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GSOC 2019 PROJECT

Integrating RRPlugins with libRoadRunner and devloping Differential Evolution optimizer plugin

LibRoadrunner is a high performance SBML based simulator that uses LLVM to generate very efficient runtime code. This enables LibRoadrunner to...

Contributor
Debashish Roy
Mentor
Herbert Sauro
Organization
National Resource for Network Biology (NRNB)Science and medicine
Program
GSoC 2019Completed

About this project

Description from the program archive

<p>LibRoadrunner is a high performance SBML based simulator that uses LLVM to generate very efficient runtime code. This enables LibRoadrunner to simulate models on par with compiled C/C++ code. By combining Libroadrunner with standard optimization algorithms it is possible to use Libroadrunner to fit models to data. At present this is done by writing code to link the standard Python optimizer available via scipy with Libroadrunner. Although this works, it is inefficient and for large models, it is not practical. In this project, we would like to develop a C/C++ based differential evolution plugin that can be used directly by Libroadrunner (after integrating it with RRPlugins) without having to go via Python. This would enable us to provide high performance optimization capabilities.</p>

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Data: Google Summer of Code public archive. This project in the official archive