Course Catalog 2012-2013
Basic

Basic Pori International Postgraduate Open University

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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
Lectures
Excercises
 2 h/week
 4 h/week


 


 


 


 
SGN-6186 2012-01 Wednesday 10 - 12, TB222
Wednesday 10 - 12, TB224

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:

Completion parts must belong to the same implementation

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
SGN-6186 2012-01 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.        

Last modified20.08.2012