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Modelling of Biosystems

Course developer

Course abstract

The aim of the study course is to review the cycle of creation and application of models of biological systems, which includes clarifying both the structure of the model and its dynamic parameters under conditions of incomplete information. Examples include models at different scales, from cellular process models to population-level models. Modeling and its use for process prediction and optimization are important skills in modern biotechnology, medicine and ecology.

Learning outcomes and their assessment

• students know about the implementation of the stages of creating computer models in accordance with the latest scientific knowledge, extracting the maximum amount of information from the available experimental data and literature - practical work, independent work
• students know how to argue the choice of modeling techniques appropriate to the available amount of information, the ability to compare and critically evaluate various literature sources - practical work, independent work
• students are able to formulate and critically analyze alternative modeling strategies, create new and adapt existing modeling techniques for the improvement of various bioprocesses - practical works

Course Content(Calendar)

1. Stages of creating a computer model of bioprocesses and classes of model optimization tasks – 2 h
2. Determining the scope of the model depending on the problem under study – 2 h
3. Defining the boundaries of the modeled system and its interaction with the environment – 2 h
4. Creating the internal structure of the model and determining the parameters of functional relationships - 2 h
5. Dynamic models, simulation experiments and their interpretation - 2 h
6. Determination of dynamic parameters of the model using experimental data – 2 h
7. Critical analysis of a successful model – 2 h
8. Applications of artificial intelligence for solving parameter determination tasks - 2 h
9. Risks of stagnation in the optimization process – 1 h
10. Optimization of the model for achieving new bioprocess properties - 2 h
11. Evaluation of stationary state - 1 h
12. Determination of the best set of parameters to be optimized for different number of parameters to be changed - 2 h
13. Effect of model nonlinearity on the duration of the optimization experiment – 2 h

Requirements for awarding credit points

To award credit points in the Modeling of Biosystems course:
• it is necessary to develop and defend all laboratory work;
• it is necessary to develop and defend independent work.

Description of the organization and tasks of students’ independent work

The organization of independent work during the semester takes place by studying literature independently, using the advice of the teaching staff.
Independent work: carrying out optimization tasks of the sugarcane computer model according to various criteria, analyzing the results and providing conclusions.

Criteria for Evaluating Learning Outcomes

The final course mark consists of: 1) participation in lectures (20%), 2) developed and defended laboratory work (20%), 3) developed and defended independent work (60%). The maximum number of % is 100%, which corresponds to 10 points in the final evaluation.

Compulsory reading

1. Palsson B.O. Systems Biology: Properties of Reconstructed networks. Cambridge: Cambridge University Press, 2006.
2. Ingalls B.P. Mathematical Modeling in Systems Biology. Massachuset: Massachusets Institute of Technology, 2013.
3. Selga T. Šūnu bioloģija. Rīga: LU Akadēmiskais apgāds, 2007.
4. Jones D.S., Sleeman B.D. Differential Equations and Mathematical Biology. Chapman &Hall/CRC, 2003.

Further reading

1. Szallasi Z., Stelling J., Periwal V. System Modelling in Cell Biology from concepts to nuts and bolts. MIT Press, 2006.

Notes

ITF Master's Academic Study Program "Information Technologies"