Reasoning Engine for Interaction Networks (RE:IN)

Reasoning Engine for Interaction Networks (RE:IN)

Established: January 1, 2012



This webpage is dedicated to the tool RE:IN, providing information on the latest version available, together with a tutorial, FAQ, and example files.


About RE:IN

The Reasoning Engine for Interaction Networks (RE:IN) is a tool that runs online in your web browser, which is designed for the synthesis and analysis of biological programs. Specifically, it encapsulates a methodology that uses automated reasoning to transform a set of critical components, possible interactions and regulation functions into a mechanistic explanation of experimental observations. Components and possible interactions are defined to construct an ‘abstract’ network topology, which implicitly defines a number of concrete topologies. Experimental observations are encoded as constraints on network trajectories. RE:IN synthesises those concrete networks that satisfy the constraints, and permits the user to query the set of consistent models to formulate predictions of untested behaviour.


To use the tool directly, please click here.

For new users of the tool, please see our tutorial. This also provides detail of the updated syntax in the latest version of RE:IN. We have also compiled a set of Frequently Asked Questions.

The following are some pre-loaded examples that correspond to published networks. The files used to generate these can be saved directly from the tool for examination.

The last three examples are explored in more detail in a publication that is currently under review, and will be updated with additional details once this manuscript is available.


This project began as a collaborative effort with Prof Austin Smith, based at the Wellcome Trust – Medical Research Council Stem Cell Institute, University of Cambridge, and Dr Graziano Martello, based at the University of Padova, Italy.