New Software Programs for the Design, Analysis and Parameter Estimation of Synthetic Intracellular Systems

Andrea Degasperi (NUID-UCD) in collaboration with Lan K. Nguyen (NUID-UCD and Monash University, Australia) developed two software programs in the context of SynSignal. The first program, Dynamics Visualization based on Parallel Coordinate (DYVIPAC), allows the user to discover whether a biochemical system, synthetic or found in nature, is capable of complex non-linear input-output dynamics such as switches or sustained oscillations. More in details, DYVIPAC is a Python-based software for Systems and Synthetic Biology for relating systems parameters with systems dynamics through visualisation. DYVIPAC uses mathematical models written in the Systems Biology Markup Language (SBML) as input, explores the model parameter space, performs stability analysis and plots the results in a parallel coordinates plot.

The second program, Parameter Estimation Pipeline for Systems and Synthetic Biology (PEPSSBI (Java/C++)), employs optimization algorithms to identify parameters of the mathematical models that make the models best fit the data. This is a key step for making the models and so our understanding of the biological systems refined and quantitative. PEPSSBI allows the user to model multiple synthetic circuits that have common components at the same time. This implies that data from different circuits can be used at the same time to constrain parameters of common components. Another interesting feature of PEPSSBI is the normalisation of the simulations. In order to compare the data, which are in arbitrary units, with the model simulations, which are in concentration or number of molecules, we apply to the simulations the same normalisation that was applied to the data, allowing a direct comparison. This is not possible out-of-the box in any other available software program, where the user needs to estimate additional parameters (scaling factors) or to modify the program themselves.