BMT-52407 Models of Gene Networks, 5 cr

Toteutuskerta BMT-52407 2019-01


From this course the student will know how to do stochastic simulations and delayed stochastic simulations, and how to create models of delayed stochastic gene regulatory networks. Students will become familiar with detailed models and experimental results related to single gene expression and its underlying mechanisms. Also, the student will be introduced to models of small- and large-scale genetic circuits and to models of gene expression at the single nucleotide level.

In 2019-20, the lectures will be at:

Lectures: Wed 12:00 - 14:00, Arvo D502 (28.8.-9.10.2019)
Exercises: Fri 16:00 - 18:00, Arvo ML72 (30.8.-11.10.2019)
Exam Wed 9-12, Arvo F213 (16.10.2019)
Exam Wed 17-20, Arvo F213 (27.11.2019)
Exam Wed 17-20, Arvo D202 (8.1.2020)


Periodi 1
Opetusmuodot Tentti
Vastuuhenkilö Andre Sanches Ribeiro


Numerical evaluation scale (0-5)


a) Exercises (must complete at least 50% of exercise points. 80% gives bonus of 0.5). Exercises solutions can be delivered until the day preceding the next exercise lecture.
b) Final exam (50% of the final grade).
c) Project work (50% of the final grade).
d) Short summary (1-5 lines) of the lecture, to be delivered at the end of each lecture. The grade of each summary is: PASS/FAIL. If 3 or more summaries have PASS grade, the student gets a bonus of 0.5 in the final grade.

Additionally, a passing grade must be achieved in project, exam, and exercises in order to pass the course.

Grading: 0 to 5 (0 fails, 1 to 5 passes). 2.5 from exam, 2.5 from project, 0.5 bonus for good performance in exercises, and 0.5 bonus for good performance lecture summaries.

Lisätietoja toteutuksesta

Exam Wed 16.10.2019 09:00 - 12:00


Tyyppi Nimi Tekijä ISBN Lisätiedot Kieli Tenttimateriaali
Journal Bioinformatics Ribeiro and Lloyd-Price SGN Sim, a Stochastic Genetic Networks Simulator English No
Journal J. Phys. Chem Gillespie, D. T. Exact stochastic simulation of coupled chemical reactions English No
Journal J. of Theor. Biol. Ribeiro and Kauffman Noisy Attractors and Ergodic Sets in Models of Genetic Regulatory Networks English No
Journal Journal of Computational Biology AS Ribeiro et al A General Modeling Strategy for Gene Regulatory Networks with Stochastic Dynamics English No
Journal Journal of Computational Biology Hidde de Jong Modeling and Simulation of Genetic Regulatory Systems: A Literature Review English No
Journal Mathematical Biosciences Andre S. Ribeiro Mathematical Biosciences English No