Dynamical Modeling Methods for Systems Biology

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About this course: An introduction to dynamical modeling techniques used in contemporary Systems Biology research. We take a case-based approach to teach contemporary mathematical modeling techniques. The course is appropriate for advanced undergraduates and beginning graduate students. Lectures provide biological background and describe the development of both classical mathematical models and more recent representations of biological processes. The course will be useful for students who plan to use experimental techniques as their approach in the laboratory and employ computational modeling as a tool to draw deeper understanding of experiments. The course should also be valuable as an…

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When you enroll for courses through Coursera you get to choose for a paid plan or for a free plan

  • Free plan: No certicification and/or audit only. You will have access to all course materials except graded items.
  • Paid plan: Commit to earning a Certificate—it's a trusted, shareable way to showcase your new skills.

About this course: An introduction to dynamical modeling techniques used in contemporary Systems Biology research. We take a case-based approach to teach contemporary mathematical modeling techniques. The course is appropriate for advanced undergraduates and beginning graduate students. Lectures provide biological background and describe the development of both classical mathematical models and more recent representations of biological processes. The course will be useful for students who plan to use experimental techniques as their approach in the laboratory and employ computational modeling as a tool to draw deeper understanding of experiments. The course should also be valuable as an introductory overview for students planning to conduct original research in modeling biological systems. This course focuses on dynamical modeling techniques used in Systems Biology research. These techniques are based on biological mechanisms, and simulations with these models generate predictions that can subsequently be tested experimentally. These testable predictions frequently provide novel insight into biological processes. The approaches taught here can be grouped into the following categories: 1) ordinary differential equation-based models, 2) partial differential equation-based models, and 3) stochastic models.

Created by:  Icahn School of Medicine at Mount Sinai
  • Taught by:  Eric Sobie, PhD, Associate Professor

    Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY)
Basic Info Course 4 of 6 in the Systems Biology and Biotechnology Specialization Commitment 8-10 hours/week Language English How To Pass Pass all graded assignments to complete the course. User Ratings 4.8 stars Average User Rating 4.8See what learners said Задания курса

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Icahn School of Medicine at Mount Sinai The Icahn School of Medicine at Mount Sinai, in New York City is a leader in medical and scientific training and education, biomedical research and patient care.

Syllabus


WEEK 1


Introduction | Computing with MATLAB
The description goes here


5 videos, 7 readings expand


  1. Материал для самостоятельного изучения: Syllabus
  2. Материал для самостоятельного изучения: Supplemental Files
  3. Video: Lecture 1 - Introduction
  4. Video: Lecture 2 - Computing with MATLAB - Part 1
  5. Материал для самостоятельного изучения: Lecture Slides
  6. Video: Lecture 3 - Computing with MATLAB - Part 2
  7. Материал для самостоятельного изучения: Lecture Slides
  8. Материал для самостоятельного изучения: Supplementary Files
  9. Video: Lecture 4 - Computing with MATLAB - Part 3
  10. Video: Lecture 5 - Computing with MATLAB - Part 4
  11. Материал для самостоятельного изучения: Lecture Slides
  12. Материал для самостоятельного изучения: Supplementary Files

Graded: Assignment 1

WEEK 2


Introduction to Dynamical Systems
The description goes here


4 videos, 5 readings expand


  1. Материал для самостоятельного изучения: MATLAB Licenses
  2. Video: Lecture 6 - Introduction to Dynamical Systems - Part 1
  3. Материал для самостоятельного изучения: Lecture Slides
  4. Video: Lecture 7 - Introduction to Dynamical Systems - Part 2
  5. Материал для самостоятельного изучения: Lecture Slides
  6. Video: Lecture 8 - Introduction to Dynamical Systems - Part 3
  7. Материал для самостоятельного изучения: Lecture Slides
  8. Video: Lecture 9 - Introduction to Dynamical Systems - Part 4
  9. Материал для самостоятельного изучения: Lecture Slides

Graded: Assignment 2

WEEK 3


Bistability in Biochemical Signaling Models
The description goes here


6 videos, 4 readings expand


  1. Video: Lecture 10 - Bistability in Biochemical Signaling Models - Part 1
  2. Video: Lecture 11 - Bistability in Biochemical Signaling Models - Part 2
  3. Материал для самостоятельного изучения: Lecture Slides
  4. Video: Lecture 12 - Bistability in Biochemical Signaling Models - Part 3
  5. Материал для самостоятельного изучения: Lecture Slides
  6. Video: Lecture 13 - Bistability in Biochemical Signaling Models - Part 4
  7. Материал для самостоятельного изучения: Lecture Slides
  8. Video: Lecture 14 - Bistability in Biochemical Signaling Models - Part 5
  9. Video: Lecture 15 - Bistability in Biochemical Signaling Models - Part 6
  10. Материал для самостоятельного изучения: Lecture Slides

Graded: Assignment 3

WEEK 4


Computational Modeling of the Cell Cycle
The description goes here


4 videos, 3 readings expand


  1. Video: Lecture 16 - Computational Modeling of the Cell Cycle - Part 1
  2. Материал для самостоятельного изучения: Lecture Slides
  3. Video: Lecture 17 - Computational Modeling of the Cell Cycle - Part 2
  4. Материал для самостоятельного изучения: Lecture Slides
  5. Video: Lecture 18 - Computational Modeling of the Cell Cycle - Part 3
  6. Video: Lecture 19 - Computational Modeling of the Cell Cycle - Part 4
  7. Материал для самостоятельного изучения: Lecture Slides

Graded: Assignment 4

WEEK 5


Modeling Electrical Signaling
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6 videos, 5 readings expand


  1. Video: Lecture 20 - Mathematical Models of Action Potentials - Part 1
  2. Материал для самостоятельного изучения: Lecture Slides
  3. Video: Lecture 21 - Mathematical Models of Action Potentials - Part 2
  4. Материал для самостоятельного изучения: Lecture Slides
  5. Video: Lecture 22 - Mathematical Models of Action Potentials - Part 3
  6. Материал для самостоятельного изучения: Lecture Slides
  7. Video: Lecture 23 - Mathematical Models of Action Potentials - Part 4
  8. Video: Lecture 24 - Mathematical Models of Action Potentials - Part 5
  9. Материал для самостоятельного изучения: Lecture Slides
  10. Video: Lecture 25 - Mathematical Models of Action Potentials - Part 6
  11. Материал для самостоятельного изучения: Lecture Slides

Graded: Assignment 5

WEEK 6


Modeling with Partial Differential Equations
The description goes here


3 videos, 2 readings expand


  1. Video: Lecture 26 - Modeling with Partial Differential Equations - Part 1
  2. Материал для самостоятельного изучения: Lecture Slides
  3. Video: Lecture 27 - Modeling with Partial Differential Equations - Part 2
  4. Video: Lecture 28 - Modeling with Partial Differential Equations - Part 3
  5. Материал для самостоятельного изучения: Lecture Slides


WEEK 7


Stochastic Modeling
The description goes here


2 videos, 1 reading expand


  1. Video: Lecture 29 - Stochastic Modeling - Part 1
  2. Video: Lecture 30 - Stochastic Modeling - Part 2
  3. Материал для самостоятельного изучения: Lecture Slides
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