SASTRA University

Thanjavur
Name of the Degree Programme : B.Tech. Bioinformatics
Integrated M.Tech. Bioinformatics
Duration : B.Tech. - 4 years
Integrated M.Tech. - 5 years
Programme Objective
To create graduates with capabilities to interpret large scale biological data in the post genome
era

To train a generation of students with strong programming skills to deelop tools and
algorithms to analyse biological se!uences" structures" gene e#pression data and for pathway
modelling
To impart skills in structural modelling" drug design and systems biology with a strong
emphasis on programming and high end computing suited for research and industry
Curriculum Design
Semester III
S No Co!e No Subject
Perio! Per "ee# Cre!it
$ T P $
% BBI$M%&'()'(
MBI$M%&'(
*ngineering Mathematics III & ( ' 4
&
BBI$BI&'+)'&
MBI$BI&'+
$ell and Molecular Biology & ( ' 4
'
BBI$BI&'&)'+
MBI$BI&'&
Biochemistry & ( ' 4
( BBI$BI&'4)'+
MBI$BI&'4
Basic Bioinformatics & ( ' 4
) BBI$BI&'5)'(
MBI$BI&'5
%lgorithms , -ata .tructures & ' ' &
* BBI$BI&'/)'+
MBI$BI&'/
Basic Biocomputing & ( ' 4
+ BBI$BI&'0)'+
MBI$BI&'0
Basic Biocomputing 1aboratory ' ' & +
, BBI$BI&'2)'+
MBI$BI&'2
Basic Bioinformatics 1aboratory ' ' & +
Total (2 5 / +0
Semester -
SNo Co!e No Subject
Perio! Per "ee# Cre!it
$ T P C
%
BBI$M%5'()'+
MBI$M%5'(
*ngineering Mathematics 3 & ( ' 4
&
BBI$BI5'+)'&
MBI$BI5'+
4rotein *ngineering & ( ' 4
'
BBI$BI5'&)'(
MBI$BI5'&
5aa for Bioinformatics & ( ' 4
( BBI$BI 5'4)'(
MBI$BI5'4
Molecular Modelling I & ( ' 4
)
BBI$BI5'5)'+
MBI$BI5'5
Machine 1earning in Bioinformatics & ( ' 4
*
BBI-BI 5'()'(6
MBI-BI5'(
BBI-BI5'+)'(6
MBI-BI5'+
-ata Mining , 7arehousing6
$linical Informatics
4 ' ' 4
+
BBI$BI5'/)'&
MBI$BI5'/
Molecular Modelling 1aboratory I ' ' & +
,
BBI$BI 5'0)'+
MBI$BI5'+
5aa 1aboratory ' ' & +
. BBI$BI5'2)'(
MBI$BI5'2
.eminar ' ' & (
%/ BBI$T45'86
MBI$T45'8
9) .kills + ' ' +
Total +( 5 8 &(
Course Outline
.emester number : &
'0%0/0(
1earning outcome for 11IC2A'/%R/%321IC2A'/%4 5N6IN55RIN6 2AT752ATICS 8 III
Course Objectives: To help the learners in understanding various transform techniques used in
Engineering disciplines and Analytic function theory in engineering computations.
UNIT I %) Perio!s
1%41%$* T)%:.;<)M.: definition = $onditions for e#istence = Transform of standard functions =
4roperties = Transform of deriaties and integrals = -eriaties and integrals of transforms. Inerse 1aplace
transforms = $onolution theorem = transform of periodic functions" unit step function and unit impulse >or
dirac delta? function. %pplications to sole higher order ordinary differential e!uations and .imultaneous
differential e!uations with constant coefficients and integro- differential e!uations. .imple *ngineering
%pplications: Bending of Beams" 7hirling of .hafts and *lectric $ircuits.
UNIT II %) Perio!s
$<M41*@ -I;;*)*:TI%TI<: 4 %nalytic functions = :ecessary conditions for analyticity = $auchy-
)iemann e!uations in cartesian and polar coordinates = .ufficient conditions for analyticity >without proof? =
4roperties of analytic functions: 9armonic functions = <rthogonal system = $onstruction of an analytic
function when its real or imaginary part is gien = $onformal mappings -
z
z z z e
z
(
" cos " sin " + and
z sinh
only = Bilinear Transformation. .imple *ngineering applications: $omple# potential functions"
.tream lines" e!uipotential" elocity potential and stream functions.
UNIT III %) Perio!s
$<M41*@ I:T*A)%TI<:: $ine and .urface Integrals- $auchyBs integral theorem = Integral formula =
TaylorBs and 1aurentBs series >without proof? = .ingularities = Ceros = 4oles and residues = $auchyBs residue
theorem = $ontour integration = ealuation of integrals of the type
( )
( )
( )

+
'
cos " sin dx
x g
x f
and d f
only.
UNIT I- %) Perio!s
;<D)I*) T)%:.;<)M.: The infinite ;ourier transforms = .ine and cosine transforms = properties =
Inersion theorem = problems = $onolution theorem = 4arsealBs identity = 4roblems = ;inite ;ourier
transforms = .ine and cosine transforms = *aluation of definite Integrals-problems .oling boundary alue
problems using finite ;ourier sine and cosine transforms.
T59T 1OO:S
(. *ngineering Mathematics >;or .emester III? by T.3eeraraEan" Tata McAraw - 9ill 4ublishers 1T-"
:ew -elhi - +'('
+. *ngineering Mathematics" 4art %" -r. M.F.3enkataraman" :ational publishing company" +''4.
R5;5R5NC5S
(. 9igher *ngineering Mathematics" B...Arewal" Fhanna publishers" +''/.
+. %danced *ngineering Mathematics" 5.*rwin FreysGig" 2
th
edition" 7iley eastern 1td." +''0.
&. %danced engineering mathematics" 5ain ).F and ..).F. Iyengar" :arosa publications" +''/.
$5ARNIN6 OUTCO25S
Dnit I The learner will hae knowledge to use the transform techni!ues in other fields of
*ngineering such as .ignal and Image processing and also to transform functions from
one domain to another domain.
Dnit II The learner will be able to apply arious concepts in %nalytic ;unction Theory in
application areas such as heat conduction" elasticity" fluid dynamics and flow of
electric current.
Dnit III The learner will be capable of ealuating complicated integrals using residue calculus.
Dnit I3 The learner will hae a strong idea of applying ;ourier transform techni!ues in
soling boundary and initial alue problems in arious branches of *ngineering.
.emester number: &
'0%0/0(
1earning outcome for 11IC1I'/&R/'321IC1I'/&4 C5$$ AND 2O$5CU$AR 1IO$O6<
Course Objective: To help the learners understand the underlying principles of various biological
processes that govern cell structure, function and other complicated processes involved in deciding the
specific characteristic of an organism.
UNIT I %) =erio!s
I:T)<-D$TI<: T< $*11 BI<1<AH: Basic properties" organiGation and functions of cell-
classification of cells- prokaryotes , eukaryotes - structure and function of plasma membrane- membrane
proteins - transport across cell membrane = diffusion facilitated moement - actie and passie transport -
cell diision- mitosis and meiosis = prokaryotic and eukaryotic cell cycle - mechanics of cell diision- M-
phase = mitosis and meiosis - chromosome segregation - microtubules in spindle assembly - structure and
functions of kinetochore" centrosomes - cytoskeletal proteins - actin and myosin
UNIT II %) =erio!s
$*11D1%) $<M4<:*:T. <; 4)< %:- *DF%)H<T*.: $ytoplasm and its features = organelles
and their structural organiGation and functions = mitochondria" endoplasmic reticulum" Aolgi apparatus"
lysosomes" ribosomes" nucleus" nuclear membrane - localiGation of genetic components - cytoskeleton in
eukaryotes and their structure and composition = microtubules" microfilaments.
UNIT III %) =erio!s
A*:* %:- T9* A*:<M*: $oncept of a gene- chemical nature - structure of -:%- basic components
and their structures - 7atson and $rick Model of -:% - forms of -:%- %"B and C -:% - replication of
-:% =types of ):% and different structures- genome wide transcription processes -transcription =
mechanism - enGymes inoled = initiation - elongation and termination - post-transcriptional processing
of m):%: $%4- polyadenylation- introns and e#ons-splicing of m):%.
UNIT I- %) =erio!s
A*:* *@4)*..I<: %:- *DF%)H<TI$ A*:* %..*MB1H: Aenetic code - amino acids and codons
= 7obble hypothesis - 0'. and 2'. ribosomes- translation = initiation" elongation and termination"
enGymes and inhibitors - translation in prokaryotes and eukaryotes - chromosomes- organiGation of -:%
= nucleosomes" chromatin network- histone proteins - modifications of histone proteins- $ontrol of
transcription and translation.
T59T1OO:
(. Bruce %lberts" %le#ander 5ohnson" 5ulian 1ewis" Martin )aff" Feith )oberts" 4eter 7alter"
Molecular Biology of the $ell" Aarland .cience" Taylor and ;rancis" :ew Hork" D.%" +''2"4e.
R5;5R5NC5 1OO:S
(. 5eremy M.Berg." 5ohn 1 TymockGo" 1ubert .tryer " Biochemistry" 7.9.;reeman." D...%." +'(("0e
2. Aerald Farp." $ell and Molecular Biology: $oncepts and *#periments" 5ohn 7iley , .ons Inc.
>51 R5;5R5NC5S
(. $ell Biology by -r. .anEukta 4atra"IIT Auwahati
http:66nptel.ac.in6syllabus6syllabus.phpIsubEectIdJ('+('&'(+
+. Molecular $ell Biology by -r. BishwaEit Fundu"IIT -elhi
http:66nptel.ac.in6syllabus6syllabus.phpIsubEectIdJ('+('+''8
&. Molecular $ell Biology by 4rof. -earaEan Farunagaran"IIT Madras
http:66nptel.ac.in6syllabus6syllabus.phpIsubEectIdJ('+('/'+5
$5ARNIN6 OUTCO25S
Dnit I The learner will understand all the concepts about cell >basic unit of life? architecture"
and its basis of multiplication to form multicellular organisms. ;urther" knowledge about
different processes inoled in moement of molecules into and out of the cell would be
proided.
Dnit II The learner will receie a thorough knowledge on different classification of organisms
and the specific roles of cellular components that is responsible for the structure and
functionality of the organism.
Dnit III The learner will be able to understand all about genes >basic unit of heredity? and gain
insight on structural and functional entity that is responsible for a particular gene
function.
Dnit I3 The learner will hae an understanding of the principles inoled in protein synthesis in
different forms of organisms. In addition" the learner will also understand the key to
modulating gene e#pression via learning different processes inoled in controlling
chromosome structure" and also the processes inoled in conerting the information
from genes to proteins.

.emester number: &
'0%0/0(
1earning outcome for 11IC1I'/'R/&3 21IC1I'/'4 1IOC752ISTR<
Course Objective: This course provides information on the basic concepts in biochemistry, underlying
the major macromolecules and chemical properties of living systems. Furthermore, the mechanisms of
major macromolecular metabolism, enzyme inetics, regulation and inhibition are also addressed here.
UNIT I %) =erio!s
$%)B<9H-)%T*." 1I4I-. %:- M*MB)%:*.4 Aeneral description of carbohydratesK
classificationK monosaccharidesK configurationsK conformationsK polysaccharidesK di and structural
polysaccharides L$hitin , $elluloseMK storage polysaccharidesK starch and glycogenK
glycosaminoglycansK glyco proteinsK their structure and functionK bacterial cell wall composition.
$lassification of lipidsK fatty acidsK phospholipidsK sphingolipidsK liposomesK structural elucidation
biological membranesK membrane proteinsK fluid mosaic modelK lipid linked proteinsK lipoproteinsK
31-1-9-1K structural elucidation.
UNIT II %) =erio!s
%MI:< %$I-. %:- 4)<T*I:.: .tructure of amino acidsK their classificationK optical actiityK
;ischer conentionK chirality and properties of amino acidsK isoelectric point and p9K 4roteinsK peptide
bondsK dihedral anglesK )amachandran plotK coalent modifications of proteinsK primaryK secondaryK
tertiary and !uaternary organiGationK protein function and diersityK binding theoriesK positie and
negatie cooperatie bindingK protein foldingK theoryK folding pathwaysK protein purificationK
se!uencing of amino acids.
UNIT III %) =erio!s
*:CHM* %:- $<-*:CHM* $9*MI.T)H: -efinitionK $lassification of enGymesK specificityK co-
enGymesK allosteric modificationsK enGyme kineticsK Michaelis Menten e!uationK enGyme inhibition
studiesK competitieK uncompetitieK mi#ed inhibitionK enGyme-substrate interactionK lock and key
mechanisms in enGyme kineticsK catalytic Mechanisms? acid-baseK coalent-metal ion catalysisK
mechanisms with releant e#amplesK structural elucidation of enGymes with lysoGyme and serine
proteasesK pyrido#al phosphateK thiamine pyrophosphateK biotinK itamins.
UNIT I- %) =erio!s
M*T%B<1I.M: $arbohydratesK glycolysisK T$% cycleK electron transport chainK regulation and
energetics of metabolic pathwayK lipids-fatty acid o#idationK ketone bodiesK general description on
steroidal hormonesK amino acid metabolismK deaminationK urea cycle.
R5;5R5NC5 1OO:S
(. -. 3oet and 5A. 3oet. NBiochemistryO" 46e" 5ohn 7iley" :ew Hork" +'((.
+. -aid 1. :elson" Michael M. $o#. !ehninger. "#rinciples of $iochemistry%, &'e, (.).Freeman and
*o, +,-,.
>51 R5;5R5NC5
(. Bio$hemistry I by 4rof. .. -asgupta" IIT Fharagpur
http:66nptel.ac.in6ideo.phpIsubEectIdJ('+('5'&4
$5ARNIN6 OUTCO25S
Dnit I The learner will be able to understand the different types of carbohydrates and lipids as
macromolecules.
Dnit II The learner will understand aminoacids that make the proteins and also their structural
organisation and se!uencing methodologies.
Dnit III The learner will understand enGyme kinetics" the different types of enGyme inhibition and
co-enGyme chemistry.
Dnit I3 The learner will hae an understanding of the principles inoled in metabolism and
bioenergetics of carbohydrate" lipids and aminoacids.
.emester number: &
'0%0/0(
1earning outcome for 11IC1I'/(R/&3 21IC1I'/(4 1ASIC 1IOIN;OR2ATICS
Course Objective: This course provides an introduction to existing tools and resources for computational
analysis of biological data, including sequences, phylogenies, microarrays, ontologies, and biomolecular
interactions.
UNIT I %( =erio!s
B%.I$. <; 9%:-1I:A A*:<MI$ -%T%: The central dogma = genome- the human genome proEect
and the need for databases and annotation" -atabases = contents" structure and annotation: file formatsK
annotated se!uence databasesK )etrieal of biological data: data retrieal with *ntreG , -BA*T61ink-BK
data retrieal with .). >se!uence retrieal system?.
$<:$*4T <; .*PD*:$I:A - -:%" ):% , proteins- :e#t Aeneration .e!uencing and data handling"
interpreting se!uence data
UNIT II %) =erio!s
.*PD*:$* B%.*- %1A<)IT9M. %:- .*%)$9*.: .e!uence similarity searchesK similarity and
identity among biological se!uences -amino acid substitution matricesK ;%.T% , B1%.TK se!uence
filtersK iteratie database searches , 4.I-B1%.T-Multiple-se!uence alignment" local and global
alignment algorithms- multiple-se!uence alignment and family relationships
49H1<A*:*TI$. - cladistics and ontologyK building phylogenetic trees and eolutionary relationships
UNIT III %+ =erio!s
.T)D$TD)%1 BI<I:;<)M%TI$.: $onceptual models of protein structureK the relationship of protein
three-dimensional structure to protein functionK protein families and pattern databasesK protein domains -
structural alignment. $lassification of proteins of known three-dimensional structure: $%T9 , .$<4 =
concept of molecular modelling = homology modelling and threading
UNIT I- %( =erio!s
BI<I:;<)M%TI$. I: -)DA -*.IA:: 4rocess of drug discoery- drug design and irtual screening =
structure and receptor based ligand design = docking = scoring =small molecular libraries = lead
optimisation = pharmacophore mapping = case study
T59T 1OO:
(. Bioinformatics =.e!uence and Aenome %nalysisB" -aid 7.Mount" $.91 4ress" :ew Hork "+''5"+e
R5;5R5NC5 1OO:S
(. Bioinformatics in the 4ost-Aenomic *ra -Aenome" Transcriptome" 4roteome" and Information-Based
Medicine" %ddison-7esley"+''4"(e
>51 R5;5R5NC5
(. Bioinformatics by 4rof. 9arish Farnick" -r. %rnab Bhattacharya and 4rof. .omenath Biswas" IIT
Fanpur
http:66nptel.ac.in6syllabus6syllabus.phpIsubEectIdJ('/('4'(2
$5ARNIN6 OUTCO25S
Dnit I The learner will hae an understanding of the concepts of human genome" gene"
arious se!uencing methods and -:% and ):%. They will also understand the
importance and outcomes of the human genome proEect. They will learn the
important biological se!uence databases and the se!uence retrieal methods.
Dnit II The learner will hae an understanding arious se!uence alignment methods and
their algorithms. They will also learn the importance of arious amino acid
substitution matrices. They will understand the importance phylogenetic analysis
in understanding the eolutionary relationship and the arious methods of
deeloping and alidating phylogenetic trees.
Dnit III The learner will understand the se!uence-structure relationships and the structure-
function relationships. They will understand the arious leels of protein
classification based on the folds and arious methods used for modelling proteins.
Dnit I3 The learner will hae an understanding of the basic concepts of medicinal
chemistry and computational drug designs. They will learn the basic structure
based and ligand based drug design methods.
.emester number: &
'0/0/0'
1earning outcome for 11IC1I'/)R/%321IC1I'/)4 A$6ORIT72S AND DATA STRUCTUR5S
Course Objective: The purpose of this course is to provide the students .ith solid foundations in the
basic concepts of programming/ data structures and algorithms. The main objective of the course is to
teach the students on ho. to choose the appropriate data structure and algorithm design method for a
specified application and also to assess ho. the choice of data structures and algorithm design methods
impacts the performance of programs.
UNIT I . =erio!s
I:T)<-D$TI<: T< %1A<)IT9M.: Introduction - problem soling aspect - top-down design -
implementation of algorithms - program erification - efficiency and analysis of algorithms
;D:-%M*:T%1 %1A<)IT9M.: *#changing alues of two ariables - summation of a set of numbers
- factorial computation - ;ibonacci series - base conersion
UNIT II %& =erio!s
%:%1H.I. <; .<)TI:A %:- .*%)$9I:A %1A<)IT9M.: .election sort - insertion sort -
e#change sort - sorting by diminishing increment and partitioning - two-way merge sort - binary search -
hash searching
)*$D).I3* %1A<)IT9M: Binary tree traersal - recursie !uick-sort - eight !ueensB problem - towers
of 9anoi problem - combination and permutation
UNIT III %& =erio!s
-%T% .T)D$TD)*.: Introduction = pseudo code -abstract data type - model of %-T
1I:F*- 1I.T.: $oncepts of linear list and linked list - linked list algorithms" processing" applications-
comple# linked list structures
.T%$F. %:- PD*D*: Basic stack operations - stack linked list implementation - stack applications -
!ueue operations - !ueue linked list design - !ueue theory and applications
UNIT I- %& =erio!s
T)**.: Basic tree concepts -binary trees - binary tree traersals - e#pression trees - 9uffman code-
binary search trees - %31 trees and implementation
A)%49.: Basic terminology = operations = graph storage structures - graph algorithms and networks -
minimum spanning tree- shortest path algorithm
-ata .tructures for *cient .tring %lgorithms".e!uences and .ubse!uences" )abin-Farp %lgorithm"
%postolico-Aiancarlo algorithm" Two 7ay algorithm" 1ongest common subse!uence problem" Minimal
longest ascending subse!uence algorithm
T59T1OO:S
(. ). A. -romey" Q9ow to .ole it by $omputerB" 4earson *ducation Inc." +''0"+e.
+. )ichard ;. Ailberg" BehrouG %. ;orouGan" Q-ata .tructures: % 4seudo code %pproach with $B"
Thomson 1earning Inc" +''4"+e.
&. Ddi Manber " QIntroduction to %lgorithmsK a $reatie %pproach:B%ddison 7esley (828
>51 R5;5R5NC5
(. -ata .tructures and %lgorithms by 4rof. :aeen Aarg" IIT -elhi
http:66nptel.ac.in6courses6('/('+'/46
$5ARNIN6 OUTCO25S
Dnit I The learner will hae an understanding of algorithm design techni!ues including
greedy" diide-and-con!uer and dynamic programming.
Dnit II The learner will understand the arious sorting algorithms and the run-time analysis
re!uired to determine their efficiencies
Dnit III The learner will hae an understanding oer the abstract data types of stacks" 1inked
1ists and !ueues" and also to select appropriate methods for organiGing data files and
implement file-based data structures.
Dnit I3 The learner will hae an understanding of the arious graph and string algorithms
commonly used in bioinformatics.
.emester number4 &
'0%0/0(
1earning outcome for 11IC1I'/*R/&3 21IC1I'/*4 1ASIC 1IOCO2PUTIN6
Course Objective: The course presents the theoretical no.ledge of the !0123 '2103 file system, the
commonly used utilities, editors, shell programming, and scripting. 0t includes instruction in soft.are
development in the 2103 '!inux environment. This course also gives an introduction to programming
.ith #erl and $ioperl.
UNIT I %) =erio!s
B%.I$ $<:$*4T. I: 1I:D@: 1I:D@- 9istory and 4rinciples = components" distributions - desktop
enironments - F-*" A:<M* " :autilus ;ile Manager" A:D 4roEect and A41 - linu# file hierarchy
concepts = absolute and relatie path-names - current working directory - changing directories - listing
directory contents - home directory - file names - creating" copying" moing" renaming and remoing files
, directories = iewing entire te#t file one screen-full at a time and getting help-man pages - installing
software from compressed archies >tar" rpm?
UNIT II %) =erio!s
1I:D@ ;I1* 4*)MI..I<:: ;ile and directory permission - user" groups and others = e#amining
permissions symbolic and numeric methods of changing file permissions
3i *-IT<): .tarting i - cursor moement - entering and leaing insert mode = changing" deleting" te#t -
undoing changes - searching for te#t - saing and e#iting - printing in linu#
.9*11 .$)I4TI:A: $ommands and comments - ariables and scripts - ariable alues input and output
- let command - control structures - test command - conditionals and logical commands looping
constructs
UNIT III %) =erio!s
4*)1: Introduction - syntactic rules for creating a script - running a script - scalar and array ariable
-numeric and string literals - decision statements looping statements = operators - basic I6< - arrays -
declaring arrays - array functions - hash introduction - key alue pairs
.T)I:A 9%:-1I:A: Built-in functions" ;ormatting strings" substring and string inde#ing" .tring
comparison operators" $onerting between %.$II characters and alues" Trimming Blanks from the *nds
of a .tring " 4arsing $omma-.eparated -ata
;I1* 9%:-1I:A: <pen and die function - reading and writing file contents
)*AD1%) *@4)*..I<:: Binding operator - pattern delimiters - matching - substitution and
transliteration operators and options = Meta characters - character classes - repetition operators
.DB)<DTI:*.: -eclaring subroutines in 4erl - global and local ariables
UNIT I- %) =erio!s
<B5*$T <)I*:T*- 4)<A)%MMI:A: 7riting 4erl modules - introduction to classes and obEects =
constructors - bless function - anonymous hash - 4*)1-$AI programming - 9TM1 form and $AI -
param>? method and $AI.pm module.
4*)1 %:- -BI: Introduction to -BI and -B- modules - connection management - !uery e#ecution -
result set processing
BI<4*)1: Introduction to Bioperl - creating a se!uence and an obEect - writing a se!uence to a file -
retrieing a se!uence from a file - retrieing a se!uence and multiple se!uences from a database -
se!uence statistics = B1%.T
I:T)<-D$TI<: T< @M1-$reating @M1 documents-$reating -T- to alidate @M1 documents-
$reating .chemas to alidate @M1 documents-$reating @.1T .tyle .heet for formatting data- .P1
4rogramming and Pueries with the databases.
T59T1OO:S
(. 5ames Tisdall" NBeginning 4erl for BioinformaticsO" <B)eilly 4ublishers" +''(
+. -aid Medinets" N4erl 5 By e#ample"O Pue" (88/
R5;5R5NC5 1OO:S
(. Maurice 5.Bach"BThe -esign of the Dni# <perating .ystemsB"4rentice 9all"+''/
+. .riram .riniasan" Q%danced 4erl 4rogrammingB" <B)eilly 4ublishers" (880
&. Bioperl : http:66www.bioperl.org6
4. 9arold" *lliotte )usty "B@M1 (.( Bible Q"7iley 4ublishers"+''4
$5ARNIN6 OUTCO25S
Dnit I The learner will understand the 1inu# <perating system and its essential concepts
and arious utility commands
Dnit II The learner will understand the concepts of ;ile permission" .hell scripting and 3i
editor.
Dnit III The learner will hae understanding of 4*)1 programming and its concepts of ;ile
9andling" )egular *#pression" defining .ubroutines and soling arious
Bioinformatics problems using aboe learned concepts.
Dnit I3 The learner will hae an understanding of <bEect oriented concepts in 4*)1 and its
applications in -BI programming " Bioperl programming and @M1
.emester number: &
/0/0'0&
1earning outcome for 11IC1I'/+R/&3 21IC1I'/+4 1ASIC 1IOCO2PUTIN6 $A1ORATOR<
Course Objective: The course provides practical aspects of solving $ioinformatics and destop problems
using #E4! scripting language and various !inux commands for processing of text files.
(? 4*)1 - 1ooping and $ontrol .tructures
+? %rrays" 9ashes and .ubroutines
&? )egular e#pression in 4erl
4? <<4s in 4*)1 " Biosuite %pplication -eelopment
5? .tring %lgorithms = Implementation
a? .e!uence %lignment and %lignment .coring with -ynamic 4rogramming
b? The Fnuth-Morris-4ratt >FM4? algorithm
c? Boyer-Moore %lgorithm
d? )egulatory motifs in -:% se!uences
e? %lgorithms based on mutation analysis in se!uences
/? 7eb serer with 4*)1-$AI
0? 4erl TF module
2? Araphics in 4erl
8? 1inu# Basics and ;ile .ystem
('? 1inu# .oftware installation =tar" rpm" gGip" Gip
((? ;ile 4ermissions in 1inu#
(+? 1inu# i editor
$5ARNIN6 OUTCO25S
( The learner will hae the ability to write programs by understanding 4*)1 synta#es "1ooping and
$ontrol .tructures
+ The learner will understand the 4*)1 concepts based on the %rrays" 9ashes and .ubroutines and
deelop scripts for soling a gien problem
& The learner will hae the understanding of )egular e#pressions concepts and write programs for
4attern matching tasks in Bioinformatics
4 The learner will hae the ability to deelop a Bioinformatics suite using <<4s concepts learned in
4*)1
5 The learner use the arious Bioinformatics algorithms and implement them using 4*)1
programming
/ The learner will be able to deelop Bioinformatics based 7eb serer using $AI programming
concepts in 4*)1
0 The learner will be familiar with designing Araphical Dser Interface based
.tandalone %pplications are designed using 4*)1 Tk modules
2 The learner will hae the e#posure in 7orking with 1inu# <perating .ystem enironment and
learning arious utility commands.
8 The learner will hae the understanding of A- module and soling arious Araphical based
%pplications
(' The learner will be able to get e#posure in installing .oftware in 1inu# using different compressed
file formats.
(( The 1earner will hae the ability to understand and apply file permissions concepts in 1inu# files
(+ The learner will be able to use 1inu# 3i editor and its arious commands and options for managing
the file contents
.emester number: &
/0/0'0&
1earning outcome for 11IC1I'/,R/&321IC1I'/,4 1ASIC 1IOIN;OR2ATICS
$A1ORATOR<
Course Objective: This computer laboratory course .ill provide students basic no.ledge and
practical sills needed for general bioinformatics database searches, genomics, and proteomics
analyses lie sequence alignment, phylogenetic construction, gene annotation and protein
structure mining.
(. ;ile transfer protocols: Telnet" 9TT4" ;T4K Basic 9TM1
+. )epresentation of biological se!uence and structural data
&. .e!uence retrieal system and se!uence similarity searches
4. .e!uence and structural alignment tools
5. Multiple .e!uence %lignment and 4hylogenetic analysis
/. 4rotein structure analysis and isualisation
0. %nalysis of se!uence repeats" motifs and domains
2. %nalysis of e#ons and introns
8. $reating and managing biological databases and web pages
$5ARNIN6 OUTCO25S
1ab I The learner will have an understanding of the concepts of various
fle transfer protocols and their importance in handling larger fle
size. They will also learn to develop simple webpages using basic
HTML codes.
1ab II The learner will hae an understanding of arious biological se!uence and structure
file formats. They will also learn how to conert one file format to another.
1ab III The learner will understand the arious se!uence retrieal system from arious
biological databases like :$BI" *MB1" --B5" 4-B etc." The learner will also
understand the concepts of arious se!uence alignment methods to perform similarity
searches and multiple se!uence alignments.
1ab I3 The learner will hae an understanding arious tools aailable for se!uence and
structure alignments. They will also understand the importance of structural
alignment in predicting the function of proteins.
1ab 3 The learner will learn the importance of performing phylogenetic trees in
understanding the eolutionary relationship and the step by step procedure for
deeloping a phylogenetic tree and the different methods for alidating the
phylogenetic tree. They will perform the analysis for both -:% and 4rotein
se!uences.
1ab 3I In this lab session the learner will understand the importance of isualiGing the
protein &- structures. They will learn the arious tools aailable for isualiGing the
macromolecules. They will also learn the arious commands for rendering
publication !uality images.
1ab 3II In this session the learner will learn the arious algorithm for motif" and domain
predictions.
1ab 3III The learner will hae an understanding of identifying the introns and e#ons for the
gien genome. They will learn and compare the different algorithms used for finding
the introns and e#ons.
1ab I@ In this lab session the students will be trained to deelop webpages using adanced
web deeloping concepts. They will also learn the database management system and
will learn about how to integrate the databases with 9TM1 pages.
Dnit III (.-escribe the role of 4rotein: -:% interactions in regulating transcription initiation
in 4rokaryotes.
+.-istinguish 4ositie regulation from :egatie regulation.
&.Dse models of gene regulatory systems" to predict the effects of mutations in
arious components.
Dnit I3 (. -escribe the role of 4rotein:-:% interactions in regulating transcription
initiation in *ukaryotes.
+. 1ist post- transcriptional modes of regulation in eukaryotes.
.emester number : 5
'0%0/0(
1earning outcome for 11IC2A)/%R/&321IC2A)/%4 5N6IN55RIN6 2AT752ATICS 8 -
Course Objective: To help the learner in understanding various 1umerical techniques and 5tatistical
methods applied to Engineering problems.
UNIT I %, Perio!s
:DM*)I$%1 .<1DTI<: <; .IMD1T%:*<D. *PD%TI<:." <)-I:%)H %:- 4%)TI%1
-I;;*)*:TI%1 *PD%TI<:. > <-*. %:- 4-*.?: .olutions of linear system by Aauss elimination"
Aauss-5ordan methods - Inerse of a matri# by Aauss elimination method = )ela#ation method = $routBs
method = Aauss-5acobi and Aauss-.eidel methods. :umerical solution of <-*: 4ower series
appro#imation = .olution by TaylorBs series = Improed and modified *ulerBs methods = )unge-Futta
method = MilneBs predictor-corrector method = :umerical solution of 4-*: $lassification of partial
differential e!uations of second order = 1aplace e!uation and its solution by 1eibmannBs process =
.olution of 4oissonBs e!uation = *#plicit and implicit schemes for soling parabolic heat conduction
e!uations = Bender-.chmidt and $rank :icholson schemes = .olution of hyperbolic wae e!uations.
UNIT II %& Perio!s
4)<B%BI1ITH" $<))*1%TI<: %:- )*A)*..I<: %:%1H.I.: Basic concepts of probability =
$onditional probability = BayesB theorem = <ne -imensional )andom 3ariable = 4robability mass
function - $umulatie distribution function = 4robability density function = -istribution function =
*#pectation - 3ariance = Moments = 1inear correlation = )ank correlation = )egression = Multiple and
partial correlation coefficients.
UNIT III %) Perio!s
.T%TI.TI$%1 M*%.D)*. %:- .%M41I:A T9*<)H: Types of biological data: %ccuracy and
.ignificant figures-;re!uency distributions- $umulatie fre!uency distributions- Measures of central
tendency-mean" median and mode-Measures of dispersion-)ange" !uartile deiation" mean deiation and
standard deiation-coefficient of ariation- skewness and kurtosis. .ampling theory-4arameters and
statistics-<ne-sample and two-sample hypothesis.
UNIT I- %) Perio!s
%:<3% %:- -*.IA: <; *@4*)IM*:T. : %nalysis of 3ariance: .ingle-factor analysis of ariance-
confidence limits for population means- power and sample siGe in analysis of ariance- nonparametric
analysis of ariance-testing for difference among seeral medians- homogeneity of ariances-
homogeneity of coefficients of ariations- effect of coding- multi-sample testing for nominal-scale data-
Turkey test.
T7<-;%$T<) %:%1H.I. <; 3%)I%:$*: Two-factor analysis of ariance with e!ual replications-
Two-factor analysis of ariance with une!ual replications- Two-factor analysis of ariance without
replications--esign of e#periments: )andomiGed block e#perimental design-)epeated measures
e#perimental design-multiple comparisons and confidence interals in two factor analysis of ariance-
power and sample siGe in two-factor analysis of ariance.
T59T 1OO:S
(. -r.M.F.3enkataraman" N:umerical Methods in .cience and *ngineeringO" 5
th
edition" The
:ational 4ublishing $ompany" +''4 >;or Dnit-(?.
+. ..$.Aupta" 3.F.Fapoor" N;undamentals of Mathematical .tatisticsO" ('
th
reised edition" .ultan
$hand and .ons publications" +''0. >;or Dnit +?
&. 5errold 9.Car" NBiostatistical %nalysisO"4
th
edition" 4earson *ducation" +''&. >;or Dnits & and 4?
R5;5R5NC5 1OO:S
(. M.F.5ain" ..).F.Iyengar and ).F.5ain" N:umerical methods for .cientific and *ngineering
$omputation" 7iley *astern 1imited" +''0.
+. -r......astry" NIntroductory methods of :umerical %nalysis" 4rentice 9all of India" +''5.
&. 7.7.-aniel" NBiostatistics: % foundation for %nalysis in the 9ealth .ciences"
0
th
edition" 5ohn 7iley .ons" +'''.
$5ARNIN6 OUTCO25S
Dnit I Mathematical skill deelopment for application of arious direct and iteratie methods for
soling system of linear e!uations and algebraic e!uations of higher degree. %pplication
of arious numerical methods for soling ordinary differential e!uations and partial
differential e!uations to ac!uire !uality solutions.
Dnit II .kill enhancement for soling problems in probability" $orrelation and )egression
analysis.
Dnit III %c!uiring skills in understanding arious statistical issues pertaining to measures of
central tendency" dispersion and statistical inferential techni!ues.
Dnit I3 4aing way for deeper understanding of design of e#periments in statistics such as single
factor analysis" obtaining confidence limits etc. to apply in their DA proEects. To hae
practice to deise design of e#periments.
.emester number: 5
'0%0/0(
1earning outcome for 11IC1I)/&R/'3 21IC1I)/&4 PROT5IN 5N6IN55RIN6
Course Objective: To provide a fundamental no.ledge of the methods used to engineer protein
molecules .ith novel properties and study the impact of the alterations on different protein functions.
UNIT I %) =erio!s
4)<T*I: .T)D$TD)* %:- ;<1-I:A: Motifs in protein structure: amino acidsK polypeptide
structureK secondary structures - alpha heli#" beta sheets and loopsK )amachandran diagramK topology
diagramsK motifs = heli#-turn-heli#" heli#-loop-heli#" hairpin beta" greek key motif and beta-alpha-beta-
multi domain proteins.
4)<T*I: ;<1-I:A: protein renaturation - determinants of protein foldingK protein disulphide
isomeraseK molecular chaperones- conformational diseases.
UNIT II %) =erio!s
4)<T*I: 4)<-D$TI<: %:- *:AI:**)I:A M*T9<-.: 4rotein e#pressionK choice of e#pression
systemsK use of E. coli and 5. cerevisiae for protein productionK post-translational manipulationsK
optimiGation of protein productionK initial purification.
in vitro MDT%A*:*.I./ principle and ariations - in vitro chemical mutagenesis = oligonucleotide -
based mutagenesis - cassette mutagenesis = 4$) based mutagenesis - saturation mutagenesis faouring
the mutantsK applications. protein engineering using non canonical amino acids - methodologiesK
applications-side chain packing - backbone mutations- dissecting collagen mutations
UNIT III %) =erio!s
.T)%T*AI*. ;<) 4)<T*I: -*.IA:: 4rotein designK strategies for the design of structure - self
assembly - ligand-induced assembly - assembly ia coalent cross-linking - assembly of peptides on a
synthetic template
.T)%T*AI*. ;<) T9* -*.IA: <; ;D:$TI<: - noel functions by retrofitting natural proteins -
incorporation of binding sites into de novo proteins - design of catalytically actie proteins - membrane
proteins and ion channels - design of new materials.
UNIT I- %) =erio!s
M<-D1%TI:A 4)<T*I: .T)D$TD)* %:- I:T*)%$TI<: BH $<M4DT%TI<:%1 -*.IA::
The core repacking problemK predicting natie protein core se!uencesK early core designsK full repacks
and surface designK hydrogen bonding and polar residues in the coreK altering protein foldsK e#perimental
ealuation.
Aeometry based designK stereochemistry based designK applications of computationally designed proteins
- biosensors - therapeutic proteins and antibodies.
T59T1OO:S
(. NIntroduction to 4rotein .tructureO" +6e" Branden $. and TooGe 5" Aarland .cience" D.%"(888.
+. N4rotein *ngineering and -esignO" (e" 4aul ). $arey" %cademic 4ress Inc" D.%" (88/.
&. N4rotein *ngineering and -esignO" (6e" .heldon 5. 4ark" 5ennifer ). $ochran." Taylor and ;rancis
Inc." $)$ 4ress" D.%"+'('.
R5;5R5NC5 1OO:S
% N4rotein *ngineering: % 4ractical %pproachO" (6e" )ees" %.)." .ternberg" M.5.*." 7etGel" )"
<#ford Dniersity 4ress" D.%" (88&.
>51 R5;5R5NC5
(. 4rotein .cience and *ngineering by 4rof. Mishra .aroE" IIT -elhi
http:66nptel.ac.in6syllabus6syllabus.phpIsubEectIdJ('+('+'((
$5ARNIN6 OUTCO25S
Dnit I
The learner will be able to understand physical aspects on protein structure" its components
and folding.
Dnit II
The learner will get the e#posure on recombinant protein production and mutagenesis
methods to engineer new protein constructs.
Dnit III
The learner can obtain knowledge in arious strategies to design protein structure and
function.
Dnit I3
The learner will able to understand the different aspects inoled in protein structure design
and interactions using computational and geometry based approaches.
.emester number: 5
'0%0/0(
1earning outcome for 11IC1I)/'R/%3 21IC1I)/'4 @A-A ;OR 1IOIN;OR2ATICS
Course Objective: The course presents the theoretical no.ledge of 6ava #rogramming syntax and
fundamentals of programming such as variables, conditional, iterative execution methods and 6ava A#0.
7bject oriented programming including defining classesand invoing methods. 8ultithreading etc. The
course gives the fundamentals of Applet #rogramming and A(T for designing 9raphical 2ser interface
applications and $io6ava for $ioinformatics pacages.
UNIT I %) =erio!s
I:T)<-D$TI<: T< 5%3% : 9istory and features of 5aa" -ifference between $" $RR , 5%3%" Eaa
irtual machine" byte code" obEect oriented principle" obEect and classes" structure of Eaa program" Eaa
keywords" ariable" data types and literals" identifiers" separators in Eaa" string" operators and casting"
5%3% .T%T*M*:T. , %))%H.: if and switch" while" do-while and for statement" Introduction to
arrays" types of arrays" new operator" break" continue statements.
*#ploring 5aa string classes and methods" 7rapper classes.

UNIT II %* =erio!s
$1%..*." 3I.IBI1ITH %:- I:T*);%$*.: $lasses and Inheritances: specifying classes" methods and
fields" creating obEects " passing obEects to methods" recursie methods" returning obEects" static fields ,
methods" oerloading method" constructor" constructor oerloading" this keyword" introduction to
inheritance" specifying sub class" types of inheritance
3I.IBI1ITH $<:T)<1: public" priate" protected" package. super keyword" oerriding methods"
dynamic method dispatch" abstract methods and classes" final methods and classes" nested classes and
inner classes.
4%$F%A*. %:- I:T*);%$*.: introduction to interface" defining and implementing interface"
e#tending interfaces" multiple interfaces" introduction to packages" naming conentions" package
statement" creating packages" import statement" accessing package" use of $1%..4%T9" adding class to
package" hiding classes.
UNIT III %( =erio!s
MD1TIT9)*%-I:A %:- %441*T 4)<A)%MMI:A I: 5%3%: Java nput !utput" Java #!
pac$age% byte#character stream% bu&ered reader # writer% fle reader # writer classes.
MD1TIT9)*%-I:A: creating and running threads" runnable interface" and methods in thread class"
setting priority" synchroniGation.
%441*T 4)<A)%MMI:A: applet s application" creating applets" life cycle" local , remote applets.
S%441*TT tag , its attributes" adding applet to 9TM1 file" running applet" methods in applets.
UNIT I- %) =erio!s
*3*:T 9%:-1I:A %:- BI< 5%3%: *ent 9andling: eent delegation model" eent source and
handler" eent categories" listeners" interfaces" controls such as te#t bo#" radio buttons"
checkbo#es" lists" choice" command buttons" te#t area etc.
5-B$: 5aa database connectiity"connecting to the Mys!l serer" issuing !ueries" result set.
BI<5%3%: .ymbols and symbol 1ists" se!uences , features" se!uence I6< basics" change eent oeriew"
change eent e#ample using distribution obEects" implementing changeable" blast-like parsing >:$BI
Blast" 7D-Blast" and 9MM*)?" and dynamic programming e#amples.
T59T1OO:
% 5aa: 9ow to 4rogram" 86e" 9. M. -eitel and 4. 5. -eitel" 4earson %sia" +'((.
R5;5R5NC5S
% 5aa + The $omplete )eference" 56e" 4atrick :aughton , 9erbert .childt" <sborne" "McAraw-9ill
$ompanies Inc."D.%" +''+.
& 5aa + 4rogramming" (6e" Feyur .hah" 5" Tata McAraw-9ill" +''(.
$5ARNIN6 OUTCO25S
Dnit I
The learner will understand synta#es in 5aa programming and semantics" arious
looping constructs and decisions making statements" %rrays and .tring 9andling.
Dnit II
The learner will understand the <bEect <riented concepts" %ccessmodifiers"
accessspecifiers and 4ackages.
Dnit III
The learner will hae understanding of ;ile 9andling concepts" %pplet 4rogramming
and Multithreading and sole programs based on these concepts.
Dnit I3
The learner will hae an understanding of %7T packages" 5-B$ connectiity and
Bio5aa and write applications programs
.emester number: 5
'0%0/0(
1earning outcome for 11IC1I)/(R/%3 21IC1I)/(4 2O$5CU$AR 2OD5$$IN6 8 I
Course objective: This course encompasses theoretical methods and computational techniques used to
model or mimic the behaviour of bio:molecules. 0t discusses theoretical and computational
methodologies, from ab initio quantum mechanics calculations of small organic molecules to molecular
mechanics simulations of macromolecular systems.
UNIT I %) =erio!s
I:T)<-D$TI<: T< M<1*$D1%) M<-*11I:A: The concepts on molecular modelling: coordinate
systemsK potential energy surfacesK molecular graphicsK molecular surfacesK molecular modelling
literature - mathematical concepts in modelling: eigen ectorsK 1agrange multipliers. .chrodinger wae
e!uation" soling the schrodinger e!uation - probability interpretation and normalisation" the phase of a
wae function" operators in !uantum mechanics" momentum and the uncertainty principle" the
conseration of probability" molecular orbital theory of homonuclear diatomicK heteronuclear diatomic
molecules.
UNIT II %) =erio!s
PD%:TDM M*$9%:I$%1 %44)<%$9*. T< M<-*11I:A BI<M<1*$D1*.: Puantum
mechanical models. one electron atoms" polyelectronic atoms and molecules" M< calculations" the
hartree-fock e!uations" basis sets" the ab initio , semi-empirical approachesK practical considerations
when performing ab initio calculationsK appro#imate molecular orbital theories" M:-<K calculating
molecular properties using !uantum mechanicsK electron density distribution , molecular orbitalsK
electrostatic potentials.
UNIT III %) =erio!s
M<1*$D1%) M*$9%:I$. : The simple molecular mechanics force fieldK general features of
molecular mechanics force fieldsK bond stretchingK angle bendingK torsional termsK out-of-plane bending
motionsK non-bonded interactionsK electrostatic interactionsK an der 7aals interactionsK hydrogen
bondingK calculating thermodynamic properties using a force field.
UNIT I- %) =erio!s
<4TIMI.%TI<: <; M<-*11*- .T)D$TD)*.: *nergy surfaces. energy minimiGationK non-
deriatie minimiGation methods" the simple# method , the se!uential uniariate methodK deriatie
minimisation methods: first-order minimiGation methodsK second deriatie methods" the :ewton-
)aphson methodK selection of minimiGation methodK applications of energy minimiGation" determination
of transition structures and reaction pathways
T59T1OO:
% Molecular Modelling" 4rinciples , %pplications" +6e" %ndrew ). 1each" 4earson *ducation Inc" +''5.
& Molecular Modelling and .imulation-%n Interdisciplinary Auide" (6e" Tamar .chlick" .pringer
3erlag" :ew Hork"+''5.
R5;5R5NC5S
% Basic Inorganic $hemistry"&6e" ;. %. $otton and A. 7ilkinson" 7iley *astern $o." (884.
$5ARNIN6 OUTCO25S

.emester number: 5
'0%0/0(
1earning outcome for 11IC1I)/)R/&3 21IC1I)/)4 2AC7IN5 $5ARNIN6 IN
1IOIN;OR2ATICS
Course Objective: To help the learner in developing intelligent algorithms applicable for identifying and
classifying biological patterns, .ith the help of 5tatistical !earning Theory.
UNIT I %) =erio!s
M%$9I:* 1*%):I:A ;<D:-%TI<: = 4)<B%BI1I.TI$ ;)%M*7<)F: Introduction to Bayesian
Modelling = The $o# 5aynes a#ioms = principle of ma#imum entropy-Aroup theoretic predictions =
Bayesian interference and induction model structures = graphical models and tricks = gradient descent -
*M 6 A*M algorithm = Marko chain and Monte $arlo methods- dynamic programming. Machine
learning algorithms

UNIT II %) =erio!s
Dnit I
The learner will be introduced to the mathematical concepts of molecular
modelling and some of their terminologies. .tudents will also understand the basic
concepts of !uantum mechanics
Dnit II
The learner will be able to learn the !uantum mechanical treatment of atoms and
molecules and the usage of ab inito and semi empirical methods of !uantum
mechanics for molecular modelling. The adantages and disadantages of the
methods will also be understood.
Dnit III
The learner will be introduced to the concept of Molecular Mechanics force fields
and their adantages oer the !uantum mechanical calculations. They will also
learn arious model of potential energy function associated with the Molecular
Mechanics force fields.
Dnit I3
The learner will be introduced to the concept of energy minimiGation and the
importance of finding local and global minimum on the potential energy surface of
a molecule. The arious energy minimiGation techni!ues and algorithms will also
be learnt.
:*D)%1 :*T7<)F. : ;undamental concepts of artificial neural networks: basic models-arious
architectures and topologies of %:: =types of actiation functions and their significance -types of
learning - learning techni!ues in %::.;eed-forward networks and superised learning: single-layer
perceptron networks =perceptron learning rule. multilayer feed-forward networksK back-propagation
algorithm.
UNIT III %) =erio!s
A*:*TI$ %1A<)IT9M. >A%? : ;undamentals of Aenetic %lgorithms: - basic concepts - biological
background - creation of offspring-search space- arious encoding schemes = fitness function-
reproduction-arious selection techni!ues.The three basic operators of A% = types of crossoer operations
= crossoer rate-inersion and deletion = mutation operator = mutation rate = other operators =
generational cycle = conergence of A%-Benefits and limitations of A%.
UNIT I- %) =erio!s
.D44<)T 3*$T<) M%$9I:*.
.upport ector classification - the ma#imal margin classifier -soft margin optimiGation -norm soft margin
-- norm soft margin -- the bo# constraint - linear programming support ector machines - support ector
regression --epsilon-insensitie loss regression - !uadratic epsilon-insensitie loss - linear epsilon-
insensitie loss - kernel ridge regression - Aaussian processes.
.4*$I;I$ %441I$%TI<:. <; T9* M*T9<-.
Marko neural model for eukaryotic promoter recognition = eolutionary granular kernel tress for protein
sub cellular prediction- superised learning methods for micro ):% studies =machine learning in .:4 =
disease based study.
T59T1OO:S
% Bioinformatics: the machine learning approach" +6e" 4ierre Baldi" .UrenBrunak" MIT 4ress" +''(.
& ;undamentals of :eural :etworks = %rchitectures" %lgorithms and %pplications"+6e" 1aurene;ausett"
4rentice 9all of India" +''4.
R5;5R5NC5 1OO:
1. Machine 1earning in Bioinformatics" (6e" Han!ing Chang" 5agath $. )aEapakse" 5ohn 7iley , .ons"
+''2.
$5ARNIN6 OUTCO25S
Dnit I
.kill deelopment for application of BayesB theorem to construct network architectures
and to learn the art of integrating dynamic programming principles for obtaining optimum
parameters of biological processes.
Dnit II
.kill deelopment for handling the data pertaining to biological studies and apply arious
ersions of %rtificial :eural :etwork techni!ues for aried applications> classification
and optimiGation? and to study the Mathematical" analysis of %::.
Dnit III
To help the learner to understand the application of arious genetic operators for
obtaining optimum alues of randomiGed population of data.
Dnit I3
To help the learner to understand .upport 3ector Machine as a tool to process large siGed
data at less computational comple#ity. The students will hae a practice of applying a
class of algorithms or their combinatorial structure in their proEect.
.emester number: 5
(0/0/0(
1earning outcome for 11ID1I)/%R/%3 21ID1I)/%4 DATA 2ININ6 AND >AR57OUSIN6
Course Objective: To help learners understand the fundamental processes, concepts and techniques of
data mining in biology .ith particular emphasis on data .arehousing, classification, clustering and
association rule mining; develop the ability to select methods and techniques appropriate for a given
biological data mining problem.
UNIT I %) =erio!s
-%T% 7%)*9<D.*%:- <1%4 T*$9:<1<AH: -ata 7arehouse - a multidimensional data model -
data warehouse architecture = data warehouse implementation - from data warehousing to data mining.
UNIT II %) =erio!s
I:T)<-D$TI<: T< -%T% MI:I:A: -ata mining- data mining functionalitiesK data preprocessing:
data cleaning: missing alues -data cleaning as a processK data integration and transformationK data
reduction: data cube aggregation - attribute subset selection -dimensionality reduction - numerosity
reductionK data discretiGation and concept hierarchy generation: discretiGation and concept hierarchy
generation for numerical data - concept hierarchy generation for categorical data.
UNIT III %) =erio!s
%..<$I%TI<: )D1*. %:- $1%..I;I$%TI<:: Basic concepts - efficient and scalable fre!uent item
set mining methods - mining arious kinds of association rules$lassification and 4rediction: decision tree
induction = attribute selection measures - tree pruning =scalability and decision tree inductionK Bayesian
classification: BayesB theorem - naVe Bayesian classificationK accuracy and error measures: classifier
accuracy measures -predictor error measures.
UNIT I- %) =erio!s
$1D.T*) %:%1H.I.: Introduction to cluster analysis and its types-hierarchical Methods:
agglomeratie and diisie hierarchical $lustering - BI)$9: balanced iteratie reducing and clustering
using hierarchies.
T59T1OO:
(. -ata Mining: $oncepts and Techni!ues" (6e" 5iawei 9an and MichelineFamber" Morgan Faufmann
4ublishers" D.%" +''/.
R5;5R5NC5S
(. -ata Mining Introductory and %danced Topics" (6e" Margaret 9. -unham" 4earson *ducation" +''&.
+. -ata 7arehousing" -ata Mining and <1%4" %le# Berson" .tephen 5. .mith" McAraw 9ill Inc. D.%"
+''(.
$5ARNIN6 OUTCO25S
Dnit I The learner will understand the arious ways to store large data for efficient data mining.
Dnit II The learner will be able to suggest suitable data preprocessing techni!ues for a gien data.
Dnit III The learner will be able to use classification as a tool to deelop predictie tools. %lso" the
learner will be able to apply algorithms for e#tracting associations in biological te#ts.
Dnit I3 The learner will be able to use clustering as a tool to identify interesting patterns in large
datasets.
.emester number: 5
(0/0/0(
1earning outcome for 11ID1I)/&R/%3 21ID1I)/&4 C$INICA$ IN;OR2ATICS
Course Objective: *linical informatics deals .ith organizing information related to the health care
industry. 0t blends information technology, computer science and medical information.
UNIT I %) =erio!s
M*-I$%1 I:;<)M%TI$. %:- :*T7<)FI:A: $omputer based patient record maintenance -
integrated network planning issues and the computer based patient record- standards and healthcare
ocabularies -te#t categoriGation6summariGation -distributed information and retrieal -decision trees and
medical decision-making -)<$ $ures -physiological signals: sampling and data handling -web-based
physiological monitoring -the road to physiologic imaging: @-)ay6$T -physiological imaging: image
display and analysis -remote access to adanced image display and analysis.
UNIT II %) =erio!s
9*%1T9 I:;<)M%TI<: .H.T*M.: %rchitecture" health data management" medical coding and
classification" medical databases" clinical data collection and ac!uisition and ealuation methodsK priacy
and security of clinical dataK clinically releant drug-drug interactions and databasesK telemedicine and
tele healthK ethics in medical informaticsK pharmacy systems and automation" drug information systems"
electronic records" informatics applications in pharmacy" surey and ealuation of on-line resources.
UNIT III %) =erio!s
M*-I$%1 T)%:.$)I4TI<:4 Dnderstanding medical terminologyK basics of document formattingK
adanced formattingK organiGation of the dataK working with multiple-page documentsK drawing toolsK
adanced tools , effectsK adanced word processingK enhancing documents with graphics.
UNIT I- %) =erio!s
$ase .tudies taken from 1iterature in $linical Informatics
T59T1OO:
% Introduction to $linical Informatics >9ealth Informatics?" +6e" 4atrice -egoulet , Marius ;ieschi"
.pringer" +''4.
$5ARNIN6 OUTCO25S
Dnit I The learner will able to understand the purpose and functions of arious types of
professional electronic patient records >doctor initiated" facility'specific" inter'facility?
as well as the personal electronic health record >initiated by the patient?. They also will
learn medical imaging and identify their characteristics.
Dnit II The learner will able to understand %ccessibility" Puality" .ustainability of 9ealth
serices and medical care and ethics.
Dnit III The learner will able to understand recording of clinical data and strategies of
enhancing documents with graphics.
Dnit I3 The learners will able to understand the principles inoled in clinical case studies and
the descriptie" e#planatory analysis of a person" group or eent about the
.emester number: 5
/0/0'0&
1earning outcome for 11IC1I)/*R/'3 21IC1I)/*4 2O$5CU$AR 2OD5$$IN6
$A1ORATOR< I
Course Objective: This lab intends to train students to perform molecular modelling using various
online and standalone soft.ares and calculate conformational energies of the molecules.
% %nalysis and 3isualisation of Brookhaen 4-B file formatted te#t file
& Molecular .ketching and <ptimisation-*nergy $alculations
' $alculation of $onformational *nergies
( *nergy 1andscape through .ystematic .ampling
) *nergy Minimisation of 4rotein Models using arious ;orce ;ields
* $alculation of *lectrostatic 4otential of 4roteins
+ $alculation of 4artial %tomic $harges
, *nergy Minimisation of 4rotein-:ucleic %cid comple#es using arious ;orce ;ields
. *nergetics of $onformational change due to Mutations
%/ $onergence $riteria and use of .teepest -escent and $onEugant Aradient
%% Identification of .hort $ontacts in 4roteins
%& *nergy $omparison using ab inito Methods
$5ARNIN6 OUTCO25S
*#. :o. ( .tudents will learn using arious isualiGation software programs to display the protein
structures.
*#. :o.+ The .tudents will get hands-on-training to draw the arious small molecules and will also
learn to optimiGe their oerall geometry.
*#. :o.& The .tudents will build the molecule using the software program in the lab and will learn
to calculate the potential energy of molecules for different conformations of a molecule
*#. :o.4 The students will be able to perform conformational systematic search by modelling
using computer and will be able to draw potential energy surface and will identify the
ma#imum and minimum energy points through isual inspection and the alues.
*#. :o.5 7ill get hands on training on the energy minimiGation of protein structures and will be
able to interpret the results of the outcome.
*#. :o./ 7ill be able to calculate electrostatic potential on the surface of the protein structures and
will be able to identify the charged regions on the surface of the molecule.
*#. :o. 0 7ill learn to construct arious molecules and will be able to calculate partial atomic
charges on each atoms that make up the molecule.
*#. :o. 2 7ill be able to perform energy minimiGation of protein-nucleic acid comple#es using the
molecular mechanics forcefields.
*#. :o. 8 7ill learn to calculate the ariations in the potential energy of the protein molecule using
in silico mutations.
*#. :o. (' 7ill learn to perform conEugate gradient and steepest -escents methods of energy
minimiGation of gien molecule and will be able to choose best method for this procedure
*#. :o. (( 7ill able to identify short-contacts in the protein structures in the 4rotein -ata Bank
using online software programs.
*#. :o. (+ 7ill be able to calculate *nergy of molecules using arious ab initio !uantum mechanical
calculations
.emester number: 5
/0/0'0&
1earning outcome for 11IC1I)/+R/&3 21IC1I)/&4 @A-A $A1ORATOR<
Course Objective: To acquire essential no.ledge and familiarity .ith the programming concepts in
6ava and to acquire a range of practical sills and develop $ioinformatics based destop applications
COR5 @A-A PRO6RA22IN6
(. .tring manipulation
+. .e!uence similarity search
&. Mutations and randomisation
4. Motifs and loops
5. %rray manipulations
/. %pplet 4rogramming
0. <bEect oriented programming
PRO6RA22IN6 IN @O5$I1 C752IN;OR2ATICS $I1RAR<
2. 5<*1ib = accessing atoms , bonds
8. Molecule operation methods , classes
('. Molecular -escriptors
1IO@A-A
((. .e!uence similarity-6homology-based searches of biological databases :$BI Blast" 7D-Blast"
9MM*)
$5ARNIN6 OUTCO25S
*#. :o.( The learner will hae the ability to write programs by understanding the 5aa .tring
handling classes and methods and soling se!uence related tasks in Bioinformatics
*#. :o.+ The learner will hae the e#posure by soling the similarity algorithms in
Bioinformatics with the help of 5aa programs
*#. :o.& The learner will hae the ability to mutate a -:% se!uence repeatedly by musing
randomiGation techni!ue and study the effect of mutations.
*#. :o.4 The learner will hae the understanding of se!uence motifs and arious looping
constructs for .earching motifs in -:% or protein se!uences
*#. :o.5 The learner will be familiar with 5aa %rray concepts and make use of it to store and
process data of one-dimensional" two-dimensional" and multi-dimensional arrays
*#. :o./ The learner will hae the understanding of %pplet 4rogrammingconcepts and deelop
Araphical user interface applications using applet classes and methods.
*#. :o.0 The learner will deelop a simple software application using the obEect oriented
%pproach
*#. :o.2 The learner will e#perience the use of 5<*1ib " free software chemical e#pert systemfor
accessing atoms and bonds of $hemical structures
*#. :o.8 The learner will hae the understanding of 5<*1ib input6output methods and classes
for $hemical structure file format
*#. :o.(' The learner will make use of 5<*1ib classes and methods for calculating Molecular
-escriptorsfor a gien structure
*#. :o.(( The learner will hae the ability to install Bio5aa packages and deelop 5aa program
for analyGing the datasets.
.emester number: 5
/0/0'0%
1earning outcome for 11IC1I)/,R/%3 21IC1I)/,4 S52INAR
Course Objective: To provide an exposure on state of the art research activities pursued in natural
sciences, and bioinformatics; and to prepare the learners in critical reading, understanding, revie. and
presentation of scientific articles.
I:T)<-D$T<)H 1*$TD)*
7hat is researchI = Bioinformatics is a multidisciplinary field - basic knowledge on scientific Eournals =
article selection releant to specialiGation = understanding key points and e#periments- improing
presentation skills = audience and presentation- announcement of selected article = deadlines - ealuation
methods.

$H$1* I
Indiidual presentation with brief background of the work" results" analysis and conclusion.
-uration: &'- 45 min
The articles should be open for discussion.
$H$1* II
Indiidual presentation with brief background of the work" results" analysis" conclusion with
candidateBs comments.
-uration: 45min
The articles should be open for discussion and candidate should able to defend the core theme of
the work.
$5ARNIN6 OUTCO25S
Introductory lecture
The candidate will get oerall idea of arious aspects of research" research
articles" and presentation procedures.
$ycle = I
The candidate will get trained in article selection" understanding key
obseration" and learn the presentation skills.
$ycle = II
The candidate will get refined in article selection" presentation and
discussion with the audience.
.emeste number: 5
/0/0&0&
1earning outcome for 11ICTP)/.321ICTP)/.4 7R S#ills I
Course Objective: To emphasise, impart and improve soft sills of the learner.
R5;5R5NC5 1OO:S
(. Body 1anguage = Hour .uccess Mantra by -r..halini 3erma
ACTI-IT< TOPICS
( .elf Introduction
+ Impromptu
& )ole 4lay
4 .7<T %nalysis
5 Body 1anguage
/ 4roduct 1aunch
0 4erson I admire 6 Book I 1ike 6 If I were
2 .elf $onfidence >Infosys *#ercise?
8 Mock 4ress
(' 1ost at .ea
(( <ut of Bo# Thinking >$reatiity , Innoatie Thinking?
(+ -ebate on $urrent %ffairs
(& Aeneral PuiG
(4 PuiG on $ 6 $RR6 IT $oncepts
2. Managing $areer by -iscoering your personality by ).M.<mkar
&. 4ersonality deelopment , .oft skills by Barun F Mitra
$5ARNIN6 OUTCO25S
Self
Intro!uction
The learner will be able to successfully introduce himself before others
Im=rom=tu The learner realiGes the importance of presence of mind and react sharply and
swiftly.
Role Play The learner will understand the importance of communication skill and
presence of mind
S>OT
Analysis
.tudents are encouraged to do a self introspection of their strengths"
weaknesses" opportunities and threats
1o!y
$anguage
The learner realiGes the importance of body language in the day to day
communication
Pro!uct
$aunch
The learner understands the importance of marketing skills and the need for
sharpening the skill.
Person I
a!mire3 1oo# I
a!mire3 If I
"ere
This inculcates the habit of reading and know about the greatness of great
people.
Self confi!ence .tudents will get to know the importance of self confidence and the ways to
improe it.
2oc# Press The learner will enhance the answering skills and the ability to articulate his
thoughts.
$ost at sea The learner will understand the importance of team skills and problem soling
skills.
Out of 1oA
thin#ing
The learner will deelop lateral thinking and encouraged to think differently.
Debate on
Current
Affairs
The learner will be e#posed to the happenings around the globe through a
debate
BuiC on CD CE
E
The learner will become familiar with the basics of $ and $RR programming to
face Eob interiew.