Bio-Curation for Cellular Signalling: The KAMI Project
The general question of what constitutes bio-curation for rule-based modelling of cellular signalling is posed. A general approach to the problem is presented, based on rewriting in hierarchies of graphs, together with a specific instantiation of the methodology that addresses our particular bio-curation problem. The current state of the ongoing development of the KAMI (Knowledge Aggregator & Model Instantiator) bio-curation tool, based on this approach, is detailed along with our plans for future development.
This work was sponsored by the Defense Advanced Research Projects Agency (DARPA) and the U.S. Army Research Office under grant numbers W911NF-14-1-0367 and W911NF-15-1-0544. The views, opinions, and/or findings contained in this report are those of the authors and should not be interpreted as representing the official views or policies, either expressed or implied, of the Defense Advanced Research Projects Agency or the Department of Defense.
The first author thanks specially Walter Fontana for many discussions over the years related to this work. Thanks also to Pierre Boutillier, John Bachman and Ben Gyori; and to Adrien Basso-Blandin and Ismaïl Lahkim Bennani who worked on prototypes of KAMI and ReGraph respectively.
- 1.Baldan, P.: Modelling concurrent computations: from contextual Petri nets to graph grammars. Ph.D. thesis, Department of Computer Science, University of Pisa (2000)Google Scholar
- 4.Danos, V., Feret, J., Fontana, W., Harmer, R., Hayman, J., Krivine, J., Thompson-Walsh, C., Winskel, G.: Graphs, rewriting and pathway reconstruction for rule-based models. In: Foundations of Software Technology and Theoretical Computer Science (2012)Google Scholar
- 6.Danos, V., Feret, J., Fontana, W., Harmer, R., Krivine, J.: Rule-based modelling and model perturbation. In: Priami, C., Back, R.-J., Petre, I. (eds.) Transactions on Computational Systems Biology XI. LNCS, vol. 5750, pp. 116–137. Springer, Heidelberg (2009). doi: 10.1007/978-3-642-04186-0_6 CrossRefGoogle Scholar
- 10.Gyori, B.M., Bachman, J.A., et al.: From word models to executable models of signaling networks using automated assembly. BioRxiv (2017)Google Scholar
- 12.Harmer, R.: Rule-Based Meta-modelling for Bio-curation. Habilitation à Diriger des Recherches, ENS Lyon (2017)Google Scholar
- 15.Laurent, J.: Causal analysis of rule-based models of signaling pathways. Master’s thesis, École Normale Supérieure, Paris, France (2015)Google Scholar
- 17.Mazurkiewicz, A.: Introduction to trace theory. In: The Book of Traces, pp. 3–41 (1995)Google Scholar
- 19.Nelander, S., et al.: Models from experiments: combinatorial drug perturbations of cancer cells. Mol. Syst. Biol. 4(1), 216 (2008)Google Scholar