Module: Praktijkopdracht Thema 8

Gegevensveld Waarde
Osiriscode BFVH3TH8
ECTS 5
Toetsvorm Opdracht
Minimum cijfer 5,5
Docent(en) FEFE
Contactpersoon FEFE
Voertaal Nederlands

Cursusdoelen (leerdoelen)

  • Begrijpen wat wiskundige modellen zijn en wat de relatie is tot de werkelijkheid
  • Kunnen interpreteren van stelsels differentiaal vergelijkingen
  • Stelsels differentiaal vergelijkingen kunnen opstellen en oplossen door simulatie in R
  • Begrijpen hoe aanpassingen in de uitgangssituatie en model parameters doorwerken in de resultaten
  • Resultaten van simulaties grafisch kunnen weergeven en interpreteren.

Inhoud

In this course you will be introduced to modelling biological systems using computer simulations. You will learn about the relations between reality, experiments and models, how to describe biological systems as mathematical models that can be simulated, and how to interpret the results. For the main assignment, you will search scientific literature for a systems biology study on a topic of your interest and repeat the study in R. The assignments are performed in couples. Larger teams are allowed for the final assignment for more complex systems. In this course, the following topics will be dealt with:

  • Modelling and simulation.
  • Differential equations.
  • Dynamics, convergence and equilibrium.
  • Setting up and running simulations using R.
  • Searching, reading (and writing) scientific articles.

Literatuur en andere bronnen

Literatuur
Literature will comprise of review articles on methods within the context of ODE and system biology, research papers demonstrating the application in a particular research project, and background literature. All materials can be found at http://www.bioinf.nl/~fennaf/thema08/

Web Blackboard course thema 8 and http://www.bioinf.nl/~fennaf/thema08/

Competenties

1(II), 2(II), 3(II), 4(II), 5(II), 6(II), 7(II), 8(I), 9(II), 10(II), 11(II), 12(II), 13(II)

Werkvormen

  • The course is a practical course with week assignments introduced by background tutorials. Week 1 till 4 are preparatory assignments to learn to work with the material. The final assignment starting in week 5 consists of reproducing and testing (part of) the systems biology modeling from the paper selected.

Ingangseisen

  • This subject cannot be done in combination with another theme practical

Ingangseisen toets

  • N. A

Voorkennis

  • Introduction level or R and basic mathematics knowledge is required

Voorkennis kan worden opgedaan met

  • Using R for Introductory Statistics

Bronnen van zelfstudie

Verplicht materiaal

  • Package deSolve: Solving Initial Value Differential Equations in R

Aanbevolen materiaal

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