Publication details
On Algorithmic Analysis of Transcriptional Regulation by LTL Model Checking
| Basic information | |
|---|---|
| Original title: | On Algorithmic Analysis of Transcriptional Regulation by LTL Model Checking |
| Authors: | Jiří Barnat, Luboš Brim, Ivana Černá, Sven Dražan, Jana Fabriková, David Šafránek |
| Further information | |
|---|---|
| Citation: | BARNAT, Jiří  - BRIM, Luboš - ČERNÁ, Ivana - DRAŽAN, Sven - FABRIKOVÁ, Jana - ŠAFRÁNEK, David. On Algorithmic Analysis of Transcriptional Regulation by LTL Model Checking. Theoretical Computer Science. ISSN 0304-3975, 2009, vol. 2009, no. 410, pp. 3128-3148. |
| Original language: | English |
| Field: | Informatika |
| WWW: |  http://dx.doi.org/10.1016/j.tcs.2009.02.017 |
| Type: | Article in Periodical |
| Keywords: | Genetic regulatory network; Piecewise-linear approximation; Model checking |
This paper is focused on the model checking approach for analysis of piecewise-linear deterministic models of genetic regulatory networks. Firstly, the qualitative simulation algorithm of de Jong et.al. that builds the heart of Genetic Network Analyzer (GNA) is revisited and its time complexity is studied in detail. Secondly, a novel algorithm that reduces the state space generation time is introduced. The new algorithm is developed as an abstraction of the original GNA algorithm. Finally, a fragment of linear time temporal logic for which the provided abstraction is conservative is identified. Efficiency of the new algorithm when implemented in the parallel model checking environment is demonstrated on a set of experiments performed on randomly modified biological models. In general, the achieved results bring a new insight into the field of qualitative simulation emerging in the context of systems biology.
Related projects:
- Highly Parallel and Distributed Computing Systems
- Verification and Analysis of Large-Scale Computer Systems
