- Brief account of cloning, Genomic research its advantages and disadvantages.
- Biotechnology in Medicine (outline idea only) : P.C.R. (Genema0chine) Antibiotics. Vaccines, Enzymes, Vitamines., Steriodis. Artificial Blood.
- Environmental Biotechnology (outline idea only) : Metal and petroleum recovery pest control waste-water treatment.
- Food drink and diary Biotechnology (outline idea only) : Fermented food production : diary products, alcoholic beverages and vinegar microbial spoilage and food preservation.
BIT-202: Discrete Mathematics
Unit-I
Sets and proposition : Cardinality, Mathematical Induction, Principle of inclusion and exclusion, derangements. Language, Phrase-structure grammar. Chain and Antichain.
Unit-II
Hasse Diagram. Pigeonhole Principle.
Group, Ring and Field : Definitions, simple examples and elementary properties only.
Unit-III
Graph, Multigraph and Pseudograph, Degree of vertex in a graph, Directed graph, Loop, Finite and Infinite graphs, Weighted graphs, Paths and Circuits, Eulerion Path and Euleriom Circuit, Traveling Salesman Problem, Planar graphs, Kuratowski's graph.
Unit-IV
Trees, Properties of trees, rooted tree, sub tree, Binary tree, Spanning tree, chromatic number.
Types of Machines, Finite state machine, Language determined by an automation, Finite state language.
Unit-V
Definition and elementary properties of lattices, Dual lattice and duality principle.
Definition and elementary theorems on Boolean algebra, Boolean expression, Boolean functions.
Books :
- C.L. Lin, "Elements of Discrete Mathematics". McGraw-Hill Book Co., 1986
- S. Lipschutz et al. Discrete Mathematics-Schaum's outlines Tata McGraw-hill Pub. Co. Ltd., New Delhi, 2006
- N. Deo, Graph Theory with Applications to Engineering and Computer Science. Prentice Hall of India, 1990
- S. Wiitala, 'Discrete mathematics - A Unified approach'. McGraw-Hill Book Co.
BIT 203: Database Management Systems
Unit I
Database architectures: Three levels of the architecture: external, conceptual and internal level], centralized and distributed.
Unit II
Database models: Hierarchical: Concepts of a Hierarchy, IMS Hierarchy], Relational [Concepts of relational model, relational algebra, relational calculus], Network [Concepts of a Network, DBTG Network, DBA Scheme declaration]
Unit III
Planning a database (tables, queries, forms, reports), Creating and editing database, customizing tables, linking tables, designing and using forms, modifying database structure, maintaining database, Sorting and Indexing database, Querying a database and generating Reports, modifying a Report, exporting a Report to another format.
Unit IV
Relational Data Structure, Database Design, Normalization, Characteristics and advantages of SQL, SQL language levels, SQL data types and Literals, SQL Operators, types of SQL commands,
Unit V
Tables, Indexes, Views, Nulls, Aggregate Functions, Select statement, Sub queries, Insert, Update and Delete operations, Joins, Unions, Data security, integrity and concurrency, Backup and recovery, numeric and text data in SQL, dealing with dates, Synonyms, Snapshots, Programming with SQL.
Reference Books:
- Ramakrishan and Gharke, Database Management Systems, Tata McGraw Hill Pub. Co. Ltd.
- Date C J, Database Management Systems, Pearson Education Asia.
- Korth H and Silberschataz A, Database System Concepts, McGraw Hill.
- Geraid V Post, Database Management Systems, Tata McGraw Hill.
- Naveen Prakash, Introduction to Database Management Systems, Tata McGraw Hill.
- Leon, and Leon, SQL, Tata McGraw Hill Pub. Co. Ltd.
- Ivan Bayross, Database Technologies, Sybex Computer Books Inc.
BIT-204 : BIOCHEMISTRY
Unit: I(1) Water Chemistry (Important properties of water): The law of mass action, dissociation of water and it's ionic product, pH, pK, Bronsted acids, ionization of weak acids and bases, Handerson-Hasselbach equation, Titration curves, buffer action and physiological buffers.
(2) Bioenergetics: Laws of thermodynamics, Entropy and role of free energy, role of ionic balance and membrane potential. Reversible and irreversible processes.
Unit: II
(3) Bio-molecules: The small molecule of life:- Sugars, organic acids, amino acids, nucleotides and fats.Macromolcules of life: polysaccharides, proteins and nucleic acids; General idea of primary, secondary, tertiary and quaternary structures.
(4) Chloroplasts : Capturing energy from the Sun, Structure, organization and function: Basic information on 'light' and 'dark' reactions of photosynthesis and participation of chloroplast in the process in C3, C4 and CAM plants.
Unit: III
(5) Enzymes: Nomenclature and classification; Coenzymes and co factors, reaction and derivation of Michaelis-Menten equation, kinetics and allosteric regulation of enzymes, isoenzyme, mode of catalysis. Enzyme inhibitors.
(6) Vitamins: Structure and physiological role of vitamins A, B group of vitamins, C, D and E.
Unit: IV
(7) Carbohydrate metabolism: Glycolysis, Kreb's cycle. Pentose phosphate pathway, glyoxylate cycle, glycogenolysis and glycogenesis, gluconeogenesis. Anaerobic respiration and basics of fermentation.
(8) Lipid metabolism : biosynthesis of odd and even carbon saturated and unsaturated fatty acids, formation of ketone bodies, biosynthesis of triacylglycerols, membrane phospholipids, cholesterol and steroids.
Unit: V
(9) Protein metabolism: metabolic fate of amino group, transamination and deamination, decarboxylation and oxidative degradation of amino acids, Nitrogen excretion and urea cycle.
(10) Nucleic Acid Metabolism: Biosynthesis and break down of purine and pyrimidine nucleotide by De novo and Salvage pathway. Phosphorus and sulphur regulation. Metabolic regulation.
BOOKS
Harper et al: Review of Physiological Chemistry, Lange Medical Pulication, Mauzaen Asian Edition
Bell & Davidson: Text book of Physiology and Biochemistry, ELBS, London
Smith et al.: Principles of Biochemistry. McGraw Hill
Conn & Stumpf: Outline of Biochemistry, Wiley Eastern Ltd.
Rao: Text Book of Biochemistry
A.L. Bhatia: Biochemistry, Indus Valley Publication
II YEAR
Integrated Course of BioInformatics
| PAPER CODE | PAPER TITLE | TEACHNG SCHEDULE (Hours/Week) * for Tutorial/Seminar | UNIVERSITY EXAM THEORY/PRACTICAL DUARATION | INTERNAL UNIVERSITY EXAM. THEORY/PRACTICAL DUARATION | TOTAL THEORY/ PRACTICAL | |||
| Lecture | Practical | Hrs | Marks | Hrs | Marks | Maximum Marks | ||
| BIT-301 | Advanced Statistics | 5+1* | 3 | 3 | 80/40 | 2 | 20/10 | 100/50 |
| BIT-302 | Object Oriented Programming Methodology | 5+1* | 3 | 3 | 80/40 | 2 | 20/10 | 100/50 |
| BIT-303 | Molecular Modelling | 5+1* | 3 | 3 | 80/40 | 2 | 20/10 | 100/50 |
| BIT-304 | Structural Biology | 5+1* | 3 | 3 | 80/40 | 2 | 20/10 | 100/50 |
| THEORY | TOTAL | 30 | 12 | 12 | 320 | 8 | 80 | 400 |
| PRACTICAL | TOTAL | 160 | 40 | 200 | ||||
- It comprises all the practicals based on the above theory papers.
- The provision of communication skill and for proficiency in English as well as Hindi should also be made in practicals (one hour duration each on Monday and Saturday in such a manner that any exercise should begin on Monday may also assign homework to be tested on Saturday throughout the session)
- Examiner is supposed to test this and allocate 20% marks in the practical.
III- Semester
| BIT-301 | Advanced Statistics |
| BIT-302 | Object Oriented Programming Methodology |
| BIT-303 | Molecular Modelling |
| BIT-304 | Structural Biology |
BIT-301-Advanced Statistics
Classification and Tabulation of Data, Frequency distribution, Mean, Median, Mode, Quartiles, Deciles and Percentiles, Range, quartile deviations, Mean deviation, Standard deviation.
Unit-II
Variance, covariance, correlation and regression analysis.
Probability of an event, Addition and Multiplication Theorems on Probability, Conditional Probability. Baye's Theorem and its applications.
Unit-III
Discrete and continuous random variables, Bionomial, Poission and Normal distribution - Mean, Variance and their applications. Chi-square, t - and z - distributions - definitions simple problems and their applications.
Unit –IV
Measures of dispersion, skewness, moments and Kurtosis. Mathematical expectations.
Unit-V
Sample, sampling variation, types of population, probability sampling techniques. Test of hypothesis, Test of significance.
Books :
- Kapur and Gupta, 'Fundamentals of Mathematical Statistics'. S.Chand and Comp. Pvt. Ltd., New Delhi
- Goon, Gupta and Dasgupta, 'Fundamentals and Statistics'.
- Agarwal, 'Basic Statistics'. New Age International Publishers, New Delhi, 1996
- Rao, 'Introduction of Bio Statistics'. Prentice Hall, India
- Rohlf and Sokal, 'Biometry : The principles and practice of Statistics in Biological Research'
BIT-302: Object Oriented Programming Methodology
UNIT- 1
Necessity of Object Oriented Programming, Essentials of OOP (Encapsulation, Constructors,
Destructors, Inheritance, Pointers to Objects, Polymorphism).
UNIT- 2:
Basic Concepts of Object Oriented Programming, Characteristics of Object-Oriented Languages, Object, Classes in C++, Constructors, Destructors, Complex Class, Matrix class; Classes, Objects and Memory;
UNIT- 3:
Structures and Classes; C++ Free Store, Static Class Data, Overload Assignment Operator, Copy Constructor, Data Conversion between Objects of different classes.
UNIT- 4:
Data structure through C++, Handling Data files (sequential and random), opening and closing files, stacks and queues, linked lists, trees. Inheritance Multiple, Private and Protected Inheritance, Virtual Functions, Objects Slicing.
UNIT- 5:
Input/Output in C++, User defined manipulators, Predefined Stream Objects, File I/O with Streams, Strstreams, Classes within classes, Smart Pointers, Templates, Exception Handling.
Reference Books
- Deitel and Deitel: How to Program C++, Addison Wesley, Pearson Education Asia, 1999.
- C. Thomas Wu, An Introduction to OOP with Java, McGraw Hill.
- Timothy Wood, An Introduction to Object Oriented Programming, Addison Wesley.
- John R. Hubbard, Programming with C++, McGraw Hill International.
BIT-303: Molecular Modelling
Unit IIntroduction: Coordinate systems, Potential energy surfaces, Molecular graphics, Surfaces, Computer hardware and software, Units of length and energy, The molecular Modelling literature, The Internet, Mathematical concepts.
An introduction to computational quantum mechanics: Introduction, One-electron atoms, Polyelectronic atoms and molecules, Molecular orbital calculations, The Hartree-Fock equations, Basis sets, Calculating molecular properties using ab initio quantum mechanics, Approximate molecular orbital theories, Semi-empirical methods, Huckel theory, Performance of semi-empirical methods.
Advanced ab initio methods: density functional theory and solid-state quantum mechanics Introduction: Open-shell systems, Electron correlation, Practical considerations when performing ab initio calculations, Energy component analysis Density functional theory, Quantum mechanical methods for studying the solid-state. The future role of quantum mechanics: theory and experiment working together.
Unit II
Empirical force field models: molecular mechanics: Introduction, Some general features of molecular mechanics force fields , Bond stretching , Angle bending , Torsional terms, Improper torsions and out-of-plane bending motions , Cross terms Class 1, 2 and 3 force fields , Introduction to non-bonded interactions, Electrostatic interactions, van -der-Waals interactions, Many-body effects, Effective pair potentials, Hydrogen bonding in molecular mechanics, Force field models for the simulation of liquid water, United atom force fields and reduced representations, Derivatives of the molecular mechanics energy function, Calculating thermodynamic properties using a force field, Force field parameterization, Transferability of force field parameters, The treatment of delocalized systems, Force fields for inorganic molecules, Force fields for solid-state systems, Empirical potentials for metals and semiconductors .
Energy minimization and related methods for exploring the energy surface: Introduction, Non-derivative minimization methods, The, Introduction to derivative minimization methods, First-order minimization methods, Second derivative methods: the Newton-Raphson method, Quasi-Newton methods, Applications of energy minimization, Determination of transition structures and reaction pathways, Solid-state systems: lattice statics and lattice dynamics
Unit III
Computer simulation methods: Introduction, Calculation of simple thermodynamic properties, Phase space, Practical aspects of computer simulation, Boundaries, Monitoring the equilibration, Truncating the potential and the minimum image convention, Long-range forces, Analyzing the results of a simulation and estimating errors.
Molecular dynamics simulation methods: Introduction, Molecular dynamics using simple models , Molecular dynamics with continuous potentials, Setting up and running a molecular dynamics simulation , Constraint dynamics, Time-dependent properties, Molecular dynamics at constant temperature and pressure, Incorporating solvent effects into molecular dynamics: potentials of mean force and stochastic dynamics ,conformational changes from molecular dynamics simulations, Molecular dynamics simulations of chain amphiphiles .
Monte carlo simulation methods: Introduction, Calculating properties by integration, Some theoretical background to the Metropolis method, Implementation of the Metropolis Monte Carlo method, Monte Carlo simulation of molecules, Models used in Monte Carlo simulations of polymers, 'Biased' Monte Carlo methods, Tackling the problem of quasi-ergodicity: Monte Carlo sampling from different ensembles, Calculating the chemical potential, The configurational bias Monte Carlo method, Simulating phase equilibria by the Gibbs ensemble Monte Carlo method, Monte Carlo or molecular dynamics?
Unit IV
Conformational analysis: Introduction ,Systematic methods for exploring conformational space, Model-building approaches, Random search methods, Distance geometry, Exploring conformational space using simulation methods, Which conformational search method should I use? A comparison of different approaches, Variations upon the standard methods.
Finding the global energy minimum: Evolutionary algorithms and simulated annealing, Solving protein structures using restrained molecular dynamics and simulated annealing, Structural databases, Molecular fitting, Clustering algorithms and pattern recognition techniques, Reducing the dimensionality of a data set, Covering conformational space: poling, A "classic" optimization problem: predicting crystal structures.
Protein structure prediction, sequence analysis and protein folding: Introduction, Some basic principles of protein structure, First-principles methods for predicting protein structure, Introduction to comparative Modelling, Sequence alignment, Constructing and evaluating a comparative model, Predicting protein structures by "threading", A comparison of protein structure prediction methods: CASP, Protein folding and unfolding .
Unit V
Four challenges in molecular Modelling: free energies, solvation, reactions and solid-state defects:-Free energy calculations, The calculation of free energy differences, The 'slow growth' method , Applications of methods for calculating free energy differences, The calculation of enthalpy and entropy differences, Partitioning the free energy ,Potential pitfalls with free energy calculations, Potentials of mean force, Approximate/"rapid" free energy methods, Continuum representations of the solvent , The electrostatic contribution to the free energy of solvation: the Born and Onsager models, Non-electrostatic contributions to the solvation free energy, Very simple solvation models, Modelling chemical reactions, Modelling solid-state defects .
The use of molecular Modelling and chemoinformatics to discover and design new molecules: Molecular Modelling in drug discovery, Computer representations of molecules, chemical databases and 2D substructure searching, 3D database searching, Deriving and using three-dimensional pharmacophores, Sources of data for 3D databases, Molecular docking, Applications of 3D database searching and docking, Molecular similarity and similarity searching, Molecular Descriptors, Selecting "diverse" sets of compounds, Structure-based de novo ligand design, Quantitative structure-activity relationships, Partial least squares, Combinatorial libraries .
References:
- Molecular Modeling: Principles and Applications (2nd Edition) - by Andrew Leach.
- Molecular Modeling: Basic Principles and Applications - by Hans-Dieter Holtje, Wolfgang Sippl, Didier Rognan, and Gerd Folkers.
- Molecular Modeling for Beginners - by Alan Hinchliffe
- Molecular Modeling and Simulation - by Tamar Schlick
- Molecular Modeling - by Warren J. Hehre
BIT 304: Structural Biology
UNIT- I
- Internal and external coordinate system Generation of cooordinates of biopolymers in Cartesian and cylindrical polar coordinate System.
- Methods of single crystal X-ray Diffraction of macromolecules: molecular replacement method and direct method
- Fiber diffraction
- Analysis of structures and correctness of structures
- Submission of data to PDB: atomic coordinates and electron density maps
- Anatomy of Proteins
- Ramachandran plot
- Secondary structures
- Motifs
- Domains
- Tertiary and quaternary structures
- Anatomy of DNA: A, B, Z DNA, DNA bending etc.
RNA structure - Structure of Ribosome
- Principles of Protein Folding
- Structural data banks Protein Data Bank, Cambridge small molecular crystal structure data bank
- Calculation of conformational energy for bio-macromolecules
- Methods for Prediction of Secondary and Tertiary structures of Proteins
- Knowledge based structure prediction
- Fold recognition
- Ab initio methods for structure prediction
- Methods for comparison of 3D structures of proteins
- Methods to predict three dimensional structures of nucleic acids, rRNA
- Electrostatic energy surface generation
- Molecular Mechanics & Molecular Dynamics of Oligopeptides, Proteins, Nucleotides, and small Molecules
- Mechanics and dynamics of bio-macromolecules
- Simulation of molecular mechanics and dynamics
- Simulations of Free Energy changes
- Force fields
- Molecular interactions of
- Protein - Protein
- Protein - DNA
- Protein - carbohydrate
- DNA - small molecules etc.
- Docking of Molecules
- Molecular Design
- Creighton, T. E. Ed.: Protein Structure: A Practical Approach. 1989.
- Creighton, T.E.: Proteins: Structure And Molecular Properties. Second Edition. New York. W. H. Freeman And Company, 1993.
- Creighton,T.: Protein Folding, 1992.
- Sternberg, M.J.E.: Protein structure prediction: a practical approach, 1996
- Pain, R.G.: Mechanisms of protein folding, 1994
- Leach.A.R: Molecular modelling: principles and applications
| PAPER CODE | PAPER TITLE | TEACHNG SCHEDULE (Hours/Week) * for Tutorial/seminar |
UNIVERSITY EXAM THEORY/PRACTICAL DUARATION | INTERNAL UNIVERSITY EXAM. THEORY/PRACTICAL DUARATION |
TOTAL THEORY/PRACTICAL | |||
| Lecture | Practical | Hrs | Marks | Hrs | Marks | Maximum Marks | ||
| BIT-401 | Fundamentals of Electronics | 5+1* | 3 | 3 | 80/40 | 2 | 20/10 | 100/50 |
| BIT-402 | Information Resources and Databases | 5+1* | 3 | 3 | 80/40 | 2 | 20/10 | 100/50 |
| BIT-403 | Phylogenetics and Molecular Evolution | 5+1* | 3 | 3 | 80/40 | 2 | 20/10 | 100/50 |
| BIT-404 | Immunoinformatics | 5+1* | 3 | 3 | 80/40 | 2 | 20/10 | 100/50 |
| THEORY | TOTAL | 30 | 12 | 12 | 320 | 8 | 80 | 400 |
| PRACTICAL | TOTAL | 160 | 40 | 200 | ||||
Practicals:
- It comprises all the practicals based on the above theory papers.
- The provision of communication skill and for proficiency in English as well as Hindi should also be made in practicals (one hour duration each on Monday and Saturday in such a manner that any exercise should begin on Monday may also assign homework to be tested on Saturday throughout the session)
- Examiner is supposed to test this and allocate 20% marks in the practical.
IV- Semester
| BIT-401 | Fundamentals of Electronics |
| BIT-402 | Information Resources and Databases |
| BIT-403 | Phylogenetics and Molecular Evolution |
| BIT-404 | Immunoinformatics |
BIT-401-Fundamentals of Electronics
Introduction of AC supply, Voltage, Current, Power, Frequency, Phase and DC supply; Fundamental electrical components like: Resistors, Capacitors, Inductors, Transformers, Transistors, Amplifiers, Oscilloscopes, Multimeters; basic RC and RL circuits, Ohm's Law and Kirchoff's Law, Series and Parallel connection of Resistors and Capacitors, Heating Effect due to current and need of fuses, Maximum Power Transform Theorem, Thevenins Theorem, Electromagnetism, Magnetic Force, Electromagnetic Induction, Resonance.
Unit II: Semiconductor Physics and Semiconductor Diode
Properties of Semiconductors, Intrinsic and Extrinsic semiconductors, P & N Type semiconductors, PN Junction, Biasing. Characteristics of Semiconductor Diodes, Symbol and Ratings of Semiconductor Diodes, Forward and Reverse Bias Characteristics. Introduction about Rectifier, Types of Rectifiers: Half wave, Full Wave, Bridge; Applications of Filters and Zener Diode
Unit III: Transistor
PNP and NPN Transistors, CB, CC, CE Configurations, Transistor as an Amplifier, Transistor as a switch, Alpha & Beta Parameters, RC coupled Transistor Amplifier & Transformer coupled Transistor Amplifier, Audio Power Amplifier, Push Pull Amplifier; Different type of Signals: Sine Ware, Saw Tooth, Triangular, Pulses, Multi vibrators.
Unit IV: Electronic Devices
Electronic Devices such as: LED, Photo Diode, Triode, FET, MOSFET; Characteristics & Applications of These Devices.
Unit V: Introduction to Digital Electronics
Introduction about digital logic circuits, Basic logic gates (AND, OR, NAND, NOR) and their truth tables, Logic Gate Symbols, Brief Idea about Half adder, Full Adder and Flip Flops; Introduction to Microprocessors and Assembly Language
References:
- Principles of Electrical Engineering and Electronics - V. K. Mehta
- Fundamentals of Electronics - Ashok Singh
- Digital Electronics and Microprocessor - Douglas Hall, McGraw Hill
- Digital Electronics - M. Moris Mano
BIT 402: Information Resources and Databases
Introduction about Bioinformatics, Use of Bioinformatics in Biology, Scope of Bioinformatics, Introduction about available Computational Tools and Databases on Bioinformatics sites, Biological Literature Information access, storage and retrieval;
Unit II: Major Information Resources
Information Resources at: NCBI, EBI, ExPasy, Entrez & SRS System Genomic Sequencing, Sequence assembly, Submission methods of Sequences on different Databases sites, Sequence databases, Sequence File Formats: genbank, embl, Swiss-prot, pdb, fasta, msf, nbrf, pir etc., Conversion between formats, Introduction about Annotation and Archival
Unit III: Databases in Bioinformatics I
Primary Sequence & Structure Databases: Genbank, SwissProt/Uniprot, EMBL, PIR, PDB, MMDB, NDB, CSD, KEGG etc.
Unit IV: Databases in Bioinformatics II
Derived (Secondary) Databases of Sequences and Structure:
Prosite, PRODOM, PRINTS, Pfam, BLOCK, INTERPRO etc
SSOP, CATH, DSSP, FSSP, RNAbase,
Genome Databases (at NCBI, EBI, TIGR, SANGER), High-throughput genomics sequences (EST, STS, GSS), ENSEMBL
Unit V: Introduction and Use of different Bioinformatics Tools
Similarity Searching Tools: BLAST and FASTA, variants of BLAST and FASTA, PSI-BLAST and PHI BLAST; Sequence Comparison
Tools: Dotplot, Dotter, Dotlet; Multiple Sequence Alignment Tools: CLUSTALW/X etc.
References:
- Information Sources in Biotechnology - Macmillann Press
- Current Protocols in Bioinformatics - by A.D. Baxevanis et al, Wiley Publishers
- Bioinformatics Basics - By Hooman H. Rashidi, Lukas K. Buehler, CRC press
- Fundamental concepts of Bioinformatics - by D.E. Krane and M.L Raymer, Pearson Education
- Bioinformatics - by David W. Mount, Cold Spring Harbor Laboratory Press
BIT-403. Phylogenetics and Molecular Evolution
Evolutionary tree of life, mechanism of evolution, structure, function of genes, mutational change of DNA, codon usage. Evolutionary change of amino acid sequences: Amino acid differences, proportion of different amino acids, Poisson correction, gamma distance, bootstrap variance, co variance, amino acid substitution matrix, mutation rate and substitution rate.
Unit II: Evolutionary change of DNA sequences
Nucleotide differences between sequences, estimation of nucleotide substitutions, gamma distances, numerical estimation of evolutionary distances, aligning of nucleotide sequence, handling sequence gaps in estimation of evolutionary distances. Synonymous and non synonymous nucleotide substitutions. Evolutionary pathway methods, likelihood methods with codon substitution
Unit III: Phylogenetic Trees and Different Methods for phylogenetic Inference
Phylogenetic trees: Types of phylogenetic trees, Topological differences, tree building methods. Phylogenetic inference- distance methods: UPGMA, LS methods, ME, NJ. Phylogenetic inference- Maximum parsimony method : finding Maximum parsimony trees, strategies of searching MP trees, consensus trees, estimation of branch lengths, weighted parsimonies, MP method for protein data, Phylogenetic inference- Maximum likelihood method: Computational procedure of ML methods, models of nucleotide substitutions protein likelihood methods, theoretical foundation of ML methods.
Unit IV: Accuracies, statistical test of phylogenetic trees and Molecular clocks & linearised trees
Accuracies, statistical test of phylogenetic trees : optimization, principle and topological errors, interior branch tests, bootstrap tests, tests of topological difference, advantages and disadvantages of different tree building methods. Molecular clocks and linearised trees: Molecular clock hypothesis, relative rate tests, phlyogenetic test, linearised trees.
Unit V: Genetic polymorphism and evolution
Ancestral amino acid and nucleotide sequences, Genetic polymorphism and evolution: evolutionary significance of genetic polymorphism, analysis of allele frequency data, DNA polymorphism, statistical tests for detecting selection. Population trees from genetic markers: genetic distance from allele frequency data, analysis of DNA sequence by restriction enzyme, analysis of RAPD data, statistical methods, genome projects, molecular biology and evolution
References:
- Molecular Evolution and Phylogenetics-by Masatoshi Nei and Sudhir Kumar
- Computational Methods in Phylogenetic Analysis - by Arun Jagota and Majid Masso
- Phylogenetic Systematics -by by Willi Hennig, D Dwight Davis
- The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny -by Marco Salemi and Anne-Mieke
- Statistical Methods in Molecular Evolution (Statistics for Biology and Health)- by Rasmus Nielsen
- Molecular Evolution: A Phylogenetic Approach - by Roderic D. Page and Edward C. Holmes
- Bioinformatics and Molecular Evolution - by Paul G. Higgs and Teresa Attwood
- Techniques in Molecular Systematics and Evolution - by Rob DeSalle, Gonzalo Giribet, Ward Wheeler, and Go
BIT-404. Immunoinformatics
Unit II: Use of Bioinformatics in Immunology
Bioinformatics strategies for better understanding of immune function, Future of computational modeling and prediction systems in clinical immunology, Role of Immunoinformatics in personalized medicine. From immunome to vaccine- epitope mapping, vaccine design tools. Insights from MHC bound peptides.
Unit III: Genotyping methods and disease gene identification
Genotyping of SNPs, classical HLA typing, MHV haplotypes, Molecular haplotyping, microhaplotyping, MHC and disease association, Definition of MHC supertypes through clustering of MHV peptide repertoires.MHC class I epitope binding- prediction trained on small data sets. BcePred: prediction of continuous B- cell epitopes in antigenic sequences using physico chemical properties.
Unit IV: Computational vaccinology
Quantitative approach, international immunogenetics information system, generating data for databases- peptide repertoire if HLA molecules, HLA nomenclature and IMGT/HLA sequence databases.
Unit V: Immunogenetics to immunomics
Functional prospects of geneand transcripts, Mathematical models of HIV and immunesystem, Immunogenomics- towards digital immunesystem, Integration of immune models using PetriNets, Viral bioinformatics- computational views of host and pathogen.
References:
- Immunology, Fifth Edition - by Richard A. Goldsby, Thomas J. Kindt, Janis Kuby, and Barbara A. Osborne
- Roitt's Essential Immunology (Essentials) - by Ivan M. Roitt, Seamus J. Martin, Peter J. Delves, and Dennis Burton
- Novartis Foundation Symposium 254 (CIBA Foundation Symposia Series) - by Novartis.
- Immunoinformatics - by Vladimir Brusic
- Computer Applications in Pharmaceutical Research and Development (Wiley Series in Drug Discovery and Development) - by Sean Ekins and Binghe Wang
- Immunogenomics and Human Disease - by Andras Falus
- Artificial Immune Systems: Third International Conference, ICARIS 2004, Catania, Sicily,
Italy, September 13-16, 2004, Proceedings (Lecture Notes in Computer Science) - by Giuseppe Nicosia, Vincenzo Cutello, Peter John Bentley, and Jonathan Ian Timmis
III YEAR
IV SEMESTER
| PAPER CODE | PAPER TITLE | TEACHNG SCHEDULE (Hours/Week) * for Tutorial/seminar | UNIVERSITY EXAM THEORY/PRACTICAL DUARATION | INTERNAL UNIVERSITY EXAM. THEORY/PRACTICAL DUARATION |
TOTAL THEORY/PRACTICAL | |||
| Lecture | Practical | Hrs | Marks | Hrs | Marks | Maximum Marks | ||
| BIT-501 | Programming & Datastructure in PERL | 5+1* | 3 | 3 | 80/40 | 2 | 20/10 | 100/50 |
| BIT-502 | RDBMS Using Oracle8i and MySql | 5+1* | 3 | 3 | 80/40 | 2 | 20/10 | 100/50 |
| BIT-503 | Pharmacogenomics | 5+1* | 3 | 3 | 80/40 | 2 | 20/10 | 100/50 |
| BIT-504 | Cheminfromatics and Drug Design | 5+1* | 3 | 3 | 80/40 | 2 | 20/10 | 100/50 |
| THEORY | TOTAL | 30 | 12 | 12 | 320 | 8 | 80 | 400 |
| PRACTICAL | TOTAL | 160 | 40 | 200 | ||||
Practicals:
- It comprises all the practicals based on the above theory papers.
- The provision of communication skill and for proficiency in English as well as Hindi should also be made in practicals (one hour duration each on Monday and Saturday in such a manner that any exercise should begin on Monday may also assign homework to be tested on Saturday throughout the session)
- Examiner is supposed to test this and allocate 20% marks in the practical.
| BIT-501 | Programming & Datastructure in PERL |
| BIT-502. | RDBMS Using Oracle8i and MySql |
| BIT-503 | Pharmacogenomics |
| BIT-504 | Cheminfromatics and Drug Design |
BIT-501: Programming and Data Structure in PERL
Unit I: Introduction to Perl I
Creating and Running Simple Perl program, Command Interpretation, Comments, Scalar Values and Scalar Variables, Assignment, Statements & Blocks, Arrays , Hashes, Operators, Operator Precedence, Basic Operations, Conditionals and Logical Operators, Binding Operators, Loops, Subroutines & Modules Unit III: Introduction to Perl II
Input/Output, Reading from and writing into files, Regular Expressions, Scalar and List Context, Built-in Functions, Exploding Strings into Arrays,Operating on Strings, Using the Perl Documentation, Data Structures and Algorithms for Biology
Unit III: Sequences & Strings, Motifs & Loops
Representing Sequence Data, A Program to Store a DNA Sequence, Concatenating DNA
Fragments,Transcription: DNA to RNA, Calculating the Reverse Complement in Perl,Reading Proteins in Files,
Flow Control,Code Layout,Finding Motifs,Counting Nucleotides
Unit IV: The Genetic Code and Mutations & Randomization
Translating DNA into Proteins, Reading DNA from Files in FASTA Format,Reading Frames,
Restriction Maps and Regular Expressions, Restriction Maps and Restriction Enzymes, Random Number Generators, A Program Using Randomization,A Program to Simulate DNA MutationGenerating Random DNA, Analyzing DNA
Unit V: Protein Data Bank, BLAST and GenBank
Overview of PDB, PDB Files,Parsing PDB Files
Obtaining BLAST, String Matching and Homology,BLAST Output Files,Parsing BLAST
Output, Presenting Data, GenBank Files, GenBank Libraries, Separating Sequence and Annotation, Parsing Annotations, Indexing GenBank with DBM.
Understanding, Bioperl Module and using it in Perl programs
Reference:
- Teach Yourself Perl in 21 Days - SAMS
- Learning Perl -O'REILLY
- Beginning Perl for Bioinformatics - James Tisdall, O'Reilly
- Mastering Perl for Bioinformatics - James Tisdall, O'Reilly
- Learning Perl, 3rd Edition by Schwartz and Christiansen, O'Reilly and Assoc., Inc.
- Programming Perl, 3rd Edition by Wall, Schwartz and Christiansen. O'Reilly and Assoc. Inc
BIT-502: RDBMS Using Oracle8i and MySql
Unit I: Oracle Environment and Basic Concepts
Introduction and Terminology, The Oracle Server and Client environment, SQL*PLUS - The Development Environment, Overview of Oracle Architecture; Data Types and Composite Structures: Strings, Numbers, Dates and Timestamps, Records and Collections, Miscellaneous Data types, Creating Tables, Indexes, Constraints and views; Unit II: Basic Concepts
Built in SQL Functions: Characters, Numeric, Date & Time, Conversion, Aggregate and Analytic; Introduction of Privileges, Types of Privileges: Object and System level; Transaction Control: Commit, Savepoint, Rollback; Introduction about VARRAY and Nested Tables
Unit III: PL/SQL
Constructing PL/SQL Subprograms, Expression and Operators, Variables and Control Structures in PL/SQL; Cursors: Defining Cursor, Cursor Variables, Cursor Types: Explicit, Implicit; Procedure and Functions: Subprogram creation, Parameter Modes, Difference between Procedure and Function; Stored Procedure, DML and Transaction Management, Packages; Triggers: Creating Triggers, Mutating Tables , Type of Triggers, Detailed knowledge about Database-Level Triggers; Exceptions and Error Handling: Declaration of Exception, Raising and Handling Exception, Scope of Exception;
Unit IV: Administration in Oracle8i and Oracle8i new features
Understanding Oracle Data Dictionary and Standard Packages, Administrative Scripts and PL/SQL, Administering Tablespaces and Datafiles, Tablespace Management , Maintaining Datafiles, Managing Indexes, Creating Indexes, Maintaining Control Files, Understanding the Redo Log Files , Maintaining Views and Sequences;
Materialized views: Show the use of MV and how they are used to improve performance of data warehouse queries; Partitioning: Review of table and index partitioning and how it effects developers; PL/SQL and Java: Calling Java methods from within PL/SQL
Unit V: MySQL
MySQL SQL syntax and use, working with data in MySQL, Query Optimization, MySQL Programs using C and PHP, MySQL Data Directory, introduction to MySQL Administration
Reference:
- Loney & Koch, Oracle8i, the Complete Reference, Osborne
- Feuerstein & Pribyl, Oracle PL/SQL Programming, 5th Edition, O' Reilly
- Gennick & Luers, Sams Teach Yourself PL/SQL in 21 Days, 2nd Edition, Sams
- MySQL The definitive guide to using, programming, and administering MySQL 4.1 Third Edition
BIT-503. Pharmacogenomics
Unit I: History and overview
Historical perspectives, current view of Pharmacogenetics, Pharmacogenetics; Biomarkers, promise of personalized medicine. Genetic drug response profiles, effect of drug on gene expression, Pharmacogenomics- in drug discovery and drug development. Current status of pharmacogenetics, drug metabolism.
Unit II:Pharmacogenetic of drug response and Functional analysis of gene variation
Role of pharmacogenomics in drug discovery and therapeutics. Pharmacogenomics of drug transporters-OATP, OAT, OCT, OCTN, PepT, MRP, MDR, white ABC transporter. Interethnic differences in drug response. Functional analysis of gene variation. Transfection assays with allele specific constructs, Allele specific variation in human gene expression, and Genome wide analysis of allele specific gene expression using oligo micro arrays, Haploclp- an in vivo assay.
Unit III: Genotyping techniques
Aselection, Denaturing HPLC for mutation detection and genotyping, Pyrosequencing of clinically relevant polymorphism, Kinetic fluorescence quenching detection assay for allele frequency estimation, Matrix associated laser desorption/ionization time of flight mass spectrometry, Fluorescent based fragment size analysis SNP genotyping, Taqman genotyping of insertion/ deletion polymorphism.
Unit IV: Pharmacogenomics and drug design
Need for protein structure information, Mutation in drug targets, Insilco drug design of small molecules, automated drug design, structure based drug design, and ligand based drug design methods. Bioinformatics, proteomics: Technologies, challenges of pharmacogenetics. Management of pharmacogenomic information PharmGKB- pharmacogenetics and pharmacogenomics knowledge base, Systems for management of pharmacogenomic information.
Unit V: Molecular diagnostics
Development of biotechnology based diagnostics, Technologies for analysis of SNP polymorphisms, application, analysis, Serial Analysis Gene Expression - transcription insights into functional, Multiplex genotyping by specialized mass spectrometry. Multiplex fluorescent mini sequencing applied to typing of genes encoding drug metabolizing enzymes.
References:
- Pharmacogenomics, Second Edition ( Drugs and the pharmaceutical Sciences) - Werner Kalow, Urs B.Meyer, and Rachel F. Tyndale
- Pharmacogenomics: Methods And Applications (Methods in Molecular Biology) - by Federico, MD, Ph.D. Innocenti
- Pharmacogenomics: The search for individualized Therapies - By Julio Lignio and Ma- Li Wong
- Pharmacogenomics In Drug Discovery and Development (Drug Discovery Series) - by Dale S. Dhanoa
- An A-Z Guide to Pharmacogenomics - by Michael G. Catania
- Pharmacogenomics: Pocket PC - by Lexi-Comp
BIT-504: Cheminfromatics and Drug Design
Unit I: Basics of Cheminformatics & Medicinal Chemistry
Introduction to Cheminformatics, Evolution of Cheminformatics, History of Chemical Information Science, Use of Cheminformatics, Prospectus of Cheminformatics
History of Medicinal Chemistry, Prodrugs and Soft Drugs , Drug Targets , Drug Solubility, Natural Resources of Lead Compounds, Pharmacokinetics & Drug Metabolism, Biological Testing and Bioassays, Preclinical Testing and Clinical Trial, Synthesis, Patenting and Manufacture, Complexes and Chelating Agents, Molecular Modeling Using Computers
Unit II: Modern Combinatorial Chemistry & Chemical Information Sources
Combinatorial Chemistry Technologies & Libraries, Solution Phase Synthesis, High-Throughput Synthesis and Screening, Combinatorial Libraries, Analytical Methods, Biopanning, Peptide Display Libraries: design and Construction
Chemical Literature, Chemical Information Searches, Chemical Information Sources, Chemical Name and Formula Searching, Analytical Chemistry (Constitutional Chemistry), Chemical History, Biography, Directories, and Industry Sources
Unit III: Cheminformatics Database Design & their Management
Chemical Database Design, Bio Catalysts Database, The MOS Database, The Failed Reaction Database, Protecting Groups Database, Solid-Phase Synthesis Database
Unit IV: Data Sequencing Mining and Visualization
An Introduction to Data Mining, Data Mining: Broad Aspects Visualizing Data Mining Models, Software- Past and Present Developments, Application Visualization System, Software for Chemical Data Mining, Data Mining & human Genome
Unit V: Drug Design and Discovery
Contour of Drugs, Development of New Drugs, chemical & physiochemical parameters in Drug design, Design of enzyme inhibitors, Drug metabolism, Structure Based drug Designing, Drug Discovery, computation techniques in drug design process.
Reference:
- An Introduction to Chemoinformatics - Andrew R. Leach, Valerie J. Gillet
- Chemoinformatics in Drug Discovery (Methods and Principles in Medicinal Chemistry) - by
- Mannhold, Raimund, Wiley-VCH Verlag publication
- .Chemoinformatics: A Textbook - by Johann Gasteiger, Thomas Engel
- Basic Cheminformatics: A Textbook - By Mercato Inglese
| 601 | Professional communication skills. | 100 |
| 602 | Industrial relations and Entrepreneurship | 200 |
| 603 | Dissertation will have 200 marks distributed as below (I) 50 marks viva voce, (2)150 marks Dissertation- its contents, quality, style of presentation. | 200 |
Only one external examiner will be appointed for each centre.
| Total | 500 |
| Total Marks for all the three years | 3500 |
601 PROFESSIONAL COMMUNICATION SKILLS
Note: Question No.1 shall consist of questions requiring short answers and shall cover entire paper. The paper is divided into four sections. Students are required to attempt five questions in all, selecting not more than one question from each section. All questions carry equal marks.
Unit- I
- Communication: Definition, Barriers in communications, Implication of Communication, Purpose of communication.
- Elements: Preparation, structure and personal interaction.
Unit- II - Oral Communication; Skill and Techniques of Speaking preparation of Speaking, Development of speaking skills, barriers to speaking, speaking structure, bridging points, time limitation/length of speech, Use of Humor.
- Visual Communication: Nature and scope of visual aids, Bolds, slides, overhead projector, cutouts.
Unit- III - Technical letter writing: Purpose of writing, space/layout, economy of words, use of verb/passive voice, type face (italics, bold, underline) and use of indentation.
- Report writing: Preparation, report structure (purpose of report, scope, shape, presentation of report, introduction of report, bridging of report, style of report, and index of report.
Unit- IV - Public communication: meetings, planning and discussion, opening procedure, timing, degree of formality, behavior, repetitive,
Unit- V - Interviews (complexity of situation, preparation of thinking, preparation of setting, preparing the interview, style of interview). Group discussion. (to enhance oral communication and debates, speeches; addresses may be introduced for Public).
BIT- 602: INDUSTRIALIZATION AND ENTREPRENEURSIDP
Unit- I: Principles of Management - The topic mentioned below are to be covered with respect to Bioindustries and Byproducts. .
Management - meaning and importance, evolution of management thoughts. Functions of management: ol type="i">
Unit- II
Communication, Mediation - theories of Motivation, Leadership styles.
Manpower planning, sources of recruitment, selection and training of staff, job evaluation, merit rating, performance appraisal, wage administration and system of wage payment, incentive, trade unions and industrial relations.
Unit- III :Purchase and Stores Management: Concepts of quotations, tenders and comparative statement, inspection and quality control, inventory - Carrying cost and fixed cost of inventors, BEP analysis, stores management, functions of storekeeper, methods of inventory LIFO, FIFO. Marketing Management: Concepts of selling, marketing, market research, Pricing-methods, penetration and Skimming pricing, Physical distribution methods, advertising and Sales promotion.
Unit- IV :Export and Import Management: Concepts of international trade, duties and antidumping duty, Costs involved in exporting a product, pricing of export product. Government assistance for export promotion, export houses, export promotion counsel, MODV AT, patent and patent rights.
Unit- V
Management Laws: Concepts of Contract act, offer and acceptance, types of Contracts, Void Contract, Concept of guarantee and warranty, introduction of MRTP and FERA.
Work Study: Work Measurement, time and motion study, flow process chart, flow diagram, Flow chart, string chart etc.Quality Management: TQM, quality management, ISO Systems.
Reference books:
- Management for Business and Industry - C.S.George Jr.
- Principles of Management - Koontz and 0 'Donnell.
- Business Organization and Management - M.C. Shukla.
- Biotechnology, Colin and Bjorn Kristiansen, Cambridge
Dissertation Based on Lab and Field Work
BIT- 603
| Dissertation will have 200 marks distributed as below (I) 50 marks viva voce, (2)150 marks Dissertation- its contents, quality, style of presentation. | 200 |
| Only one external examiner will be appointed for each centre. | |
| Total | 500 |
| Total Marks for all the three years | 3500 |