Software

Becker-Doring Simulator

Simulator of Becker-Doring Systems in Python
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Input-Output GraphTool

Tool to verify Input-Output monotonicity on Chemical Reaction Networks.
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Translator of Threshold Boolean Networks into Reaction Systems

Implementation of the encoding of threshold Boolean networks into Reaction Systems in C.
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Formula-based predictors

Tool for the computation of formula-based predictors for Reaction Systems
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Social Network Simulator

Simulator of social networks developed in Java.
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Safety-critical Human Multitasking Modeling

Formal executable framework for the modeling and analysis of safety-critical human multitasking. Developed in Real-Time Maude.
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Simulator of Human Attention

Java implementation of a simulation algorithm of human attention
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Simulator of Internet Addiction

Simulation tools of the model of the dopaminergic system used to stude Internet addiction phenomena in social networks.
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Objective/MC

Objective/MC is a prototype high level model checking language. ObjMC is a compiler for the Objective/MC language, generating a DTMC PRISM model.
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Spatial P systems

Simulator for the territorial fish and herring models presented in the paper "Simulation of spatial P system models" by Roberto Barbuti, Andrea Maggiolo-Schettini, Paolo Milazzo, and Giovanni Pardini.
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Grid Systems modelling and simulation tool

A Java modelling and simulation tool for ecological systems described by Grid Systems. This software has been developed in the context of the Ph.D. thesis "Formal Modelling for Population Dynamics" by Suryana Setiawan
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DelaySim

A library to perform stochastic simulation of biological systems with delays. This software has been developed to perform simulations described in the Ph.D. thesis "Formal Modeling and Simulation of Biological Systems With Delays" by Giulio Caravagna
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Translation of the Lac operon model into NuSMV input language

The model developed for the paper "Modular Verification of Interactive Systems with an Application to Biology"
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Stochastic Antitumour-Immune System

The software developed for the paper "Antitumour Immune Surveillance Through Stochastic Oscillations". Journal of Theoretical Biology, Volume 265, Issue 3, pages 336-345
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AMSR2PRISM translator

A translator of Abstract Multiset Rewriting (AMSR) models into models for the PRISM model checker, that allows model checking of biological systems with uncertainty on kinetic rates
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SPECsim simulator

A simulator for studying phenomena of sympatric speciation by sexual selection in populations with different genotypes
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The Stochastic CLS machine

A simulator of biological systems based on the Stochastic Calculus of Looping Sequences (Stochastic CLS)
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