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Tailor-made bioinformatics training programs

We have been particularly leaders in training in NGS data analysis in India, and have conducted more than 15 hands-on training courses/workshops since 2009. Shodhaka has also conducted training for ICMR scientists across India twice. Our course participants have been very happy with the learning experience (see feedback from our participants).

Areas of training

Next generation sequencing (NGS) data analysis
Drug discovery, homology modeling and other structural analysis
Proteomics data analysis
Microarray & other gene expression data analysis
Databases & tools: selection & use in genomics, transcriptomics & proteomics
Biocuration, and basic data mining and analysis
Programming for life sciences
Biostatistical analysis

Course structures:

Shodhaka has carefully designed compact training sessions - with or without related background theory sessions. The programs are interactive, and include lectures and discussions. But the demonstrations and meticulously designed practice sessions (with case studies) make bulk of our workshops/courses.

Indicative CONTENTS of some of the hands on training program from Shodhaka:
Overview and introduction of microarray technology, EST, SAGE, MPSS.
NGS (RNA-seq) in transcriptomics, analysis & current trends in research.
Software (including 'R') & databases used for microarray- & NGS-based gene expression analysis.
Alternative splice-form, regulatory networks, TFBS & ChIP data analysis.
Single Nucleotide Polymorphism (SNP)
SNP analysis, current research trends.
Optimal use of SNP databases and interpretations.
Next Generation Sequencing (NGS) data analysis
Overview, de novo assembly & reference assembly.
RNA sequencing, ChIP data.
Metagenomics in various contexts.
SNP/indel analysis.
Repeat sequence analysis.
Protein-protein interactions (PPIs) and pathway analysis
Introduction to and current research on PPIs.
Apt use of PPI databases & interpretations.
Apt use of pathway databases & interpretations.
General network analysis.
Primer & probe designing
Principles and applications.
Case-specific resources (mutation analysis, cloning, microarray probes, junctional probes, etc).
DNA motif detection tools
Case-specific selection & use of tools.
Transcription factor databases & binding site analysis; regulatory networks.
Structural protein studies & drug/biosimilars
Drug designing.
Ligand docking.
Homology modeling.
Target identification, drug discovery process and related data analysis.
Basic and advanced data mining & biocuration
Fundamentals concepts, significance to biological experiments
Characteristics of common types biological data points
Commonly used tests in biological experiments
Commonly used computational methods in biostatistics, and data presentation
We have also been conducting two special programs regularly:
a) career planning workshop for students & fresh graduates/post-graduates and
b) biotechnology & bioinformatics in simple terms: a day program for experts from non-bio domains.

In addition, we are keen to conduct short courses in GMPs, GCPs, IPR, Tech. transfer, Pharmacovigilance & other industrially relevant courses.

Examples of the training programs:
  1. Two-day genomics workshop for students (Rajalakshmi Engg College, Chennai, 2016).
  2. One day training on NGS & SNP data analysis for ICMR scientists (NIN, Hyderabad, 2011).
  3. Four-day workshop on gene ontology, biocuration and advanced literature search for scientists from all over India (NIRRH, Mumbai, 2011).
  4. One to four weeks crash course for bio-students in use of databases and tools (genomics, transcriptomics & proteomics, including multiplatform analysis, de novo assembly and reference alignment, RNA seq, ChIP-seq, metagenomics, microarray, mass-spec, protein interactions etc.) (DY Patil College, Navi Mumbai, 2010; New Horizon College, Bengaluru, 2012).
  5. 10 days (crash course) workshop on major resources for genomics, transcriptomics & proteomics (contents as in the above-course, conducted every year for students, teachers, scientists and other professionals) (repeated almost every year from 2010 till 2018).
  6. 3 to 8 hours quick introduction to basic biotechnology and bioinformatics in simple terms for IT professionals (a multinational IT company, 2011).
  7. One day career planning workshop for life science students, including biotechnology (PES College, Bengaluru 2011).

Internship/ project/ summer training

************************************************************************** Applications are invited for internship/project work/summer training from biotechnology, bioinformatics and other life sciences students/freshers in the following areas:


  • Getting new insights into the molecular basis of cancer growth and identifying new biomarkers
  • NGS and/or microarray data analysis in the context of specific human and plant disorders
  • Comparative analysis of bioinformatic resources from a biologist's perspective


  • Development of software / databases for biological research
  • Programming in bioinformatics
  • Genomics, transcriptomics and proteomics
  • Drug designing and molecular structural biology
  • Biostatistics

C. Students interested in MARKETING and OTHER BUSINESS-RELATED experiences can also apply.

We NEVER CHARGE for project work/internship! Minimum charges apply for initial training only, as we find it essential for a meaningful completion of project work for most students, but we also waive training fees for talented ones. Students are encouraged to apply in group and get discount for training fees also (best student in the group may get a fee waiver for training also).

Shodhaka is on constant look out talented students and grow with them, and does not consider training as a means of generating profits. In fact, we have identified best performers in many batches and offered them jobs or helped them to find jobs, and - in some cases promoted their plans for higher studies. Our experts frequently provide counseling for higher studies, CSIR-NET & other competitive exams, finding jobs and planning career. Some of the interns have done a splendid work and are proud co-authors in our research papers published in peer-reviewed high-quality of journals. But only students serious about studies and project work should apply. Hard work and sincerity are a must during the training and project work!

Procedure to apply:

Email the following information:

Current course, semester, college/university, & department
Duration of the project
Expected start date (at least approximate week or month)
and attach your CV.
Email id: shodhaka.ls@gmail.com

Options and types:

Summer training in biotechnology or bioinformatics: duration will be 1 week to 30 days. Part of the training (in the areas listed above) will be for 5 to 15 days followed by assignment or project-based training on a specific aspect.

Summer project work in biotechnology or bioinformatics: duration will be 30 to 90 days. Initial part will consist of training (in the areas listed above) for 5 to 15 days. The candidate has to simultaneously read and begin taking a responsibility for a specific research project

Summer internship in biotechnology or bioinformatics: As above. The project work is same as internship.

Summer training/projects are designed for making a better use of vacation time by students.

Project work in biotechnology or bioinformatics: Expected duration is 4 to 12 months. Initial part will consist of training (in the areas listed above) for about 30 days. The candidate has to simultaneously read and begin taking a responsibility for a specific research project. Biotechnology projects will involve topics such as gene expression regulation mechanism but involve biological analysis of experimental data. This type of work is not bioinformatics. But it does not involve any wet-laboratory experiments also.

Internship in biotechnology or bioinformatics: As above. The project work is same as internship

These long term projects or internships are open to not only students, but also freshers who would like to use their time to learn more and gain experience. After all, not having a job to continue the growth doesn't mean the growth should stop! In fact, we have many such freshers who have grown with us by making a better use of time, and we even publish research papers with them.

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Personalized Online Training Programs
by the discoverers!

Get trained by scientists who are not only routinely involved in omics data analysis, but have also been systematically compiling and comparing bioinformatics databases, software and methods (e.g., J Biomed Inform. Jan 2020, Nature precedings 2011, BMC Genomics 2010, resources related to NGS, genomics, transcriptomics, proteomics and other data analysis: startbioinformatic.com).


(scroll down for contents, fees and duration;
you can also write to: shodhaka.ls@gmail.com)
Note: Our training modules do not involve simple lecture-videos or pre-set tutorials. All topics include carefully planned multiple one-to-one active and live sessions with experienced professionals. The sessions would focus on hands-on practice sessions using specific databases and software that suit each exercise, but would be preceded by theoretical discussions from research and analysis perspectives, and/or detailed demonstrations.

NGS & data analysis
Functional OMICS data analysis
Microarray & data analysis, including 'R'
Biostats and R
Drug designing
Bioinformatics for biotechnologists, microbiologists, etc (along with an overview of system biology, big data biology & synthetic biology)
Career planning

Details of some of the modules (can be custom-designed further):

An overview of NGS technology; Concepts, relevance and NGS applications to genomics & transcriptomics, metagenomics and other related omics; quality of sequencing data, depth and coverage of reads; NGS data retrieval using SRA & ENA; Quality analysis and trimming of raw reads; Reference alignment of NGS reads; NGS whole-genome & exome sequencing, and reference assembly; k-mer optimization; SNP analysis concepts & resources; Reference genomes retrieval using UCSC; filtering and annotation de novo assembly concepts and annotation process; de novo assembly of reads to contigs; RNA-sequencing and concepts; Identification of gene & transcript levels, and differential expression; system-level analysis and system biology approaches - concepts; an overview of functional analysis following transcriptomics and proteomics (see the module below for details); Metagenomics, the need & approach, and resources; Metagenomics analysis from NGS reads; OTU identification and analysis; network analysis and functional analysis of microbiomes.

Relevance of transcriptomics & proteomics: mass scale gene expression techniques and corresponding data; Protein-interaction retrieval and analysis; Analysis of non-coding RNAs; ontology and pathway analysis; Case studies on molecular interactions, Case studies on pathways; Gene Ontology information retrieval, gene enrichment and functional analysis using different resources such as DAVID; Regulatory network analysis; System biology approaches.

Microarray, ESTs & related Data Analysis:
Gene expression studies, microarray technology: an overview; Data files, and analysis workflow; Applications and resources; Data retrieval using GEO & ArrayExpress; Normalization and clustering principles; Differential expression analysis; Microarray data analysis using R package; Microarray resources, and data retrieval; Network analysis using 'R'; Case studies using microarray resources with BioGPS ; Microarray data analysis using online tools.

Bioinformatics exercises for molecular cloning: Selecting genes based on disease relevance or expression patterns; gene-, mRNA-, ncRNA- and protein- based data mining; Advanced strategies in literature-based data mining and biocuration; Case studies for selected genes, proteins and diseases; Retrieving and analyzing sequences of RNA or genes; Primer designing & restriction site analysis; Concepts in sequence analysis; Basic sequence analysis exercises; Advanced sequence analysis exercises.

IPR, GMP, GLP, Drug discovery, Clinical trials & GCPs:
Introduction to key concepts in each of these industrially relevant topics; definitions, types and significance of intellectual properties; differences in regulations across countries; prior art searching; claim drafting; stages of patent filing; GMP, GCP and GLP relevance in various sectors; regulatory aspects of GMPs and GCPs, and differences across countries; SOPs; case studies; quality checks - internal and external; regulatory bodies in different countries; Drug discovery, drug designing and pharma industry, and relevance of clinical studies and basic research; Homology modeling; Molecular docking process; Small molecule databases and cheminformatics.

Biostats & 'R':
Basic principles in statistics and relevance to biological research; variable types with examples in life sciences; sampling patterns; study designs; Parametric and non-parametric tests with biological case studies; central tendencies and distribution patterns; case studies in t-test, ANOA, non-parametric equivalents, chi-square test, correlation coefficient, tabulations and graphical representations with illustrations from biological research; case studies with gene expression profiling data and 'R' applications; common tests in omics and case studies in 'R'.

Total duration:
Contact sessions (skype or google hangout can be used for online classes): Multiple short sessions (each may vary between 20 to 60 minutes, depending on what you already know); the duration and number of sessions shall be decided based on a basic simple assessment in the beginning.

Amount per contact session will be decided after initial discussions depending on the topic as well as prior knowledge and expertise of the trainee.

Write to: shodhaka.ls@gmail.com Phone: +91- 98 440 271 25