Computational Systems Biology

By Prof. Karthik Raman   |   IIT Madras
Learners enrolled: 978
Every living cell is the result beautifully concerted interplay of metabolic, signalling and regulatory networks. Systems biology has heralded a systematic quantitative approach to study these complex networks, to understand, predict and manipulate biological systems. Systems biology has had a positive impact on metabolic engineering as well as the pharmaceutical industry. This course seeks to introduce key concepts of mathematical modelling, in the context of different types biological networks. The course will cover important concepts from network biology, modelling of dynamic systems and parameter estimation, as well as constraint-based metabolic modelling. Finally, we will also touch upon some of the cutting-edge topics in the field. The course has a significant hands-on component, emphasizing various software tools and computational methods for systems biology.

INTENDED AUDIENCE : Interested learners
PREREQUISITES : Basic knowledge of a high-level programming language (preferably MATLAB)
INDUSTRY SUPPORT : Bioprocess industries / Computational Biology Companies, e.g. MedGenome, Vantage Research
Course Status : Completed
Course Type : Elective
Duration : 12 weeks
Category :
  • Biological Sciences & Bioengineering
Credit Points : 3
Level : Undergraduate/Postgraduate
Start Date : 27 Jan 2020
End Date : 17 Apr 2020
Enrollment Ends : 03 Feb 2020
Exam Date : 25 Apr 2020 IST

Note: This exam date is subjected to change based on seat availability. You can check final exam date on your hall ticket.

Page Visits

Course layout

Week 1  :  Introduction to Mathematical Modelling
Week 2  :  Introduction to Static Networks 
Week 3  :  Network Biology and Applications
Week 4  :  Reconstruction of Biological Networks
Week 5  :  Dynamic Modelling of Biological Systems: Introduction, Solving ODEs & Parameter Estimation
Week 6  :  Evolutionary Algorithms, Guest Lectures on Modelling in Drug Development
Week 7  :  Constraint-based approaches to Modelling Metabolic Networks 
Week 8  :  Perturbations to Metabolic Networks
Week 9  :  Elementary Modes, Applications of Constraint-based Modelling
Week 10:  Constraint-based Modelling Recap, 13C Metabolic Flux Analysis
Week 11:  Modelling Regulation, Host-pathogen interactions, Robustness of Biological Systems
Week 12:  Advanced topics: Robustness and Evolvability, Introduction to Synthetic Biology, Perspectives & Challenges

Thanks to the support from MathWorks, enrolled students have access to MATLAB for the duration of the course.

Books and references

  • Voit E (2012) A First Course in Systems Biology. Garland Science, 1/e. ISBN 0815344678
  • Klipp E (2009) Systems biology: a textbook. Wiley-VCH, 1/e. ISBN 9783527318742
  • Newman MEJ (2011) Networks: an introduction. Oxford Univ. Press. ISBN 9780199206650

Instructor bio

Prof. Karthik Raman

IIT Madras
Dr. Karthik Raman is an Associate Professor at the Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras. Karthik’s research group at IIT Madras works on the development of algorithms and computational tools to understand, predict and manipulate complex biological networks. The key areas of research in his group encompass in silico metabolic engineering, biological networks and biological data analysis. Karthik also co-ordinates the Initiative for Biological Systems Engineering at IIT Madras and is a core member of the Robert Bosch Centre for Data Science and Artificial Intelligence (RBC-DSAI).

Course certificate

• The course is free to enroll and learn from. But if you want a certificate, you have to register and write the proctored exam conducted by us in person at any of the designated exam centres.
• The exam is optional for a fee of Rs 1000/- (Rupees one thousand only).
• Date and Time of Exams: 25th April 2020, Morning session 9am to 12 noon; Afternoon Session 2pm to 5pm.
• Registration url: Announcements will be made when the registration form is open for registrations.
• The online registration form has to be filled and the certification exam fee needs to be paid. More details will be made available when the exam registration form is published. If there are any changes, it will be mentioned then.
• Please check the form for more details on the cities where the exams will be held, the conditions you agree to when you fill the form etc.

• Average assignment score = 25% of average of best 8 assignments out of the total 12 assignments
 given in the course. 
• Exam score = 75% of the proctored certification exam score out of 100
• Final score = Average assignment score + Exam score

• If one of the 2 criteria is not met, you will not get the certificate even if the Final score >= 40/100.
• Certificate will have your name, photograph and the score in the final exam with the breakup.It will have the logos of NPTEL and IIT Madras. It will be e-verifiable at nptel.ac.in/noc.
• Only the e-certificate will be made available. Hard copies will not be dispatched.

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