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About bioNuSMV

bioNuSMV is a fork and extension of NuSMV-a by Hannes Klarner (hklarner), which adds a handful of features to ease the use of model checking by modellers of biological processes, in particular, in the context of the verification of qualitative regulatory networks.

It was implemented by André Mendes (Patriq) as part of the FCT funded research project ERGODiC, under the supervision of Pedro T. Monteiro (ptgm) at INESC-ID/Instituto Superior Técnico (Taguspark campus).

Features

With respect to the original NuSMV 2.6.0, this version adds the following features:

  • -a command line option, for printing and saving the set of accepting states (see NuSMV-a)
  • ARCTL (Action Restricted CTL) operators, for the verification of Mixed Transition Systems (see NuSMV-ARCTL-TLACE)
  • -ctlei command line option (or equivalently by the SPEC_E keyword), where a given CTL expression becomes TRUE if it is valid by at least one state in the set of the initial states (default is for all states in the set of initial states)
  • High-level RS and RAS operators, for the verification of weak and strong reachability, respectively
  • Recursive CTL operators

Below we present a small description of each of the functionalities.

-a command line option

The command line option -a adds support for printing initial states, accepting states and initial and accepting states of a BDD representing a CTL specification to the NuSMV model checking procedure. For a complete description of this functionality, please check the original NuSMV-a.

ARCTL operators

The first version of NuSMV with ARCTL operators was developed by Simon Busard, Franco Raimondi, José Vander Meulen , with the purpose of extending CTL (Computation Tree Logic) with action-restricted operators, for the verification of Mixed Transition Systems.

Here is a list of all ARCTL operators: EAX, EAU, AAX, AAU, EAF, AAF and AAG. The syntax for all these operators is: OPERATOR(action_expression)(ctl_expression) where action_expression is a restriction over transitions labels (i.e., variables under the VAR keyword) and ctl_expression is a restriction over state labels (i.e., variables under the VAR keyword).

Check tests/latch.smv for an example.

-ctlei command line option and the SPEC_E expression

For a given specification, the command line option -ctlei adds support to interpret each CTL expression, as TRUE if it is satisfied by at least one state in the set of the initial states (default is for all states in the set of initial states) You can use the flag both in interactive and batch mode.

Alternatively, one can use the SPEC_E keyword, replacing the SPEC keyword, in order to interpret each of the subsequent CTL expressions as TRUE if and only if it is satisfied by at least one state in the set of initial states.

RS and RAS operators

Each one of these operators is an alias to an already existing operators:

  • RS(ctl_expression) is an alias to EF ( ctl_expression & AG ( ctl_expression ))
  • RAS(action)(ctl_expression) is an alias to EAF (action)( ctl_expression & AAG ( action )( ctl_expression ))

Recursive CTL and ARCTL operators

We have included the following set of recursive CTL/ARCTL operators, in order to simplify the specification of nested CTL/ARCTL operators:

  • bla
  • bla

Using CTL:

  • it aliases OPERATOR(ctl_expresion_a, ctl_expresion_b, ..., ctl_expresion_z) to OPERATOR(ctl_expresion_a & ( OPERATOR ctl_expresion_b & ... & (OPERATOR ctl_expresion_z)))

Using ARCTL:

  • it aliases EAX(action_expression)(ctl_expresion_a, ctl_expresion_b, ..., ctl_expresion_z) = EAX(action_expression)(ctl_expresion_a & EAX(action_expression)(ctl_expresion_b & ... & EAX(action_expression)(ctl_expresion_z)))

This syntax only works for all CTL and ARCTL unary operators.