Pre-Symposium Workshop – National Symposium on Recent Trends in Omics in Plant Biology (20 May 2025)
As part of the National Symposium on Recent Trends in Omics in Plant Biology, ICAR–Indian Institute of Spices Research, Kozhikode, organized a full-day Pre-Symposium Workshop on 20 May 2025, featuring four specialized hands-on training sessions conducted in two parallel tracks. The workshop was designed to provide researchers, students, and scientists with focused training on cutting-edge computational methods in modern plant biology.
Parallel Session I included a forenoon session on Computational Metagenomics, handled by Dr. Ratna Prabha (ICAR–Indian Agricultural Research Institute), offering participants practical exposure to metagenomic data processing, taxonomic profiling, and functional annotation. In the afternoon, Dr. Sajitha S Lulu (Vellore Institute of Technology) conducted an intensive session on Machine Learning in Plant Genomics, introducing participants to ML workflows, predictive modeling, and applications in genomic data analysis.
Parallel Session II began with a session on Genome Wide Association Studies (GWAS) led by Dr. P. Supriya (ICAR–National Academy of Agricultural Research Management), where participants learned GWAS concepts, statistical models, and interpretation of association signals. The final workshop session, Transcriptomics: From Reads to Pathways, was delivered by Dr. Sarika Sahu (ICAR–Indian Agricultural Statistics Research Institute), focusing on RNA-seq analysis pipelines, differential expression, and pathway-level interpretation.
The Pre-Symposium Workshop offered participants a unique opportunity to receive expert-driven training across multiple domains of computational plant biology, setting the stage for the scientific sessions of the symposium.
From Bench to Bytes – An Interactive Workshop in Bioinformatics (15–21 May 2024)
The workshop “From Bench to Bytes”, held from 15–21 May 2024 provided an intensive, hands-on introduction to essential and emerging areas of bioinformatics. The programme opened with a welcome address by Dr. T. E. Sheeja, Head, Crop Improvement and Biotechnology Division, followed by an overview of the workshop by Dr. Sona Charles, Scientist (Agricultural Bioinformatics), and introductory remarks by Dr. K. Kandiannan, HRD Nodal Officer, ICAR-IISR.
Across the week, participants were trained through a series of interactive sessions led by experts from ICAR-IISR and collaborating institutions. Dr. Sona Charles handled major modules including Introduction to Bioinformatics, Introduction to R, Biological Databases, and Data Visualization using R, offering both conceptual grounding and hands-on practice. Dr. Mukesh Sankar S contributed to training in Next-Generation Sequencing and guided practical sessions in R programming. Ms. Ayisha Jabbar and Mr. Akash A supported participants in system setup and basic command-line operations.
Advanced topics were delivered by invited scientists: Dr. Merlin Lopez covered Linux, Metagenomics, and Biodiversity Informatics, while Dr. Vimala Mathew (NIELIT, Calicut) introduced participants to Machine Learning and Generative AI, highlighting their growing role in biological data interpretation.
The workshop offered a comprehensive blend of lectures, demonstrations, and practical exercises, enabling participants to gain confidence in handling biological datasets, performing exploratory analyses, and understanding computational workflows. The event concluded with participant feedback, evaluations, and a valedictory session presided over by Dr. R. Dinesh, Director, ICAR-IISR, followed by the distribution of certificates.
R for Bioinformatics (4–8 November 2024)
An intensive five-day online workshop titled “R for Bioinformatics” was conducted by the Bioinformatics and Integrative Genomics Facility, ICAR–Indian Institute of Spices Research, from 4–8 November 2024. The program brought together 60 participants from various prestigious institutions across India, including scientists, research scholars, and postgraduate students.
The workshop began with a welcome address by Dr. T.E. Sheeja, Head, Division of Crop Improvement & Biotechnology. Dr. Sona Charles, Scientist (Bioinformatics), introduced the course and led the pre-workshop evaluation.
Over the five days, participants were trained through a combination of lectures and hands-on practical sessions covering fundamental and advanced concepts in R. Dr. Sona Charles handled sessions on Introduction to R, basic concepts, sequence analysis, data visualization, and differential expression analysis. Ms. Shahana Arif led practical sessions on Data Wrangling and Differential Gene Expression analysis. Dr. J. Sreekumar (ICAR-CTCRI) delivered sessions on basic statistics using R, while Dr. Merlin Lopez (IIT Palakkad) taught Biodiversity Informatics. A special lecture on data visualization using R was conducted by Dr. Ravindra Kumar (NIT Calicut). Dr. Mukesh Sankar S also engaged participants through a dedicated module on R for plant breeding applications.
The workshop concluded with participant feedback, post-workshop evaluation, and closing remarks delivered by Dr. D. Prasath, Project Coordinator, AICRP (Spices), followed by a vote of thanks from Dr. Mukesh Sankar S. The interactive nature of the sessions, combined with expert-led training, ensured that participants gained a strong foundation in applying R for biological data analysis.
Biological Data Exploration and Visualization using R (6–8 Nov 2023)
A three-day online hands-on workshop titled “Biological Data Exploration and Visualization using R” was organized by the Bioinformatics and Integrative Genomics Facility, ICAR–Indian Institute of Spices Research, Kozhikode from 6–8 November 2023. The workshop was inaugurated with a welcome address and introductory remarks by Dr. T. E. Sheeja, Head, Crop Improvement and Biotechnology Division, ICAR–IISR. The course overview was presented by Dr. Sona Charles, Scientist (Bioinformatics), ICAR–IISR.
The technical sessions included lectures and practical demonstrations on key topics such as Introduction to R, Basic Statistics, Statistics using R, Data Visualization, dplyr package, and Bioinformatics-oriented data visualization workflows. Sessions were handled by Dr. Sona Charles (ICAR–IISR), Dr. Sreekumar J, Head, Section of Social Sciences and Extension (ICAR–CTCRI), and Dr. Manimaran B, Scientist (Nematology), Division of Crop Protection (ICAR–IISR).
The workshop attracted 53 participants, including scientists, research scholars, postgraduate students, and project fellows from diverse academic and research institutions. Through interactive lectures and live coding sessions, participants gained practical skills in handling biological datasets, performing statistical analyses, and generating high-quality visualizations using R.
Life Science meets Programming. (13-15 September)
A three days hands-on workshop was organised by the Bioinformatics Centre, ICAR- Indian Institute of Spices Research, Kozhikode from 13-15 September 2022 for Research Scholars, Scientists and Assistant Professors. The inaugural talk was delivered by Dr. Santhosh J Eapen, former Director, ICAR-IISR. The sessions were handled by Ms. Sona Charles, Mr. MukeshSankar S and Mr. Jayarajan from ICAR-IISR, Dr. Prashanth N Suravajhala from Amrita Vishwa Vidyapeetham, Mr.Subeesh A from ICAR - Central Institute of Agricultural Engineering, Bhopal and Dr. Merlin Lopez from MS Swaminathan Research Foundation. The workshop included theory as well as hands-on sessions on basic Bioinformatics, introduction to R, Python, Linux and Galaxy. 15 participants were selected from over 200 applicants for the workshop from various ICAR institutes, Universities and colleges. The questions from the participants were answered during the discussion.
R for Biologists. (6-8 October)
A three days hands-on workshop was organised by the Bioinformatics Centre, ICAR- Indian Institute of Spices Research, Kozhikode from 6-8 October, 2021 for PG students, Research Scholars and Project Fellows / JRFs. The sessions we handled by Ms. Sona Charles, Dr. Divya P Syamaladevi, Dr. Santhosh J Eapen from ICAR-IISR and Dr. Sreekumar J from ICAR-CTCRI, Thiruvananthapuram. The workshop included theory as well as hands-on sessions on basic Bioinformatics, introduction to R, statistics using R and data visualization using R packages. 48 participants were selected from over 150 applicants for the workshop from various ICAR/ SAUs and colleges. The questions from the participants were answered during the discussion.
Short-term training / workshops
NGSDAT 2019 - DBT Funded training on Bioinformatics for metagenome data analysis
19 Mar 2019 - 22 Mar 2019, 19 participants
Workshop in Basic Bioinformatics
20 Mar 2018 - 21 Mar 2018, 40 participants
Training on Bioinformatics for Transcriptome Sequencing (NGSDAT 2017)
20 Mar 2017 - 25 Mar 2017, 14 participants
Training on Bioinformatics for Whole Genome Sequencing (NGSDAT 2016)
27 Jan 2016 - 30 Jan 2016, 16 participants
Training on NGS: Data Analysis & Annotation
17 Mar 2014 - 20 Mar 2014, 15 participants
Training on NGS: Data Analysis & Annotation
12 Mar 2013 - 16 Mar 2013, 14 participants
Training on Cheminformatics- Tools & Applications
19 Feb 2013 - 22 Feb 2013, 14 participants
Training on Whole genome sequencing and annotation
21 Feb 2012 - 25 Feb 2012, 14 participants
Testimonials
“The workshop was excellent and well organized. The lectures and hands-on were very useful in learning and using programming tools like R, Linux, Python. Overall it is a good start for me for using programming tools in genomics. Introduction to Galaxy is very useful. I have some transcriptome data and I hope I may be able to do some analysis. This workshop has certainly given confidence in data handling. I thank ICAR-IISR and the organisers, especially Dr. Sona Charles for conducting this workshop in a fruitful manner. I look forward for future help from the Bioinformatics team of IISR. Thanks.”
- Shahnawaz Ali, Sr. Scientist, ICAR-DCR
“I just had the basics with me before attending, but the 3 day workshop helped me to use those basics to have good analysis and visualization .Thank you for organizing such a beautiful virtual session. Thank you”
-Neha Rose Pious, Junior Bioinformatics Scientist, Anderson Diagnostic Services Private Limited
“I heard about R programming before, but never tried to explore as I wasn't knowing the basics. The workshop helped and inspired me immense to learn, practice and explore more on R programming.”
- Aswathi M K (St. Joseph's College, Lecturer, Devagiri)
“Being a plant breeder, biplot techniques would be helpful in analysing multi-environmental data. The training also has given a confidence to explore R in different dimensions for statistical analysis. This would be helpful in representing the data in the form of graphs in our future publications”.
- Ameena Premnath., PhD, TNAU
Contact Us
Dr. Sona Charles, MSc, ARS Coordinator
Bioinformatics Centre
ICAR-Indian Institute of Spices ResearchP.B. No. 1701, Marikunnu Post, Kozhikode - 673 012, Kerala, India
Phone : (+91) 495 2731410 Extn. 202
sona.charles@icar.gov.in
