Abstract
We introduce a programming language called BlenX. It has been specifically designed and implemented to model and simulate biological systems and is strongly inspired to process calculi. We describe all the features of BlenX together with its supporting tools and show the application of the language on real case studies.
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Notes
- 1.
One of the two boxes (or even both of them, even if it has little meaning) can be a Nil, a fake box that does nothing.
- 2.
Debugging is a computer-related term that refers to the process of finding errors in a program (or a model, in this case) and correcting them.
- 3.
A graph layout is an algorithm that decides, based on some criteria, how to place nodes and vertices in a 2D or 3D space.
- 4.
Layouts and algorithms can be added using a plug-in system, so that more can be easily added.
- 5.
Consider that at the beginning the monomer is free and thus it is in state 1.
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Dematté, L., Larcher, R., Palmisano, A., Priami, C., Romanel, A. (2010). Programming Biology in BlenX. In: Choi, S. (eds) Systems Biology for Signaling Networks. Systems Biology. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-5797-9_31
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DOI: https://doi.org/10.1007/978-1-4419-5797-9_31
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