2IF35 Formal Modelling in Cell Biology (academic year 2010/2011)
News
-
The course 2IF35 will be organized this year as a working group.
Kick-off meeting is on Monday September 27, 2010 at 13.45 hours,
auditorium 16. Meetings are weekly.
We will be working on the modelling of a number of biological
casestudies (of increasing complexity) with a number of
model checkers and simulators.
Assessment is by means of a written report in January on one's own
working group activities, in particular discussing the modelling
efforts and results.
Students interested in following this working group are kindly
requested to send an email to the lecturer, E.P. de Vink, mentioning
surname, first name and student number.
Tools
-
BetaBW, a collection of tools based on BlenX, a language explicitly
designed to represent biological entities and their interactions
- BioCHAM,
modelling environment for systems biology, with some unique features
for inferring unknown model parameters from temporal logic constraints
- BioPEPA,
a process algebra for the modelling and the analysis of biochemical
networks
- COPASI,
a user-friendly software application for simulation and analysis of
biochemical networks and their dynamics
- GINsim,
a computer tool for the modeling and simulation of genetic regulatory
networks with facilities for stable state search and path finding
- kappa,
a rule-based language for modeling protein interaction networks
- mCRL2,
a general purpose formal specification language with associated
toolset for modelling, validation and verification of concurrent systems
and protocols
- PRISM,
a probabilistic model checker for formal modelling and analysis of
systems which exhibit random or probabilistic behaviour
- SPiM,
a programming language for designing and simulating computer models
of biological processes
- SPIN,
a open-source software tool for formal verification of distributed
software systems using LTL
Literature
A short description of the two-variable model of bacteriophage lambda
can be found in
H. Siebert and A. Bockmayr,
Temporal constraints in the logical analysis of regulatory
networks,
Theoretical Computer Science 391(3):258-275, 2008
Planning
| 27/9 |
kick-off |
[slides] |
| 4/10 |
progress report on tool installation and basic examples |
|
| 11/10 |
progress report and further examples |
|
| 8/11 |
quantitative analysis: circadian clock |
[slides] |
| 15/11 |
no meeting |
|
| 22/11 |
progress report |
|
| 29/11 |
further examples |
[slides] |
| 6/12 |
presentations |
|
| 13/12 |
consultancy hours |
|
| 10/1 |
consultancy hours |
|
Report
To be decided.
Lecturer
Dr. E.P. de Vink, HG 6.72, evink (at) win.tue.nl, 040-2473146