Abstract
In this paper we present KAMIStudio, an environment for biocuration of cellular signalling knowledge based on the KAMI framework. The environment provides an interface for the aggregation of decontextualized knowledge about individual protein-protein interactions, its interactive visualization, instantiation into signalling models and the subsequent generation of Kappa scripts that can be further used to study the dynamics of the modelled systems.
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Boutillier, P., Ehrhard, T., Krivine, J.: Incremental update for graph rewriting. In: Yang, H. (ed.) ESOP 2017. LNCS, vol. 10201, pp. 201–228. Springer, Heidelberg (2017). https://doi.org/10.1007/978-3-662-54434-1_8
Danos, V., Feret, J., Fontana, W., Harmer, R., Krivine, J.: Rule-based modelling of cellular signalling. In: Caires, L., Vasconcelos, V.T. (eds.) CONCUR 2007. LNCS, vol. 4703, pp. 17–41. Springer, Heidelberg (2007). https://doi.org/10.1007/978-3-540-74407-8_3
Faeder, J.R., Blinov, M.L., Hlavacek, W.S.: Rule-based modeling of biochemical systems with bionetgen. In: Systems Biology, pp. 113–167. Springer, Cham (2009). https://doi.org/10.1007/978-1-59745-525-1_5
Gyori, B.M., Bachman, J.A., Subramanian, K., Muhlich, J.L., Galescu, L., Sorger, P.K.: From word models to executable models of signaling networks using automated assembly. Mol. Syst. Biol. 13(11), 954 (2017)
Harmer, R.: Rule-based modelling and tunable resolution. EPTCS 9, 65–72 (2009)
Harmer, R., Le Cornec, Y.S., Légaré, S., Oshurko, I.: Bio-curation for cellular signalling: the KAMI project. In: CMSB 2017, pp. 3–19 (2017)
Romers, J.C., Krantz, M.: rxncon 2.0: a language for executable molecular systems biology. BioRxiv, p. 107136 (2017)
Todorov, P.V., Gyori, B.M., Bachman, J.A., Sorger, P.K.: INDRA-IPM: interactive pathway modeling using natural language with automated assembly. Bioinformatics, btz289 (2019)
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Harmer, R., Oshurko, E. (2019). KAMIStudio: An Environment for Biocuration of Cellular Signalling Knowledge. In: Bortolussi, L., Sanguinetti, G. (eds) Computational Methods in Systems Biology. CMSB 2019. Lecture Notes in Computer Science(), vol 11773. Springer, Cham. https://doi.org/10.1007/978-3-030-31304-3_20
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DOI: https://doi.org/10.1007/978-3-030-31304-3_20
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