Modeling and Simulation

Seminar: Stochastic Simulation Techniques
Lecturer: Verena Wolf
Assistant: Linar Mikeev, Alexandr Andreychenko, David Spieler

Schedule: Block seminar on November 7th and 8th, 2011.
Registration: Please, make an appointment with Dr. Wolf to register for the seminar and fix a topic.
Registration deadline: September 1st

Credits: 7 ECTS points

Contents:
The seminar discusses several research papers related to simulation techniques. The seminar mainly focuses on stochastic models in quantitative biology and related fields.

Prerequisites:
The seminar is designed for students of computer science or bioinformatics. Basic knowledge about Markov chains is helpful for a successful participation. During the registration procedure, the participants of the lectures “Data Networks” or “Modeling and Simulation” are treated preferably, since stochastic simulation has been discussed in these lectures. The language of the seminar is English (presentation and write-up).

Requirements for successful participation (“Schein”)
Presentation:
Every participant will give a presentation of 30 to 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 before Christmas. 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.

Consultation:
Participants must present their slides to the seminar supervisor not later than two weeks before the block seminar.

Topics:
In order to improve the understanding of the papers listed below, it is helpful to read the first sections (at least until Section 2.3) of Gillespie’s introduction at http://www.springerlink.com/content/r21347m26lv1x387/ (if you do not have access to the pdf, send an email to V. Wolf).

• (1) Gillespie Simulation (introductory talk given by V. Wolf).
• (2) Gibson Bruck Algorithm: M. A. Gibson and J. Bruck, (2000). “Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels”. J. Phys. Chem. A 104: 1876–1889. doi:10.1021/jp993732q (already assigned to B. Bhattarai, 1. opponent: S. C. Dhinakaran, 2. opponent: V. Ingalalli)
• (3) Explicit Tau-leaping: D. Gillespie (2001).
  “Approximate accelerated stochastic simulation of chemically reacting systems” J. Chem. Phys. 115, 1716 doi:10.1063/1.1378322
  (topic is already assigned to S. Zickenrott, 1. opponent: A. Graf-Brill, 2.opponent: D. Kumar)
• (4) Approximate Simulation: Haseltine and Rawlings (2002) “Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics”. JOURNAL OF CHEMICAL PHYSICS VOLUME 117, NUMBER 15
  (topic is assigned to S. C. Dhinakaran, 1. opponent: A. Graf-Brill 2. opponent: P. Yadava)
• (5) 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
  (topic is assigned to A. Graf-Brill, 1. opponent: S. Zickenrott, 2.opponent: D. Kumar)
• (6) Hybrid Stochastic Simulation: Salis, H; Kaznessis, Y (2005). “Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions”. Journal of Chemical Physics 122 (5): 054103. doi:10.1063/1.1835951 (topic is assigned to D. Kumar, 1. opponent: A. Podosinnikova, 2. opponent: S. C. Dhinakaran)
• (7) Discrete-Time Conversion: Werner Sandmann (2007).
  Stochastic Simulation of Biochemical Systems via Discrete-Time Conversion. Proc. 2nd Conference on Foundations of Systems Biology in Engineering, FOSBE 2007, pp. 267-272, Stuttgart, Germany, 9-12 September, Fraunhofer IRB Verlag, 2007.
  (Topic is assigned to P. Yadava, 1. opponent: S. Zickenrott, 2. opponent: B. Bhattarai)
• (8) Multiple Perturbations: Werner Sandmann (2007).
  Simultaneous Stochastic Simulation of Multiple Perturbations in Biological Network Models.
  Proc. 2007 International Conference on Computational Methods in Systems Biology, CMSB 2007, Edinburgh, Scotland, 20-21 September 2007, Lecture Notes in Computer Science, Volume 4695, pp. 15-31, Springer, 2007. (Topic is assigned to V. Ingalalli, 1. opponent: A. Podosinnikova, 2. opponent: B. Bhattarai)
• (9) Method of moments: Stefan Engblom (2006).
  Computing the moments of high dimensional solutions of the master equation.
  Appl. Math. Comput., 2006. (Topic is assigned to A. Podosinnikova, 1. opponent: P. Yadava, 2. opponent: V. Ingalalli)