Table 1.
Available formats.
| File extension | Multi-valued | Import | Export | Description and associated tools |
|---|---|---|---|---|
| sbml | x | x | x | SBML qual Exchange format (Chaouiya et al., 2013) |
| bnet | x | x | (Py)BoolNet (Müssel et al., 2010; Klarner et al., 2017) | |
| booleannet | x | x | booleannet (Albert et al., 2008) | |
| boolfunction | x | x | Boolean functions | |
| boolsim | x | x | boolsim (genYsis) (Garg et al., 2008) | |
| cnet | x | x | BNS (Dubrova and Teslenko, 2011) | |
| ginml | x | x | GINsim (Naldi et al., 2018a) | |
| mnet | x | x | x | Custom text format for multi-valued models |
| tt | x | x | x | Truth table |
| an | x | x | Pint automata network (Paulevé, 2017) | |
| apnn, pnml, ina | x | x | Conversion to Petri Net formats (Chaouiya et al., 2011) | |
| gna | x | x | GNA (Piecewise-linear formalism) (Batt et al., 2012) | |
| bnd | x | MaBoSS (Stochastic Boolean model) (Stoll et al., 2017) |
The Import/Export capabilities are listed in the corresponding columns (all formats can be exported). The formats natively supporting multi-valued models are also identified, other formats rely on implicit model booleanization.