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MODEL CHECKING AND STATE MACHINES
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Boutillier, P., Maasha, M., Li, X., Medina-Abarca, H. F., Krivine, J., Feret, J., … Fontana, W. (2018). The Kappa platform for rule-based modeling. Bioinformatics, 34(13), i583–i592. https://doi.org/10/gdrhw6
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Brown, R., & Porter, T. (2008). Category Theory and Higher Dimensional Algebra: potential descriptive tools in neuroscience. ArXiv:Math/0306223. Retrieved from http://arxiv.org/abs/math/0306223
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Dal Lago, U., & Hoshino, N. (2019). The Geometry of Bayesian Programming (pp. 1–13). https://doi.org/10/ggdk85
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Danos, V., Feret, J., Fontana, W., Harmer, R., & Krivine, J. (2008). Rule-Based Modelling, Symmetries, Refinements. In J. Fisher (Ed.), Formal Methods in Systems Biology (pp. 103–122). Berlin, Heidelberg: Springer. https://doi.org/10/dc5k68
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Fages, F., Calzone, L., & Soliman, S. (2006). BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge. Bioinformatics, 22(14), 1805–1807. https://doi.org/10/dfv
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Fages, F. (2014). Cells as Machines: Towards Deciphering Biochemical Programs in the Cell. In R. Natarajan (Ed.), Distributed Computing and Internet Technology (pp. 50–67). Cham: Springer International Publishing. https://doi.org/10/ggdf96
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Fages, F., Martinez, T., Rosenblueth, D. A., & Soliman, S. (2018). Influence Networks Compared with Reaction Networks: Semantics, Expressivity and Attractors. IEEE/ACM Trans. Comput. Biol. Bioinformatics, 15(4), 1138–1151. https://doi.org/10/ggdf94
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Lack, S., & Sobociński, P. (2005). Adhesive and quasiadhesive categories. RAIRO - Theoretical Informatics and Applications - Informatique Théorique et Applications, 39(3), 511–545. https://doi.org/10/fntwvv
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Wilkinson, D. J. (2006). Stochastic Modelling for Systems Biology. CRC Press.
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