Reasoning Engine for Interaction Networks (RE:IN)

Reasoning Engine for Interaction Networks (RE:IN)

Established: January 1, 2012

Publications

Overview

This webpage is dedicated to the tool RE:IN, providing information on the latest version available.

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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 dynamic explanation of experimental observations. Components and possible interactions are defined to construct an ‘abstract’ network topology, which implicitly defines a number of concrete topologies. This formalism allows us to capture some of the uncertainty in the interactions that may or may not exist between biological components due to noisy or limited experimental data. 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.

Software design patterns provide abstract, reusable solutions to frequently encountered problem. In this project, we will explore whether biology also exploits design patterns in the regulatory programs controlling cellular behaviours. We will focus on the role of small regulatory motifs that are known to be enriched in living systems, and which cluster in specific ways, and employ formal methods to understand how structure gives rise to function in these motifs. A new regulatory system based on engineered RNA interactions will be developed to allow for the reliable creation of large regulatory circuits, which will then be used to implement novel regulatory programs from motif-based design rules.

4-year PhD Scholarship, Supervisor: Dr Thomas Gorochowski (School of Biological Sciences, University of Bristol, UK) Co-supervisors: Dr Boyan Yordanov, Dr Sara-Jane Dunn (Biological Computation Group, Microsoft Research Cambridge, UK) and Lucia Marucci (Engineering Mathematics, University of Bristol, UK).

Find out more information here.


 

Using RE:IN

There is computational interface with notebooks for the underlying Reasoning Engine on Github.

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