RNAdev Models implemented as ODE systems and written in the SBML format
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translational
README.md
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README.md

SBML Models

In this git repository we set up a system to model RNA designs over time. Therefore we built a network context, which models important cellular processes such as transcription, translation and degradation as system of ordinary differential equations (ODEs) with a more or less “realistic” parameter set.

We investigated a system published in 2011 by the Keasling lab [Carothers et. al 2011], which has been used to evaluate self-cleaving ribozymes and ligand triggered aptazymes. We modularized the ODE system such that different regulatory mechanisms, e.g. translational ON switches based on sRNA-mRNA interaction or a riboswitch sensor, can be encoded into the framework.

First, the original ODE system was reduced to model transcription, translation and degradation of an mRNA and the produced protein. Subsequently this system was extended to describe translational ON/OFF and transcriptional ON/OFF switches.

The developed models are available in the according sub-directory:

There we provide a short summary of each model and their implementation in ODE and SBML format. We are happy to provide further details about the system setups, e.g. used parameters, upon request.