Cadbiom (Computer Aided Design of BIOlogical Models) is a discrete modeling software.

What is Cadbiom?

Cadbiom is an free modeling software (GPL licensed). Based on Guarded transition semantic, it gives a formal framework to help the modelling of biological systems such as cell signaling network.

Who could use it?

Cadbiom offers a user friendly interface, making it as simply as possible to use. Molecular biologist, systems biologist, computer scientist and people interesting in biological systems modeling could use it.

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What sorts of analyses can I perform on Cadbiom?

Once you have a model, you could simulate it or check for a property. The simulation gives you the evolution of the model during a finite number of steps. With the checker you can search for example "how to reach a property?".

What kind of data do I need to use Cadbiom?

You could create a model with qualitative data; no protein concentration or reaction rates needed. The nodes usally represent biomolecules, like an activated receptor or a phosphorylated protein; while guarded transitions represent a biological reaction, like translocation, transcription, complex association. But you are free to make a model with your own level of interpretation and abstraction.

Thanks to the module biopax2cadbiom, the translation from various databases or ontologies formalized in BioPAX is an automatic feature.

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You can also use Pathway Interaction Database (PID) as data source. The automatic translation of PID pathway is a feature of this software (see user manual to get more precise information on the translation scheme).

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How to install it?

Cadbiom package is available on PyPI (Python Package Index), the official third-party software repository for Python language.

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