Gene Regulation in the Pi Calculus: Simulating Cooperativity at the Lambda Switch

Notes:

  • The lambda switch is a standard model of a bacterial gene regulation mechanism. Lambda is a virus infecting E. coli.
  • The lambda switch incorporates both positive and negative feedback, as well as many different kinds of feedback loop. Only transcriptional control was considered in this talk.
  • Lambda can operate in two phases: the lysogenic and the lytic phases. In lysogeny, the lambda genome is passivated and incorporated into the host cell, being replicated by the host across generations, to be reactivated into the lytic phase in some later generation. Unprompted reactivation is very rare, and is induced artificially ("induction signal") for experimental purposes.
  • [Aside: with our "alternative model" strategy for encoding biochemical reactions, does bisimulation still compute something relevant?]
  • The paper covers various implementations tricks (handshakes, timers) for encoding the various interactions of proteins — there wasn't time to cover the techniques during the talk.
  • Modularity within models is a major challenge - the implementation tricks required seemed to make the model monolithic (?)
  • Accessibility of π-based modelling tools to non-computer-scientists is also very important
  • A question from the end: the table in the slides listing the various states of each reagent ("states of molecular actors") is a-priori information on the control flow in the system (is it related to the lack of ambients?). The question was: how might that table be automatically derived rather than input a-priori? </ul>