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Decision-Making in Stem Cells
Decision-Making in Stem Cells

Pluripotency is the unique characteristic of embryonic stem (ES) cells, which demonstrate the capacity to generate all somatic cell lineages. But how ES cells decide to transition to a given adult cell type remains unknown. In this project, we combine formal verification, model-checking and model synthesis into a new tool for uncovering the transcriptional program of pluripotency: a reasoning engine for interaction networks.

This project is a collaborative effort with Graziano Martello and Prof Austin Smith, based at the Wellcome Trust Centre for Stem Cell Research, University of Cambridge.


RE:IN is made available as an in-browser tool. To use the tool, please click here. To read the user tutorial for RE:IN, please click here.


The tool can also be run with examples pre-loaded. For further information on these examples, please refer to the tutorial.

  • Simple four-component example
  • Basic stem cell pluripotency example, constrained against 15 experimental observations
  • Stem cell pluripotency example, constrained against 23 experimental observations 
  • Identifying the minimal transcriptional network governing pluripotency. In this example, set the interaction limit to 17.

Sample Files

The examples that are referred to throughout the tutorial are available here. These can be loaded and run as instructed.