Adding new functionality to COPASI, a software for simulation of biological circuits in systems biology
Broto Vispe, José Manuel
Vaqueiro de Castro Alves, Rui Carlos
Universitat de Lleida. Escola Politècnica Superior
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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.
European research projects
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