Dynamical Modeling Methods for Systems Biology from Coursera

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.

What's inside

Syllabus

Introduction | Computing with MATLAB

The description goes here

Introduction to Dynamical Systems

Bistability in Biochemical Signaling Models

Computational Modeling of the Cell Cycle

Modeling Electrical Signaling

Modeling with Partial Differential Equations

Stochastic Modeling

Good to know

Know what's good

, what to watch for

, and possible dealbreakers

Students who come in with graduate-level academic training in Systems Biology are best suited to take this course, as it is advanced

Students who hope to use computational modeling as a tool for deeper understanding of experiments are well-suited to take this course

Students who intend to conduct original research in modeling biological systems should take this course

Students interested in an introduction to MATLAB or other programming will not find it here, as this course assumes some comfort with coding

Students who are uncomfortable with math are not well-suited for this course, as it uses concepts from calculus and linear algebra

Reviews summary

Helpful and practical biology course

Learners say Dynamical Modeling Methods for Systems Biology is a helpful and practical course that offers engaging assignments and clear explanations. Many students comment on the course's excellent material, especially for students interested in molecular biology and computational biology. However, some learners mention that the assignments can be challenging. Overall, students find the course comprehensive and well-organized, with knowledgeable instructors.

Assignments enhance learning

""The assignments seemed very tough. Other than that this course was very knowledgeable.""

""Very good course. The first 5 weeks are incredible, the last couple weeks are decidedly of a lower quality with no assignments to accompany the material. ""

""The tests are not easy but I liked the homework style approach. It forces you to understand the subject better than the regular quizzes.""

Straightforward teaching aids learning

""New to systems biology and I am really impressed with the clear explanations.""

""Amazing and clearly explained course that helped me understand all the ODE, PDE, and finally also a little bit of stochatic methods.""

""The content of the course are very straight forward and comprehensive.""

Missing files affect course experience

""I really enjoyed the course. However, project files (*.sboj) were missing from downloads.""

Activities

Be better prepared before your course. Deepen your understanding during and after it. Supplement your coursework and achieve mastery of the topics covered in Dynamical Modeling Methods for Systems Biology with these activities:

Connect with experts in Systems Biology

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Seek guidance and support from experienced researchers in the field to enhance your learning.

Browse courses on Systems Biology

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Identify potential mentors through conferences, research papers, or online platforms.
Reach out to mentors via email or LinkedIn.

Review requisites: Linear algebra

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Reinforce your understanding of linear algebra, which is essential for modeling complex biological systems.

Browse courses on Linear Algebra

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Revisit key concepts such as vector spaces, matrices, and linear transformations.
Practice solving systems of linear equations.
Review matrix theory, including eigenvalues and eigenvectors.

Explore MATLAB tutorials

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Familiarize yourself with MATLAB, a powerful tool for numerical simulations and data analysis in Systems Biology.

Browse courses on MATLAB

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Complete beginner tutorials to understand the MATLAB environment.
Follow guided exercises on data manipulation and visualization.

Five other activities

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Review probability and statistics

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Strengthen your understanding of probability and statistics, which are crucial for analyzing and interpreting biological data.

Browse courses on Probability

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Revisit basic concepts of probability distributions.
Practice statistical hypothesis testing.

Practice ODE modeling in MATLAB

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Enhance your skills in solving and simulating ordinary differential equations using MATLAB.

Browse courses on MATLAB

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Solve simple ODEs analytically.
Implement numerical methods (e.g., Euler, Runge-Kutta) in MATLAB.
Simulate and analyze ODE models of biological systems.

Discuss modeling approaches with peers

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Engage in discussions with classmates to exchange ideas, clarify concepts, and learn from diverse perspectives.

Browse courses on Systems Biology

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Join online forums or study groups.
Participate in discussions, asking and answering questions.

Develop a simple cell cycle model

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Apply your knowledge to build a computational model that simulates the cell cycle.

Browse courses on Systems Biology

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Understand the key events and phases of the cell cycle.
Translate biological mechanisms into mathematical equations.
Implement the model in MATLAB and simulate it.
Analyze the simulation results and compare them to experimental data.

Participate in modeling challenges

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Test your skills and gain recognition by participating in modeling competitions.

Browse courses on Systems Biology

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Identify relevant modeling challenges.
Develop and submit a computational model.
Analyze and present your results.

Career center

Learners who complete Dynamical Modeling Methods for Systems Biology will develop knowledge and skills that may be useful to these careers:

Systems Biologist

Systems Biologists model complex biological systems using a range of mathematical and computational techniques. A background in dynamical modeling prepares you for this role by providing you with the foundational knowledge of how to approach such problems. Specifically, this course will provide you with hands-on experience developing and analyzing dynamical models of biological systems.

See salaries and explore the career path for Systems Biologist

Computational Biologist

Computational Biologists use computational techniques to solve problems in biology. The models and techniques you will learn in this course will provide you with a strong foundation for this field.

See salaries and explore the career path for Computational Biologist

Biostatistician

Biostatisticians use statistical methods to analyze data in the biological sciences. The skills you will learn in this course in developing and analyzing mathematical models will be valuable preparation for this career.

See salaries and explore the career path for Biostatistician

Quantitative Analyst

Quantitative Analysts use mathematical and statistical methods to analyze data in the financial industry. The skills you will learn in this course in developing and analyzing mathematical models will be valuable preparation for this career.

See salaries and explore the career path for Quantitative Analyst

Actuary

Actuaries use mathematical and statistical methods to assess risk and uncertainty. The skills you will learn in this course in developing and analyzing mathematical models will be valuable preparation for this career.

See salaries and explore the career path for Actuary

Market Researcher

Market Researchers use mathematical and statistical methods to analyze market data. The skills you will learn in this course in developing and analyzing mathematical models will be valuable preparation for this career.

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Data Scientist

Data Scientists use data to solve problems in a variety of fields. The skills you will learn in this course in developing and analyzing mathematical models will be valuable preparation for this career.

See salaries and explore the career path for Data Scientist

Operations Research Analyst

Operations Research Analysts use mathematical and statistical methods to solve problems in a variety of industries. The skills you will learn in this course in developing and analyzing mathematical models will be valuable preparation for this career.

See salaries and explore the career path for Operations Research Analyst

Financial Analyst

Financial Analysts use mathematical and statistical methods to analyze financial data. The skills you will learn in this course in developing and analyzing mathematical models will be valuable preparation for this career.

See salaries and explore the career path for Financial Analyst

Bioinformatician

Bioinformaticians use computational methods to analyze biological data. The skills you will learn in this course in developing and analyzing mathematical models will be valuable preparation for this career.

See salaries and explore the career path for Bioinformatician

Public Health Scientist

Public Health Scientists use mathematical and statistical methods to study public health problems. The skills you will learn in this course in developing and analyzing mathematical models will be valuable preparation for this career.

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Epidemiologist

Epidemiologists use mathematical and statistical methods to study the distribution and determinants of health-related states or events in populations. The skills you will learn in this course in developing and analyzing mathematical models will be valuable preparation for this career.

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Research Scientist

Research Scientists use mathematical and statistical methods to conduct research in a variety of fields. The skills you will learn in this course in developing and analyzing mathematical models will be valuable preparation for this career.

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Science Writer

Science Writers use writing skills to communicate scientific information to a variety of audiences. The skills you will learn in this course in developing and analyzing mathematical models will help you to understand the technical details of scientific research and to communicate them effectively to your audience.

See salaries and explore the career path for Science Writer

Teacher

Teachers use a variety of methods to teach students about a variety of subjects. The skills you will learn in this course in developing and analyzing mathematical models will help you to understand the technical details of your subject matter and to communicate them effectively to your students.

See salaries and explore the career path for Teacher