BINC BioInformatics Syllabus -  Basic

Major Bioinformatics Resources: NCBI, EBI, ExPASy, RCSB

The knowledge of various databases and bioinformatics tools available at these resources, organization of databases: data contents and formats, purpose and utility in Life Sciences

Open access bibliographic resources and literature databases:

Open access bibliographic resources related to Life Sciences viz., PubMed, BioMed Central, Public Library of Sciences (PloS), CiteXplore

Sequence databases: Formats, querying and retrieval; Nucleic acid sequence databases: GenBank, EMBL, DDBJ; Protein sequence databases: Uniprot-KB: SWISS-PROT, TrEMBL, UniParc; Repositories for high throughput genomic sequences: EST, STS GSS, etc.; Genome Databases at NCBI, EBI, TIGR, SANGER – Viral Genomes; Archeal and Bacterial Genomes; Eukaryotic genomes with special reference to model organisms (Yeast, Drosophila, C. elegans, Rat, Mouse, Human, plants such as Arabidopsis thaliana, Rice, etc.)

Structure Database: PDB, NDB, PubChem, ChemBank

Derived Databases

Knowledge of the following databases with respect to: basic concept of derived databases, sources of primary data and basic principles of the method for deriving the secondary data, organization of data, contents and formats of database entries, identification of patterns in given sequences and interpretation of the same – Sequence: InterPro, Prosite, Pfam, ProDom; Structure: FSSP, DSSP

Extraction of knowledge from resources on Immunology, Plant, animal and infectious diseases: databases and servers published in the NAR Database and Web server Issues and other Bioinformatics journals viz. BMC Bioinformatics etc.

Sequence Analysis

Various file formats for bio-molecular sequences: GenBank, FASTA, GCG, MSF etc

Basic concepts of sequence similarity, identity and homology, definitions of homologues, orthologues, paralogues and xenologues

Scoring matrices: basic concept of a scoring matrix, Matrices for nucleic acid and proteins sequences, PAM and BLOSUM series, principles based on which these matrices are derived

Database Searches: Keyword-based Entrez and SRS; Sequence-based: BLAST & FASTA; Use of these methods for sequence analysis including the on-line use of the tools and interpretation of results from various sequence and structural as well as bibliographic databases

Pairwise sequence alignments: basic concepts of sequence alignment, Needleman and Wunsch, Smith and Waterman algorithms for pairwise alignments, gap penalties, use of pairwise alignments for analysis of Nucleic acid and protein sequences and interpretation of results

Multiple sequence alignments (MSA): the need for MSA, basic concepts of various approaches for MSA (e.g. progressive, hierarchical etc.). Algorithm of CLUSTALW and PileUp and their application for sequence analysis (including interpretation of results), concept of dandrogram and its interpretation

Sequence patterns and profiles: Basic concept and definition of sequence patterns, motifs and profiles, various types of pattern representations viz. consensus, regular expression (Prosite-type) and sequence profiles; profile-based database searches using PSI-BLAST, analysis and interpretation of profile-based searches

Taxonomy and phylogeny: Basic concepts in systematics, taxonomy and phylogeny; molecular evolution; nature of data used in Taxonomy and Phylogency, Definition and description of phylogenetic trees and various types of trees

Protein and nucleic acid properties: Computation of various parameters using proteomics tools at the ExPASy server, GCG utilities and EMBOSS

Comparative genomics: Basic concepts and applications, whole genome alignments: understanding significance. Artemis as an example

Structural Biology

Proteins: Principles of protein structure; anatomy of proteins – Hierarchical organization of protein structure – Primary. Secondary, Super secondary, Tertiary and Quaternary structure; Hydrophobicity of amino acids, Pacing of protein structure, van der Waal and Solvent accessible surface, Internal coordinates of proteins; Derivation, significance and applications of Ramachandran Map, protein folding

DNA and RNA: types of base pairing – Watson-Crick and Hoogstein; types of double helices A, B, Z and their geometrical as well as structural features; structural and geometrical parameters of each form and their comparison; various types of interactions of DNA with proteins, small molecules

RNA secondary and tertiary structures, t-RNA tertiary structure

Carbohydrates: The various building blocks (monosaccharides), configurations and conformations of the building blocks; formations of polysaccharides and structural diversity due to the different types of linkages

Glyco-conjugates: various types of glycolipids and glycoproteins

Structure analysis and validation: PDB Goodies, Procheck, ProsaII, PDBsum

3-D structure visualization and simulation: Visualization of structures using Rasmol or SPDBV or CHIME or VMD

Basic concepts in molecular modeling: different types of computer representations of molecules. External coordinates and Internal Coordinates

Concepts of force fields: representations of atoms and atomic interactions, potential energy representation

Classification and comparison of protein 3D structures:

Purpose of 3-D structure comparison and concepts, Algorithms such as FSSP, CE, VAST and DALI, Fold Classes

Databases of structure-based classification; CATH and SCOP

Secondary structure prediction: Algorithms viz. Chou Fasman, GOR methods; analysis of results and measuring the accuracy of predictions using Q3, Segment overlap, Mathew’s correlation coefficient

Tertiary Structure prediction: Fundamentals of the methods for 3D structure prediction (sequence similarity/identity of target proteins of known structure, fundamental principles of protein folding etc.) Homology Modeling, fold recognition, threading approaches, and ab-initio structure prediction methods

Fundamentals of docking small and macromolecules to proteins and nucleic acids

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BINC Information Technology Syllabus – Basic

Concepts in Computing

Overview and functions of a computer system

Input and output devices

Storage devices: Hard Disk, Diskette, Magnetic Tape, RAID, ZIP devices, Digital Tape, CD-ROM, DVD, etc (capacity and access time)

Main Circuit Board of a PC: Chips, Ports, Expansion slots, etc

Memory: Register, buffer, RAM, ROM, PROM, EPROM, EEPROM (comparison)

Types of Processing: Batch, Real-Time, Online, Offline

History of Computers: Evolution, Generation of computers (I, II, III, IV, V), Classification of computers (mainframes, mini computers, microcomputers, special purpose) – comparison with memory, power, cost, size – then and now

Types of modern computing: Workstations, Servers

An overview of computer viruses: What is a virus? Virus symptoms, How do they get transmitted? What are the dangers, General Precautions?

Introduction to operating systems: Operating System concept, Windows 2003/XP, Windows Vista, UNIX/LINUX

The Internet and its Resources, World Wide Web (WWW): Associated tools, services, resources and various terminologies

Programming in C

Introduction to Database Systems

Concepts of various types of databases

Data Abstraction

Data Models

Instances and Schemes

E-R Model: Entity and entity sets; Relations and relationship sets; E-R diagrams; Reducing E-R Diagrams to tables

Network Data Model: Basic concepts

Hierarchical Data Model: Basic Concepts

Text Databases

Multimedia Databases – Basic Concepts and Applications; Indexing and Hashing

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BINC  Mathematics Statistics Physics and Chemistry Syllabus – Basic

Functions and Graphs: Functions, Relations, notation and representation. Graphs. Review of basic functions. Functions of several variables

2D coordinate geometry: Equation of a line, circle, ellipse, parabola, hyperbola

3D geometry: Equation of sphere, cone, direction cosines, equation of line

Basic trigonometric functions

Matrix algebra: Addition, subtraction, multiplication, transpose

Introduction to principles of statistical sampling from a population, random sampling

Frequency distributions and associated statistical measures, Probability distributions – normal and binomial

Particle dynamics, Newton’s laws of motion, velocity, acceleration, momentum

Pressure, temperature, volume relationship

First law of thermodynamics, isothermal process, entropy and second law of thermodynamics, reversible and irreversible processes; Concepts of enthalpy, internal energy and potential energy; Inter-relation between potential energy and force

Concept of pH, pK, chemical equilibrium, Henderson-Hasselbach equation, structure of water, chemical forces, hydrophilic and hydrophobic forces, hybridization states of atoms, electronic structure of molecules, and concept of bonding (chemical bonds, ionic bonds, covalent bonds, hydrogen bond, coordinate bonds)

Bio-Informatics National Certification (BINC) 2010 Syllabus

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BINC Biology Syllabus -  Basic

Cell Biology

Basic aspects of Prokaryotic and eukaryotic cells (plant and animal cells); membranes and cellular compartments, cell organelles, structure and function

Cell motility and shape: cytoskeletal elements, cilia and flagella; motor proteins

Cell-cell interactions: Intercellular junctions

Photosynthesis, transportation of proteins in cells, transpiration, Electron transport chain

Cell cycle and its regulation; events during mitosis and meiosis

Genetics

Mendelian principles of inheritance, sex linked inheritance

Concept of linkage, linkage maps and recombination

Mutations – molecular, point and chromosomal mutations, hotspots

Phenotype and genotype relationships, role of environment, from gene to phenotype, gene interactions. Study of quantitative traits

Genetics of populations, genetics and evolution

Immunology

Immune systems: Innate and adaptive immunity in vertebrates

Antigen processing and presentation

Antibodies: Immunoglobulins, Immunoglobulin classes and subclasses, CDR and LDR regions and sequence numbering

Concepts of generation of diversity and specificity in immune system; Immunological methods

Molecular Biology

Prokaryotic genome organization and structure

Prokaryotic gene expression, factors involved in gene regulation

Eukaryotic genome organization and structure, Mechanism of gene expression in Eukaryotes, Basic mechanism of transcription and translation

Mechanisms by which genome undergoes changes, recombination, mutation, inversion, duplication, transposition

Biochemistry

Carbohydrates and lipids, their importance in cells

Proteins: Amino acids and their physiocochemical properties, peptide bond and peptides

Nucleic acids: nucleosides, nucleotides, RNA and DNA. Denaturation and renaturation of DNA

Enzymes: Units of activity, coenzymes and metal cofactors, temperature and pH effects, Michaelis-Menten kinetics, inhibitors and activators, active site

Organization of metabolic systems: enzyme chains, multienzyme complexes, multifunctional enzymes and regulatory enzymes

Concept of biochemical regulation, feed back and feed forward systems, biochemical oscillations

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BINC BioInformatics Syllabus- Advanced

Sequence analysis

Scoring matrices: Detailed method of derivation of the PAM and BLOSUM matrices

Pairwise sequence alignments: Needleman and Wuncsh, Smith and Waterman algorithms and their implementation

Multiple sequence alignments (MSA): Use of HMM-based Algorithm for MSA (e.g. SAM method)

Taxonomy and phylogeny: Phylogenetic analysis algorithms such as maximum Parsimony, UPGMA, Transformed Distance, Neighbors-Relation, Neighbor-Joining, Probabilistic models and associated algorithms such as Probabilistic models of evolution and maximum likelihood algorithm, Bootstrapping methods, use of tools such as Phylip, Mega, PAUP

Sequence patterns and profiles:

Algorithms for derivation of and searching sequence patterns: MeMe, PHI-BLAST, SCanProsite and PRATT

Algorithms for generation of sequence profiles: Profile Analysis method of Gribskov, HMMer, PSI-BLAST

Protein and nucleic acid properties: e.g. Proteomics tools at the ExPASy server and GCG utilities and EMBOSS

Structural Biology

Identification/assignment of secondary structural elements from the knowledge of 3-D structure of macromolecule using DSSP and STRIDE methods

Prediction of protein structure: PHD and PSI-PRED methods

Tertiary structure: Detailed protocols/algorithms for Homology modeling, fold recognition and ab-initio approaches

Structures of oligomeric proteins and study of interaction interfaces

Molecular modeling and simulations

Macro-molecular force fields, salvation, long-range forces

Geometry optimization algorithms: Steepest descent, conjugate gradient

Various simulation techniques: MD, Monte Carlo, docking strategies etc

Molecular mechanics, conformational searches

Genomics

Large scale genome sequencing strategies

Genome assembly and annotation

Genome databases of Plants, animals and pathogens

Metagenomics

Gene networks: basic concepts, computational model such as Lambda receptor and lac operon

Prediction of genes, promoters, splice sites, regulatory regions: basic principles, application of methods to prokaryotic and eukaryotic genomes and interpretation of results

Basic concepts on identification of disease genes, role of bioinformatics-OMIM database, reference genome sequence, integrated genomic maps, gene expression profiling; identification of SNPs, SNP database (DbSNP). Role of SNP in Pharmacogenomics, SNP arrays

Basic concepts in identification of Drought stress response genes, insect resistant genes, nutrition enhancing genes

Epigenetics

DNA microarray: database and basic tools, Gene Expression Omnibus (GEO), ArrayExpress, SAGE databases

DNA microarray: understanding of microarray data, normalizing microarray data, detecting differential gene expression, correlation of gene expression data to biological process and computational analysis tools (especially clustering approaches)

Comparative genomics:

Basic concepts and applications, BLAST2, MegaBlast algorithms, PipMaker, AVID, Vista, MUMmer, applications of suffix tree in comparative genomics, synteny and gene order comparisons

Comparative genomics databases: COG, VOG

Functional genomics:

Application of sequence based and structure-based approaches to assignment of gene functions – e.g. sequence comparison, structure analysis (especially active sites, binding sites) and comparison, pattern identification, etc. Use of various derived databases in function assignment, use of SNPs for identification of genetic traits

Gene/Protein function prediction using Machine learning tools viz. Neural network, SVM etc

Proteomics

Protein arrays: basic principles

Computational methods for identification of polypeptides from mass spectrometry

Protein arrays: bioinformatics-based tools for analysis of proteomics data (Tools available at ExPASy Proteomics server); databases (such as InterPro) and analysis tools

Protein-protein interactions: databases such as DIP, PPI server and tools for analysis of protein-protein interactions

Modeling biological systems

Systems biology – Use of computers in simulation of cellular subsystems

Metabolic networks, or network of metabolites and enzymes

Metabolic pathways: databases such as KEGG, EMP

Study of plant pathways –MetaCyc, AraCyc

Signal transduction networks

Gene regulatory networks

Bioinformatics Resources at the species level

ICTV Database, AVIS, VirGen, Viral genomes at NCBI, VBRC, VBCA, PBRC and Subviral RNA database, Species 2000, TreeBASE etc

Drug design

Drug discovery process

Role of Bioinformatics in drug design

Target identification and validation, lead optimization and validation

Structure-based drug design and ligand based drug design

Modeling of target-small molecule interactions

Vaccine design:

Reverse vaccinology and immunoinformatics

Databases in Immunology

B-cell epitope prediction methods

T-cell epitope prediction methods

Resources to study antibodies, antigen-antibody interactions

Structure Activity Relationship – QSARs and QSPRs, QSAR Methodology, Various Descriptors used in QSARs: Electronics; Topology; Quantum Chemical based Descriptors. Use of Genetic Algorithms, Neural Networks and Principle Components Analysis in the QSAR equations

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BINC Information Technology Syllabus – Advanced

Local area networking, network devices, IP address, computational cluster

Parallel processing/computing, cluster computing, grid computing, etc

Java and Perl programming

Introduction to distributed database processing; understand, appreciate and implement relational database design

SQL and front end development

Select statement

Data definition statements

Data manipulation statements

Data control statements

Other database objects: Views, Sequences, Synonyms

Application development using visual basic

Working with code and forms

Variables, procedures and controlling program executor

Standard controls

Data access using Data control

Connecting to Oracle database using visual basic

Using Oracle DBMS as backend, SQL skills and basic skill in using VB as a front end

Computer graphics and visualization

Introduction

Scientific and Engineering opportunities

Visualization techniques: Software, Hardware, Color representation – RGB, CMY, gray-scale

Interactive graphics

Interaction devices and techniques

Geometric transformations

Viewing in three dimensions. Stereo-pairs, perspective, depth-cue

Rendering

Standards – CGI, GKS, PHIGS

Programming in C

Concepts of flowcharts, algorithm development, pseudo codes etc

Computer assignments based on the following topics in ‘C’ programming: Data types, operatos and expressions, Hierarchy of operators, control statements including decision (if, if-else), loops (while, do-while, for), branching (switch, break, continue), functions, arrays (1D, 2D- all matrix operations including inverse of a matrix), strings, Pointers, file handling, data structures etc,

OR

Programming in Object Oriented Languages

JAVA

An introduction to JAVA programming

Object-oriented programming and Java

Java basics

Working with objects

Arrays, Conditionals and Loops

Creating classes and applications in Java

More about methods

Java applets basics

Graphics, Fonts and Color

Simple Animation and threads

Advanced animation, images and sound

Managing simple events and interactivity

Creating user interfaces with AWT

Modifiers, Access control and class design

Packages and Interfaces

Exception

Multithreading

Streams and I/O

Using Native methods and libraries

Java programming tools

Working with data structures and Java

Image filters,

OR

Perl

What is Perl? Why use Perl in Bioinformatics? History of Perl, Availability, Support, Basic concepts.

Scalar data: What is Scalar Data? Numbers, strings, scalar operators, scalar variables, scalar operators and functions

Arrays and list data: What is a list or array? Literal representation, variables, arrays operators and functions, scalar and list context

Control structures: Statement blocks

Hashes: What is a Hash? Hash variables, Literal representation of a Hash, Hash Functions, Hash Slices

Basic I/O

Regular expressions: Concepts about regular expressions, simple uses of regular expressions, patterns, matching operator, substitutions, the split and join functions

Subroutines: System and user functions, the local operator, variable-length parameter lists, lexical variables

Miscellaneous control structures

Filehandles and file tests: What is a filehandle? Opening and closing a filehandle, using pathnames and filenames, die, using filehandles, The –x file tests, the stat function

Formats: What is a format? Defining a format, invoking a format

Directory access: Directory tree, globbing, directory handles, opening and closing a directory handle, reading a directory handle

File and directory manipulation

Process management: Using system and exec, using backquotes

Other data transformation: Finding a substring, extracting and replacing a substring

Formatting data: Sorting, Transliteration

System information: Getting User and Machine information, Packing and Unpacking Binary data, getting network information

Database manipulation: DBM databases and DBM Hashes, Opening and closing DBM Hashes, Fixed-length random-access databases, Variable-Length (Text) Databases, Win32 Database Interfaces

CGI programming: The CGI.pm Module, CGI program in context, simple CGI programs, passing parameters via CGI, Perl and the Web

Object oriented perl: Introduction to modules, Creating Objects

Bioperl: Introduction, Installation procedures, Architecture, Uses of bioperl

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BINC Mathematics, Statistics, Physics and Chemistry Syllabus – Advanced

Number integration. Interpolation and approximate methods

Vector – addition, subtraction, dot, cross, scalar triple product, divergence and curl.

System of linear equations. Matrix inverse, eigenvalue, eigenvector, principalm component analysis

Mathematical modeling and simulation

Methods of least squares, chi-square test, systematic and random sampling, accidental and systematic errors, correlation and regression analysis. Poisson and extreme value distributions

Multivariate analysis, Hypothesis testing, Markov process

Bayesian Statistics

Basics of classical mechanics and quantum mechanics

Laws of motion

Refraction of light, focal length of lens, magnification. Definition of resolution, optical and electron microscope

Principles of lasers

Luminescence, fluorescence and phosphorescence (basic concepts and applications)

Non-covalent bonding in protein structure

Biophysical techniques for determining size and shape of macromolecules – ultra centrifugation, electrophoresis and chromatography. Application of spectroscopy (fluorescence and absorption spectroscopy) and X-ray diffraction for determination of biomolecular secondary and tertiary structure – CD, NMR, X-ray crystallography, mass spectroscopy of biological molecules

Basic principle of chemical kinetics – Zero order and first order kinetics, energy of activation. Reversible and irreversible thermodynamics

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BINC Biology Syllabus – Advanced

Cell Biology and Genetics

Vesicular transport and protein traffic in cells

Different mechanisms of signal transduction, concepts in signal network, second messenger, molecules involved in various signaling pathways such as G-protein coupled receptors, protein kinases, calcium binding proteins

X-linked and autosomal diseases, mitochondrial related disease, QTL methods for diagnostics

Extra-chromosomal inheritance

Immune response, autoimmune disorders, ELISA method

Molecular genetics and genetic disorders

Molecular Biology

Genome organization, Initiation, elongation and termination of transcription-template and enzyme properties, promoter and regulator sequences. Regulation of translation, Post transcriptional modifications

Methods for studying gene expression and regulatory sequences, large-scale expression analysis, use of microarrays

Genetic information transfer, details of regulation in eukaryotes and prokaryotes, horizontal gene transfer

Operons – positive and negative regulation, Processing of RNA and Proteins – Transport and Stability

Organization of eukaryotic genome, Methods for studying variation and polymorphism at genome level, PCR, northern, southern, western blotting, RFLP, fingerprinting, RAPDs, DNA and protein sequencing methods

Epigenetic mechanisms of inheritance regulatory RNA molecules (RNA; miRNA, siRNA), antisense RNA and their applications

Biochemistry

Enzyme kinetics, Lineweaver-Burk plot, Competitive and non competitive inhibition

Molecular mechanisms of interactions of small and large molecules including ions, regulation of protein pathways, mechanism of enzyme action, ribozyme and abzymes

Isoenzymes, allosteric enzymes, regulation by covalent modification

Carbohydrate metabolism: Glycolysis, gluconeogenesis, glycogenolysis, glycogenesis, TCA cycle and oxidative phosphorylation

Pentose phosphate pathway; hormonal control, β-oxidation and biosynthesis of fatty acids

Transamination and deamination of amino acids, ketogenic and glycogenic amino acids, urea cycle

Purine and pyrimidine biosynthesis

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