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Course Catalog 2011-2012
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
Project work (20% of the final grade), weekly exercises (1 per exercises lesson, 40% of the final grade) and final exam (40% of the final grade).
The student is required to pass the course:
a) must execute all the three requirements.
b) must attend and complete at least 50% of the exercises lessons
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. | Biological background of different cellular systems. | ||
| 2. | Deterministic and stochastic methods to model the dynamical behavior of cellular systems. | ||
| 3. | Simulation of deterministic and stochastic models. |
Evaluation criteria for the course
The final grade comes from the exam. The grade is incremented by one if weekly exercises and assignment are done.
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 | T. Manninen, H. Mannerstrom, A. Ribeiro | English | ||||
| Research | Scientific articles | English |
Prerequisites
| Course | Mandatory/Advisable | Description |
| MAT-33506 Differential equations | Advisable | |
| MAT-45706 Introduction to scientific computing | Advisable | |
| SGN-6106 Computational Systems Biology | Advisable |
Additional information about prerequisites
The students ought to have basic knowledge of calculus, but the methods to solve first order ODEs will be revisited.
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, which special focus on the modeling and simulation of chemical reactions in cellular systems. 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. |