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Course Catalog 2012-2013
SGN-6186 Mathematical Modeling of Cellular Systems, 5 cr |
Additional information
Course is lectured every year.
Suitable for postgraduate studies
Person responsible
Andre Sanches Ribeiro
Lessons
| Study type | P1 | P2 | P3 | P4 | Summer | Implementations | Lecture times and places |
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Requirements
To pass the course, the student is required to:
a) Execute the project work (20% of the final grade)
b) Execute the weekly exercises (1 per exercises lesson, 40% of the final grade)
c) Do the final exam (40% of the final grade).
d) All three requirements above are needed to complete the course.
Completion parts must belong to the same implementation
Learning outcomes
After completing the course, the student will be able to create mathematical models, both deterministic and stochastic, of cellular systems, implement them, and solve their behavior computationally by running simulations. Systems include signal transduction, metabolism, and single cells. Moreover, the student will be able to explain the differences between deterministic and stochastic methods and chose the appropriate method in each case. After the course, the student will have the necessary skills to use MATLAB environment in modeling.
Content
| Content | Core content | Complementary knowledge | Specialist knowledge |
| 1. | Deterministic modeling of chemical reactions | Numerical simulation of deterministic models of chemical reactions | |
| 2. | Stochastic modeling of chemical reactions | Numerical simulation of stochastic models of chemical reactions | |
| 3. | Reaction-diffusion modeling | Deterministic and stochastic solutions of reaction-diffusion models. | |
| 4. | Deterministic and stochastic modeling of neurons | Deterministic and stochastic solutions of models of neurons. |
Evaluation criteria for the course
To complete the course, the student is required to: a) Execute the project work (20% of final grade) b) Execute weekly exercises (1 per exercises lesson, 40% of final grade) c) Final exam (40% of the final grade). d) All three requirements above are needed to complete the course. Grading from 0 to 5 (0 fails, 1 to 5 passes).
Assessment scale:
Numerical evaluation scale (1-5) will be used on the course
Partial passing:
Study material
| Type | Name | Author | ISBN | URL | Edition, availability, ... | Examination material | Language |
| Lecture slides | Mathematical Modeling of Cellular Systems | A. Ribeiro, I Potapov | English | ||||
| Research | Scientific articles | English |
Prerequisites
| Course | Mandatory/Advisable | Description |
| MAT-33506 Differential equations | Advisable | |
| SGN-6106 Computational Systems Biology | Advisable |
Additional information about prerequisites
Basic knowledge of Calculus is required.
Prerequisite relations (Requires logging in to POP)
Correspondence of content
There is no equivalence with any other courses
More precise information per implementation
| Implementation | Description | Methods of instruction | Implementation |
| This course presents methods and modeling strategies of biological systems, focusing on the modeling and simulation of chemical processes in cells using either Differential Equations or Numerical methods. After completing the course, the student will be able to create mathematical models of cellular systems, both deterministic and stochastic, implement them, and solve them by analytical or numerical methods. Systems include simple processes, signal transduction, and gene expression. Moreover, the student will learn how to choose appropriately between deterministic and stochastic methods. After the course, the student will have gained multiple skills in using the MATLAB environment in modeling of dynamical processes. |