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Bioinformatics Summer Training

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NTHRYS provides Bioinformatics Summer Training for interested candidates at its Hyderabad facility, Telangana. Please refer below for more details including Fee strctures, Eligibility, Protocols and Modules etc.,. Please do call / message / whatsapp for more details on 9014935156 [India - +91]

Eligibility: BSc / BTech / MSc / MTech / MPhil / PhD in any Life Sciences studying or completed students

Protocols / Techniques Covered

    In the present scenario as the demand for accurate, faster and qualitative research increased, this led to the advent of bioinformatics. Bioinformatics as a tool where errors made can be corrected to open newer approaches in R&D fields. With the advent of Bioinformatics we can develope and carry out research in various areas like nanotechnology, biochemistry, crop research, environmental biotechnology. The basic information of biology one can gains through training in bioinformatics is now a pre-requisite for any life sciences graduate.The recent rise in organism specific genome projects coming up from scientist desks, bioinformatics becomes the foundation to start these projects. It helps to develope research, start new research, maintain and organize the data and decode the results. On a global perspective in order to receive faster results bioinformatics is a necessary tool to embark on a career in life sciences division is bioinformatics.
    Bioinformatics Training Program at NTHRYS is provided under three different modules:

  1. Basic Bioinforrmatics Training Module

    Module I

    Theory

    Practical

    Tools

    History

    Biological Databases

    NCBI,MMDB,EMBL,DDBJ,SwissProt

    Origin

    Structure DB

    PDB,CATH,SCOP,InterproScan,Signal Scan

    Scope of Bioinformatics

    Importance of Tools

    N/A

    Origin of Tools

    Sequence DB’s

    Scan,Prosite,Prodom, MotifScan,PFam

    Sequence File Formats

    Types

    Genebank file format,FASTA format,EMBL format,UniprotKB/Swiss-Prot format, PIR/NBRF format

    Module II

    Application of Bioinformatics

    Gene Prediction & Functional Analysis

    ORF finder, GeneScan,GeneMark,Webgene

    Sequence Comparison

    EXPASy, EMBOSS

    BLAST,Clustalw,DIALIGN

    Structure File Formats

    Repeat detection

    Repeat Masker, dnadot

    General Introduction to Molecular Biology

    Hydrophobicity

    Protparam

    Restriction Site Mapping

    Restriction site Detection

    Webcutter,NEBCutter

    Visualiztion  Software

    System Biology Vs /w

    RasMol,SPDBV,JMol,Cn3D

    Phylogenetic Analysis

    Evolutionary Relationship

    Phylogeny,HHperd, Biology workbench

    Bioinformatics Dogma

    Thermodynamics

    ProTherm

    Minor Project Concerning the concepts learnt

  2. Advanced Bioinformatics Training Module

    Theory

    Practical

    Tools

    Module III

    Statistical significance of Alignments

    RNA sequence Analysis

    Expasy

    Sequence Databases for similar sequences

    RNA fold Recognition

    MFOLD,PFOLD

    RNA sequence analysis

    Secondary Structure Prediction

    GOR4, ChouFasman, Predator, Phobious, HMMTOP

    RNA structure Prediction

    Abinitio Structure Prediction

    QUARK,Bhageerath

    Submitting Sequence

    To NCBI

    N/A

    Scoring Types

    PAM,BLOSUM

    N/A

    Types of Alignment

    Global & Local

    Grapics Sequences Pairwise BLAST & EMBOSS Aligns

    Module IV

    Molecular Phylogeny Prediction

    Molecular evolutionary genetic Analysis

    MEGA5,PHYLIP

    EST and Gene Discovery

     

    dbEST

    Genome Analysis

     

    Genid,FGNEGH,GLIMMER,GRAIL

    Comparative modeling

    Homology Modeling

    MODELER, Swiss Model

    Fold recognition

    Threading

    RAPTOR,3DPSSM,HHPRED

    Model Evaluation

    Structure Refinement

    WHATCHECK,SAVES Server

    Structure Validation

    RMSD plot

    CASP Server

    Module V

    Molecular Dynamics

    Molecular Simulation

    GROMACS,HOOMD blue,PYMOL

    Molecular Modeling

     

    CHARM-GUI,Amber

    Primer Desinging

    Three Primer designing tools along with concepts of behind tools

    FastPCR,PRIMER3,Gene Fisher

    Concepts of Biostatistics,biophysicsand biochemistry to help in dealing with databases/tools

    Various tools  used to useges, of subject with bioinformatics

    Risk assessment tools,KinCohort software MultAssoc,Genetic Pathway analysis software

    Minor project work in desired topic

    Major project in desired topic

    Note: Major project as well as Minor project can also done by the student after selected time and respective certification can be issued on the respective date. For example if a MSc first year student joins in this training module he/she can complete the training module and take Training and take training certificate at the time and later come back after few months continue doing the minor project and then collect the certificate and come later at the time of final year academic project time and do the major project and collect the certificate for the same in respective dates and make use of the three certifications for a single fee structure.
    This module was designed after considering the advices given by the Bioinformatics Head of the departments of many reputed universities.

  3. Pofessional Bioinformatics Training Module

    Theory Practicals Tools Used

    Module VI

    Reconstruction Of Metabolic Pathway

    Various pathway construction tools including KEGG

    Pathway Databases

    KEGG [all databases ]

    Monte Carlo Simulation

    Molecular dynamics tools

    Docking of Small Molecules

    Docking Software

    GOLD, HYPERCHEM, AutoDOCK, Hex, Argus Lab

    Module VII

    Energy minimization

    QSAR Studies

    Build QSAR

    Geometry Optimization

    Descriptor Database

    E-Dragon

    Force Fields

    Primer Designing

    Primer3, FastPCR

    Descriptors

    BioPERL

    BioPERL / PERL programming

    Antibody engineering

    Designing and modeling antibodies

    HTML concepts

    HTML

    Concepts on designing a bioinformatics database

    Concepts on various biotechnology aspects

    Major project work in any one of the fields present in NTHRYS Bioinformatics Projects section.

  4. Expertise Training Module on QSAR

    Module VIII
    Topic Practical Approaches Software / Tools
    Free Energy Relationships Hansch method : Linear Free Energy Relationships (physicochemical properties) QSAR-PC: PAR
    Martin & Kubinyi : Non Linear Free Energy Relationships (physicochemical properties)
    Free Wilson mathematical model (structural elements)
    Molecular Modeling Curation KNIME
    Molecular Descriptors (0D, 1D, 2D, 3D, 4D, 5D, 6D) Chemistry Development Kit, PADel, RDKit, MOE, PubChem, Chemotypes
    Modeling Methods
    1. K-Nearest Neighbors (kNN)
    2. Random Forest
    3. Support Vector Machines (SVM)
    ACD/ChemSketch, ACD/3D Viewer, Biomer, MOLEKEL, The Molecular Modelling Toolkit etc.,
    Quantum Mechanical Model
    1. Linear Scaling Methods
    2. QM/MM (Quantum Mechanics /Molecular Mechanics)
    3. QM Simulation
    4. Protonation States
    5. Cation-π and π-π interactions
    6. Using QM to calculate molecular properties
      1. QM derived FFs (Force Fields)
      2. QM Derived Partial Charges
      3. QM Descriptors in QSAR/QSPR (Quantitative Structure Property Relationship)
      4. Molecular Quantum similarity measures
      5. Variation particle number approach for molecular design
    AlgoGen, ProToss, Epik etc.,
    Topological Method
    1. The Wiener Index
    2. The Platt and Gordon-Scantlebury Indices
    3. The Hosoya Index
    4. The Zagreb Indices
    5. The Balaban J Index
    6. Information Content Indices
    7. Autocorrelation Descriptors
    8. WHIM Descriptors
    9. Topochemical Atom Indices
    10. The Centric Index
    11. Triplet Indices
    12. The Randić Index
    13. Molecular Connectivity Indices
    14. Kappa Indices
    15. Flexibility Indices
    16. The Variable Connectivity Index
    17. Topological Descriptors in Inverse QSAR
    18. Electrotopological State Indices
    19. Biodescriptors
    20. Chirality
    ADAPT, CODESSA, MathChem, MDL QSAR, TOPIX, etc.,
    Pattern Recognization    

    Fee for Module VIII

    Module VIII (Online Mode Only) - $1500 for 1 Month Duration (Training + 1 Minor Project) , $3000 for 3 Months Duration (Training + 1 Major Project + Publication Assistance as Co author Only), $2000 additional for First Authorship Publication Project Assistance along with training.

Fee Structures for Bioinformatics Summer Training

Fee details in Rs per student
Fee 5 Days 10 Days 20 days 1 Month 45 Days
Individual 11900 12500 15800 19600 23200
Group 2 - 4 11400 11400 15100 18700 22100
Group 5 - 7 11200 11200 14900 18500 21900
Group 8 - 10 11100 11100 14800 18300 21700


Note: NTHRYS currently operates through three registered entities: NTHRYS BIOTECH LABS (NBL), NTHRYS OPC PVT LTD (NOPC), and NTHRYS Project Greenshield (NPGS).

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