Participating Partners: UCD
NUID UCD TA will provide Users with access to expertise and computational services on mechanistic modelling of bionano interactions, calculation of nano-descriptors at the molecular and quantum level, statistical modelling for predicting nanomaterial and protein descriptors, evaluation of interaction constants and corona structure, as well as probabilities of MIEs and KEs for relevant AOPs. It will set up and maintain modelling servers, accessible via web interface.
Examples of the tools developed by NUID UCD include:
Dynamics Visualisation 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. 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.
Parameter Estimation Pipeline for Systems and Synthetic Biology (PEPSSBI (Java/C++)), employs optimisation 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, PEPSSBI applies 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.
The computation tools offered by NUID UCD for TA fall under two categories:
- Predictive nanotoxicology
- AOP search and Data visualisation