Jakob L. Andersen, Christoph Flamm, Daniel Merkle & Peter F. Stadler (2016):
A Software Package for Chemically Inspired Graph Transformation..
Lecture Notes in Computer Science 9761,
pp. 73–88,
doi:10.1007/978-3-319-40530-8_5.
Paolo Baldan (2000):
Modelling Concurrent Computations: from Contextual Petri Nets to Graph Grammars.
Computer Science Department - University of Pisa.
Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer, Jonathan Hayman, Jean Krivine, Chris Thompson-Walsh & Glynn Winskel (2012):
Graphs, rewriting and pathway reconstruction for rule-based models.
Proceedings of FSTTCS 2012 18,
pp. 276–288,
doi:10.4230/LIPIcs.FSTTCS.2012.276.
Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer & Jean Krivine (2007):
Rule-Based Modelling of Cellular Signalling, invited paper.
Proceedings of the 18th CONCUR 4703,
pp. 17–41,
doi:10.1007/978-3-540-74407-8_3.
Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer & Jean Krivine (2008):
Rule-Based Modelling, Symmetries, Refinements.
Proceedings of Formal Methods in Systems Biology FMSB,
pp. 103–122,
doi:10.1007/978-3-540-68413-8_8.
Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer & Jean Krivine (2010):
Abstracting the Differential Semantics of Rule-Based Models: Exact and Automated Model Reduction.
Proceedings of the 25th Annual IEEE Symposium on Logic in Computer Science,
pp. 362–381,
doi:10.1109/LICS.2010.44.
Vincent Danos, Jérôme Feret, Walter Fontana & Jean Krivine (2007):
Scalable Simulation of Cellular Signaling Networks.
Proceedings of Programming Languages and Systems: 5th Asian Symposium APLAS,
pp. 139–157,
doi:10.1007/978-3-540-76637-7_10.
Vincent Danos & Cosimo Laneve (2004):
Formal Molecular Biology.
Theoretical Computer Science 325(1),
pp. 69–110,
doi:10.1016/j.tcs.2004.03.065.
H. Ehrig, K. Ehrig, U. Prange & G. Taentzer (2006):
Fundamentals of Algebraic Graph Transformation (Monographs in Theoretical Computer Science. An EATCS Series).
Springer-Verlag New York, Inc.,
Secaucus, NJ, USA.
H. Ehrig, R. Heckel, M. Korff, M. Löwe, L. Ribeiro, A. Wagner & A. Corradini (1997):
Algebraic Approaches to Graph Transformation. Part II: Single Pushout Approach and Comparison with Double Pushout Approach.
In: Handbook of Graph Grammars and Computing by Graph Transformation.
Springer-Verlag New York, Inc.,
Secaucus, NJ, USA,
pp. 247–312,
doi:10.1142/9789812384720_0004.
Available at http://dl.acm.org/citation.cfm?id=278918.278930.
James R. Faeder, Michael L. Blinov & William S. Hlavacek (2009):
Rule-Based Modeling of Biochemical Systems with BioNetGen.
Systems Biology,
pp. 113–167,
doi:10.1007/978-1-59745-525-1_5.
Daniel T Gillespie (1977):
Exact stochastic simulation of coupled chemical reactions.
The Journal of Physical Chemistry 81(25),
pp. 2340–2361,
doi:10.1021/j100540a008.
Jean Krivine (2017):
Systems Biology.
ACM SIGLOG News 4(3),
pp. 43–61,
doi:10.1145/3129173.3129182.
Leen Lambers, Hartmut Ehrig & Fernando Orejas (2006):
Conflict Detection for Graph Transformation with Negative Application Conditions.
Proceedings of Graph Transformations: Third International Conference, ICGT,
pp. 61–76,
doi:10.1007/11841883_6.
Ugo Montanari & Francesca Rossi (1993):
Graph rewriting for a partial ordering semantics of concurrent constraint programming.
Theoretical Computer Science 109(1),
pp. 225 – 256,
doi:10.1016/0304-3975(93)90069-6.
eptcs@eptcs.org