Cadbiom (Computer Aided Design of BIOlogical Models) is a discrete modeling software system.
Cadbiom is a free modeling software system (GPL licensed). Based on Guarded transition semantic, it gives a formal framework to help modeling of biological systems such as cell signaling network.
Cadbiom provides a user-friendly interface, making it as simply as possible, to use for biologists and computer scientists interested in biological systems modeling.
Cadbiom allows simulating rule-based models and properties checking. Simulating the model shows the evolution of the model during a finite number of steps. Model checking provides solutions to reach properties.
You can either create you own model or import models already formalized using BioPAX language. Thanks to the module biopax2cadbiom, the translation from various databases or ontologies formalized in BioPAX is an automatic feature
To create your own model, you need to describe the relationships (reaction) between nodes (gene, protein, complex). The reactions are described as transitions (translocation, transcription, complex association etc) from an origin node to a target node. The guard of the transition is composed a logical formula with nodes as variables and ∨, ∧ and ¬ as logical operator.
You can also use Pathway Interaction Database (PID) as data source. The automatic translation of PID pathways toward Cadbiom formalism is a feature of this software (see user manual to get more information on the translation scheme).
Cadbiom package is available on PyPI (Python Package Index), the official third-party software repository for Python language.