18 R. Harmer et al.
Acknowledgements.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 con-
tained in this report are those of the authors and should not be interpreted as represent-
ing 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 Isma ̈ıl Lahkim Bennani who worked on pro-
totypes ofKAMIandReGraphrespectively.
References
- Baldan, P.: Modelling concurrent computations: from contextual Petri nets to
graph grammars. Ph.D. thesis, Department of Computer Science, University of
Pisa (2000) - Basso-Blandin, A., Fontana, W., Harmer, R.: A knowledge representation meta-
model for rule-based modelling of signalling networks. EPTCS 204 , 47–59 (2016) - Corradini, A., Heindel, T., Hermann, F., K ̈onig, B.: Sesqui-pushout rewriting.
In: Corradini, A., Ehrig, H., Montanari, U., Ribeiro, L., Rozenberg, G. (eds.)
ICGT 2006. LNCS, vol. 4178, pp. 30–45. Springer, Heidelberg (2006). doi:10.1007/
118418834 - 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) - 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). doi:10.1007/978-3-540-74407-8 3 - 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 - Danos, V., Harmer, R., Winskel, G.: Constraining rule-based dynamics with types.
MSCS 23 (2), 272–289 (2013) - Demir, E., et al.: The BioPAX community standard for pathway data sharing. Nat.
Biotechnol. 28 (9), 935–942 (2010) - Gerhart, J.: 1998 Warkany lecture: signaling pathways in development. Teratology
60 (4), 226–239 (1999) - Gyori, B.M., Bachman, J.A., et al.: From word models to executable models of
signaling networks using automated assembly. BioRxiv (2017) - Harmer, R.: Rule-based modelling and tunable resolution. EPTCS 9 , 65–72 (2009)
- Harmer, R.: Rule-Based Meta-modelling for Bio-curation. Habilitation `a Diriger
des Recherches, ENS Lyon (2017) - Harris, L.A., et al.: BioNetGen 2.2: advances in rule-based modeling. Bioinformat-
ics 32 (21), 3366–3368 (2016) - Janes, K.A., et al.: A systems model of signaling identifies a molecular basis set
for cytokine-induced apoptosis. Science 310 (5754), 1646–1653 (2005)