IITM-EBI modelling workshop


 Monday 2 Thursday 5 December 2019


Indian Institute of Technology Madras - IIT P.O.Chennai,  Tamil Nadu,  600 036, India

Application opens: 

Wednesday 25 September 2019

Application deadline: 

Thursday 07 November 2019


Open application with selection


IBSE Workshop Team

Registration fee: 

Student/Postdoc ₹2,500 / Faculty ₹5,000 / Industry ₹10,000

Registration closed

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Course Overview

Computer models are increasingly used by researchers as well as the pharmaceutical industry to investigate disease initiation, progression and therapy. Modelling of biochemical pathways deregulated in disease condition offers mechanistic insights into the pathology; helps to elucidate mechanisms behind dug action and predict dose required for treatment and thereby greatly facilitates fundamental research and drug discovery. Such modelling requires a background in both molecular biology and mathematics. 

The four days workshop will train researchers from life science and mathematics to communicate and work together to learn to build and analyse computer models using user-friendly open-source software. The workshop will be jointly organised by EBI and Indian Institute of Technology Madras (IITM; https://www.iitm.ac.in/), more specifically, BioModels team from EBI along with  Initiative for Biological Systems Engineering (IBSE; https://ibse.iitm.ac.in/) and Robert Bosch Centre for Data Sciences and Artificial Intelligence (RBC-DSAI; https://rbcdsai.iitm.ac.in/) from IITM. This national-level workshop will be organised locally at IITM. Various modelling approaches and tools will be introduced to the participants. They will explore a few of the disease-specific computer models from a recent publication, freely available in BioModels repository (//www.ebi.ac.uk/biomodels/).

Other EBI resources including Reactome, IntAct, OmicsDI, PRIDE, ExpressionAtlas will be introduced to the participants  BioModels team will lead the training on kinetic modelling of signalling pathways, curation and annotation of mathematical models as well as standards in modelling (SBML, SED-ML, etc). IITM/IBSE team will partner in the training on kinetic modelling approaches, and also introduce other paradigms such as constraint-based modelling (e.g. Flux Balance Analysis (FBA)) for the analysis of metabolic pathways.   

An essential agenda in the meeting will be group projects where participants from both experimental and theoretical background would work to getter to curate mathematical models and submit them to the BioModels repository. This workshop will allow EBI to partner with IITM to share expertise on kinetic modelling and gain expertise on the curation of non-kinetic models in BioModels repository. Furthermore, this join workshop would be used as an opportunity for long term partnership with IITM to establish training for EBI resources in India, explore the possibility of joint data curation engagement and scientific collaboration.


Participants from both experimental and theoretical backgrounds would benefit from this workshop.

Learning outcomes



Day one: Monday 2 December 2019

08.30-09.30 Registration
09.30-10.00 Inauguration
10.00-11.00 Opening Keynote: “Insights into human metabolism from kinetic modelling”
Dr. K. V. Venkatesh, IIT Bombay
11.00-11:30 Tea
11.30-13.00 Workshop Lecture 1: Introduction to Kinetic Modelling
Dr. Karthik Raman, IIT Madras
13-14.30 Lunch
14.30-15.30 Workshop Lecture 2: Data and Resources for Modelling
Dr. Henning Hermjakob, EBI
15.30-16.00 Tea
16.00-17.30 Hands-on 1: Model curation
Dr. Rahuman Sheriff, EBI
17.30-18.30 Posters
19.00 Dinner

Day two: Tuesday 3 December 2019

09.30-10.00 The QSP Approach in Pharma R&D: Quantitative Integrative Approaches Mitigate Risk in Drug Development
Dr. Rukmini Kumar, Vantage Research, Chennai



Workshop Lecture 3: Parameter Estimation
Dr. Nirav Bhatt, IIT Madras

12.30-14.00 Lunch
14.00-15.30 Workshop Lecture 4: Modelling Databases and Standards
Dr. Rahuman Sheriff, EBI
15.30-16.00 Tea
16.00-17.30 Hands-on 2: Model Annotation with COPASI
Dr. Rahuman Sheriff, EBI
17.30-18.00 Introduction to Group Projects
18.00-19.00 Posters
19.00 Dinner

Day three: Wednesday 4 December 2019


Introduction to Constraint-based Modelling
Dr. Karthik Raman, IIT Madras

11.00-11:30 Tea
11.30-13.00 Projects
13.00-14.30 Lunch
14.30-15.30 Poster Flash Talks
15.30-19.00 Projects
19.00 Dinner

Day four: Thursday 5 December 2019

09.30-11.00 Projects




13.00-14.00 Lunch
14.00-15.30 Project presentations
15.30-16.00 Tea
16.00-17.00 Project presentations
17.00-18.00 Closing keynote: “Towards a functional cure of HIV infection”
Dr. Narendra Dixit, IISc Bengaluru
18.00-18.30 Awards and valedictory
19.00 Dinner