Bioinformatics Summer Training

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.

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 K-Nearest Neighbors (kNN) Random Forest Support Vector Machines (SVM)	ACD/ChemSketch, ACD/3D Viewer, Biomer, MOLEKEL, The Molecular Modelling Toolkit etc.,
Quantum Mechanical Model	Linear Scaling Methods QM/MM (Quantum Mechanics /Molecular Mechanics) QM Simulation Protonation States Cation-π and π-π interactions Using QM to calculate molecular properties QM derived FFs (Force Fields) QM Derived Partial Charges QM Descriptors in QSAR/QSPR (Quantitative Structure Property Relationship) Molecular Quantum similarity measures Variation particle number approach for molecular design	AlgoGen, ProToss, Epik etc.,
Topological Method	The Wiener Index The Platt and Gordon-Scantlebury Indices The Hosoya Index The Zagreb Indices The Balaban J Index Information Content Indices Autocorrelation Descriptors WHIM Descriptors Topochemical Atom Indices The Centric Index Triplet Indices The Randić Index Molecular Connectivity Indices Kappa Indices Flexibility Indices The Variable Connectivity Index Topological Descriptors in Inverse QSAR Electrotopological State Indices Biodescriptors 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