270
Views
20
CrossRef citations to date
0
Altmetric
Original Articles

Compositionality, stochasticity, and cooperativity in dynamic models of gene regulation

, &
Pages 17-28 | Received 22 Jun 2007, Accepted 13 Sep 2007, Published online: 07 Sep 2010
 

We present an approach for constructing dynamic models for the simulation of gene regulatory networks from simple computational elements. Each element is called a “gene gate” and defines an input/output relationship corresponding to the binding and production of transcription factors. The proposed reaction kinetics of the gene gates can be mapped onto stochastic processes and the standard ordinary differential equation (ODE) description. While the ODE approach requires fixing the system's topology before its correct implementation, expressing them in stochastic π‐calculus leads to a fully compositional scheme: network elements become autonomous and only the input/output relationships fix their wiring. The modularity of our approach allows to pass easily from a basic first‐level description to refined models which capture more details of the biological system. As an illustrative application we present the stochastic repressilator, an artificial cellular clock, which oscillates readily without any cooperative effects.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.