A. Bachman and P. Sorger, New approaches to modeling complex biochemistry, Nature Methods, vol.6, issue.2, pp.130-131, 2011.
DOI : 10.1038/nmeth0211-130

L. Blinov, J. Yang, J. R. Faeder, and W. S. Hlavacek, Graph Theory for Rule-Based Modeling of Biochemical Networks, Proc. CSB, number 4230, 2006.
DOI : 10.1007/11905455_5

T. Corradini, F. Heindel, B. Hermann, and . König, Sesqui-Pushout Rewriting, Proc. ICGT, 2006.
DOI : 10.1007/11841883_4

J. Danos, W. Feret, R. Fontana, J. Harmer, and . Krivine, Abstracting the Differential Semantics of Rule-Based Models: Exact and Automated Model Reduction, 2010 25th Annual IEEE Symposium on Logic in Computer Science, 2010.
DOI : 10.1109/LICS.2010.44

URL : https://hal.archives-ouvertes.fr/hal-00520112

J. Danos, W. Feret, J. Fontana, and . Krivine, Scalable Simulation of Cellular Signaling Networks, Proc. APLAS, 2007.
DOI : 10.1007/978-3-540-76637-7_10

URL : https://hal.archives-ouvertes.fr/inria-00528409

J. Danos, W. Feret, J. Fontana, and . Krivine, Abstract Interpretation of Cellular Signalling Networks, Proc. VMCAI, 2008.
DOI : 10.1007/978-3-540-78163-9_11

URL : https://hal.archives-ouvertes.fr/inria-00528352

R. Danos, G. Harmer, and . Winskel, Constraining rule-based dynamics with types, Mathematical Structures in Computer Science, vol.2006, issue.02, 2012.
DOI : 10.1007/978-3-540-74407-8_3

URL : https://hal.archives-ouvertes.fr/hal-00694492

C. Danos and . Laneve, Formal molecular biology, Theoretical Computer Science, vol.325, issue.1, 2004.
DOI : 10.1016/j.tcs.2004.03.065

URL : https://hal.archives-ouvertes.fr/hal-00164591

J. Ehrig, U. Padberg, A. Prange, and . Habel, Adhesive high-level replacement systems: A new categorical framework for graph transformation, Proc. ICGT '04, 2006.

T. Hayman and . Heindel, Pattern Graphs and Rule-Based Models: The Semantics of Kappa, 2012.
DOI : 10.1007/978-3-642-37075-5_1

URL : https://hal.archives-ouvertes.fr/hal-00925345

C. Hayman, G. Thompson-walsh, and . Winskel, Simple containment structures in rulebased modelling of biochemical systems, Proc. SASB, 2011.

. Heckel, DPO Transformation with Open Maps, Proc. ICGT, number 7562 in LNCS, 2012.
DOI : 10.1007/978-3-642-33654-6_14

. Hermann, Permutation equivalence of DPO derivations with negative application conditions based on subobject transformation systems, ECEASST, vol.16, 2008.

. Löwe, Algebraic approach to single-pushout graph transformation, TCS, vol.109, 1993.

M. Winskel and . Nielsen, Models for concurrency, Handbook of Logic and the Foundations of Computer Science. OUP, 1995.