This webpage is dedicated to the tool RE:IN, providing information on the latest version available, together with a tutorial, FAQ, and example files.
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.
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.
- A simple toy example, with two input signals and three components.
An embryonic stem cell pluripotency example, with 23 experimental constraints.
Identifying the minimal transcriptional network governing pluripotency. In this example, use the 'Find Minimal Models' functionality.
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.
- Yoli Shavit, Boyan Yordanov, Sara-Jane Dunn, Christoph M. Wintersteiger, Youssef Hamadi, and Hillel Kugler, Switching Gene Regulatory Networks, in 10th International Conference on Information Processing in Cells and Tissues (IPCAT 2015), Springer, September 2015.
- Sara-Jane Dunn, Graziano Martello, Boyan Yordanov, Stephen Emmott, and Austin Smith, Defining an essential transcriptional factor program for naïve pluripotency, in Science, vol. 344, no. 6188, pp. 1156 - 1160, 6 June 2014.
- Boyan Yordanov, Christoph M. Wintersteiger, Youssef Hamadi, and Hillel Kugler, Z34Bio: An SMT-based Framework for Analyzing Biological Computation, in SMT'13, July 2013.
- Boyan Yordanov, Christoph M. Wintersteiger, Youssef Hamadi, and Hillel Kugler, SMT-based Analysis of Biological Computation, in NASA Formal Methods Symposium 2013, Springer Verlag, May 2013.
- Boyan Yordanov, Christoph M. Wintersteiger, Youssef Hamadi, and Hillel Kugler, Z3-4biology SMT-based analysis of biological computation, no. MSR-TR-2012-31, 12 March 2012.
Windows bug-testing software cracks stem cell programs - New Scientist
Minimal toolkit for stem cell self-renewal - The Scientist
Theorem prover sheds new light on stem cell behaviour - Inside Microsoft Research