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Bibliography
The list of bibliographic references pertaining to parasim may be found in references.
The concept of biological system's robustness is summarized in Kitano 2007. Parasim is based on behaviour-oriented robustness and its properties, most importatly on property robustness in a point of perturbation space corresponding to the property satisfiability in its neighbourhood. This is discussed thouroughly in Fainekos 2009.
For property specification, parasim uses signal temporal logic defined in Maler 2006. [Donzé 2010a](Robust satisfaction of temporal logic over real-valued signals) deals with robustness computation over formulae of this logic. Point sampling used in parasim is similar to sampling proposed in Donzé 2007.
STL* is an extension of STL (Signal Temporal Logic) which defines a signal-value freeze operator (see Dluhos 2012).
There are several tools for robustness computation. Breach Toolbox (see [Donzé 2010b](Breach, A Toolbox for Verification and Parameter Synthesis of Hybrid Systems)) is the most similar to parasim, as parasim is built on the same theoretical basis. Another tool, which computes property-oriented robustness (in contrast to behaviour-oriented robustness), is BIOCHAM (see Rizk2008).
Parasim is developed in Java language on Java Standard Edition 7 platform. Its configuration is stored in XML. Models used in parasim are specified via SBML language (see Hucka 2003).
Parasim uses the JSBML library (see Drager 2011) to load models and GNU Octave to simulate trajectories during experiment analysis.
There are several sample experiments in parasim distribution:
- Band2012_DII-Venus_FullModel -- see Band 2012.
- SIR -- epidemiologic model introduced in Kermack 1927.
- SIR-vital -- epidemiologic SIR model with vital dynamics with constant non-specific death rates introduced in Kermack 1933.
- angiogenesis -- see Karagiannis 2004
- lorenz84 -- Lorenz system (see Lorenz2010)
- lotkav -- Lotka-Volterra predator-prey model introduced in Lotka 1925 and Volterra 1926.