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LABORATORY SETUP
  • One Bench top cold centrifuge.
  • One Thermocycler (Amersham Biosciences) [48 well]
  • Tissue Culture set up with one Laminar Air Flow Cabinet.
  • Autoclave.
  • Biochemistry laboratory (fully equipped).
  • Vertical and Submarine gel apparatus.
  • Bioinformatics
    What is Bioinformatics ?
    The term bioinformatics was coined by Paulien Hogeweg in 1979 for the study of informatic processes in biotic systems. Its primary use since at least the late 1980s has been in genomics and genetics.

    Bioinformatics is the field of science in which biology, computer science, and information technology merge to form a single discipline. The ultimate goal of the field is to enable the discovery of new biological insights as well as to create a global perspective from which unifying principles in biology can be discerned. At the beginning of the “genomic revolution”, a bioinformatics concern was the creation and maintenance of a database to store biological information, such as nucleotide and amino acid sequences. Development of this type of database involved not only design issues but the development of complex interfaces whereby researchers could both access existing data as well as submit new or revised data.

    Ultimately, however, all of this information must be combined to form a comprehensive picture of normal cellular activities so that researchers may study how these activities are altered in different disease states. Therefore, the field of bioinformatics has evolved such that the most pressing task now involves the analysis and interpretation of various types of data, including nucleotide and amino acid sequences, protein domains, and protein structures. The actual process of analyzing and interpreting data is referred to as computational biology. Important sub-disciplines within bioinformatics and computational biology include:

  • The development and implementation of tools that enable efficient access to, and use and management of, various types of information.
  • The development of new algorithms (mathematical formulas) and statistics with which to assess relationships among members of large data sets, such as methods to locate a gene within a sequence, predict protein structure and / or function, and cluster protein sequences into families of related sequences.
  • Why Is Bioinformatics So Important ?
    The rationale for applying computational approaches to facilitate the understanding of various biological processes includes:

  • A more global perspective in experimental design.
  • The ability to capitalize on the emerging technology of database-mining – the process by which testable hypotheses are generated regarding the function or structure of a gene or protein of interest by identifying similar sequences in better characterized organisms
  • Evolutionary Biology
    New insight into the molecular basis of a disease may come from investigating the function of homologs of a disease gene in model organisms. In this case, homology refers to two genes sharing a common evolutionary history. Scientists also use the term homology, or homologous, to simply mean similar, regardless of the evolutionary relationship.

    Equally exciting is the potential for uncovering evolutionary relationships and patterns between different forms of life. With the aid of nucleotide and protein sequences, it should be possible to find the ancestral ties between different organisms. Thus far, experience has taught us that closely related organisms have similar sequences and that more distantly related organisms have more dissimilar sequences. Proteins that show a significant sequence conservation, indicating a clear evolutionary relationship, are said to be from the same protein family. By studying protein folds (distinct protein building blocks) and families, scientists are able to reconstruct the evolutionary relationship between two species and to estimate the time of divergence between two organisms since they last shared a common ancestor.
    Protein Modeling
    The process of evolution has resulted in the production of DNA sequences that encode proteins with specific functions. In the absence of a protein structure that has been determined by X–ray crystallography or nuclear magnetic resonance (NMR) spectroscopy, researchers can try to predict the three-dimensional structure using protein or molecular modeling. This method uses experimentally determined protein structures (templates) to predict the structure of another protein that has a similar amino acid sequence (target).

    Although molecular modeling may not be as accurate at determining a protein’s structure as experimental methods, it is still extremely helpful in proposing and testing various biological hypotheses. Molecular modeling also provides a starting point for researchers wishing to confirm a structure through X–ray crystallography and NMR spectroscopy. Because the different genome projects are producing more sequences and because novel protein folds and families are being determined, protein modeling will become an increasingly important tool for scientists working to understand normal and disease-related processes in living organisms.
    Genome Mapping
    Genomic maps serve as a scaffold for orienting sequence information. A few years ago, a researcher wanting to localize a gene, or nucleotide sequence, was forced to manually map the genomic region of interest, a time-consuming and often painstaking process. Today, thanks to new technologies and the influx of sequence data, a number of high-quality, genome-wide maps are available to the scientific community for use in their research.

    Computerized maps make gene hunting faster, cheaper, and more practical for almost any scientist. In a nutshell, scientists would first use a genetic map to assign a gene to a relatively small area of a chromosome. They would then use a physical map to examine the region of interest close up, to determine a gene’s precise location. In light of these advances, a researcher’s burden has shifted from mapping a genome or genomic region of interest to navigating a vast number of Web sites and databases.
    Major Bioinformatics Companies in India
    HH Biotechnologies Pvt. Ltd.
    Location: Agra, India.
    HH Bio is a Research and Development arm of Agra based Harihar group and is presently focusing on raising of Bio–pharmaceuticals and similar other products with the help of transgenic plants. The parent company Harihar Biotech holds a state–of–the–art 2–acre campus at the city of Taj, where it is engaged in the tissue culture based production of various plants. HH Bio is having its research laboratory at Biotech Park Lucknow, to explore the possibilities of various bio pharmaceuticals based proteins, which can be expressed in plants by using transgenic molecular biology techniques and through computational proteomics approach.
    Metahelix Life Sciences Pvt. Ltd.
    Location: Bangalore, India.
    Metahelix is an agricultural biotechnology company focusing on developing traits and technologies for crop protection & improved productivity. Hybrid Seeds and traits are commercialized by its wholly owned subsidiary seeds business Dhaanya Seeds. Metahelix also provides customized research to select global Ag–biotech business using its proprietary technologies in crop transformation and functional genomics.
    Strand Genomics
    Location: Bangalore, India.
    Strand Life Sciences, formerly Strand Genomics, is a premier in silico technologies Innovation Company. Strand leverages its core strengths in Data Mining, Predictive Modeling, Computational Chemistry, Software Engineering and Research Biology to develop Technologies and offer various Products for research biology, chemistry and drug discovery. Strand also offers custom Solutions based on its technologies.
    Biobase Inc
    Location: Bangalore, India.
    BIOBASE is the leading content provider of biological databases, knowledge tools and software for the life science industry. We offer our customers well-structured data, assembled by highly qualified subject-matter experts, organized in an accessible and easily searchable manner that enables researchers to identify connections between disparate pieces of information and to apply that knowledge to their specific topic of interest.
    Genbios
    Location: Bangalore, India.
    GENBIOS is a start–up bioinformatics firm working in the areas of microbial products, database design, literature curation and bio-software tool development. We intend to serve Pharmaceutical, Food, Cosmetics, Diagnostics, Health care and other Biotechnological industries. Our team has post–graduates and doctorates from the fields of Information Technology, Life Sciences and Bioinformatics. GENBIOS is virtually incubated at IBAB, Institute of Bioinformatics and Applied Biotechnology (www.ibab.ac.in). The skill base of GENBIOS is Bionformatics. Our Products and Services include designing key, ready to use reliable, cost–effective software solutions for the biotechnology / pharmaceutical / diagnostics industry with a range of products and an array of custom services including Data mining, Algorithm development, Gene identification, Multiple–platform software development, Database creation and manipulation, Literature curation, and tools for image analysis.
    BioCOS
    Location: Bangalore, India.
    BioCOS mainly is focussing on following research and application activities – Microarray data processing – Biomarkers and drug candidate identification – Biomedical imaging solutions – Algorithms for non invasive biomedical devices – Network biology.
    ADI Biosolution
    Location: Chandigarh, India.
    ADI is committed to provide premium solutions world wide to the life science industry. The company offers curated and compiled biological software’s and databases products with expert bioinformatics services, educational services and essential IT applications and resources for bio–medical research, that bridge the gap between information gathering and knowledge generation.
    Read more
    Barat Bioinformatics Research Institute
    Location: Chennai, India.
    Barat Bioinformatics Research Institute (BBRI) is consultancy and service provider in the field of Bioinformatics and Information Technology. We aim at delivering innovative and customized Insilico solutions matched to the special needs of biotechnological and pharmaceutical origin. We can ready to prepare the database which will be related to systems biology and drug discovery according to the company needs like Pharma, Agriculture, Biotechnology.
    Neozene Bio Sciences
    Location: Chennai, India.
    Computational Biology, which includes both Bioinformatics and Cheminformatics, has now become a necessary area that is to be present in the research community. As, the requirements for Bioinformatics and Cheminformatics drastically increase we Neozene Bio Sciences, venture into Computational Biology to ravel the mysteries of biological molecules by identifying Biomarkers, Therapeutics and Drug targets.
    Neogen Biosolutions
    Location: Chennai, India.
    A division of NEOGEN Research Foundation, started with a finishing school concept to bridge the gap between Academics & Industries. The Mission of the NeoGen Life Sciences is to become a world– class centre of excellence for bioinformatics research and training. The centre will mainly emphasis on bioinformatics research and learning across the country and will facilitate the development of integrated research from the diverse fields associated with bioinformatics. The aim and vision of the institute is to pave a platform for individuals, professionals, R&D Organizations, Pharmaceutical & Software companies to utilize and harness the Indian bioinformatics potential.
    Informatics Outsourcing
    Location: Chennai, India.
    Informatics Outsourcing, an analytics and research company based in Chennai, India, provides expert services and cater to the outsourcing needs of Pharmaceutical and Biotech clients around the globe. We have carved out a niche for ourselves on domains in the Pharma and Biotech industries that require outsourcing. Our accomplished scientists provide innumerable reasons for customers to utilize our offerings. Our expertise can complement yours and our technologies can be accessed through collaboration. Our services can be utilized to handle multitude of complex computational challenges faced by Pharmaceutical and Biotechnological Companies and Research Institutions.
    BionteQ Bioscience Private Limited
    Location: Chennai, India.
    We are a Bioinformatics outsourced and offshore organization offering our services from India with a team of highly qualified, experienced and expert Bioinformaticians. BionteQ provides informatics solutions to accelerate biological research by its various services, thereby enabling effective decision making. Along with its life science informatics services, the company also provides services and products for biomedical application. By providing prompt knowledge and computational solutions, BionteQ helps to cut costs, make therapeutic and other decisions at the right time and to pursue the research based on well–defined objectives and tasks.
    Liatris Biosciences
    Location: Cochin, India.
    Provides contract research services in custom scientific data curation, Computational chemistry, Chemical name to structure, Bioindexing, Microarray data analysis, Patent search, biostatistics and Clinical data management, Biological database development.
    BioAxis DNA Research Centre
    Location: Hyderabad, India.
    BioAxis DNA Research Centre pvt is an autonomous Research Organization, devoted for Vaccines and Drugs Research with the Bioinformatics/Biotechnology and Molecular Biology Applications. BDRC works to create a platform conductive for the growth promotion and partnering in the field of Biological sciences. We at BDRC are dedicated to provide a backbone to the Biological Research, for proper utilization of the advancements in the field of life sciences by taking together students, professional, academics, organizations through consultative, advisory, educative process which will provide growth and partnership opportunities for organization, academics, students, the society and mankind as a whole.
    Eminent Biosciences
    Location: Indore, India.
    Eminent Biosciences established in the year of 2008, November and is located in Indore, a bustling hub of 1.5 million inhabitants located atop central India’s Deccan. We provide solutions to core bioinformatics problems by innovative ideas, advanced algorithms and top notch software development for research in Life science and Pharma Industry. We serve companies involved in Life science, Pharmaceutical and other R&D Organizations by helping them to work in computational analysis. For widening our services we undertakes contract research on Genomics, Proteomics, Clinical Genomics, Toxicogenomics, Microarray, Drug Discovery, Drug Designing, Virtual Screening, QSAR studies and other various fields of Bioinformatics.
    Medha Innovation and Development
    Location: Indore, India.
    Medha Innovation and Development, develops advanced algorithms based on innovative research, providing solutions to fundamental bioinformatics problems. This small, adaptable group is committed to serving the needs of pharmaceutical, biotechnological and academic scientists and to the progression of drug discovery research.
    SooryaKiran Bioinformatics (P) Ltd.
    Location: Trivandrum, India.
    SooryaKiran Bioinformatics (P) Ltd focuses on algorithm design and software development in the areas of bioinformatics, computational biology and synthetic biology. Our service portfolio ranges from customized and dedicated life science software development to sophisticated insilico reconstruction and simulation of metabolic pathways.
    Modular Course (S) in Bioinformatics
    Course BI01: Introduction to Bioinformatics
    Duration: 30 Hours.
    Introduction to Biology (10 hours):
  • DNA, RNA and PROTEIN Structure.
  • The Central Dogma and the Processes involved (DNA REPLICATION, TRANSCRIPTION, RNA PROCESSING, TRANSLATION, POST TRANSLATIONAL MODIFICATIONS).
  • DNA SEQUENCING AND AMINO ACID SEQUENCING.
  • INTRODUCTION TO PROTEIN 3D STRUCTURE DETERMINATION.
  • GENOMIC AND PROTEOMIC TECHNIQUES.
  • Introduction to Bioinformatics (20 Hours): (PRACTICAL AND DEMONSTRATION)
  • BASIC REQUIREMENTS OF A COMPUTER SYSTEM TO PERFORM BIOINFORMATICS ANALYSES.
  • TYPES OF SEQUENCE FORMATS.
  • DATABASE AND DATAWAREHOUSE CONCEPT: BIOLOGICAL DATABASES – NCBI, SWISS PROT, EBI, SCOP, PDB, CATH, KEGG, miRBASE.
  • INTRODUCTION TO BASIC LOCAL ALIGNMENT SEARCH TOOL AND ITS VARIANTS.
  • INTRODUCTION TO MULTIPLE SEQUENCE ALIGNMENT AND JALVIEW.
  • IDENTIFICATION OF DOMAINS AND MOTIFS USING WEBSERVERS.
  • MAXIMUM INTAKE CAPACITY: 30 Students per batch.
    INSTITUTIONAL REQUIREMENTS: ONE LECTURE THEATRE for 3 hours per day.

    THE INSTITUTION CAN REQUEST THE WAIVER OF FEES FOR TWO NEEDY BUT MERITORIUS STUDENTS
    Course BI02: Structure Analysis and Molecular Modelling
    Duration: 40 Hours
    STRUCTURAL BIOLOGY (10 HOURS):
  • DNA, RNA and PROTEIN Structure.
  • INTRODUCTION TO PROTEIN 3D STRUCTURE DETERMINATION.
  • CONCEPT OF FREE ENERGY OF THE SYSTEM.
  • INTRODUCTION TO PROTEIN – PROTEIN INTERACTION.
  • PROTEIN EVOLUTION AND PROTEIN FAMILIES.
  • STRUCTURE ANALYSIS AND MODELLING (30 Hours): (PRACTICAL AND DEMONSTRATION)
  • INTRODUCTION TO STRUCTURAL PARAMETERS OF INTEREST: ACCESSIBLE SURFACE AREA, POCKET IDENTIFICATION.
  • DETERMINATION OF ACCESSIBLE SURFACE AREA OF A MOLECULE: ASA VIEW/VADAR.
  • DETERMINATION OF INTERACTING RESIDUES.
  • DETECTING HOMOLOGIES USING PDB BLAST.
  • MOLECULAR MODELLING USING SWISS – MODEL WORKBENCH.
  • MOLECULAR MODELLING USING MC FOLD.
  • APPLICATION OF 3D SURFER.
  • VISUALIZING PROTEINS AND NUCLEIC ACIDS USING RASMOL.
  • MAXIMUM INTAKE CAPACITY: 25 Students per batch.
    INSTITUTIONAL REQUIREMENTS: ONE LECTURE THEATRE for 2 hours per day. (For 20 days)

    THE INSTITUTION CAN REQUEST THE WAIVER OF FEES FOR ONE NEEDY BUT MERITORIUS STUDENT
    Course BI03: Interactomics and Molecular Dynamic Simulation
    Duration: 40 Hours
    STRUCTURAL BIOLOGY (10 HOURS):
  • DNA, RNA & PROTEIN STRUCTURE.
  • CONCEPT OF FREE ENERGY OF THE SYSTEM.
  • INTRODUCTION TO PROTEIN – PROTEIN INTERACTION.
  • TYPES OF PROTEIN – PROTEIN AND NUCLEIC ACID – PROTEIN INTERACTIONS AND THEIR APPLICATION IN BIOLOGY.
  • METHODS OF STUDYING PROTEIN – PROTEIN AND NUCLEIC ACID – PROTEIN INTERACTIONS IN THE WET LAB – YEAST ONE HYBRID AND TWO HYBRID ASSAYS, EMSA, IMMUNOCHEMICAL METHODS.
  • MOLECULAR DYNAMIC SIMULATIONS: (25 Hours) (PRACTICAL AND DEMONSTRATION)
  • INTRODUCTION TO MOLECULAR DYNAMIC SIMULATIONS.
  • DETERMINATION OF THE LIGAND INTERACTING SITES.
  • DETECTION OF INTERACTING RESIDUES.
  • USING HEX TO SIMULATE AN INTERACTION ENVIRONMENT.
  • ANALYZING THE COMPLEXES USING CHIMERA.
  • MAXIMUM INTAKE CAPACITY: 25 Students per batch.
    INSTITUTIONAL REQUIREMENTS: ONE LECTURE THEATRE for 2 hours per day. (For 20 days)

    THE INSTITUTION CAN REQUEST THE WAIVER OF FEES FOR ONE NEEDY BUT MERITORIUS STUDENT
    Programming Using Java, Bioperl C & C++ & Support Vector Machine Approaches For Bioinformatics
    Duration: 40 Hours
    THE BASICS OF PROGRAMMING (20 hours)
  • CONCEPT OF PROGRAMMING
  • ALGORITHMS IN BIOINFORMATICS TO WHICH PROGRAMMING CAN BE APPLIED
  • INTRODUCTION TO C and C++
  • INTRODUCTION TO JAVA
  • INTRODUCTION TO BIOPERL
  • INTRODUCTION TO SUPPORT VECTOR MACHINE
  • APPLICATION OF PROGRAMMING BASICS (20 Hours)
  • APPLICATION OF JAVA.
  • APPLICATION OF C and C ++.
  • APPLICATION OF BIOPERL.
  • APPLICATION OF SUPPORT VACTOR MACHINES.
  • INTEGRATING ALL THE APPROACHES TO DEVELOP A BASIC BIOINFORMATICS TOOL.
  • MAXIMUM INTAKE CAPACITY: 25 Students per batch.
    INSTITUTIONAL REQUIREMENTS: ONE LECTURE THEATRE for 2 hours per day. (For 20 days)

    THE INSTITUTION CAN REQUEST THE WAIVER OF FEES FOR ONE NEEDY BUT MERITORIUS STUDENT