ADB Syllabus 2019 280921

BVDU-RGITBT-ADB (Advanced
Diploma in Bioinformatics, Post

Graduate Diploma) Syllabus
2019
BVDU-RGITBT-ADB (ADVANCED DIPLOMA IN BIOINFORMATICS, POST GRADUATE DIPLOMA) SYLLABUS
BHARATI VIDYAPEETH DEEMED TO BE UNIVERSITY

PUNE
REVISED SYLLABUS FOR

Advanced Diploma in Bioinformatics
(Post Graduate Diploma)
UNDER
FACULTY OF INTERDISCIPLINARY STUDIES
SYLLABUS OF SEM I – SEM II
UNDER
CREDIT SYSTEM
To be effective from Academic Year
2019-20
BVDU-RGITBT-ADB (ADVANCED DIPLOMA IN BIOINFORMATICS, POST GRADUATE DIPLOMA) SYLLABUS
BVDU-RGITBT-ADB
INTRODUCTION
The Advanced Diploma in Bioinformatics (ADB) is a full time post graduate diploma
offered by Bharati Vidyapeeth (Deemed to be University (BVDU)) in its constituent unit,
Rajiv Gandhi Institute of IT and Biotechnology (RGITBT). The course was initiated in the
year 2010 and was designed to facilitate empowerment of students to face cutting edge
technological applications in bioinformatics sector. 21st century biology has been
transformed into integrative biology due to paradigm shift from reductionist to holistic
approach. The data explosion is one of the obvious causes of the transformation to
holistic or systems biology mode. In order to have deeper insights in to biological
systems, integration of the data from genome to phenome levels to generate dynamic
models has surfaced as key area of bioinformatics. On its implementation for 10 years,
the curriculum is being revised two times to embrace newer emerging disciplines and
value added courses. The revised ADB is a full time 60 credits Program to be
implemented in Rajiv Gandhi Institute of IT and Biotechnology from the academic year
2019-20. The feedback of students, alumni, faculty, employers and parents has a
substantial contribution in designing of this curriculum.
OBJECTIVES
1. To impart deep knowledge of the discipline

2. Develop skills in relevant areas to enhance employment opportunities
3. Introduce emerging areas of NGS, Drug designing and data mining
4. Build interdisciplinary approach
5. Foster global competence among students
6. Inculcate social and moral values and sense of scientific responsibilities in
students
ELIGIBILITY FOR ADMISSION TO THE COURSE
Candidates satisfying following criteria are eligible to apply for ADB Course
1. A student who has obtained Bachelor’s degree with minimum 45% in (i) B.Sc.
(Biotechnology / Microbiology / Biochemistry / Zoology / Botany / Chemistry
/Agriculture/ Mathematics /Statistics / Computer Science). (ii)B. Pharm (iii).
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BVDU-RGITBT-ADB
MBBS (iv) BDS (v) BAMS (vi) BHMS (vii) B.E. in Computer Science or Information
technology or Biomedical Engineering will be considered eligible for admission to
M.Sc. Bioinformatics course or 40% aggregate marks for SC / ST category
respectively at graduate level university examination.
2. Subject to above conditions, the admission will be based on first come first serve
basis.
DURATION OF THE COURSE
The course will be executed in two semesters. The medium of instruction and
examination will be only English.
RULES FOR THE COURSE
1. The entire course is of 60 credits.

2. One credit for theory course is equivalent to 15 lectures/tutorials; while one
credit for practical course is equivalent to 25 – 30 hrs. of lab /field work or
demonstration.
3. The curriculum comprises of core, advanced and value added courses. The Core
and Advanced Courses are compulsory where as Value Added are elective.
4. The Core Courses are aimed at providing fundamental knowledge of the
discipline. The advanced courses are designed to develop manpower for
bioinformatics industries as per current need. The Value Added Courses are
intended to inculcate the thrust of new domains of bioinformatics within
students.
5. The teaching schedule for the 3 credits and 2 credits theory courses will be 3 and
2 lectures per week respectively. All courses will have one tutorial fortnightly.
6. The respective elective course will be implemented only if more than 10 students
enroll for that course.
7. All core courses will be evaluated by University Examination. The elective courses
will be evaluated by University Examination and Continuous Assessment.
8. Two extra credits will be awarded to students if there is any significant outcome
of their dissertation study. The research outcome in terms of publication in
indexed national/International journal; filing of patent; or commercialization of
technology will be considered for the award of credits.
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BVDU-RGITBT-ADB
RULES FOR EXAMINATION
A: Nature of Examination:
1. Each course will have 40% marks for internal assessment and 60% marks for
semester-end examination.
2. The assessment for 1, 2 and 3 Credits courses will be as given in following table:
Table 1: Evaluation pattern for one to three Credit Courses
Course Marks for Marks for Total Marks for

Credits UE (60% Weightage) IE (40% weightage) evaluation
1 15 10 25
2 30 20 50
3 45 30 75
4 60 40 100
3. The duration of 60 Marks UE theory paper will be 3.00 Hrs; for 30 Marks 1.30
Hrs. respectively.
4. The Internal Assessments (IA) will be conducted by the Institute and an end-of-
the term University Examination (UE) conducted by the university. The UE will be
based on the entire syllabus.
5. The performances at UE and IA will be combined to obtain the Grade Point
Average (GPA) for the course.
STANDARD OF PASSING
A: Grading System: A 10-point absolute grading system will be adapted for grading
in each head of passing. The system will have seven grade points, the highest being
10. The grading system shall be as shown in Table-2 below. The performance
indicators O, A+, A, B+, B, C, and D shall respectively mean Outstanding, Excellent,
Very Good, Good, Average, Satisfactory, and Poor.
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BVDU-RGITBT-ADB
Table-2: The grading system under CBCS
Range of Marks Grade Point Grade

(out of 100)
80 ≥Marks ≤ 100 10 O
70 ≥ Marks ≤ 80 9 A+
60 ≥Marks ≤ 70 8 A
55 ≥Marks ≤ 60 7 B+
50 ≥Marks ≤ 55 6 B
40 ≥Marks ≤ 50 5 C
Marks <40 0 D
1. The grade point average (GPA) for a course shall be calculated by first finding the
total marks out of 100 for the course. The corresponding GP (as per the table-2)
shall be the GPA for the course.
2. Two kinds of performance indicators, namely, the Semester Grade Point Average
(SGPA) and the Cumulative Grade Point Average (CGPA) shall be computed at the
end of each term. The SGPA measures the cumulative performance of a learner
in all the courses in a particular semester, while the CGPA measures the
cumulative performance in all courses up to and including the current semester.
The CGPA of a student when he/she completes the program is his/her final
result.
3. The SGPA is calculated by the formula , SGPA = ∑ Ck x GPAk where Ck is the
∑ Ck
Credit-value assigned to a course and GPAk is the GPA obtained by the student in
the course. In the above, the sum is taken over all the courses that the student
has undertaken for the study during the semester, including those in which
he/she might have failed or those for which he/she remained absent. The SGPA
shall be calculated up to two decimal place accuracy.
4. The CGPA is calculated by the formula , CGPA = ∑ Ck x GPAk where Ck is the
∑ Ck
Credit-value assigned to a course and GPAk is the GPA obtained by the student in
the course. In the above, the sum is taken over all the courses that the student
has undertaken for the study from the time of his/her enrolment and also the
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BVDU-RGITBT-ADB
during the semester for which CGPA is calculated, including those in which
he/she might have failed or those for which he/she remained absent. The CGPA
shall be calculated up to two decimal place accuracy.
5. The CGPA, calculated after the minimum credits specified for the program are
‘earned’, will be the final result grace marks of 1, 2 or 3 may be awarded to a
candidate at UE as per the university rules.
B: Standards of Passing and ATKT rules:
1. For all Core Courses, both UE and IA
Constitute separate heads-of-passing (HoP). In order to pass in such courses and

to ‘earn’ the assigned credits
(a) the learner must obtain a minimum grade point of 5.0 (40% marks) at UE
and also a minimum grade point of 5.0 (40% marks) at IA;
OR
(b) If he/she fails in IA, then also the learner passes in the course, provided
that a minimum of 25% is obtained in IA and GPA for the course is at
least 6.0 (50%marks ) in aggregate. The GPA for a course will be
calculated only if the learner passes in that course.
2. A student who fails at UE in a course has to reappear only at UE as a backlog
candidate and clear the HoP. Similarly, a student who fails in a course at IA has to
reappear only at IA as a backlog candidate and clear the HoP. A student who
passes in aggregate in a course need not reappear even if he failed at IA if
he/she obtains 25% at IA.
3. The students of Semester I and II & III will be admitted to next Semester even if
he/she gets backlog in any of the course. They can reappear in the next semester
examination as a backlog candidate.
C: AWARD OF HONOURS:
1. A student who has completed the minimum credits specified for the program
shall be declared to have passed in the program. The final result will be in terms
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BVDU-RGITBT-ADB
of letter grade and CGPA only and is based on the CGPA of all courses studied
and passed. The criteria for the award of honors are given in Table 3.
Table 3: Criteria for the award of honors at the end of the program
Range of CGPA Final Grade Performance Equivalent Range of

Descriptor Marks (%)
9.50 ≥ CGPA≤ 10.00 O Outstanding 80 ≥ Marks ≤ 100
9.00 ≥CGPA≤ 9.49 A+ Excellent 70 ≥ Marks ≤ 80
8.00 ≥CGPA≤ 8.99 A Very Good 60 ≥Marks ≤ 70
7.00 ≥CGPA≤ 7.99 B+ Good 55 ≥ Marks ≤ 60
6.00 ≥CGPA≤ 6.99 B Average 50 ≥ Marks ≤ 55
5.00 ≥CGPA≤ 5.99 C Satisfactory 40 ≥ Marks ≤ 50
CGPA Below 5.00 F Fail Marks below 40
THE FORMAT OF THE TRANSCRIPTS
The transcripts may be acquired by the students indicating his/her performance

in every semester examination. The transcript shall show the performance indicators
given in the following table, in addition to any other information.
Course Course Number University IA/CA Grade Result

Number Description of Credits Examination Point
Average
Grade Grade Grade Grade
(GPA)
Point Point
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BVDU-RGITBT-ADB
Total Cumulative SGPA CGPA Equival Note: GPA is calculated by adding the UE
Credits Completed ent marks out of 60 and IA marks out of 40.
The total marks out of 100 are
Marks
converted to Grade Point, which will be
(%) GPA
PATTERN FOR ASSESSMENT
A: Pattern of Evaluation for Internal Assessment of Theory Courses:
The weightage for Internal Assessment is 40%. Students for IA of every theory course
will be assessed for total of 40 marks for 3 credit course and for 20 marks for 2 credit
course which will be cumulative marks obtained in two separate assessments specified
below.
1. Two internal written examinations of 20 marks each for 3 credit course and 10
marks each for 2 credit course. A total of the two tests will be considered.
2. An optional assignment/ oral/ open book examination may be undertaken if
desired.
B. Pattern of Evaluation for Internal Assessment of Practical Courses:
The Internal Assessment for every practical course will be of 20 Marks for 2 credits and
40 marks for 4 credits practical courses. The students for IA will be assessed on the basis
of;
1. Performance for every practical: 10 Marks/20 Marks for 2/4 Credits practical
courses respectively. (Marks to be distributed depending on total number of
practical)
2. Assignment/ Oral examination/Tour Report: 10/20 Marks for 2/4 Credits courses
C: Pattern of question paper at University Examination
University Examination for 3 credit and 2 credit theory course will be of 60 marks and 30
marks respectively. For 3 credit course, the question paper will comprise of 6
7
BVDU-RGITBT-ADB
questions, 3 questions each in section I and section II. Each question will be of 10 marks.
All questions will be compulsory. The pattern of question paper will be as given on next
page.
PATTERN OF QUESTION PAPER FOR 3 CREDIT COURSE OF UNIVERSITY THEORY

EXAMINATION OF ADB 2019 Credit System Based Course (TOTAL MARKS: 60, TME:
2.00 HRS.)
Instructions to Paper Setter:
1. Question paper of each course will comprise of total 6 questions,

2. Section I will have 3 questions and Section II 3 questions.
3. All questions will be compulsory. Each question will carry an internal option of
one extra sub-question.
4. Q. no 1 will be objective, comprising of 7 questions of 2 mark each. They will be
based on entire portion of Section I. Students will have to attempt any 5 out of
these.
5. Q no 4 will be objective, comprising of 7 questions of 2 mark each. They will be
based on entire portion of Section II. Students will have to attempt any 5 out of
these.
6. Questions 2 & 3 of Section I and 5 & 6 of Section II will be descriptive and
contain 3 sub-questions of 5 marks each out of which students will attempt any
two.
7. Q 2 and 3 will be based solely on Unit I and II whereas Q 5 and 6 will be based on
Unit III and IV of the syllabus respectively.
8. Students will attempt answers to Section I and Section II in separate answer
books
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BVDU-RGITBT-ADB
SECTION I
Q.1 Attempt Any FIVE of the following:(Define, Explain why, Fill in the (10)
blanks, Give examples, Answer in brief)
a
b
c
d
e
f
g
Q.2 Attempt Any Two of the following: (Answer the following, Differentiate (10)
Between, Give neat labeled diagram of)
a
b
c
Q.3 Write short notes on Any Two of the following (10)
a
b
c
SECTION II
Q.4 Attempt Any five of the following: :(Define, explain why, Fill in the (10)
a
b
c
d
e
f
g
Between, Give neat labeled diagram of)
a
b
c
Q.6 Write short notes on Any Two of the following (10)
a
b
c
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BVDU-RGITBT-ADB
QUESTION PAPER PATTERN FOR 2 CREDITS THEORY COURSE AT UNIVERSITY

EXAMINATION
For 2 credit course, the question paper will comprise of 4 questions, 2 questions each in
section I and section II. Q1 of section I and Q3 of section II will be of 7 marks each while
Q2 and Q4 will be of 8 marks each .All questions will be compulsory. The pattern of
question paper will be as given on next page.
Pattern of question paper for 2 credit course of university theory examination of ADB
2019 Credit System Based Course (Total Marks: 30, Tme:1.50 Hrs.)
Instructions to Paper Setter:
1. Question paper of each course will comprise of total 4 questions,

2. Section I will have 2questions and Section II 2 questions.
3. All questions will be compulsory. Each question will carry an internal option of
one extra sub-question.
4. Questions 1 of section I and 3 of section II will be objective, and contain 7
questions of 1 mark each out of which students will attempt any 5. They will be
based on entire portion of Section I and section II respectively.
5. Questions 2 of Section I and 4 of Section II will be descriptive and contain 3 sub-
questions of 5 marks each out of which students will attempt any two.
6. Q 2 and 4 will be based solely on Unit I and II of the syllabus respectively.
7. Students will attempt answers to Section I and Section II in separate answer
books
SECTION I
Q.1 Attempt Any Five of the following: :(Define, Explain why, Fill in the (05)
a
b
c
d
e
f
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BVDU-RGITBT-ADB
Between, Give neat labeled diagram of, Write short notes on)
a
b
c
SECTION II
Q.3 Attempt Any Five of the following: :(Define, Explain why, Fill in the (05)
a
b
c
d
e
f
g
h
Between, Give neat labeled diagram of, Write short notes on)
a
b
c
D: PATTERN FOR QUESTION PAPER OF UNIVERSITY PRACTICAL EXAMINATION OF ADB

2019 Credit System Based Course
(Total Marks: 30/60 for 2/4 credit courses, Time: 3 .00/6.00 Hrs.)
Q. 1 Major Practical (10/20)
Q. 2 Spotting/Minor Experiment (10/20)
Q. 3 Viva (05/10)
Q. 4 Journal (05/10)
---------------
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BVDU-RGITBT-ADB
Course structure of Advanced Diploma in Bioinformatics

Under Credit System Based Course 2019-20
SEMESTER I
Course No. & Title Credits IA Univ. Total

Description Exam Credits
ADB 101
Cell Biology (C) 2 20 30
Basic Course-Theory
ADB 102
Biochemistry(C) 2 20 30
Basic Course –Theory
ADB 103
Biomathematics(C) 2 20 30
ADB 104
Biostatistics(C) 2 20 30
ADB 105 C Programming and
3 40 60
Basic Course –Theory Data structure(C)
ADB 106 Biological
2 20 30
Basic Course – Theory Informatics(C)
ADB 107 DBMS & MongoDB
3 40 60
Basic Course – Theory (C)
28
ADB 108
Python 2 20 30
Core Course - Theory
ADB 109 Cell Biology and
2 20 30
Basic Course –Practical Biochemistry Lab (C)
C Programming and
ADB 110
Data Structure Lab 2 20 30
Basic Course –Practical
(C)
ADB 111 Biological
2 20 30
Basic Course –Practical Informatics Lab (C)
ADB 112 DBMS & MongoDB
2 20 30
Basic Course –Practical lab(C)
ADB 113
Python Lab 2 20 30
Core Course - Practical
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BVDU-RGITBT-ADB
SEMESTER II
Course No. & Title Credits IA Univ. Total

Description Exam Credits
ADB 201 Statistical Analysis
System (SAS) (C) 2 20 30
Core Course –Theory
ADB 202 R and Data Analytics
3 40 60
Core Course –Theory (C)
ADB 203 JAVA and BioJAVA
3 40 60
Core Course –Theory Programming (C)
ADB 204
Science of Omics (C) 3 40 60
Core Course –Theory
ADB 205
Proteomics (C) 2 20 30
Core Course - Theory
ADB 206 Advanced
2 20 30
Advance Course -Theory Bioinformatics
ADB 207 Data Mining through 2 20 30
Advance Course -Theory Machine Learning
ADB 208 Molecular Modeling

3 40 60 32
Advance Course-Theory & Drug Designing
ADB 209 SAS and Data
2 20 30
Core Course - Practical Analytics lab (C)
JAVA and BioJAVA
ADB 210
Programming lab 2 20 30
Core Course - Practical
(C)
ADB 211 Omics Analysis Lab
2 20 30
Core Course - Practical (C)
ADB 212 Advanced
2 20 30
Advance Course - Practical Bioinformatics Lab
Data Mining through
ADB 213
Machine Learning 2 20 30
Advance Course- Practical
Lab
Molecular Modeling
ADB 214
& Drug Designing 2 20 30
Advance Course- Practical
Lab
Total Credits Offered: 28 C, Sem I+ 32 C, Sem II = 60
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SEMESTER I
BVDU-RGITBT-ADB: SEM I
ADB 101: Cell Biology (C) Total

Basic Course – Theory; 2 Credits 30L
UNIT I
1. Cell as a basic unit of life. 4

Basic structure, organization and composition of prokaryotic and eukaryotic cell.
Plasma membrane structure and functions, Membrane models. Components of
blood & their functions (Plasma, RBC, WBC, Platelets).
2. Cytoskeleton: Organization and functions cytoskeleton, Actin filaments, actin 3
binding proteins, Intermediate filaments, Microtubules
3. Cell Junctions: 2
Gap junctions, Tight junctions, Cell adhesion-integrins, selectins, cadherins.
desmosomes and hemidesmosomes, plasmodesmata
4. Membrane Transport: 6
Transport across membrane- passive diffusion, osmosis, active transport, Ion
Channels, Na+ and K+ pump, Ca2+ ATPase pump, co-transport, symport, antiport,
endocytosis and exocytosis.
UNIT II
6. Cell Cycle: Molecular events of cell division and cell cycle, regulation of cell cycle 5
events- Cyclins, Cyclin dependent kinases, inhibitors.
7. Cell Signaling: General principles of cell signaling, signaling via G-protein 6

coupled receptors, kinase receptors, role of secondary messengers.
8. Ageing and apoptosis, abnormal development and teratogenesis in animals 4
References:
1. Alberts, B., Bray, D., Lewis, J., Raf, M., Roberts, K., Watson, J.D. (1994).
Molecular Biology of the Cell
2. Cooper, G.M. (1997).The Cell: A molecular approach, ASM Press, USA.
3. Darnell, J., Lodish, H., Baltimore, D. (1990). Molecular Cell Biology.
Scientific American Books Inc. NY.
4. Hallwell, B., Gutteridge, J.M.C. (2002). Free Radicals Biology and Medicine.
Oxford Press.UK.
5. Karp, G. (1996). Cell and Molecular Biology concepts and experiments, John
Wiley and Sons Inc. NY.
14
ADB 102: Biochemistry (C) Total

UNIT I
1. Introduction to Biomolecules: Carboydrates, Lipids and Proteins – their 1

biological roles and functions
2. Carbohydrates: Classification-on basis of carbon no & functional grs.; 3

Structure with molecular formulae; Stereochemistry (structural and
conformational isomers); isomers with one and more chiral centres, properties
of stereoisomers; cyclization of sugars; conformations of cyclic forms (chair
& boat forms).
3. Important monosaccharides: 6 C sugars- glucose, fructose, mannose, 1

galactose, 5 C sugars- ribose, deoxyribose, important modified
monosaccharides (2-keto-3-deoxy-D-manno-octulosonic acid (KDO), 2-keto-
3-deoxy-D-glycero-D-galacto-nonulosonic acid (KDN), sialic acids,
aminosugars, sugar acids (their biological role/ occurrence)
4. Linkages in Sugars: Structure and functions of important di-saccharides 1

(sucrose, lactose, maltose, cellobiose) and poly-saccharides (homo and
heteropolymers, storage and structural polymers – starch, glycogen, cellulose,
chitin, peptidoglycan)
5. Physico-chemical properties of carbohydrates:Reducing-non-reducing 2

properties; Exploitation for detection and separation –Benedict’s test;
Introduction to conjugate sugars (Glycoproteins and glycolipids and their
importance)
6. Significance of carbohydrates in microbial, plant and animal system: 2

ABO blood groups, heparin, lectins, carbohydrate vaccines
7. Lipids: Occurrence/sources: plant derived oils, ghee 1

8. Structure :Structure of fatty acids, triglycerides; Classification viz., simple 2
and compound, structural and storage with examples; unsaturated-saturated,
Oils (refined/unrefined significance); fats, waxes, rancidity/spoilage of fats
(microbial, oxidative)
9 Functions:Functions in a living system: significance of hydrophobicity and 2

water immiscibility for compartmentalisation, in vitamins, cofactors, for
signalling, pigments
10. Lipid conjugates:Important conjugates and their functions: phospholipids, 3

glycerophospholipids, sphingolipids; structure of membranes, micellar
15
structures, Cholesterol- Structure, function and significance
11. Liposomes:Liposomes in drug delivery, soaps, bio-surfactants 1

12 Physico-chemical properties of carbohydrates and lipids: Compare and
contrast of properties arising due to differences in C:O ratio
UNIT II
12. Amino acids, peptides and proteins: Occurrence/sources, Naturally 3

occurring amino acids; structures; abbreviated names; stereoisomerism;
amphoteric nature of amino acids, Classification of amino acids (on basis of
functional groups, essential/non-essential); Chemical reactivity due to
functional group (amide, acid, amine); peptides & proteins peptide bond,
bond properties, N-Terminal, C-Terminal, Complex proteins– Proteoglycans,
Lipoproteins, metalloproteins, phosphoproteins, chromoproteins and their
significance
13. Protein structure: Primary, secondary (α helix and β conformation), tertiary 4

and quaternary structure. Forces stabilizing molecular structure (covalent
bond, ionic bond, hydrogen bond, salt linkage, van der Waal’s forces) a brief
over view of Ramchandran plot, Structure-Function relationship in proteins
with examples of Fibrous proteins, Collagen, Hemoglobin; importance of
sequence of amino acids for structure and function of protein (eg. Sickle cell
anaemia),
14. Introduction to enzymes as biocatalysts: Enzyme-substrate interaction, 4

Rates of enzyme reaction, Concept of Km, Vmax
References:
1. Biochemistry, Berg, J.M., Tymoczko, J. L. and Stryer, L. W.H. Freeman and

Co., New York, USA (2003).
2. Principles of Biochemistry by Lehninger, A., Nelson, D. L. and Cox,

M.M. W.H. Freeman and Co., New York, USA (2008).
3. Biochemistry, Satyanarayan, U. Books and Allied (P) Ltd., Kolkata, India
(2008).
16
ADB 103: Mathematics (C) Total

UNIT I
1. Calculus: Limits, Continuity, Differentiation (1D & Partial), Definite 8

Integrals.
2. Numerical Techniques: Vector algebra, Matrices, Finding Eigen values 3
& Eigen vectors
3 2Dimensional & 3Dimensional Geometry: Cartesians and Polar 4
Coordinates, Locus, Equation of a straight line, Pair of straight lines,
Circle, Ellipse, Parabola, Hyperbola. 3D Coordinate System, Spherical
and Cylindrical Coordinates.
UNIT II
4. Ordinary & Partial Differential Equation: 1’st Order & 2’nd Order 5
Ordinary Differential Equations. Nature of Partial Differential
Equations, Method of Separation of Variables, Methods for Solving
Equations, Solving ODE & PDE.
5. Integral transform: Fourier Series, Fourier Transform, Laplace 7
Transform
6. Applications To Mathematical Biology: Enzyme kinetics, Immunology, 3

Population genetics, Tumor modeling, Applications of ordinary &
partial differential equations to Biology.
References:
1. Introduction to mathematical methods in bioinformatics by Isaev, Alexander Berlin
Springer, 2004.
2. Mathematics in chemistry by K. V. Raman & Pal, Sourav, New Delhi, Vikas
publishing house Pvt. ltd., 2005
3. Calculations in molecular biology and biotechnology: a guide to mathematics in the
laboratory by Stephenson, F.H. Amsertdam, Academic Press, 2003.
4. Mathematics and computer science in medical imaging by Viergever, Max A.&
Todd-Pokropek, Andrew.,1988.
5. Mathematical Methods for Physicists by G. Arfken, Academic Press, New
York,1970.
6. Mathematical Biology, by J. D. Murray Springer Verlag, 1989.
7. Mathematical Models in Molecular and Cellular Biology by Segal, L., ed. 1980.
Cambridge: Cambridge University Press.
8. Numerical Methods by Balaguruswamy, TMH.
17
ADB 104: Biostatistics (C) Total

UNIT I
1. Probabilities, Random Variables, Multiple Random Variables, Distributions, 7

Random Sampling, Maximum Likelihood Estimators, Bayes Estimators,
Mean Squared Error. Hypothesis Testing., t-tests, Likelihood Ratio Tests ,
Interval Estimation
2. Analysis of Variance ,One-Way Analysis of Variance , Two-Way Analysis 8

of Variance , Regression Models, Simple Linear Regression, Logistic
Regression
UNIT II
3. Bayesian Method with Examples, basics of Markov chains, Dynamic 7

Programming and Hidden Markov Model, Metropolis–Hastings Algorithm
and Gibbs Sampling.
Gene Expression and Microarray Analysis ,Unsupervised Learning ,
Supervised Learning Sequence Alignment, Pair-Wise Sequence Analysis,
Multiple Sequence Alignment , Sequence Pattern Discovery
4. Some Common Tools and Techniques : (Brief introduction and case studies 8
only)
Classification and clustering ( Use WEKA)
Artificial Neural Networks.
Fuzzy Sets and Fuzzy Logic
Genetic Algorithms
Note: Practice on XLminer analysis tool-pack or R (no hand computations). Theory to

focus on basic concepts, applications and interpretations/inferencing with secondary
data, no mathematical derivations
References:
1. Basics of Bioinformatics, Rui Jiang Xuegong Zhang Michael Q. Zhang Editors

2. “Basic Statistics for Bioinformatics,”(free open-source package called R. /XL Miner
for solving problems / No hand computation, Use of XL-miner in practicals - 10
excercises, focus should be on estimating and interpreting outputs)
18
3. Probability statistics, and reliability for engineers by Boca Raton, Ayyub B. M. &
McCuen, R H, CRC Press, 1997.
4. Statistics: concepts and applications by Frank, Harry & Althoen, S. C., Cambridge
University Press, 1995.
5. Statistical methods in bioinformatics: an introduction by Ewens, W. J. & Grant, G.
R., New York. Springer, 2001.
19
ADB 105: C Programming and Data Structure (C) Total

UNIT I
1. Introduction and First Program 3
 Why Programming
 Types of Programming
 Introduction to C
 C programming features
 Benefits of C
 Some Facts about C
 Understanding First C Program
2. Variables and Data Types 3
 Identifiers
 Keywords
 Data Types
 Variables
 Constants
3. Console IO Operations 2
 printf function
 scanf function
 Unformatted Functions
4. Operators and Expressions 2

 Expressions
 Types of Operators
 Type Casting
5. Control Flow Statements 2
 Decision Making in C
 If Statement
 Switch Statement
 Unconditional Branching
 While Loop
 Do…While Loop
 For Loop
 Break and continue statements
UNIT II
6. Working with Functions 5

 What is a Function
20
 Benefits of a Function
 Function Terminology
 Array of Structures
 How does Function Works
 Scope and Lifetime of Variables in function
 Storage Classes of Variables
 Call by value and call by reference
 Recursion
7. Working with Arrays and Strings 5
 Understanding Arrays
 Arrays Declaration and Initialization
 Sample Programs
 Multidimensional Arrays.
 Arrays and Functions
 String operation
UNIT III
8. Pointers 4
 Understanding Pointers
 Declaring and Initializing Pointers
 Function and Pointer Parameters
 Pointer Arithmetic
 Pointer and Arrays
 Two Dimensional Arrays and Pointers
 void Pointer
 Dynamic allocation of memory
 Difference between malloc and calloc
9. Structure and Unions 4

 Overview of Structures
 Defining and Using a Structure
 Structures within a Structure
 typedef keyword
 Passing Structures to Functions
 Structure and Pointers
 Unions
10. File Handling 4
 What is a Stream
 Opening and Closing of Files
 Writing and Reading in Text Format
 Writing and Reading in Binary Format
21
Unit IV
11. Introduction to Data Structures 2

Data Structures- Data structure, Abstract Data Types (ADT), Concept of
linear and Non-linear, static and dynamic data structures, and relationship
among data, data structure
10. Linked Lists 3

Concept, Comparison of sequential and linked organizations, Primitive
operations, Realization of Linked Lists, Linked list operations, Head
pointer and header node, Types of linked list- Linear and circular linked
lists, Doubly Linked List and operations, Circular Linked List, Singly
circular linked list, Doubly circular linked list.
11. Stacks 2
Stacks- concept, Primitive operations, stack operations, Applications of
Stack- Expression, Evaluation and Conversion, Need for prefix and
postfix expressions, Postfix expression evaluation, Recursion- concept,
Backtracking algorithmic strategy, use of stack in backtracking.
12. Queues 2
Concept, Realization of Queues Using Arrays , Circular Queue,
Advantages of using circular queues, operations on queue
13. Sorting and Searching 2

Searching- Search Techniques, Sequential search, Binary search.
Sorting methods- Bubble sort, Insertion sort, Selection sort, Quick sort,
Heap sort, Shell sort, Comparison of All Sorting Methods.
References:
1. C& Data structures - P. Padmanabham, B.S. Publications.
2. The C Programming Language, B.W. Kernighan, Dennis M.Ritchie, PHI/Pearson
Education.
3. C Programming with problem solving, J.A. Jones & K. Harrow, Dreamtech
Press.
4. Programming in C - Stephen G. Kochan, III Edition, Pearson Eductaion.
5. Data Structures and Program Design in C, R.Kruse, C.L. Tondo, BP Leung,
Shashi M, Second Edition, Pearson Education.
6. Computer science, A structured programming approach using C, B.A. Forouzan
and R.F. Gilberg, Third edition, Thomson.
7. DataStructures Using C - A.S.Tanenbaum, Y. Langsam, and M.J.
Augenstein, PHI/Pearson education.
8. Let us C – Yashwant Kanetkar
22
ADB 106: Biological Informatics (C) Total

UNIT I
1. Introduction to Bioinformatics 5
 Nature of biological data types

 Overview of available Bioinformatics resources on the web
 Primary Resource Institutes: NCBI, EMBL & DDBJ
 Hierarchy of Biological databases: Primary, Secondary & Derived
2. Biological Databases & Tools 10
 Database search engines: Entrez, SRS

 Nucleic acid databases: GenBank, ENA, Gententry
 Protein sequence databases: NCBI Protein, EMBL Protein, PIR-
PSD , SwissProt/ UniProtKB/ TrEMBL, Expasy
 Structural Databases: PDB, SCOP, CATH, NDB, CCSD, CSD
 Molecular visualization tools: RasMol, Cn3D, SPDBV, Chime,
Mol4D, etc
 Databases and search methods for chemical compounds:
PubChem Compound, PubChem Substance, ChEBI, ChEMBL,
PDBeChem, RESID, EuroCarbDB
 Sequence Submission Tools: Sequin, BankIt, ENA, IMGT/HLA,
DGVa, SPIN, Metagenomics
UNIT II
3. Overview/concepts in Sequence Analysis 7
 Local & Global alignment, DotPlot, Gap Penalties

 Dynamic Programming, Heuristic Methods
 Pairwise Sequence Alignment algorithms: Needleman & Wunsch,
Smith & Waterman
 Scoring matrices for Nucleic acids and proteins: PAM/MDM,
BLOSUM, CSW
4. Database Similarity Searches 8
 BLAST & FASTA
23
Other Tools: LALIGN, Dotlet

 Multiple Sequence Alignment: ClustalW, ClustalX, PRAS
Other Tools: DbClustal, Kalign, MAFFT, MUSCLE, MView, T-
Coffee
 Motifs, Pattern & Profiles
 Derived Databases: PROSITE, BLOCK, ProDom, Pfam, PRINTS,
SBASE
References:
1. Introduction to Bioinformatics by Attwood, T.K. & Parry-Smith, D.J.,

Delhi, Pearson Education (Singapore) Pte.Ltd., 2001.
2. Bioinformatics: Sequence and Genome Analysis by Mount, David, New
York, Cold Spring Harbor Laboratory Press, 2004.
3. Current Protocols in Bioinformatics by Baxevanis, A.D., Davison, D.B.,
Page, R. D. M. & Petsko, G.A., New York, John Wiley & Sons Inc., 2004.
4. Claverie, J.M. and Notredame C. 2003 Bioinformatics for Dummies. Wiley
Editor.
5. Letovsky, S.I. 1999 Bioinformatics. Kluwer Academic Publishers.
6. Baldi, P. and Brunak, S. 1998 Bioinformatics. The MIT Press.
7. Setubal, J. and Meidanis, J. 1996 Introduction to Computational Molecular
Biology. PWS Publishing Co., Boston.
8. Lesk, A.M. 2002 Introduction to Bioinformatics. Oxford University Press.
9. Rastogi, S.C., Mendiratta, N. and Rastogi, P. 2004 Bioinformatics:
Concepts, Skills & Applications. CBS Publishers & Distributors, New
Delhi.
10. Vyas, S.P. and Kohli, D.V., Methods in Biotechnology and
Bioengineering.
11. Genetic Library Construction and Screening: Advanced Techniques and
Applications: Lab Manual
12. Mont, D.W., Bioinformatics: Sequence and Genome Analysis.
13. Pierre Baldi and Soren Brunak, Bioinformatics: The Machine Learning
Approach.
24
ADB 107: DBMS & MongoDB (C) Total

UNIT I
1. DBMS 10
 Database designing, data capturing
 Data Abstraction
 Data Models
 Instances & Schemes
 E-R Model - Entity and entity sets
 Relations and relationship sets
 E-R diagrams
Reducing E-R Diagrams to tables
UNIT II
2. Basic concepts in Indexing and hashing 15

 Types of Indexing
 Data warehousing
 Data mining
 Oracle Architecture
 Basic concepts in Oracle:
o Table space
o Data files
o Blocks
o Extents
o Segments
o Oracle Background Processes
o Control files
o Oracle Memory Management
o Rollback
o Redo logs etc.
 Oracle Report generation, Grants, Roles, Privileges
 Introduction to SQL
UNIT III
3. MongoDB 10
 Introduction of mongoDB
 Uses and Advantages
25
 RDBMS/SQL vs. MongoDB

 Structure of MongoDB
 Database, Collection – operation
 Data type
UNIT IV
4.  CRVD commands 10
 Limit Records, Sorting Record
 Indexing, Aggregation
 Covered queries
 ObjectID
 Regular Expression
References:
1. Database System Concepts by Hanery Korth and Abraham Silberschatz,

McGraw Hill publication.
2. An Introduction to Database Systems by C.J. Date, Addison-Wesley.
3. Database systems by Nilkamal Surve, Tech Max publications.
4. Data Mining: Concepts and Techniques by Jiawei Han and Micheline Kamber,
Morgan Kaufmann Publishers.
5. Oracle PL/SQL Programming by Steven Feuerstein, Bill Pribyl, O-Reilly
Media.
6. The Relational Database Dictionary by C.J. Date, O'Reilly Media
7. Fundamentals of Database Systems by Elmasri and Navathe, Pearson
Education.
8. Database Design and Relational Theory by C.J. Date, O'Reilly Media.
9. Oracle Database 11g A Beginners Guide by Ian Abramson, Michael Abbey,
Michael J. Corey and Michelle Malcher, McGraw Hill publication.
10. Developing Bioinformatics Computer Skills by Gibas, & Jambeck, O-Reilly.
11. Linux : The Complete Reference 6th Edition by Richard Petersen, Tata
McGraw-Hill Education (2007)
26
ADB 108: Python Total

Core Course – Theory; 2 Credits 30L
UNIT I
1. Introduction and Overview of Python 4
 Installation and understanding Python Environment

 Introduction to Python variables
 basic Operators, keywords, python blocks
2. Data types and Program Flow Structures 6
 Numeric data types: int, float, complex, string data type and string
operations,
 Control Structure: if, else and elif , nested control structures
 Python Loop : for loops in python using ranges, string, list and
dictionaries, while loops in python, Controlling loop using pass,
continue, break and else
3. String , Lists, Tuples & Dictionaries 5
 String: String operators, String manipulation using in built methods

 Lists: list operations, slicing, list methods, - list comprehension.
 Tuples: definition, assignment, tuple operations.
 Dictionaries: definition, operations and methods
UNIT II
4. Functions , Modules & Packages 4
 Function: Definition, Function calling, lambda function

 Modules: Introduction to inbuilt Modules, User defined Modules
 Package: Understanding in built package, building own package,
27
importing package
5. File Handling & Exceptional Handling 6
 File Handling: Opening a file, Read and Write operations, File and
Directory related methods
 Exceptional Handling: try-except-else, Assert, try-finally, Raise,
Exception Names & descriptions, User defined exceptions.
6. Python Database Interaction 5
 Python Database interaction, Insertion and retrieval information

in database.
 Reading and storing information on database.
References:
1. Python: The Complete Reference Paperback – 20 Mar 2018, Martin C.

Brown
2. Python Programming: A modular approach by Pearson Paperback – 26
Sep 2017, by Taneja Sheetal , Kumar Naveen
3. Python Machine Learning By Example Paperback – Import, 31 May 2017
4. by Yuxi (Hayden) Liu
5. Artificial Intelligence with Python Paperback – Import, 27 Jan 2017,
by Prateek Joshi
6. Python Deep Learning Paperback – Import, 28 Apr 2017, by Valentino
Zocca , Gianmario Spacagna , Daniel Slater, Peter Roelants
28
ADB 109:Cell Biology and Biochemistry Lab (C) Total

(2 Credits, 1 P, 4.00 Hr., Basic Course Practical) 20 P
Cell Biology Lab

1. Chloroplast isolation from spinach leaves 1
2. Staining of prokaryotic cell organelles: 2
Staining of capsule, spore, cell wall and metachromatic granule
3. Study of mitosis with onion root tip chromosomes 2
4. Observation of permanent slides of meiosis 1
5. Isolation of nuclei from rat liver 2
6. To determine Erythrocyte (RBC) count of a blood sample 1
7. To determine Leucocytes (WBC) count of a blood sample 1
8. Temporary mounting of mitochondria by Janus green B 1
Biochemistry Lab
9. Preparation of buffers-acetate buffer & Preparation of biochemical reagents 2
(Benedict’s reagent)
10. Isolation of biomolecules 2
a. Isolation of starch from corn (separation on the basis of density)
b. Isolation of protein from a suitable source
c. Extraction of triglycerides from oilseeds (separation on the basis of
differential solubility)
11. Quantitative estimation of Glucose by DNSA method 1
12. Quantitative estimation of Protein by Biuret method and absorption at 280 nm 2
13. Acid value or saponification value. Determination with reference to fatty acids. 2
References:
1. An Introduction to Practical Biochemistry, Plummer, D.T.,

Tata‐McGraw‐Hill Publishing Co., New Delhi (2005).
2. Principles and Techniques of Biochemistry and Molecular Biology,
Wilson, K. and Walker, J., Cambridge University Press, New York (2005).
29
3. Laboratory Manual in Biochemistry, Jayraman J., New Age International

(P) Ltd., New Delhi (2007).
4. Alberts B. and Jhonson A. 4th edition (2002) Molecular Biology of the
cell, Garland science.
5. Berg J., Tymcoczko J, and Styrer L, 5th edition (2002) Biochemistry, W. H.
Freeman and company, New York.
6. Cooper G.M., Hausman R. E. The cell: A molecular approach. 5th edition.
ASM Press and Cinauer Associates Inc. 2009
7. Practical Microbiology: Principles and Techniques, (2005), 1st Edn., Kale,
V and Bhusari, K. Himalaya Publishing House, New Delhi.
30
ADB 110: C Programming and Data Structure Lab (C) Total

1. Laboratory assignments based on the following topics in ‘C’ programming: 5

 Data types, operators and expressions, Hierarchy of operators,
 control statements including decision (if, if-else), loops (while, do-while,
for), branching statements(switch, break, continue),
 Functions,
 Arrays (1D, 2D- all matrix operations including inverse of a matrix),
 Strings,
 File handling etc.
10
2. Writing C programs for Bioinformatics applications:
 Extract a protein or nucleic acid sequence from any of the databank files
(GenBank entry, Swiss-Prot, EMBL entry etc.)
 Interconverting the sequence from one databank format to the other eg.
GenBank format to FASTA format, FASTA to PIR format etc.
 Determining the base composition in a nucleic acid sequence and amino
acid composition in a protein sequence.
 Generating the complimentary sequence of a DNA sequence o Pattern
search algorithms o Search for a specific oligonucleotide pattern (eg.
GAACATCC) in a given DNA sequence.
 Find the position where a specific sequence say “GGTCCCGAC” will
hybridize a given DNA sequence.
 Find the restriction enzyme cleavage sites eg. where PVUZ, ECORI etc.
will cut the DNA.
 Locate palindromic sequence stretches in a DNA sequence. Count the
number of Open Reading frames (ORF’s) in a DNA sequence.
 Calculate the codon usage in a nucleic acid sequence.
 Translate a DNA sequence into protein sequence in the forward and reverse
frames.
 Implementation of the Needleman-Wunsch algorithm for pair wise
31
alignment and testing alignment score with randomized pairs of sequences

also.
 Numerical Techniques (4 assignments)
 Basic Formalism, Methods for Solving Equations, Finding Eigen values &
Eigenvectors (5 assignments)
References:
1. Let Us C by Yashavant Kanetkar, BPB Publications.

2. The C programming language by Kerighan and Richie, PHI Publication.
3. Programming in ANSI C by Balaguruswamy, Tata McGraw-Hill
Education.
4. Sams Teach Yourself C in 21 Days Peter Aitken and Bradley L. Jones,
Macmillan Computer publishing.
32
ADB 111: Biological Informatics lab (C) Total

1. Exploring the integrated database system at NCBI server and querying the 1
PUBMED and GenBank databases using the ENTREZ search engine.
2. Exploring the integrated database system at EBI server and searching the 1
EMBL Nucleotide database using the SRS search engine.
3. Exploring & querying SWISSPROT & UniProtKB. 1
4. Exploring and querying the PIR database. 1
5. Exploring tools on ExPASY. 1
6. Exploring utilities in EMBOSS packages. 1
7. Explore Pair-wise global alignments. 1
8. Explore Pair-wise local alignments. 1
9. Database (homology) searches using different versions of BLAST and FASTA 2
interpretation of the results to derive the biologically significant relationships of
the query sequences (proteins/DNA) with the database sequences.
Exploring other databases: LALIGN, Dotlet
10. Multiple sequence alignments: CLUSTALW, Clustal Omega, DbClustal, 2
Kalign, MAFFT, MUSCLE, MView, T-Coffee.
11. Exploring Alignment Analysis tools: AMAS, CINEMA, MaxAlign, 1
PhyloGibbs, SVA, PVS.
12. Exploring and using the derived databases: PROSITE, PRINTS, BLOCKS, 1
Pfam and Prodom for pattern searching, domain searches etc.
13. Studying the format & content of structural databases & visualization of 1
structure using Rasmol, Cn3D and other utilities.
References:
1. Bioinformatics: A Practical Guide to the analysis of Genes and Proteins

(3rd Ed.) by Baxevanis, A.D. & Ouellettee, B., F. F., New York, John
Wiley & Sons, Inc. Publications, 2004.
2. Practical Bioinformatics, Michael Agostino, 1stEdition,
33
ISBN:9780815344568 , September 26, 2012

3. Bioinformatics: A Practical Approach, Shui Qing Ye, CRC Press, 20-
Aug-2007
4. Bioinformatics: Methods Express, Paul Dear (Editor) , Publication
Date: September 18, 2007 | ISBN-10: 190484216X | ISBN-13: 978-
1904842163 | Edition: 1st Edition
5. Current Protocols in Bioinformatics by Baxevanis, A.D., Davison, D.B.,
Page, R. D. M. & Petsko, G.A., New York, John Wiley & Sons Inc.,
2004.
6. Bioinformatics: Sequence, Structure and Databanks: A Practical
Approach [Paperback]
34
ADB 112: DBMS & MongoDB lab (C) Total

1. Part I: ORACLE 2
Assignment based on “Data Definition Language”.
 A set of SQL commands used to create table, modify table structure,
drop table, rename table.
2. Assignment based on “Data Manipulation Language” 2
 A set of SQL commands used to change the data within the database.
 Insertion of records in the tables, updating of all or specific set of
records in tables.
 Viewing the attributes of table’s column.
3. Assignment based on “Data Query Language” 2
 Different forms of Select statement
 Arithmetic and logical operators.
 Range searching and pattern matching.
4. Assignment based on defining Constraints. 2
 Types: I/O constraints like Primary Key, Foreign key, Null and Unique
 Constraints. Business constraints like check constraints.
5. Assignment based on using joins. 2
 Joining multiple tables, joining a table to it.
6.  Granting rights on user objects such as Tables, Views, and Sequences. 2
 Revoking rights on user objects such as Tables, Views, and Sequences.
 XAMPP for MySQL

7. Part II: MongoDB based practical 8
References:
1. Database System Concepts by Hanery Korth and Abraham Silberschatz, McGraw

Hill publication.
2. An Introduction to Database Systems by C.J. Date, Addison-Wesley.
35
3. Database systems by Nilkamal Surve, Tech Max publications.

4. Data Mining: Concepts and Techniques by Jiawei Han and Micheline Kamber,
Morgan Kaufmann publishers.
5. Oracle PL/SQL Programming by Steven Feuerstein, Bill Pribyl, O-Reilly Media.
6. The Relational Database Dictionary by C.J. Date, O'Reilly Media
7. Fundamentals of Database Systems by Elmasri and Navathe, Pearson Education.
8. Oracle Database 11g A Beginners Guide by Ian Abramson, Michael Abbey,
Michael J. Corey and Michelle Malcher, McGraw Hill publication.
36
ADB 113: Python lab Total

(2 Credits, 1 P, 4.00 Hr., Core Course Practical) 20 labs
1. Basic Python Programming 10
 Python Basic
 Python Basic (Part -II)
 Python Data Types - String
 Python Data Types - List
 Python Data Types - Dictionary
 Python Data Types - Tuple
 Python Data Types - Sets
 Python Array
 Python Conditional statements and loops
 Python functions
2. Python Data Structures and Algorithms 3
 Data Structure
 Search and Sorting
 Recursion
3.  Python Date Time 7

 Python Class
 Python Math
 Python File Input Output
 Python Regular Expression
References:
1. https://www.w3resource.com/python-exercises/
2. Python: The Complete Reference Paperback – 20 Mar 2018, Martin C.
Brown
3. Python Programming: A modular approach by Pearson Paperback – 26 Sep
2017, by Taneja Sheetal , Kumar Naveen
4. Python Machine Learning By Example Paperback – Import, 31 May 2017
5. by Yuxi (Hayden) Liu
6. Artificial Intelligence with Python Paperback – Import, 27 Jan 2017,
by Prateek Joshi
7. Python Deep Learning Paperback – Import, 28 Apr 2017, by Valentino
Zocca , Gianmario Spacagna , Daniel Slater, Peter Roelants
37
SEMESTER II
BVDU-RGITBT-ADB- SEM II
ADB 201: Statistical Analysis System (SAS) (C) Total

UNIT I
1. Introduction to SAS 1
 An overview of SAS foundation
 Introduction to SAS programs submitting a SAS program
 Working with SAS program syntax
2. Accessing Data 1
 Examining SAS data sets
 Accessing SAS libraries- Proc contents
3. Reading and Creating SAS Data sets 2
 Introduction to SAS Data sets
 Reading from existing SAS Data Sets
 Reading Spreadsheet and Database Data
 Reading Raw Data Files
o Reading standard delimited data
o Reading nonstandard delimited data
o Handling missing data
o Reading raw data files with formatted input
o Controlling when a record loads
4. Formatting Data Values 1
 Using SAS formats
 Creating user-defined formats
5. Manipulating Data 2
 using SAS functions
 conditional processing
6. CoADBning SAS Data Sets 2
 Concatening
 Merging - one-one, one-many, merging with non-matches
7. Processing Data in groups 1
38
8. Processing Data Iteratively 2

 DO loop processing
 conditional DO loop processing
 SAS array processing
 using SAS arrays
9. Restuction / Rotating SAS Data Set 1
10. Creating Summary Reports 2

 Proc Print
 Proc Freq
 Proc Report
 Proc Tabulate
 Report Enhancement
UNIT II
11. SAS Macros Language 1

 Purpose of Macro Facility
 Program Flow
12. Macro Variables introduction to macro variables 2

 Automatic macro variables
 Macro variable references
 User-defined macro variables
 Delimiting macro variable references
13. Macro Definitions defining and calling a macro 2

 Macro parameters
 DATA Step and SQL Interfaces creating macro variables in the
DATA step
14. DATA Step and SQL Interfaces creating macro variables in the 2
39
DATA step
 Indirect references to macro variables
 Creating macro variables in SQL
15. Macro Programs conditional processing 2
 Parameter validation
 Iterative processing
 Global and local symbol tables
16. SAS SQL – Language 1

 Introduction to SAS- SQL
 Basic Queries
 Overview of the SQL procedure
 Specifying columns
 Specifying rows
17. Types of Joins 1
18. Introduction to Subqueries 2
19. Set Operators 2
References:
1. Berger, J. O. (1985), Statistical Decision Theory and Bayesian
Analysis, 2nd Edition, New York: Springer-Verlag.
2. Cameron, A. C. and Trivedi, P. K. (1998), Regression Analysis
of Count Data, Cambridge: Cambridge University Press.
3. Gallant, A. R. (1987), Nonlinear Statistical Models, New York:
John Wiley & Sons.
4. Gelman, A., Carlin, J. B., Stern, H. S., and Rubin, D. B. (2004) ,
Bayesian Data Analysis, 2nd Edition, London: Chapman & Hall.
5. Powers, D. A. and Xie, Y. (2000), Statistical Methods for
Categorical Data Analysis, San Diego: Academic Press.
6. Schervish, M. J. (1995), Theory of Statistics, New York:
Springer-Verlag.
40
ADB 202: R and Data Analytics (C) Total

Core Course – Theory; 3 Credits 45 L
UNIT I
1. An Introduction to R and Basic Programming 5

 Overview
 Environment set up (Note: Only for Lab Demonstration)
 Data Types
 Variables
 Operator
 Decision making
2. R Core Programming 5
 Loops
 Functions
 Strings
 Vector
 List
 Matrix
UNIT II
3. R Core Programming 5
 Arrays
 Factors
 Data Frames
 Packages
 Data Shaping
 Library
4. R Charts and Graphs 5
 R-Pie Chart
 R – Bar Chart
41
 R- Box Plots
 R - Histogram
 R- Line Graph
 R- Scatter Plots
UNIT III
5. R Data Interfaces 1 5
 R-CSV
 R-Excel
 R-Binary files
 R-XML files
6. R Data Interfaces 1 5
 R-JSON files
 R-Web Data
 R-Database
 R- NoSQL
UNIT IV
7. Analytics with R Statistics 6

 Mean, Median, Mode
 Normal Distribution
 Multiple regression
 Supervised Model
 Unsupervised Model
8. Algorithm 9
 Logistic regression
 Linear Regression
 Decision tree
 Random Forest
 SVM model
42
References:
1. Data Analysis with R: A comprehensive guide to manipulating, analyzing, and

visualizing data in R, Tony Fischetti, 2nd Edition Paperback – Import, 28 Mar
2018
2. Python Machine Learning, Uxi (Hayden) Liu By Example Paperback,–
Import, 31 May 2017
3. Data Analytics for Beginners: Basic Guide to Master Data
Analytics Paperback – November 3, 2016, by Paul Kinley
4. Data Analytics Made Accessible: 2019 edition Kindle Edition by Anil
Maheshwari
5. Learn R in a Day, 2013, Kindle Edition, by Steven Murray
6. Beginning R: The Statistical Programming Language, 2013 by Mark
Gardener, Paperback
7. Statistical Programming in R, 5 June 2017 by K.G. Srinivasa and G.M.
Siddesh Paperback
43
ADB 203: JAVA and BioJAVA Programming (C) Total

UNIT I
1. An Introduction to Java 2
A Short History of Java
 Features or buzzwords of Java
 Comparison of Java and C++
 Java Environment
 Simple java program
 Java Tools – jdb, javap, javadoc
 Java IDE – Eclipse/NetBeans (Note: Only for Lab
Demonstration)
2. An Overview of Java 4
 Types of Comments
 Data Types
 Final Variable
 Declaring 1D, 2D array
 Accepting input using Command line argument
 Accepting input from console (Using Buffered Reader class)
3. Objects and Classes 6
 Defining Your Own Classes
 Access Specifiers (public, protected, private, default)
 Array of Objects
 Constructor, Overloading Constructors and use of ‘this’
Keyword
 Static block, static Fields and methods
 Predefined class – Object class methods (equals(), toString(),
hashcode(),getClass())
 Creating, Accessing and using Packages
 Creating jar file and manifest file
44
 Wrapper Classes
 Garbage Collection (finalize() Method)
UNIT II
4. Inheritance and Interface 7

 Inheritance Basics (extends Keyword) and Types of
Inheritance
 Superclass, Subclass and use of Super Keyword
 Method Overriding and runtime polymorphism
 Use of final keyword related to method and class
 Use of abstract class and abstract methods
 Defining and Implementing Interfaces
 Runtime polymorphism using interface
 Object Cloning
5. Exception Handling 4
Dealing Errors
 Exception class, Checked and Unchecked exception
 Catching exception and exception handling
 Creating user defined exception
 Assertions
UNIT III
6. Strings, Streams and Files 5

 String class and StringBuffer Class
 Formatting string data using format() method
 Using the File class
 Stream classes
 Byte Stream classes
 Character Stream Classes
 Creation of files
 Reading/Writing characters and bytes
45
 Handling primitive data types

 Random Access files
7. Collection 6
Introduction to the Collection framework
 List – ArrayList, LinkedList and Vector,Stack,Queue
 Set - HashSet, TreeSet, and LinkedHashSet
 Map – HashMap, LinkedHashMap, Hashtable and TreeMap
 Interfaces such as Comparator, Iterator, ListIterator,
Enumeration
UNIT IV
8. Database Programming 6
 The design of jdbc, jdbc configuration
 Types of drivers
 Create and Execute sql statements, query execution
 The Result Set Object
9. Multithreading 3
 What are threads?
 Life cycle of thread
 Running and starting thread using Thread class
 Thread priorities
 Running multiple threads
 The Runnable interface
 Synchronization and interthread communication
10. Networking 2
Networking basics – Protocol, Addressing, DNS, URL, Socket, Port
 The java.net package – InetAddress, URL, URLConnection
class
 SocketServer and Socket class
 Creating a Socket to a remote host on a port (creating TCP
client and server)
46
 Simple Socket Program Example
References:

Delhi, Complete reference Java by Herbert Schildt(5th edition)
2. Java 2 programming black books, Steven Horlzner
3. Programming with Java , A primer ,Forth edition , By E. Balagurusamy
4. Core Java Volume-I-Fundamentals, Eighth Edition, Cay S. Horstmann,
Gary Cornell,
Prentice Hall, Sun Microsystems Press
5. Core Java Volume-II-Advanced Features, Eighth Edition, Cay S.
Horstmann, Gary
6. Cornell, Prentice Hall, Sun Microsystems Press
47
ADB 204: Science of Omics (C) Total

UNIT I
1.  Introduction to Genomics: 5
 Genome sequencing:
o Strategies & Approaches
o Conventional DNA sequencing methodologies
o NGS(Next generation sequencing)
 Introduction, Next-generation sequencing methods,
 NGS File formats (Recognizing different file formats related to
genome sequencing data),
 NGS data quality check & cleaning,
o Third generation sequencing
2.  Genome Assemblies: 6
o Reference assembly, Assembly statistics & visualization,
o De-novo assemblies & assemblers for genome makeup(MIRA, RAYMETA
etc)
 Basic Aspects of Genome Annotation
 Genome mapping techniques: Genetic Mapping and Physical mapping
 Structural Genomics and Functional Genomics
UNIT II
3. Genomics and Comparative genomics Databases: 6

 Genome Databases: Genome Sequence DataBase (GSDB), Genome
Database (GDB), 1000 Genomes Project , AceDB, FlyBase, UCSC
Genome Browser, Wormbase, MaizeGDB, MGI
 Comparative Genomics Databases: COG, VirGen, CORG, HOBACGEN,
Homophila, XREFdb, Gramene
 Genetic Disorders Databases: OMIM, OMIA, Genetic Association
48
Database, Genetic Disorder Guide, IGDD, DisGenet, Genetic Disorder

UK
4. Genomics and Comparative genomics Tools: 6
 Genome Alignments tools:BLAST2, MUMmer, PipMaker, VISTA
 Comparison of Gene Order :GeneOrder, Gene Synteny
 Prediction of genes: ORFs, Prediction of Signal sequences (Promoters, Primers,
splice sites, UTRs etc.), Operons
 Primer Designing Tools: Primer, Primer3, NetPrimer, Primerfinder
 DNA/RNA Sequence Analysis: CENSOR, Gene Finder, GENEID,
GenHunt, GENIE, GRAIL, ORD ID, ORF Finder, ORFGene, Pol3Scan,
tRNAscan
 Translation Tools: Translation Tool, The Protein Machine, 6 Frame
Translation Tool, Reverse Translation Tools
 Restriction Analysis Tools: WEB Cutter, ENZFINDER, TACG
UNIT III
5. Transcriptomics: 6
 Biology of Transcription
 Search for transcription factor binding sites
 RNA Sequencing & Techniques of RNA analysis RNA-Seq,
Microarrays, Regulatory RNAs: small or large, Computational prediction
of miRNA target genes, RNA Darkmatter
 Generating Transcriptome expression Data
6. Metagenomics: 6
 Introduction & Study of metagenomics

 Metagenomics Samples
 Qualitative and quantitative analysis of metagenome: DGGE, T-RFLP,
RT-PCR, NGS
 Sequence to identification of biodiversity
 Metagenomics Algorithms (metagenomics data analysis): RAST, IMG/M,
49
MEGAN
UNIT IV
7. Metabolomics: 5
 Fundamental concept,
 Tools of metabolomics- Capillary electrophoresis, Gas chromatography,
Electrochemical detectors
 Case studies.
8. Lipidomics: 2
Basic concepts and tools Case studies
9. Degradomics: 3
 Techniques and concepts
 Approaches to identify the protease and protease-substrate repertoires, or
 'degradomes', on an organism-wide scale
 Uncover new roles for proteases in vivo.
 Identification of new pharmaceutical targets to treat disease (Emerging
degradomic )
References:
1. She Has Her Mother's Laugh: The Powers, Perversions, and Potential of
Heredity Hardcover – May 29, 2018, Dutton; 1st Edition by Carl Zimmer
2. The Gene: An Intimate History Paperback – May 2, 2017, by Siddhartha Mukherjee
3. Introduction to genomics by Arthur M. Lesk, 2007, Published by OUP Oxford
4. Bioinformatics and Functional Genomics, Textbook by Jonathan Pevsner, 2003, Wiley
publication
5. Metabolomics- Methods and Protocols by Wolfram Weckwerth, Humana Press.
6. Lipidomics- Technologies and Applications by Kim Ekroos, Wiley-VCH.
7. Web/Journal Resources.
8. Transcriptomics: Expression Pattern Analysis, Virendra Gomase, Somnath Tagore; VDM
Publishing, 2009 – Science
50
ADB 205: Proteomics (C) Total

UNIT I
1. Overview of Proteomics: 7
 Introduction and scope of proteomics
 Protein separation techniques:
o ion-exchange
o size-exclusion and
o affinity chromatography techniques
o Polyacrylamide gel electrophoresis
o Two dimensional PAGE for proteome analysis; Image analysis of
2D gels
2.  Determination of Amino acid composition 1
o Hydrolysis
o Separation
o Quantitative analysis
3.  Protein sequencing Methods 1
o Sanger’s method
o Edman’s method
4.  Protein structure determination methods: 3
o X ray crystallography,
o Mass spectrometry
o NMR
5. Proteomics tools: 3
 Protein Databases
 Structural databases: PDB, MMDB, SCOP, CATH.
 3D structure visualization tools: Rasmol, Pymol, SPDBV, Cn3D
(already covered in ADB 106)
 Secondary structure prediction algorithms: Chou-Fasman, Jpred,
Psipred, GOR methods; PHD
51
 3D structure validation databases: PROSA, Ramchandran Plot,

Procheck
 Proteomics tools on Expasy
UNIT II
6.  Protein modifications: Post transcriptional and post translational 9

 Applications of proteome analysis to drug; Protein-protein interaction
(Two hybrid interaction screening)
 Protein engineering, Protein chips and functional proteomics
 Clinical and biomedical application of proteomics
 Proteome databases
 Proteomics industries
7. Protein-protein interaction Databases : 6
 BIND - Biomolecular Interaction Network Database,
 STRING
 DIP (Database of Interacting Proteins)
 PPI Server
 BIND - Biomolecular Interaction Network Database
 PIM -Hybrigenics
 PathCalling Yeast Interaction Database
 MINT - a Molecular Interactions Database
 GRID - The General Repository for Interaction Datasets
 InterPreTS - protein interaction prediction through tertiary structure
References:
1. Fundamentals of Data Mining in Genomics and Proteomics, By Werner Dubitzky,

Martin Granzow, Daniel P. Berrar, 2007, Springer Science + Bussiness Media,
LLC.
2. Protein Arrays, Biochips and Proteomics: The Next Phase of Genomic Discovery
edited by Joanna S. Albala, Ian Humphery-Smith, ISBN-0-8247-4212-1, 2003,
52
Marcel Dekker.
3. Proteomics: Methods Express (Methods Express Series) Paperback – Import,
2007, by C. David O'Connor (Editor), B. David Hames (Editor)
4. Proteomics: A Comprehensive Study of Proteins Hardcover – Import, 30 Jun
2017 by Tanner Perry (Editor)
5. Principles of Proteomics, English, Paperback, Twyman, 2004
6. Introduction to Proteomics -Tools for the New Biology by Daniel C. Liebler,
Humana Press
7. Mass Spectrometry for Biotechnology by Gary Siuzdak, Academic Press.
8. Proteomics for Biological Discovery by Timothy Veenstra and John Yates,
Wiley.
53
ADB 206: Advanced Bioinformatics Total

Advance Course – Theory; 2 Credits 30L
UNIT I
1. Linux: Linux Essentials, Hands-on Exercises 3

Querying Biological Databases with SQL
2. Statistics and graphing software: GraphPad Prism 3
Creating Phylogenetic Trees with MEGA
3. NGS: 4
 QC'ing Reads
 Mapping Next Generation Sequence Reads
 Analysis of ChIP-seq data in Galaxy
 Analysis of RNA-seq data in Galaxy
 Analysis of differential gene expression
 Finding and annotating indels in Human genome
 Bedtool: Toolset for genome arithmetic
5. Structural Variant Analysis 5
 Variant detection: VarScan and SVDetect
 Variant annotation: TASSEL, GATK
UNIT II
6. Advanced Genomics 5
Visualizing Genomes: Browsers
Introduction to ENSEMBL
Integrative Genomics Viewer (IGV)
Juggling Genome Coordinates
Gene list enrichment analysis
Visualizing Genomes: Circos Plots
7. Introduction to Microarray 6
DNA and Protein Array
Microarray data Analysis pipeline
Microarray Techniques
Data analysis with R/Bioconductor
Clustering and Displaying Microarray Data
Expression Atlas
Cool BaRC Web Tools
8. Sequence analysis using DotPlot 4
GeneGo: Bioinformatics Technology for Systems Biology
Visualizing Networks: Cytoscape
54
References:
1. Next-Generation DNA Sequencing Informatics,Stuart M. Brown, New York

University School of Medicine 2013 ISBN 978-1-936113-87-3
2. Chip Technology, Volume 77,Jörg D. Hoheisel, Alvis Brazma,
illustratedPublisherSpringer, 2002, ISBN3540432159, 9783540432159
3. Microarray biochip technology, Mark Schena , illustratedPublisherEaton
Pub., 2000, Original fromthe University of California, ISBN1881299376,
9781881299370
4. Discovering Statistics Using R, Andy Field, Jeremy Miles, Zoë Field,
SAGE, 2012, ISBN1446258467, 9781446258460
5. The R Book, Michael J. Crawley, John Wiley & Sons,
2012ISBN1118448944, 9781118448946
6. A Guide to MATLAB: For Beginners And Experienced Users, Brian R.
Hunt, Ronald L. Lipsman, Jonathan M. Rosenberg, Edition2,
illustratedPublisherCambridge University Press, 2006, ISBN1139452533,
9781139452533
7. MATLAB Guide, Desmond J. Higham, Nicholas J. Higham, Edition2,
illustratedPublisherSIAM, 2005ISBN0898715784, 9780898715781
8. MATLAB Primer, , Kermit Sigmon, Timothy A. Davis, Edition7, CRC
Press, 2004ISBN1420034952, 9781420034950
9. Foundations of Comparative Genomics, Arcady R. Mushegian, Academic
Press, 2010ISBN0080546099, 9780080546094
10. Essentials of Genomic and Personalized Medicine, Geoffrey S. Ginsburg,
Huntington F Willard, Academic Press, 2009ISBN0080958117,
9780080958118
55
ADB 207: Data Mining through Machine Learning Total

Advance Course – Theory; 2 Credits 30L
UNIT I
1. Introduction to Machine Learning (ML) 2

 .Introduction to Artificial Intelligence & Machine Learning,
 Elements of ML,
 Life Cycle of ML,
 Applications of Machine Learning.
2. Introduction to Data Mining 3

 Data Science and Visualization
 Important Python Libraries
 pandas
 numpy
 scikit-learn
 matplotlib
 seaborn.
3. Biological Data and its Application in Machine Learning 1
4. Genetic Algorithm 1
 What is genetic algorithm?
 Types of genetic algorithm
 Introduction to feature selection
5.  Introduction to Linear Regression 3
 loss functions
 over fitting
 gradient descent
6. Classification Algorithm 6
 Logistic Regression,
 Support Vector Machine
56
 Naïve Bayes Classifier.
UNIT II
7. Introduction & Types of Unsupervised Learning 1
8. Neural Computation 2
 Introduction to Neural computation
 Neural network model
9. Evolutionary computation 4
 Introduction to evolutionary Processes
 Genetic Operators
 Evolutionary Optimization Algorithms
10. Fuzzy Computation 3

 Introduction
 Fuzzy sets & systems
 Ant colony Optimization (ACO)
11. Introduction to Human Language Technology & Machine Learning 2
 Stochastic Grammar & linguistics,Language models
 Statistical language Model,
 Markov model
 Hidden Markov Model
12. Optimization Techniques 2
 Conjugate Gradient,
 Newton Raphson,
 Steepest descent,
 Simulated annealing
57
References:
1. Data Mining: Concepts and Techniques by Han and Kamber, Morgan

Kaufmann.
2. Machine Learning by Tom Mitchell, McGraw Hill.
3. Data Mining: Practical Machine Learning Tools and Techniques by Witten and
Frank, Elsevier.
4. Biological Sequence Analysis: probabilistic models of proteins and nucleic
acids by Durbin, R., Eddy, S., Krogh, A. & Mitchison, G.Cambridge Univ.
Press, 1998.
5. Optimization Theory and Application by Rao, S.S., 1984.
6. Discrete optimization by Parker, R. G. & Rardin, R. L., 1988.
7. Stochastic simulation by Repley, Brian D, Wiley series, 1987.
8. Methods of microarray data analysis III by Johnson, K.F. & Lin, S.M. Boston.
Kluwer academic publishers, 2003.
9. Exploration and analysis of DNA microarray and protein array data by
Amaratunga, D. & Cabrera, J.New Jersey. John Wiley & Sons Inc., 90 BVDU-
RGITBT-M.Sc. BIOINFORMATICS- SEM III 2004.
10. Ant colony optimization by Dorigo, Marco & Stutzle, Thomas New Delhi,
Prentice-Hall of India Pvt Ltd, 2004.
11. Data mining: introductory and advanced topics by Dunham, M.H.:New Delhi,
Pearson Education, 2003.
12. An introduction to bioinformatics algorithms by Jones, Neil.C. & Pevzner,
Pavel A. New Delhi, Anne Books, 2005.
13. Fuzzy sets and fuzzy logic: theory and applications by Klir, G.J. & Yuan Bo,
New Delhi. Printice Hall of India, 2002. 81-203-1136-1.
14. Fuzzy and neuro-fuzzy systems in medicine by Teodorrescu, HoriaNicolai,
Kandel, Abraham. & Jain, Lakhmi, C New York, CRS Press
58
ADB 208:Molecular Modeling& Drug Designing Total

Advance Course –Theory;3 Credits 45L
UNIT I
1. Homology Modeling, fold recognition, and ab-initio structure prediction 3

methods - protocols/algorithms.
2. General features- bond stretching, angle bending, improper torsions, cross 3
terms, non-bonded interactions, point charges, calculation of atomic
charges, polarization, Van Der Waals interactions, hydrogen bond
interactions, Water models.
3. Types of force field - all atoms force field, united atom force field, etc. 2
4. Molecular Energy minimization methods:steepest descent, conjugate 3
gradient– derivatives, First order steepest decent and conjugate gradients.
UNIT II
5. Second order derivatives Newton-Raphson, Minima, maxima saddle points 3

and convergence criteria.-non derivatives minimization methods, the
simplex.
6. Molecular Dynamics Simulation:Newtonian dynamics, Periodic boundary 3
conditions and minimum image convention, Potential truncation, Neighbor
list, Force calculations.
7. Classical Monte Carlo: Random numbers, Evaluating integrals using 3
random numbers, Importance sampling, Metropolis algorithm.
8. Analysis of simulated trajectories: Radial distribution functions, Self 3
diffusion coefficient.
UNIT III
9. Drug discovery and QSAR 11

 Drug discovery process, role of Bioinformatics in drug design.
59
 Target identification and validation, lead optimization and

validation.
 Structure-based drug design and ligand based drug design.
 Concept of de novo design for lead identification.
 Structure Activity Relationship:QSARs and QSPRs, QSAR
Methodology, Training data, test data and external validation data,
applicability domain in QSAR
 3D QSAR techniques: CoMFA and CoMSIA.
UNIT I V
10. Pharmacophore and molecular docking 11

 Pharmacophore features, Pharmacophore model, Receptor-based
and ligand-based pharmacophore modeling.
 Virtual screening based on pharmacophore model.
 Receptor site, molecular docking study, flexible docking, rigid
docking, molecular interactions.
 Scoring functions, correlation between ligand-based and receptor-
based studies.
References:
1. Molecular Modeling Principles and Applications (2nd Ed.) by Andrew R.
Leach, 2001, Prentice Hall, USA.
2. Principles of Protein Structure by G. E. Schulz, 2009, Springer
3. Textbook of Structural Biology by Anders Liljas, Lars Liljas, Jure Piskur
and GÃranLindblom, World Scientific Publishic Co. Pvt. Ltd.
4. Structural Bioinformatics, Edited by Jenny Gu, Philip E. Bourne, Wiely
Blackwell
5. Computational Structural Biology: Methods and Applications by
orstenSchwede, TorstenSchwede, Manuel C. Peitsch, 2008, World
Scientific Publishing Company.
6. Molecular Modeling Of Nucleic Acids, Leontis N.B. and SantaLucia J. Jr.
(eds), 1998, American Chemical Society.
7. Molecular Modeling of Proteins by Andreas Kukol, 2008, Humana Press.
8. Molecular Modeling and Simulation: An Interdisciplinary Guide by Schlick
T., 2012, Springer.
9. Biological Modeling and Simulation: A Survey of Practical Models,
Algorithms, and Numerical Methods (Computational Molecular Biology)by
Russell Schwartz, The MIT Press, Cambridge, Massachusetts, London,
England
60
ADB 209: SAS and Data Analytics lab (C) Total

(2 Credits, 1 P, 4.00 Hr., Core Course Practical) 20P
1. SAS based practical 10
2. Data Analysis lab 10

 Install R from CRAN and setup R studio
 Write a Program to print list of Student, Marks and Percentage
considering
o Different data types variables in R using logical, numeric
o integer, complex, character and raw
o Valid/invalid variables declaration
o Variable assignment
o Getting variables in environment
o Class of variables
o Deleting variables
o Vectors declaration
o Different operators demonstration using Arithmetic Operators,
Relational Operators, Logical Operators, Assignment Operators,
Miscellaneous Operators
o if-else demonstration for negative, positive and zero number test
o Switch case for different operations
 Write program to classify odd and even number to demonstrate For,
While and Repeat loops with break and next keywords
 Create a function to calculate Area and circumference of
circle/rectangle
o calling a function with/without arguments
o calling by argument position and names
 Write R program to demonstrate string functions in R , String
manipulations in R
o Vector declaration
o Accessing vector elements
61
o Vector manipulations
 Create a list and modify
o Name elements
o Access elements
o Manipulate the list
o Merging list
o convert list to vector
 Create a numeric matrix
o Access elements
o Matrix computation
o Demonstration
 Create array name columns, rows, matrix, Access array elements
matrix computations
 Create a categorical vector and convert it to
o Factor
o Factor validations
o Generating levels
o Order change
 Create a data frame
o Get structure and summary
o Extract data from DF
o Expand the data frame add column and rows
o Check packages
o Install packages
o Load package
o Join cols/rows in DF
o Merge DF
o Melting and casting
 Read/write files and access from
o CSV files
o Binary file
o Xls file
62
 Read access and manipulate JSON data

o Download and load data from website
o Connect to mysql/oracle DB and access data from table
o Working with MongoDB/Redis
 Create data records and create
o Plot Pie chart for Profit sharing among individuals. Percentage
plotting , pie chart
o Plot a bar graph for monthly revenue. Group bar graph/stacked
chart
o Plot a boxplot for match data mpg vs cylinder
o Create a vector and plot a histogram , Ranged histogram
o Create a vector and plot line, point both graph
o Plot scatterplot for mtcars$wt and mtcars$mpg
 Create data from Hospital, Patient, and disease use case
o Calculate mean, median, mode of a distribution for data
o Demonstration of dnorm, pnorm, qnorm and rnorm
o Demonstration of multiple regression with mtcar dataset
 Get records and perform below
o Use case of admission into university
o Use case for weight calculation
o Use case for Titanic survival prediction
o Use case for Car acceptability
o Use case for Heart disease recognition with caret package
References:
1. Data Analysis with R: A comprehensive guide to manipulating, analyzing,

and visualizing data in R, Tony Fischetti, 2nd Edition Paperback –
Import, 28 Mar 2018
2. Python Machine Learning, Uxi (Hayden) Liu By Example Paperback,–
Import, 31 May 2017
3. Data Analytics for Beginners: Basic Guide to Master Data
63
Analytics Paperback – November 3, 2016, by Paul Kinley

4. Data Analytics Made Accessible: 2019 edition Kindle Edition by Anil
Maheshwari
5. Learn R in a Day, 2013, Kindle Edition, by Steven Murray
6. Beginning R: The Statistical Programming Language, 2013 by Mark
Gardener, Paperback
7. Statistical Programming in R, 5 June 2017 by K.G. Srinivasa and G.M.
Siddesh Paperback
64
ADB 210: JAVA and BioJAVA programming Lab (C) Total

Core Course – Theory; 2 Credits 20 P
1.  Class and Method Implementation by – 2

o Method overloading
o Constructor Overloading
o Static members and methods
2.  Implementation of Multiple Inheritance using Interface. 1
3.  Implementation of Inheritance by 2
o Method overriding
o super constructor and super keyword
o abstract class
4.  Implementation of Package 1
5.  Program to read basic data types from keyboard using 1
Scanner/BufferedReader and check the entered values’ data type
for its appropriateness.
6.  Exception Handling for – 2
o Divide by zero error
o Null values
7.  Program to read the data from user and save it to two different 2
files, display the contents and exchange the contents of those two
files using IO package.
8.  Synchronization of threads. 9
 Develop an animation program using Multithreading viz.
Bouncing Ball.
 Implementation of Client / Server mechanism using Socket
classes.
 Design Database program for Employee details and implement
INSERT,
 SELECT, DELETE, UPDATE queries.
 Design concurrent server that will handle multiple clients using
 Multithreading.
65
 Develop a simple client-server application using RMI.

 Programs using IO streams.
 Programs using files.
References:

Delhi, Complete reference Java by Herbert Schildt(5th edition)
2. Java 2 programming black books, Steven Horlzner
3. Programming with Java , A primer ,Forth edition , By E. Balagurusamy
4. Core Java Volume-I-Fundamentals, Eighth Edition, Cay S. Horstmann,
Gary Cornell,
Prentice Hall, Sun Microsystems Press
5. Core Java Volume-II-Advanced Features, Eighth Edition, Cay S.
Horstmann, Gary
6. Cornell, Prentice Hall, Sun Microsystems Press
66
ADB 211: Omics Analysis Lab (C) Total

Core Course – Theory; 2 Credits 20P
1. Browsing & viewing genome data 1

Ensembl@EBI
 MapViewer@NCBI
2. Explore comparative genomics resources and NCBI and EBI 1
3. Viewing regions exhibiting Synteny 1
 Genome assembly
 Genome Annotation:
Using integrated genome annotation servers such as the
server
developed at IMTech, Chandigadh
(http://imtech.res.in/raghava/gp.html)
4. Gene Prediction and Gene Modeling 2
 Prediction of genes and gene structures (gene modeling)
using online (web) servers of different methods tailored for
prokaryotic and eukaryotic organisms such as GLIMMER,
GeneMark, Grail, GENSCAN etc. Interpretation of results
and comparison with known gene models (where available).
Evaluation of accuracy of the methods.
 Prediction of promoters using methods such as Neural
Network Promoter Prediction (NNPP) at Berkeley
Drosophila Genome Project server, Genome inspector for
coADBned analysis of multiple signals in genomes etc.
Using Promoter databases.
 Prediction of alternate splice sites using methods such as
Splice Site Prediction by Neural Network (at Berkeley
Drosophila Genome Project server), GenScan, NetGene2
GeneSplicer etc. Prediction of PCR primers using Primer 3,
ePCR etc.
67
5. Comparison of full / partial genomic sequences using following methods 2

to identify conserved genes and map/compare the annotations of the two
sequences
 BLAST2
 MegaBLAST and Discontiguous MegaBLAST
 MUMmer
 PipMaker
 VISTA
 Artemis
6. Compare gene order of given genomic sequences using the GeneOrder 1
tool
7. Explore and query the comparative genomics databases: COG, VirGen, 1
CORG, HOBACGEN, Homophila, XREFdb, Gramene etc.
8. Explore and query SNP and SNP-related databases 1
9. RNA seq data Analysis 1
10. Transcriptomics data analysis 1
11. Metagenomics Data Analysis 1
12. Explore and query the protein-protein interaction databases: DIP, PPI 2
Server,
BIND, PIM, PathCalling, MINT, GRID, InterPreTS
13. Gene annotation of unknown sequence 1
14. Functional Genomics 4
Using primary databases (such as UniProt) and derived
databases such as InterPro, PRINTS, BLOCKS, PRODOM, Pfam etc.
along with advanced sequence analysis tools such as profiles searches,
pattern searches for function annotation of genomic sequences.
Validation and verification of results for known case studies
 Using sequence-based and structure-based Function Annotation
Servers such as: ProKnow (http://www.doe-
ADB.ucla.edu/Services/ProKnow/)
 Joined Assembly of Function Annotations (JAFA) at
http://jafa.burnham.org/learnMore.html etc. which are integrated
68
services for function annotation

 ProFunc (http://www.ebi.ac.uk/thornton-srv/databases/ProFunc)
References:
1. Fundamentals of Data Mining in Genomics and Proteomics, By Werner

Dubitzky, Martin Granzow, Daniel P. Berrar, 2007, Springer Science +
Bussiness Media, LLC.
2. Protein Arrays, Biochips and Proteomics: The Next Phase of Genomic
Discovery edited by Joanna S. Albala, Ian Humphery-Smith, ISBN-0-8247-
4212-1, 2003, Marcel Dekker.
3. Proteomics: Methods Express (Methods Express Series) Paperback –
Import, 2007, by C. David O'Connor (Editor), B. David Hames (Editor)
4. Principles of Proteomics, English, Paperback, Twyman, 2004.
5. Dale Jeremy, Schantz Malcolm Von. From genes to genomes: concepts and
applications of DNA technology. Publisher: John Wiley & Sons Ltd., 2007.
ISBN:9780470017340.
9. Brown, T.A., Genomes, 3rd edition Garland Science publishers, 2006.
ISBN:
1859960294.
10. Primrose Sandy B., Twyman Richard. Principles of Gene Manipulation and
Genomics. Publisher: Wiley-Blackwell. 7th edition 2006. ISBN:
1405135441.
69
ADB 212: Advanced Bioinformatics Lab Total

(2 Credits, 1 P, 4.00 Hr., Advance Course Practical) 20P
1. Linux: Linux Essentials, Hands-on Exercises 2

Querying Biological Databases with SQL
2. Statistics and graphing software: GraphPad Prism 2
Creating Phylogenetic Trees with MEGA
3. NGS: 4
 QC'ing Reads
 Mapping Next Generation Sequence Reads
 Analysis of ChIP-seq data in Galaxy
 Analysis of RNA-seq data in Galaxy
 Analysis of differential gene expression
 Finding and annotating indels in Human genome
 Bedtool: Toolset for genome arithmetic
5. Structural Variant Analysis 2
 Variant detection: VarScan and SVDetect
 Variant annotation: TASSEL, GATK
6. Advanced Genomics 4
Visualizing Genomes: Browsers
Introduction to ENSEMBL
Integrative Genomics Viewer (IGV)
Juggling Genome Coordinates
Gene list enrichment analysis
Visualizing Genomes: Circos Plots
7. Introduction to Microarray 4
DNA and Protein Array
Microarray data Analysis pipeline
Microarray Techniques
Data analysis with R/Bioconductor
Clustering and Displaying Microarray Data
70
Expression Atlas
Cool BaRC Web Tools
8. Sequence analysis using DotPlot 2
GeneGo: Bioinformatics Technology for Systems Biology
Visualizing Networks: Cytoscape
References:
1. Next-Generation DNA Sequencing Informatics,Stuart M. Brown, New York

University School of Medicine 2013 ISBN 978-1-936113-87-3
2. Chip Technology, Volume 77,Jörg D. Hoheisel, Alvis Brazma,
illustratedPublisherSpringer, 2002, ISBN3540432159, 9783540432159
3. Microarray biochip technology, Mark Schena , illustratedPublisherEaton
Pub., 2000, Original fromthe University of California, ISBN1881299376,
9781881299370
4. Discovering Statistics Using R, Andy Field, Jeremy Miles, Zoë Field,
SAGE, 2012, ISBN1446258467, 9781446258460
5. The R Book, Michael J. Crawley, John Wiley & Sons,
2012ISBN1118448944, 9781118448946
6. A Guide to MATLAB: For Beginners And Experienced Users, Brian R.
Hunt, Ronald L. Lipsman, Jonathan M. Rosenberg, Edition2,
illustratedPublisherCambridge University Press, 2006, ISBN1139452533,
9781139452533
7. MATLAB Guide, Desmond J. Higham, Nicholas J. Higham, Edition2,
illustratedPublisherSIAM, 2005ISBN0898715784, 9780898715781
8. MATLAB Primer, , Kermit Sigmon, Timothy A. Davis, Edition7, CRC
Press, 2004ISBN1420034952, 9781420034950
9. Foundations of Comparative Genomics, Arcady R. Mushegian, Academic
Press, 2010ISBN0080546099, 9780080546094
10. Essentials of Genomic and Personalized Medicine, Geoffrey S. Ginsburg,
Huntington F Willard, Academic Press, 2009ISBN0080958117,
9780080958118
71
ADB 213: Data Mining through Machine Learning Lab Total

20P
(2 Credits, 1 P, 4.00 Hr., Advance Course Practical)
Implementation of following Algorithms using Python Programming
20
1. Logistic Regression,
2. Support Vector Machine,
3. Naïve Bayes Classifier. :
4. K- Nearest Neighbors,
5. Random Forest Classifier.
6. K-means Clustering
7. Association Rule Mining
8. Ant colony optimization
9. Simulated annealing algorithm for energy minimization
10. Estimator of transition probabilities for markov models based
on various sample sizes
References:
1. Data Mining: Concepts and Techniques by Han and Kamber, Morgan
Kaufmann.
2. Machine Learning by Tom Mitchell, McGraw Hill.
3. Data Mining: Practical Machine Learning Tools and Techniques by
Witten and Frank, Elsevier.
4. Biological Sequence Analysis: probabilistic models of proteins and
nucleic acids by Durbin, R., Eddy, S., Krogh, A. & Mitchison,
G.Cambridge Univ. Press, 1998.
5. Optimization Theory and Application by Rao, S.S., 1984.
6. Discrete optimization by Parker, R. G. & Rardin, R. L., 1988.
7. Stochastic simulation by Repley, Brian D, Wiley series, 1987.
8. Methods of microarray data analysis III by Johnson, K.F. & Lin, S.M.
Boston. Kluwer academic publishers, 2003.
9. Exploration and analysis of DNA microarray and protein array data by
Amaratunga, D. & Cabrera, J.New Jersey. John Wiley & Sons Inc., 90
BVDU-RGITBT-M.Sc. BIOINFORMATICS- SEM III 2004.
10. Ant colony optimization by Dorigo, Marco & Stutzle, Thomas New
Delhi, Prentice-Hall of India Pvt Ltd, 2004.
11. Data mining: introductory and advanced topics by Dunham, M.H.:New
Delhi, Pearson Education, 2003.
12. An introduction to bioinformatics algorithms by Jones, Neil.C. &
Pevzner, Pavel A. New Delhi, Anne Books, 2005.
13. Fuzzy sets and fuzzy logic: theory and applications by Klir, G.J. & Yuan
Bo, New Delhi. Printice Hall of India, 2002. 81-203-1136-1.
72
ADB 214: Molecular Modeling & Drug Designing Lab Total
(2 Credits, 1 P, 4.00 Hr., Advance Course Practical) 20P
Molecular Modeling:
 Homology Modeling 10
 Conformational Analysis
 Molecular dynamics simulations
 Molecular Dynamics analysis
Drug Design:
 Development of 2D QSAR models. 10
 Development of 3D QSAR models.
 Pharmacophore model.
 Molecular docking study.

o Rigid Docking
o Flexible Docking
o Self Docking
 Virtual Screening.
References:
1. Molecular Modeling Principles and Applications (2nd Ed.) by Andrew R.

Leach, 2001, Prentice Hall, USA.
2. Principles of Protein Structure by G. E. Schulz, 2009, Springer
3. Textbook of Structural Biology by Anders Liljas, Lars Liljas, Jure Piskur
and GÃran Lindblom, World Scientific Publishic Co. Pvt. Ltd.
4. Structural Bioinformatics, Edited by Jenny Gu, Philip E. Bourne, Wiely
Blackwell
73
5. Computational Structural Biology: Methods and Applications by orsten

Schwede, Torsten Schwede, Manuel C. Peitsch, 2008, World Scientific
Publishing Company.
6. Molecular Modeling Of Nucleic Acids, Leontis N.B. and SantaLucia J.
Jr. (eds), 1998, American Chemical Society.
7. Molecular Modeling of Proteins by Andreas Kukol, 2008, Humana Press.
8. Molecular Modeling and Simulation: An Interdisciplinary Guide by
Schlick T., 2012, Springer.
9. Biological Modeling and Simulation: A Survey of Practical Models,
Algorithms, and Numerical Methods (Computational Molecular Biology)
by Russell Schwartz, The MIT Press, Cambridge, Massachusetts,
London, England.
74

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BVDU-RGITBT-ADB (Advanced

Diploma in Bioinformatics, Post

BHARATI VIDYAPEETH DEEMED TO BE UNIVERSITY

REVISED SYLLABUS FOR

SYLLABUS OF SEM I – SEM II

1. To impart deep knowledge of the discipline

DURATION OF THE COURSE

RULES FOR THE COURSE

1. The entire course is of 60 credits.

RULES FOR EXAMINATION

Table 1: Evaluation pattern for one to three Credit Courses

Course Marks for Marks for Total Marks for

Table-2: The grading system under CBCS

Range of Marks Grade Point Grade

B: Standards of Passing and ATKT rules:

1. For all Core Courses, both UE and IA

Constitute separate heads-of-passing (HoP). In order to pass in such courses and

Range of CGPA Final Grade Performance Equivalent Range of

9.00 ≥CGPA≤ 9.49 A+ Excellent 70 ≥ Marks ≤ 80

8.00 ≥CGPA≤ 8.99 A Very Good 60 ≥Marks ≤ 70

7.00 ≥CGPA≤ 7.99 B+ Good 55 ≥ Marks ≤ 60

6.00 ≥CGPA≤ 6.99 B Average 50 ≥ Marks ≤ 55

5.00 ≥CGPA≤ 5.99 C Satisfactory 40 ≥ Marks ≤ 50

CGPA Below 5.00 F Fail Marks below 40

THE FORMAT OF THE TRANSCRIPTS

The transcripts may be acquired by the students indicating his/her performance

Course Course Number University IA/CA Grade Result

PATTERN FOR ASSESSMENT

A: Pattern of Evaluation for Internal Assessment of Theory Courses:

C: Pattern of question paper at University Examination

PATTERN OF QUESTION PAPER FOR 3 CREDIT COURSE OF UNIVERSITY THEORY

Instructions to Paper Setter:

1. Question paper of each course will comprise of total 6 questions,

QUESTION PAPER PATTERN FOR 2 CREDITS THEORY COURSE AT UNIVERSITY

Instructions to Paper Setter:

1. Question paper of each course will comprise of total 4 questions,

D: PATTERN FOR QUESTION PAPER OF UNIVERSITY PRACTICAL EXAMINATION OF ADB

Q. 1 Major Practical (10/20)

Q. 2 Spotting/Minor Experiment (10/20)

Course structure of Advanced Diploma in Bioinformatics

Course No. & Title Credits IA Univ. Total

Course No. & Title Credits IA Univ. Total

ADB 208 Molecular Modeling

ADB 101: Cell Biology (C) Total

1. Cell as a basic unit of life. 4

7. Cell Signaling: General principles of cell signaling, signaling via G-protein 6

8. Ageing and apoptosis, abnormal development and teratogenesis in animals 4

ADB 102: Biochemistry (C) Total

1. Introduction to Biomolecules: Carboydrates, Lipids and Proteins – their 1

2. Carbohydrates: Classification-on basis of carbon no & functional grs.; 3

3. Important monosaccharides: 6 C sugars- glucose, fructose, mannose, 1

4. Linkages in Sugars: Structure and functions of important di-saccharides 1

5. Physico-chemical properties of carbohydrates:Reducing-non-reducing 2

6. Significance of carbohydrates in microbial, plant and animal system: 2

7. Lipids: Occurrence/sources: plant derived oils, ghee 1

9 Functions:Functions in a living system: significance of hydrophobicity and 2

10. Lipid conjugates:Important conjugates and their functions: phospholipids, 3

structures, Cholesterol- Structure, function and significance

11. Liposomes:Liposomes in drug delivery, soaps, bio-surfactants 1