Seminar: Stochastic Modelling in the Biological Sciences – SS14

Responsible professor: Verena Wolf
Assistants: Linar Mikeev, Alexandr Andreychenko, David Spieler, Charalampos Kyriakopoulos

Schedule: weekly meeting during the summer term (slot will be determined via a doodle), Building E1 3 – Room 326
Distribution of topics/ registration: starts on Feb 5th via email to wolf@cs …

Credits: 7 ECTS points

Contents:
The seminar is a follow-up of the lecture “Stochastic Dynamics in Systems Biology” and mainly focuses on stochastic models and simulation techniques in quantitative biology and related fields such as the neurosciences.

Prerequisites:
The seminar is designed for students of computer science or bioinformatics. Participants that did not attend the lecture “Stochastic Dynamics in Systems Biology” should at least have participated in the lecture “Modeling and Simulation“. During the registration procedure, the participants of the lecture “Stochastic Dynamics in Systems Biology” are treated preferably. The language of the seminar is English (presentation and write-up).

Requirements for successful participation (“Schein”)
Presentation:
Every participant will give a presentation of 45 min about one of the topic listed below. Participants that give presentations of very low quality have to repeat their presentation to get a “Schein”.

Write-up:
Every participant has to submit a write-up about the corresponding topic until one week after the last regular meeting. The write-up should be at least 5 pages and submitted electronically as pdf-file.

Paper reading: Each participant has to be the “opponent” for at least two speakers, i.e., she/he has to read the related paper(s) in advance and prepare questions for the speaker.

Regular attendance:
It is expected that the participants attend all seminar meetings except if they have an excused absence (which generally means either obtaining permission in advance or getting a doctor’s note attesting the inability to attend the seminar).

Consultation:
Participants must present their slides to the seminar supervisor not later than one week before the talk is given.

Topics:

more to be announced soon

 

1) Stochastic Lotka-Volterra Systems:
Coexistence versus extinction in the stochastic cyclic Lotka-Volterra model
link: http://pre.aps.org/abstract/PRE/v74/i5/e051907
(supervisor: Linar Mikeev)

2) Implicit Tau-leaping:
M. Rathinam, L. R. Petzold, Y. Cao, and Daniel T. Gillespie, (2003).
“Stiffness in stochastic chemically reacting systems: The implicit tau-leaping method”. Journal of Chemical Physics 119 (24):
12784-12794. doi:10.1063/1.1627296
(supervisor: David Spieler)
Assigned to: Miriam Bah

3) Method of moments:
Computing the moments of high dimensional solutions of the master equation. Stefan Engblom, Appl. Math. Comput., 2006.
and
A general moment expansion method for stochastic kinetic models, Ale et al. 2013
(supervisor: Alexander Andreychenko)

4) Stochastic Models of Neurons
Avalanches in a Stochastic Model of Spiking Neurons
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000846
(supervisor: Verena Wolf)
Assigned to: Stefan Neumann

5) Linear Noise Approximation:
“A New Perspective on the Linear Noise Approximation”
Wallace et al.
(supervisor: Verena Wolf)
Assigned to: Vanessa Morguet

6) Rule-based modelling:
Yang, J., Monine, M.I., Faeder, J.R. & Hlavacek, W.S. Kinetic Monte Carlo
method for rule-based modeling of biochemical networks. Phys. Rev. E 78,
031910 (2008).
(supervisor: Thilo Krüger)
Assigned to: Gerrit Grossmann

7) Oscillatory behavior
Ursula Kummer, Borut Krajnc, Jurgen Pahle, Anne K. Green, C. Jane Dixon, Marko Marhly
Transition from Stochastic to Deterministic Behavior in Calcium Oscillations (link)
(supervisor: Alexander Andreychenko)

8) Heat shock response mechanism
Mizera A., Gambin B.
Stochastic modelling of the eukaryotic heat shock response. (link)
(supervisor: Alexander Andreychenko)
Assigned to: Alexander Marx