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Introduction to Dynamical Models in Biology

By Prof. Biplab Bose   |   IIT Guwahati
Learners enrolled: 638
ABOUT THE COURSE:
Mathematical modeling has become an integral part of different fields of biology, from ecology to cell biology. This course will introduce students of biology to elementary mathematical concepts and tools for dynamical models. The course will focus on modeling using ordinary differential equations (ODEs). We will start with basic mathematical concepts of ODE-based models and then connect those with experimental biology. Mathematical models will be on cellular and molecular processes in biology, like cell signaling, and transcriptional networks. Students will learn basics of analytical techniques, graphical techniques, and numerical simulation.


INTENDED AUDIENCE : Students of Biotechnology, Biology, Mathematical Biology, and allied subjects.

PREREQUISITES : Must have studied Mathematics at 10+2 level. Have studied graduate-level Biochemistry and Molecular Biology. Knowledge of Computer Programming will be helpful but not a necessity. 

INDUSTRY SUPPORT : Bio-pharma industries use cellular level as well organism level mathematical models. This course would help to initiate biologists to such modeling.
Summary
Course Status : Completed
Course Type : Elective
Language for course content : English
Duration : 4 weeks
Category :
  • Biological Sciences & Bioengineering
  • Computational Biology
Credit Points : 1
Level : Undergraduate/Postgraduate
Start Date : 22 Aug 2022
End Date : 16 Sep 2022
Enrollment Ends : 22 Aug 2022
Exam Date : 30 Oct 2022 IST

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

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Course layout

Week 1 :
  1. L1: Introduction to mathematical modeling in biology
  2. L2: How to start modeling?
  3. L3: Basic concepts of modeling using ODEs: Modeling the spread of infectious disease
  4. L4: Basic concepts of modeling using ODEs: Modeling population growth
  5. L5: Numerical solution of ODE-based models - I
  6. L6: Numerical solution of ODE-based models - II
Week 2 :
  1. L1: Simulating ODE-based models: Introduction to JSim
  2. L2: Simulating ODE-based models: Examples of simulation in JSim
  3. L3: Steady state and stability analysis: Understanding steady state
  4. L4: Steady state and stability analysis: Stability of steady states
  5. L5: Phase plane analysis - I
  6. L6: Phase plane analysis - II
Week 3 :
  1. L1: Concepts of bifurcation
  2. L2: Bifurcation in Biological systems
  3. L3: Modeling molecular processes in cell
  4. L4: Modeling molecular processes-I: Ligand-receptor binding
  5. L5: Modeling molecular processes-II: Enzymatic reaction
  6. L6: Modeling molecular processes-III: Transcription and translation
Week 4 :
  1. L1: Modeling a signal transduction circuit: Negative feedback
  2. L2: Modeling a signal transduction circuit: Positive feedback
  3. L3: Modeling a signal transduction circuit: Incoherent feedforward
  4. L4: Modeling transcriptional circuits – I
  5. L5: Modeling transcriptional circuits - II
  6. L6: Online resources for mathematical modeling in biology

Books and references

  1. Mathematical Modeling in Systems Biology: An Introduction, Brian P. Ingalls, MIT Press, 2013
  2. Modeling the Dynamics of Life: Calculus and Probability for Life Scientists, Frederick R. Adler, Brooks/Cole, 2012
  3. Biocalculus: Calculus for Life Sciences, James Stewart, Troy Day, Cengage Learning, 2015

Instructor bio

Prof. Biplab Bose

IIT Guwahati
Dr. Biplab Bose is an Associate Professor in the Department of Biosciences and Bioengineering at IIT Guwahati. Over the years, he has developed and taught courses on Systems Biology, Computational Biology, and Data Analysis. He uses Dynamical Systems and Statistical Physics to understand emergent and dynamical phenomena in Biology – particularly cell signaling, cell-cell interaction, and information processing in a cell.

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: 30 October 2022 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.

CRITERIA TO GET A CERTIFICATE

Average assignment score = 25% of average of best 3 assignments out of the total 4 assignments given in the course.
Exam score = 75% of the proctored certification exam score out of 100

Final score = Average assignment score + Exam score

YOU WILL BE ELIGIBLE FOR A CERTIFICATE ONLY IF AVERAGE ASSIGNMENT SCORE >=10/25 AND EXAM SCORE >= 30/75. 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 Guwahati .It will be e-verifiable at nptel.ac.in/noc.

Only the e-certificate will be made available. Hard copies will not be dispatched.

Once again, thanks for your interest in our online courses and certification. Happy learning.

- NPTEL team


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