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GSOC 2020 PROJECT

Integrating RRPlugins with libRoadRunner

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

Contributor
Debashish Roy
Mentors
Kiri Choi, Herbert Sauro
Organization
National Resource for Network Biology (NRNB)Science and medicine
Program
GSoC 2020Completed

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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 optimizers 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 continue the work to develop a C/C++ based optimization plugins that can be used directly by LibRoadrunner with the help of RRPlugins. RRPlugins is a software that uses Libroadrunner as a dependency to load plugins and perform optimization tasks. Now if we build roadrunner we need to build plugins again since plugins are designed in such a way that they use LibRoadRunner and RRPlugins both as a dependency. To overcome this we decided to integrate both LibRoadRunner and RRPlugins and 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