Adding new functionality to COPASI, a software for simulation of biological circuits in systems biology
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Date
2019-07
Authors
Broto Vispe, José Manuel
Other authors
Bartolomé, Jordi
Vaqueiro de Castro Alves, Rui Carlos
Universitat de Lleida. Escola Politècnica Superior
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Abstract
Currently there are many software available to build and simulate biological systems, but almost none of them is capable of implementing functions like the Power Laws, the Saturating Cooperative and the Saturating. The objective of this project was to add these functions to the COPASI software, so it can be more profitable for its users. COPASI is one of the most popular systems biology standalone programs currently available. It’s is programmed in C++ and Qt (GUI). To do these modifications, we had to analyze and understand the COPASI source code, and then we added the desired modifications. This was not a trivial modification, as these three functions share a common problem: they are declared differently depending on the number of substrates and modifiers of the reaction in which is selected. Usually, functions are defined as static functions, but these three were dynamic functions and that is why it was a complex problem to implement this modification. The objective has been fulfilled successfully and now it is more usable by the users. A comparison test between original COPASI and the modified COPASI was carried out by building the Overall Feedback model on both version. In this test it has been possible to appreciate the effectiveness of the implemented functions by decreasing the time by half in the complete creation of the model. The time has been highly reduced as in the modified version user must not implement manually any kind of function.