Seminar: Rule-Based and Hybrid Simulation of Reaction Networks — WS15/16

Instructor: Prof. Dr. Verena Wolf
Tutors: Mayank Goyal, Thilo Krüger

Schedule: Winter-term 2015/2016

Credits: 7 ECTS points

The seminar focuses on simulation techniques for Markov models. The main focus is on the simulation of rule-based models.

The seminar is designed for students of computer science or bioinformatics. Basic knowledge about Markov models is helpful for a successful participation. The language of the seminar is English (presentation and write-up).

The seminar can be participated by up to 12 students. There will be up to four sessions with up to three talks each. The topics for the course have to be distributed consecutively, therefore in each session, the talks for the next session will be distributed. Then there are at least three weeks left for preparing the talks for the next session. We start with session 1 and talks 1a(, 1b) and 1c. These first talks will be distributed by mail. If you have questions concerning this organisation, you can write an e-mail to thilo.krueger [at] and ask.

If you want to register, please send an e-mail with your name and matriculation number to thilo.krueger [at] You will have to confirm your registration at the beginning of the winter-term.

Requirements for successful participation (“Schein”)
Every participant have to be present in all seminar sessions.

In order to improve the understanding of the talks, it is helpful to read the first sections (at least until Section 2.3) of Gillespie’s introduction at (if you do not have access to the pdf, send an email to Thilo.).

Every participant will give a presentation of 30 to 45 min about one of the topics listed below. Participants that give presentations of very low quality have to repeat their presentation to get a “Schein”.

Every participant has to submit a write-up about the corresponding topic. 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.

Participants must meet with the organizers of the seminar to

  • get advice for introductory reading
  • discuss the assigned paper
  • present their slides

The participants must prepare for the seminar by learning some of the background of modeling and simulation. We will offer some material to do so. The following talks are planned for the seminar:

First Session: 16.11.2015, 14:15, 328, E1 3:

1b) Sruti Subramanian: Rule-based representation of reaction networks
Faeder, James R., Michael L. Blinov, and William S. Hlavacek. “Graphical rule-based representation of signal-transduction networks.” Proceedings of the 2005 ACM symposium on Applied computing. ACM, 2005.
Supervisor: Mayank Goyal
Opponents: Mehwish Hanif, Fabian Kosmale

Second Session: tba

2a) Popular rule-based modeling languages
James R. Faeder, Michael L. Blinov, and William S. Hlavacek. “Rule-Based Modeling of Biochemical Systems with BioNetGen.” Methods in Molecular Biology, Systems Biology, vol. 500 2009
Supervisor: Mayank Goyal

2b) From rules to ODEs
Feret, Jérôme, et al. “Internal coarse-graining of molecular systems.” Proceedings of the National Academy of Sciences 106.16 (2009): 6453-6458.
Supervisor: Mayank Goyal

2c) Generate-first and on-the-fly simulation of rule-based models
Lok, Larry, and Roger Brent. “Automatic generation of cellular reaction networks with Moleculizer 1.0.” Nature biotechnology 23.1 (2005): 131-136.
Supervisor: Mayank Goyal

3a) Network-free simulation 1
Danos, Vincent, et al. “Scalable simulation of cellular signaling networks.” Programming Languages and Systems. Springer Berlin Heidelberg, 2007. 139-157.
Supervisor: Thilo Krüger

3b) Network-free simulation 2
Yang, Jin, et al. “Kinetic Monte Carlo method for rule-based modeling of biochemical networks.” Physical Review E 78.3 2008.
Supervisor: Thilo Krüger

3c) Network-free simulation 3
Colvin, Joshua, et al. “RuleMonkey: software for stochastic simulation of rule-based models.” BMC bioinformatics 11.1 2010.
Supervisor: Thilo Krüger