The paper describing KappaNEURON that Oksana Sorokina, Douglas Armstrong and I presented at the Workshop on Hybrid Systems Biology 2014, Vienna and which has been already published on the arXiv finally appeared late last year in the proceedings volume. The paper describes an algorithm which incorporates stochastic rule-based models into deterministic compartmental models of neurons, and presents our implementation (KappaNEURON) of this hybrid system using the SpatialKappa and NEURON simulators.

  • Sterratt, D. C., Sorokina, O. and Armstrong, J. D. (2015). ‘Integration of rule-based models and compartmental models of neurons’. In O. Maler, Á. Halász, T. Dang and C. Piazza, eds., Hybrid Systems Biology: Second International Workshop, HSB 2013, Taormina, Italy, September 2, 2013 and Third International Workshop, HSB 2014, Vienna, Austria, July 23-24, 2014, Revised Selected Papers, vol. 7699 of Lecture Notes in Bioinformatics, pp. 143–158. Springer International Publishing, Cham. doi: 10.1007/978-3-319-27656-4_9. Preprint at arXiv:1411.4980