O. Andrei, A Rewriting Calculus for Graphs: Applications to Biology and Autonomous Systems, 2008.
URL : https://hal.archives-ouvertes.fr/tel-00337558

O. Andrei and &. Calder, A Model and Analysis of the AKAP Scaffold, Proc. of CS2Bio'10, 2010.
DOI : 10.1016/j.entcs.2010.12.002

O. Andrei, L. Ibanescu, and &. Kirchner, Non-intrusive Formal Methods and Strategic Rewriting for a Chemical Application, Algebra, Meaning, and Computation, pp.194-215, 2006.
DOI : 10.1007/11780274_11
URL : https://hal.archives-ouvertes.fr/inria-00115521

O. Andrei and &. Kirchner, A Higher-Order Graph Calculus for Autonomic Computing, Graph Theory, pp.15-26, 2009.
DOI : 10.1007/978-3-540-73449-9_5
URL : https://hal.archives-ouvertes.fr/inria-00328554

O. Andrei and &. Kirchner, A Port Graph Calculus for Autonomic Computing and Invariant Verification, Proceedings of the Fifth International Workshop on Computing with Terms and Graphs, pp.17-38, 2009.
DOI : 10.1016/j.entcs.2009.10.015
URL : https://hal.archives-ouvertes.fr/inria-00418560

D. Auber, Tulip ??? A Huge Graph Visualization Framework, Graph Drawing Software. Mathematics and Visualization Series, pp.105-126, 2003.
DOI : 10.1007/978-3-642-18638-7_5

D. Balasubramanian, A. Narayanan, C. P. Van-buskirk, and &. Gabor-karsai, The Graph Rewriting and Transformation Language: GReAT, 2006.

O. Bournez, G. Côme, V. Conraud, H. Kirchner, and L. Ibanescu, A Rule-Based Approach for Automated Generation of Kinetic Chemical Mechanisms, Lecture Notes in Computer Science, vol.2706, pp.30-45, 2003.
DOI : 10.1007/3-540-44881-0_4
URL : https://hal.archives-ouvertes.fr/inria-00099621

L. P. Cordella, P. Foggia, C. Sansone, and &. M. Vento, A (sub)graph isomorphism algorithm for matching large graphs, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.26, issue.10, pp.1367-1372, 2004.
DOI : 10.1109/TPAMI.2004.75

B. Courcelle, Graph Rewriting: An Algebraic and Logic Approach Handbook of Theoretical Computer Science, Volume B: Formal Models and Semantics, pp.193-242, 1990.

V. Danos and &. Laneve, Formal molecular biology, Theoretical Computer Science, vol.325, issue.1, pp.69-110, 2004.
DOI : 10.1016/j.tcs.2004.03.065
URL : https://hal.archives-ouvertes.fr/hal-00164591

H. Ehrig and G. Engels, Handbook of Graph Grammars and Computing by Graph Transformations, 1997.

H. Ehrig and H. Kreowski, Handbook of Graph Grammars and Computing by Graph Transformations, 1997.

C. Ermel, M. , and G. Taentzer, THE AGG APPROACH: LANGUAGE AND ENVIRONMENT, [12]. World Scientific, pp.551-603, 1997.
DOI : 10.1142/9789812815149_0014

J. R. Faeder, M. L. Blinov, &. William, and S. Hlavacek, Rule-Based Modeling of Biochemical Systems with BioNetGen, Methods in Molecular Biology, pp.133-168, 2009.
DOI : 10.1007/978-1-59745-525-1_5

M. Fernández, H. Kirchner, and O. Namet, A strategy language for graph rewriting. Submitted, see http, 2010.

M. Fernández and &. Namet, Strategic programming on graph rewriting systems, Proc. of the 1 st International Workshop on Strategies in Rewriting, Proving, and Programming, 2010.
DOI : 10.4204/EPTCS.44.1

C. Fox and S. Lappin, Lambda Calculus, Type Theory, and Natural Language II, Journal of Logic and Computation, vol.18, issue.2, p.203, 2008.
DOI : 10.1093/logcom/exm090
URL : http://logcom.oxfordjournals.org/cgi/content/short/18/2/203

R. Geiß, G. Veit-batz, D. Grund, S. Hack, and &. Szalkowski, GrGen: A Fast SPO-Based Graph Rewriting Tool, Lecture Notes in Computer Science, vol.4178, pp.383-397, 2006.
DOI : 10.1007/11841883_27

J. Krivine, R. Milner, and A. Troina, Stochastic Bigraphs, Electronic Notes in Theoretical Computer Science, vol.218, pp.73-96, 2008.
DOI : 10.1016/j.entcs.2008.10.006
URL : https://hal.archives-ouvertes.fr/hal-00530712

Y. Lafont, Interaction nets, Proceedings of the 17th ACM SIGPLAN-SIGACT symposium on Principles of programming languages , POPL '90, pp.95-108, 1990.
DOI : 10.1145/96709.96718

U. Nickel, J. Niere, and A. Zündorf, The FUJABA environment, Proceedings of the 22nd international conference on Software engineering , ICSE '00, pp.742-745, 2000.
DOI : 10.1145/337180.337620

D. Plump, The Graph Programming Language GP, Lecture Notes in Computer Science, vol.5725, pp.99-122, 2009.
DOI : 10.1007/978-3-642-03564-7_6

A. Rensink, The GROOVE Simulator: A??Tool for State Space Generation, AGTIVE. Lecture Notes in Computer Science, vol.3062, pp.479-485, 2003.
DOI : 10.1007/978-3-540-25959-6_40

A. Schürr, A. J. Winter, and A. Zündorf, THE PROGRES APPROACH: LANGUAGE AND ENVIRONMENT, [12]. World Scientific, pp.479-546, 1997.
DOI : 10.1142/9789812815149_0013

J. R. Ullmann, An Algorithm for Subgraph Isomorphism, Journal of the ACM, vol.23, issue.1, pp.31-42, 1976.
DOI : 10.1145/321921.321925
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.361.7741

D. Zhang and &. Zhang, Reserved Graph Grammar: A Specification Tool for Diagrammatic VPLs, Proc. of VL'97, p.284, 1997.