springer.bib

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@inproceedings{DBLP:conf/ismb/ReddyML93,
  author    = {Venkatramana N. Reddy and
               Michael L. Mavrovouniotis and
               Michael N. Liebman},
  title     = {Petri Net Representations in Metabolic Pathways},
  booktitle = {Proceedings of the 1st International Conference on Intelligent Systems
               for Molecular Biology},
  pages     = {328--336},
  year      = {1993},
  publisher = {{AAAI}},
}

@article{DBLP:journals/jsamas/HofestadtH94,
  author    = {Ralf Hofest{\"{a}}dt},
  title     = {A {P}etri net application of metabolic processes},
  journal   = {Journal of System Analysis, Modeling and Simulation},
  volume    = {16},
  pages     = {113--122},
  year      = {1994}
}

@article{DBLP:journals/jamia/PelegRA05,
  author    = {Mor Peleg and
               Daniel L. Rubin and
               Russ B. Altman},
  title     = {Using {P}etri Net Tools to Study Properties and Dynamics
               of Biological Systems},
  journal   = {{Journal of the American Medical Informatics Association}},
  volume    = {12},
  number    = {2},
  pages     = {181--199},
  year      = {2005},
  doi       = {10.1197/jamia.M1637}}
}

@article{DBLP:journals/fuin/Popova-ZeugmannHK05,
  author    = {Louchka Popova{-}Zeugmann and
               Monika Heiner and
               Ina Koch},
  title     = {Time {P}etri Nets for Modelling and Analysis of Biochemical Networks},
  journal   = {Fundamenta Informaticae},
  volume    = {67},
  number    = {1-3},
  pages     = {149--162},
  year      = {2005}
}

@article{DBLP:journals/isb/HofestadtT98,
  author    = {Ralf Hofest{\"{a}}dt and
               S. Thelen},
  title     = {Quantitative modeling of biochemical networks},
  journal   = {In Silico Biology},
  volume    = {1},
  number    = {1},
  pages     = {39--53},
  year      = {1998},
  url       = {http://content.iospress.com/articles/in-silico-biology/isb00006}
}

@article{DBLP:journals/isb/VossHK03,
  author    = {Klaus Voss and
               Monika Heiner and
               Ina Koch},
  title     = {Steady state analysis of metabolic pathways using {P}etri nets},
  journal   = {In Silico Biology},
  volume    = {3},
  number    = {3},
  pages     = {367--387},
  year      = {2003},
  url       = {http://content.iospress.com/articles/in-silico-biology/isb00102}
}

@article{DBLP:journals/nc/MatsunoNM11,
  author    = {Hiroshi Matsuno and
               Masao Nagasaki and
               Satoru Miyano},
  title     = {Hybrid {P}etri net based modeling for biological pathway simulation},
  journal   = {Natural Computing},
  volume    = {10},
  number    = {3},
  pages     = {1099--1120},
  year      = {2011},
  url       = {https://doi.org/10.1007/s11047-009-9164-6},
  doi       = {10.1007/s11047-009-9164-6}
}
@article{DBLP:journals/bib/Chaouiya07,
  author    = {Claudine Chaouiya},
  title     = {Petri net modelling of biological networks},
  journal   = {Briefings in Bioinformatics},
  volume    = {8},
  number    = {4},
  pages     = {210--219},
  year      = {2007},
  url       = {https://doi.org/10.1093/bib/bbm029},
  doi       = {10.1093/bib/bbm029}
}


@article{DBLP:journals/nc/BaldanCMS10,
  author    = {Paolo Baldan and
               Nicoletta Cocco and
               Andrea Marin and
               Marta Simeoni},
  title     = {Petri nets for modelling metabolic pathways: a survey},
  journal   = {Natural Computing},
  volume    = {9},
  number    = {4},
  pages     = {955--989},
  year      = {2010},
  doi       = {10.1007/s11047-010-9180-6},
  timestamp = {Sun, 28 May 2017 13:24:56 +0200},
  biburl    = {https://dblp.org/rec/bib/journals/nc/BaldanCMS10},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}

@article{PNsynthetic,
	Author = {Monika Heiner},
	Bibsource = {dblp computer science bibliography, https://dblp.org},
	Biburl = {https://dblp.org/rec/bib/journals/nc/Heiner11},
	Date-Added = {2019-07-03 14:30:01 +0000},
	Date-Modified = {2019-07-03 14:30:08 +0000},
	Doi = {10.1007/s11047-011-9253-1},
	Journal = {Natural Computing},
	Number = {2},
	Pages = {633--638},
	Timestamp = {Sun, 02 Jun 2019 20:43:43 +0200},
	Title = {Preface: Petri nets for Systems and Synthetic Biology},
	Url = {https://doi.org/10.1007/s11047-011-9253-1},
	Volume = {10},
	Year = {2011},
	Bdsk-Url-1 = {https://doi.org/10.1007/s11047-011-9253-1},
	Bdsk-Url-2 = {http://dx.doi.org/10.1007/s11047-011-9253-1}}

@inproceedings{RC19,
	Author = {Anna Philippou and Kyriaki Psara and Harun Siljak},
	Bibsource = {dblp computer science bibliography, https://dblp.org},
	Biburl = {https://dblp.org/rec/bib/conf/rc/PhilippouPS19},
	Booktitle = {Reversible Computation - 11th International Conference, {RC} 2019},
	Crossref = {DBLP:conf/rc/2019},
	Date-Added = {2019-07-03 13:42:03 +0000},
	Date-Modified = {2019-07-03 13:49:31 +0000},
	Doi = {10.1007/978-3-030-21500-2\_15},
	Pages = {238--245},
	Timestamp = {Mon, 17 Jun 2019 13:44:52 +0200},
	Title = {Controlling Reversibility in Reversing {P}etri Nets with Application 
          to Wireless Communications},
	Url = {https://doi.org/10.1007/978-3-030-21500-2\_15},
	Year = {2019},
	Bdsk-Url-1 = {https://doi.org/10.1007/978-3-030-21500-2%5C_15},
	Bdsk-Url-2 = {http://dx.doi.org/10.1007/978-3-030-21500-2%5C_15}}

@proceedings{DBLP:conf/rc/2019,
	Bibsource = {dblp computer science bibliography, https://dblp.org},
	Biburl = {https://dblp.org/rec/bib/conf/rc/2019},
	Date-Added = {2019-07-03 13:42:03 +0000},
	Date-Modified = {2019-07-03 13:42:03 +0000},
	Doi = {10.1007/978-3-030-21500-2},
	Editor = {Michael Kirkedal Thomsen and Mathias Soeken},
	Isbn = {978-3-030-21499-9},
	Publisher = {Springer},
	Series = {Lecture Notes in Computer Science},
	Timestamp = {Mon, 17 Jun 2019 13:44:07 +0200},
	Title = {Reversible Computation - 11th International Conference, {RC} 2019, Lausanne, Switzerland, June 24-25, 2019, Proceedings},
	Url = {https://doi.org/10.1007/978-3-030-21500-2},
	Volume = {11497},
	Year = {2019},
	Bdsk-Url-1 = {https://doi.org/10.1007/978-3-030-21500-2},
	Bdsk-Url-2 = {http://dx.doi.org/10.1007/978-3-030-21500-2}}

@article{PNbiology,
	Author = {Bl{\"a}tke, Mary Ann and Heiner, M and Marwan, Wolfgang},
	Date-Added = {2019-07-03 12:35:52 +0000},
	Date-Modified = {2019-07-03 12:36:07 +0000},
	Journal = {Technical Report, Otto-von-Guericke University Magdeburg},
	Title = {Petri nets in systems biology},
	Year = {2011}}

@book{PNs,
	Author = {Wolfgang Reisig},
	Bibsource = {dblp computer science bibliography, https://dblp.org},
	Biburl = {https://dblp.org/rec/bib/books/daglib/0032298},
	Date-Added = {2019-07-02 16:11:53 +0000},
	Date-Modified = {2019-07-02 16:11:53 +0000},
	Doi = {10.1007/978-3-642-33278-4},
	Isbn = {978-3-642-33277-7},
	Publisher = {Springer},
	Timestamp = {Tue, 16 May 2017 14:01:34 +0200},
	Title = {Understanding Petri Nets - Modeling Techniques, Analysis Methods, Case Studies},
	Url = {https://doi.org/10.1007/978-3-642-33278-4},
	Year = {2013},
	Bdsk-Url-1 = {https://doi.org/10.1007/978-3-642-33278-4},
	Bdsk-Url-2 = {http://dx.doi.org/10.1007/978-3-642-33278-4}}

@article{RPNJournal,
	Author = {Anna Philippou and Kyriaki Psara},
	Date-Added = {2019-07-02 16:05:41 +0000},
	Date-Modified = {2019-07-02 16:05:41 +0000},
	Journal = {Under submission},
	Title = {Reversing {P}etri nets with cyclic structures},
	Year = {2019}}

@inproceedings{BoundedPNs,
	Author = {Kamila Barylska and {\L}ukasz Mikulski and Marcin Pi{\c a}tkowski and Maciej Koutny and Evgeny Erofeev},
	Booktitle = {Proceedings of CS{\&}P 2016},
	Date-Added = {2019-07-02 16:03:59 +0000},
	Date-Modified = {2019-07-02 16:03:59 +0000},
	Pages = {74--85},
	Publisher = {CEUR-WS.org},
	Series = {{CEUR} Workshop Proceedings},
	Title = {Reversing Transitions in Bounded {P}etri Nets},
	Volume = {1698},
	Year = {2016}}

@inproceedings{PetriNets,
	Author = {Kamila Barylska and Maciej Koutny and {\L}ukasz Mikulski and Marcin Pi{\ a}tkowski},
	Booktitle = {Proceedings of RC 2016},
	Date-Added = {2019-07-02 16:03:51 +0000},
	Date-Modified = {2019-07-02 16:03:51 +0000},
	Pages = {105--118},
	Publisher = {Springer},
	Series = {LNCS 9720},
	Title = {Reversible Computation vs. Reversibility in {P}etri Nets},
	Year = {2016}}

@inproceedings{betabinders,
	Abstract = {This paper presents binders and operators, in the process calculi tradition, to reason about biological interactions.},
	Author = {Priami, Corrado and Quaglia, Paola},
	Booktitle = {Computational Methods in Systems Biology},
	Editor = {Danos, Vincent and Schachter, Vincent},
	Isbn = {978-3-540-25974-9},
	Pages = {20--33},
	Publisher = {Springer},
	Title = {Beta Binders for Biological Interactions},
	Year = {2005}}

@article{pmid19399430,
	Author = {Faeder, J. R. and Blinov, M. L. and Hlavacek, W. S.},
	Journal = {Methods in Molecular Biology},
	Pages = {113--167},
	Title = {{{R}ule-based modeling of biochemical systems with {B}io{N}et{G}en}},
	Volume = {500},
	Year = {2009}}


@inproceedings{RPNs,
  author    = {Anna Philippou and
               Kyriaki Psara},
  title     = {Reversible Computation in Petri Nets},
  booktitle = {Reversible Computation - 10th International Conference, {RC} 2018,
               Leicester, UK, September 12-14, 2018, Proceedings},
  pages     = {84--101},
  year      = {2018},
  crossref  = {DBLP:conf/rc/2018},
  url       = {https://doi.org/10.1007/978-3-319-99498-7\_6},
  doi       = {10.1007/978-3-319-99498-7\_6},
  timestamp = {Tue, 14 May 2019 10:00:38 +0200},
  biburl    = {https://dblp.org/rec/bib/conf/rc/PhilippouP18},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}

@proceedings{DBLP:conf/rc/2018,
  editor    = {Jarkko Kari and
               Irek Ulidowski},
  title     = {Reversible Computation - 10th International Conference, {RC} 2018,
               Leicester, UK, September 12-14, 2018, Proceedings},
  series    = {Lecture Notes in Computer Science},
  volume    = {11106},
  publisher = {Springer},
  year      = {2018},
  url       = {https://doi.org/10.1007/978-3-319-99498-7},
  doi       = {10.1007/978-3-319-99498-7},
  isbn      = {978-3-319-99497-0},
  timestamp = {Tue, 14 May 2019 10:00:38 +0200},
  biburl    = {https://dblp.org/rec/bib/conf/rc/2018},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}


@incollection{RPNsold,
	Author = {Anna Philippou and Kyriaki Psara},
	Booktitle = {Proceedings of {RC} 2018},
	Date-Added = {2019-06-27 18:14:30 +0000},
	Date-Modified = {2019-07-03 14:19:36 +0000},
	Doi = {10.1007/978-3-319-99498-7\_6},
	Pages = {84--101},
	Publisher = {Springer},
	Series = {Lecture Notes in Computer Science},
	Title = {Reversible Computation in {P}etri Nets},
	Year = {2018},
	Volume = {11106}}

@inproceedings{RPNtoCPN,
	Author = {Kamila Barylska and Anna Gogoli\'{n}ska and {\L}ukasz Mikulski and Anna Philippou and 
Marcin Pi{\c a}tkowski and Kyriaki Psara},
	Booktitle = {Proceedings of ATAED 2018},
	Date-Added = {2019-06-27 18:14:30 +0000},
	Date-Modified = {2019-06-27 18:14:30 +0000},
	Pages = {91--111},
	Series = {{CEUR} Workshop Proceedings},
volume = 2115,
	Title = {Reversing Computations Modelled by Coloured {P}etri Nets},
	Year = {2018}}

@article{GrahamSolomons04,
	Abstract = {Phosphoglucose isomerase (PGI) is an enzyme of glycolysis that interconverts glucose 6-phosphate (G6P) and fructose 6-phosphate (F6P) but, outside the cell, is a multifunctional cytokine. High-resolution crystal structures of the enzyme from mouse have been determined in native form and in complex with the inhibitor erythrose 4-phosphate, and with the substrate glucose 6-phosphate. In the substrate-bound structure, the glucose sugar is observed in both straight-chain and ring forms. This structure supports a specific role for Lys518 in enzyme-catalyzed ring opening and we present a ''push--pull'' mechanism in which His388 breaks the O5--C1 bond by donating a proton to the ring oxygen atom and, simultaneously, Lys518 abstracts a proton from the \{C1\} hydroxyl group. The reverse occurs in ring closure. The transition from ring form to straight-chain substrate is achieved through rotation of the C3--C4 bond, which brings the C1--C2 region into close proximity to Glu357, the base catalyst for the isomerization step. The structure with \{G6P\} also explains the specificity of \{PGI\} for glucose 6-phosphate over mannose 6-isomerase (M6P). To isomerize \{M6P\} to \{F6P\} requires a rotation of its C2--C3 bond but in \{PGI\} this is sterically blocked by Gln511. },
	Author = {J.T. Graham Solomons and Ella M. Zimmerly and Suzanne Burns and N. Krishnamurthy and Michael K. Swan and Sandra Krings and Hilary Muirhead and John Chirgwin and Christopher Davies},
	Doi = {http://dx.doi.org/10.1016/j.jmb.2004.07.085},
	Issn = {0022-2836},
	Journal = {Journal of Molecular Biology},
	Keywords = {X-ray crystallography},
	Number = {3},
	Pages = {847--860},
	Title = {The Crystal Structure of Mouse Phosphoglucose Isomerase at Resolution and its Complex with Glucose 6-Phosphate Reveals the Catalytic Mechanism of Sugar Ring Opening},
	Url = {http://www.sciencedirect.com/science/article/pii/S0022283604009258},
	Volume = {342},
	Year = {2004},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0022283604009258},
	Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.jmb.2004.07.085}}

@article{psystems,
	Abstract = {We introduce a new computability model, of a distributed parallel type, based on the notion of a membrane structure. Such a structure consists of several cell-like membranes, recurrently placed inside a unique ``skin'' membrane. A plane representation is a Venn diagram without intersected sets and with a unique superset. In the regions delimited by the membranes there are placed objects. These objects are assumed to evolve: each object can be transformed in other objects, can pass through a membrane, or can dissolve the membrane in which it is placed. A priority relation between evolution rules can be considered. The evolution is done in parallel for all objects able to evolve. In this way, we obtain a computing device (we call it a P system): start with a certain number of objects in a certain membrane and let the system evolve; if it will halt (no object can further evolve), then the computation is finished, with the result given as the number of objects in a specified membrane. If the development of the system goes forever, then the computation fails to have an output. We prove that the P systems with the possibility of objects to cooperate characterize the recursively enumerable sets of natural numbers; moreover, systems with only two membranes suffice. In fact, we do not need cooperating rules, but we only use catalysts, specified objects which are present in the rules but are not modified by the rule application. One catalyst suffices. A variant is also considered, with the objects being strings over a given alphabet. The evolution rules are now based on string transformations. We investigate the case when either the rewriting operation from Chomsky grammars (with respect to context-free productions) or the splicing operation from H systems investigated in the \{DNA\} computing is used. In both cases, characterizations of recursively enumerable languages are obtained by very simple P systems: with three membranes in the rewriting case and four in the splicing case. Several open problems and directions for further research are formulated },
	Author = {Gheorghe P{\v{a}}un},
	Doi = {http://dx.doi.org/10.1006/jcss.1999.1693},
	Issn = {0022-0000},
	Journal = {Journal of Computer and System Sciences},
	Keywords = {natural computing},
	Number = {1},
	Pages = {108--143},
	Title = {Computing with Membranes},
	Url = {http://www.sciencedirect.com/science/article/pii/S0022000099916938},
	Volume = {61},
	Year = {2000},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0022000099916938},
	Bdsk-Url-2 = {http://dx.doi.org/10.1006/jcss.1999.1693}}

@article{psystemssynanti,
	Abstract = {In the attempt to have a framework where the computation is done by communication only, we consider the biological phenomenon of trans-membrane transport of couples of chemicals (one say symport when two chemicals pass together through a membrane, in the same direction, and antiport when two chemicals pass simultaneously through a membrane, in opposite directions). Surprisingly enough, membrane systems without changing (evolving) the used objects and with the communication based on rules of this type are computationally complete, and this result is achieved even for pairs of communicated objects (as encountered in biology). Five membranes are used; the number of membranes is reduced to two if more than two chemicals may collaborate when passing through membranes.},
	Author = {P{\v{a}}un, Andrei and P{\v{a}}un, Gheorghe},
	Doi = {10.1007/BF03037362},
	Issn = {1882-7055},
	Journal = {New Generation Computing},
	Number = {3},
	Pages = {295--305},
	Title = {The power of communication: P systems with symport/antiport},
	Url = {http://dx.doi.org/10.1007/BF03037362},
	Volume = {20},
	Year = {2002},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/BF03037362}}


@article{irekNGC2019,
        Author = {P{\v{a}}un, Andrei and P{\v{a}}un, Gheorghe},
        Journal = {New Generation Computing},
        Number = {3},
        Pages = {295--305},
        Title = {The power of communication: P systems with symport/antiport},
        Volume = {20},
        Year = {2019}}

@article{irekNGC2018,
  author    = {Irek Ulidowski and
               Iain Phillips and
               Shoji Yuen},
  title     = {Reversing Event Structures},
  journal   = {New Generation Comput.},
  volume    = {36},
  number    = {3},
  pages     = {281--306},
  year      = {2018},
  url       = {https://doi.org/10.1007/s00354-018-0040-8},
  doi       = {10.1007/s00354-018-0040-8},
  biburl    = {https://dblp.org/rec/bib/journals/ngc/UlidowskiPY18}
}


@inproceedings{cham,
	Acmid = {96717},
	Address = {New York, NY, USA},
	Author = {Berry, Gerard and Boudol, Gerard},
	Booktitle = {Proceedings of the 17th ACM SIGPLAN-SIGACT Symposium on Principles of Programming Languages, POPL '90},
	Doi = {10.1145/96709.96717},
	Isbn = {0-89791-343-4},
	Location = {San Francisco, California, USA},
	Numpages = {14},
	Pages = {81--94},
	Publisher = {ACM},
	Title = {The Chemical Abstract Machine},
	Url = {http://doi.acm.org/10.1145/96709.96717},
	Year = {1990},
	Bdsk-Url-1 = {http://doi.acm.org/10.1145/96709.96717},
	Bdsk-Url-2 = {http://dx.doi.org/10.1145/96709.96717}}

@article{pmid23812977,
	Author = {Masaaki Kotera and Yasuo Tabei and Yoshihiro Yamanishi and Toshiaki Tokimatsu and Susumu Goto},
	Journal = {Bioinformatics},
	Number = {13},
	Pages = {135--144},
	Title = {{{S}upervised de novo reconstruction of metabolic pathways from metabolome-scale compound sets}},
	Volume = {29},
	Year = {2013}}

@misc{regev2000,
	Author = {Aviv Regev and William Silverman and Ehud Shapiro},
	Note = {\url{http://www.wisdom.weizmann.ac.il/~biospi/pi_draft.ps}. Accessed 5-May-2016},
	Title = {Representing biomolecular processes with computer process algebra: $\pi$-calculus programs of signal transduction pathways},
	Url = {http://www.wisdom.weizmann.ac.il/~biospi/pi_draft.ps},
	Year = {2000},
	Bdsk-Url-1 = {http://www.wisdom.weizmann.ac.il/~biospi/pi_draft.ps}}

@inproceedings{regev2001a,
	Address = {Berlin},
	Author = {Aviv Regev},
	Booktitle = {2nd Workshop on Computation of Biochemical Pathways and Genetic Networks},
	Editor = {Ralph Gauges and C. van Gend and U. Kummer},
	Pages = {109--115},
	Publisher = {Logos},
	Title = {Representation and simulation of molecular pathways in the stochastic pi-calculus},
	Year = {2001}}

@inproceedings{regev2001b,
	Author = {Aviv Regev and William Silverman and Ehud Shapiro},
	Booktitle = {Pacific Symposium on Biocomputing 2001},
	Editor = {Russ B. Altman and A. Keith Dunker and Lawrence Hunker},
	Pages = {459--470},
	Publisher = {World Scientific},
	Title = {{{R}epresentation and simulation of biochemical processes using the $\pi$-calculus process algebra}},
	Year = {2000}}

@inbook{Regev2004old,
	Author = {Regev, Aviv and Shapiro, Ehud},
	Booktitle = {Modelling in Molecular Biology},
	Editor = {Ciobanu, Gabriel and Rozenberg, Grzegorz},
	Isbn = {978-3-642-18734-6},
	Pages = {219--266},
	Publisher = {Springer},
	Title = {The $\pi$-calculus as an abstraction for biomolecular systems},
	Year = {2004},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/978-3-642-18734-6_11}}

@inproceedings{Regev2004,
author="Regev, Aviv
and Shapiro, Ehud",
editor="Ciobanu, Gabriel
and Rozenberg, Grzegorz",
title="The $\pi$-calculus as an Abstraction for Biomolecular Systems",
bookTitle="Modelling in Molecular Biology",
year="2004",
publisher="Springer",
pages="219--266",
abstract="Biochemical processes, carried out by networks of proteins, underlies the major functions of living cells ([8, 60]). Although such systems are the focus of intensive experimental research, the mountains of knowledge about the function, activity, and interaction of molecular systems in cells remain fragmented. While computational methods are key to addressing this challenge ([8, 60]), they require the adoption of a meaningful mathematical abstraction [50s]. The research of biomolecular systems has yet to identify and adopt such a unifying abstraction.",
isbn="978-3-642-18734-6",
doi="10.1007/978-3-642-18734-6_11",
url="https://doi.org/10.1007/978-3-642-18734-6_11"
}


@article{CiocchettaBiopepa,
	Acmid = {1570750},
	Address = {Essex, UK},
	Author = {Ciocchetta, Federica and Hillston, Jane},
	Doi = {10.1016/j.tcs.2009.02.037},
	Issn = {0304-3975},
	Issue_Date = {August, 2009},
	Journal = {Theoretical Computer Science},
	Keywords = {Analysis, Biochemical networks, Modelling, Process algebras},
	Number = {33-34},
	Numpages = {20},
	Pages = {3065--3084},
	Publisher = {Elsevier Science Publishers Ltd.},
	Title = {Bio-{PEPA}: A Framework for the Modelling and Analysis of Biological Systems},
	Url = {http://dx.doi.org/10.1016/j.tcs.2009.02.037},
	Volume = {410},
	Year = {2009},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.tcs.2009.02.037}}

@article{danos2004kappa,
	Author = {Danos, Vincent and Laneve, Cosimo},
	Journal = {Theoretical Computer Science},
	Number = {1},
	Pages = {69--110},
	Publisher = {Elsevier},
	Title = {Formal molecular biology},
	Volume = {325},
	Year = {2004}}

@incollection{danos2004ccsr,
	Author = {Danos, Vincent and Krivine, Jean},
	Booktitle = {CONCUR 2004 - Concurrency Theory},
	Editor = {Gardner, Philippa and Yoshida, Nobuko},
	Isbn = {978-3-540-22940-7},
	Language = {English},
	Pages = {292--307},
	Publisher = {Springer},
	Series = {Lecture Notes in Computer Science},
	Title = {Reversible Communicating Systems},
	Volume = {3170},
	Year = {2004},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/978-3-540-28644-8_19}}

@article{Danos2007ccsr,
	Abstract = {We present CCS-R, a reversible variant of Milner's \{CCS\} offering a backtracking mechanism. Formalization of biological systems satisfying a ``perfect mix'' assumption within CCS-R is discussed. },
	Author = {Vincent Danos and Jean Krivine},
	Doi = {http://dx.doi.org/10.1016/j.entcs.2004.01.040},
	Issn = {1571-0661},
	Journal = {Electronic Notes in Theoretical Computer Science},
	Keywords = {backtracking mechanism},
	Note = {Proceedings of the First Workshop on Concurrent Models in Molecular Biology (BioConcur 2003)},
	Number = {3},
	Pages = {31--49},
	Title = {Formal Molecular Biology Done in CCS-R},
	Url = {http://www.sciencedirect.com/science/article/pii/S1571066107004963},
	Volume = {180},
	Year = {2007},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S1571066107004963},
	Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.entcs.2004.01.040}}

@book{Milner1980,
	Author = {Robin Milner},
	Isbn = {9783540102359},
	Publisher = {Springer},
	Series = {Lecture Notes in Computer Science},
	Title = {A Calculus of Communicating Systems},
	Volume = {92},
	Year = {1980}}

@book{MilnerBook,
	Author = {Robin Milner},
	Isbn = {9780131150072},
	Publisher = {Prentice Hall PTR},
	Timestamp = {2014.07.03},
	Title = {Communication and Concurrency (Prentice Hall International Series in Computer Science)},
	Totalpages = {272},
	Url = {http://amazon.com/o/ASIN/0131150073/},
	Year = {1995},
	Bdsk-Url-1 = {http://amazon.com/o/ASIN/0131150073/}}

@book{MilnerPi,
	Address = {New York, NY, USA},
	Author = {Milner, Robin},
	Isbn = {0-521-65869-1},
	Publisher = {Cambridge University Press},
	Title = {Communicating and Mobile Systems: The $\pi$-calculus},
	Year = {1999}}

@book{HoareBook,
	Author = {Charles A. R. Hoare},
	Edition = {1st},
	Isbn = {9780131532717},
	Publisher = {Prentice-Hall},
	Series = {Prentice Hall International Series in Computing Science},
	Timestamp = {2014.07.03},
	Title = {Communicating Sequential Processes},
	Totalpages = {256},
	Url = {http://amazon.com/o/ASIN/0131532715/},
	Year = {1985},
	Bdsk-Url-1 = {http://amazon.com/o/ASIN/0131532715/}}

@article{Irek2007,
	Abstract = {Reversible computation has a growing number of promising application areas such as the modelling of biochemical systems, program debugging and testing, and even programming languages for quantum computing. We formulate a procedure for converting operators of standard algebraic process calculi such as \{CCS\} into reversible operators, while preserving their operational semantics. We define forward--reverse bisimulation and show that it is preserved by all reversible operators. },
	Author = {Iain Phillips and Irek Ulidowski},
	Doi = {http://dx.doi.org/10.1016/j.jlap.2006.11.002},
	Issn = {1567-8326},
	Journal = {The Journal of Logic and Algebraic Programming},
	Keywords = {Congruence result},
	Number = {1-2},
	Pages = {70--96},
	Title = {Reversing algebraic process calculi},
	Url = {http://www.sciencedirect.com/science/article/pii/S1567832607000379},
	Volume = {73},
	Year = {2007},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S1567832607000379},
	Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.jlap.2006.11.002}}

%	Doi = {10.1007/978-3-642-36315-3_18},
%	Bdsk-Url-1 = {http://dx.doi.org/10.1007/978-3-642-36315-3_18}
@incollection{Irek2012,
	Author = {Phillips, Iain and Ulidowski, Irek and Yuen, Shoji},
	Booktitle = {Reversible Computation, 4th International Workshop, RC 2012},
	Editor = {Gl{\"u}ck, Robert and Yokoyama, Tetsuo},
	Isbn = {978-3-642-36314-6},
	Language = {English},
	Pages = {218--232},
	Publisher = {Springer},
	Series = {Lecture Notes in Computer Science},
	Title = {A Reversible Process Calculus and the Modelling of the {ERK} Signalling Pathway},
	Url = {http://dx.doi.org/10.1007/978-3-642-36315-3_18},
	Volume = {7581},
	Year = {2013},
}

@incollection{Irek2013,
	Author = {Phillips, Iain and Ulidowski, Irek and Yuen, Shoji},
	Booktitle = {Reversible Computation, 5th International Conference, RC 2013},
	Doi = {10.1007/978-3-642-38986-3_12},
	Editor = {Dueck, Gerhard W. and Miller, D. Michael},
	Isbn = {978-3-642-38985-6},
	Language = {English},
	Pages = {141--154},
	Publisher = {Springer},
	Series = {Lecture Notes in Computer Science},
	Title = {Modelling of Bonding with Processes and Events},
	Url = {http://dx.doi.org/10.1007/978-3-642-38986-3_12},
	Volume = {7948},
	Year = {2013},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/978-3-642-38986-3_12}}

@article{RegevBioambients,
	Abstract = {Biomolecular systems, composed of networks of proteins, underlie the major functions of living cells. Compartments are key to the organization of such systems. We have previously developed an abstraction for biomolecular systems using the π-calculus process algebra, which successfully handled their molecular and biochemical aspects, but provided only a limited solution for representing compartments. In this work, we extend this abstraction to handle compartments. We are motivated by the ambient calculus, a process algebra for the specification of process location and movement through computational domains. We present the BioAmbients calculus, which is suitable for representing various aspects of molecular localization and compartmentalization, including the movement of molecules between compartments, the dynamic rearrangement of cellular compartments, and the interaction between molecules in a compartmentalized setting. Guided by the calculus, we adapt the BioSpi simulation system, to provide an extended modular framework for molecular and cellular compartmentalization, and we use it to model and study a complex multi-cellular system. },
	Author = {Aviv Regev and Ekaterina M. Panina and William Silverman and Luca Cardelli and Ehud Shapiro},
	Doi = {http://dx.doi.org/10.1016/j.tcs.2004.03.061},
	Issn = {0304-3975},
	Journal = {Theoretical Computer Science},
	Keywords = {Simulation},
	Number = {1},
	Pages = {141--167},
	Title = {BioAmbients: an abstraction for biological compartments},
	Url = {http://www.sciencedirect.com/science/article/pii/S030439750400235X},
	Volume = {325},
	Year = {2004},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S030439750400235X},
	Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.tcs.2004.03.061}}

@incollection{CardelliBraneCalculi,
	Author = {Cardelli, Luca},
	Booktitle = {Computational Methods in Systems Biology},
	Doi = {10.1007/978-3-540-25974-9_24},
	Editor = {Danos, Vincent and Schachter, Vincent},
	Isbn = {978-3-540-25375-4},
	Language = {English},
	Pages = {257--278},
	Publisher = {Springer},
	Series = {Lecture Notes in Computer Science},
	Title = {Brane Calculi},
	Url = {http://dx.doi.org/10.1007/978-3-540-25974-9_24},
	Volume = {3082},
	Year = {2005},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/978-3-540-25974-9_24}}

@article{StochasticBrane,
	Author = {Giorgio Bacci and Marino Miculan},
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Ee = {http://dx.doi.org/10.1016/j.tcs.2011.12.055},
	Journal = {Theor. Comput. Sci.},
	Pages = {117--136},
	Title = {Measurable stochastics for Brane Calculus},
	Volume = {431},
	Year = {2012}}

@article{bartocci2010shape,
	Author = {Bartocci, Ezio and Corradini, Flavio and Di Berardini, Maria Rita and Merelli, Emanuela and Tesei, Luca},
	Journal = {Scientific Annals of Computer Science},
	Number = {1},
	Pages = {1--31},
	Publisher = {Universitatea" Al. I. Cuza" din Iasi},
	Title = {Shape Calculus. A Spatial Mobile Calculus for 3D Shapes},
	Volume = {20},
	Year = {2010}}

@article{buti2010bioshape,
	Author = {Buti, Federico and Cacciagrano, Diletta and Corradini, Flavio and Merelli, Emanuela and Tesei, Luca},
	Journal = {Procedia Computer Science},
	Number = {1},
	Pages = {827--835},
	Publisher = {Elsevier},
	Title = {BioShape: a spatial shape-based scale-independent simulation environment for biological systems},
	Volume = {1},
	Year = {2010}}

@article{PriamiStochasticPi,
	Abstract = {We extend the π-calculus, a model of concurrent processes based on the notion of naming, to cope with performance modelling. The new language is called the stochastic π-calculus (Sπ). We obtain a more expressive language than classical stochastic process algebras because Sπ is given in the classical structural operational approach. In order to effectively computer performance measures, we define a stratified transition system that is finitely branching. We give a transition rule to directly yield a continuous time Markov chain from an Sπ specification, with no transition system manipulation.},
	Author = {Corrado Priami},
	Doi = {10.1093/comjnl/38.7.578},
	Eprint = {http://comjnl.oxfordjournals.org/content/38/7/578.full.pdf+html},
	Journal = {The Computer Journal},
	Number = {7},
	Pages = {578--589},
	Title = {Stochastic $\pi$-Calculus},
	Url = {http://comjnl.oxfordjournals.org/content/38/7/578.abstract},
	Volume = {38},
	Year = {1995},
	Bdsk-Url-1 = {http://comjnl.oxfordjournals.org/content/38/7/578.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1093/comjnl/38.7.578}}

@article{PriameRegev,
	Abstract = {We describe a novel application of a stochastic name-passing calculus for the study of biomolecular systems. We specify the structure and dynamics of biochemical networks in a variant of the stochastic π-calculus, yielding a model which is mathematically well-defined and biologically faithful. We adapt the operational semantics of the calculus to account for both the time and probability of biochemical reactions, and present a computer implementation of the calculus for biochemical simulations.},
	Author = {Corrado Priami and Aviv Regev and Ehud Shapiro and William Silverman},
	Doi = {http://dx.doi.org/10.1016/S0020-0190(01)00214-9},
	Issn = {0020-0190},
	Journal = {Information Processing Letters},
	Keywords = {Stochastic -calculus},
	Number = {1},
	Pages = {25--31},
	Title = {Application of a stochastic name-passing calculus to representation and simulation of molecular processes},
	Url = {http://www.sciencedirect.com/science/article/pii/S0020019001002149},
	Volume = {80},
	Year = {2001},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0020019001002149},
	Bdsk-Url-2 = {http://dx.doi.org/10.1016/S0020-0190(01)00214-9}}

@inproceedings{spim,
	Abstract = {<p>In this paper, an abstract machine is presented for a variant of the
                stochastic pi-calculus, in order to correctly model the stochastic simulation of
                biological processes. The machine is first proved sound and complete with respect
                to the calculus, and then used as the basis for implementing a stochastic
                simulator. The correctness of the stochastic machine helps ensure that the
                simulator is correctly implemented, giving greater confidence in the simulation
                results. A graphical representation for the pi-calculus is also introduced.</p>},
	Author = {Andrew Phillips and Luca Cardelli},
	Booktitle = {Concurrent Models in Molecular Biology},
	Title = {A Correct Abstract Machine for the Stochastic Pi-calculus},
	Url = {http://research.microsoft.com/apps/pubs/default.aspx?id=65228},
	Year = {2004},
	Bdsk-Url-1 = {http://research.microsoft.com/apps/pubs/default.aspx?id=65228}}

@incollection{causalpi,
	Author = {Curti, Michele and Degano, Pierpaolo and Tatiana Baldari, Cosima},
	Booktitle = {Computational Methods in Systems Biology},
	Doi = {10.1007/3-540-36481-1_3},
	Editor = {Priami, Corrado},
	Isbn = {978-3-540-00605-3},
	Keywords = {Concurrency; Causality; Reduction Semantics; Bio-informatics; Formal Description of Biochemical Processes},
	Language = {English},
	Pages = {21--34},
	Publisher = {Springer},
	Series = {Lecture Notes in Computer Science},
	Title = {Causal $\pi$-Calculus for Biochemical Modelling},
	Url = {http://dx.doi.org/10.1007/3-540-36481-1_3},
	Volume = {2602},
	Year = {2003},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/3-540-36481-1_3}}

@article{Irek2007entcs,
	Acmid = {1298827},
	Address = {Amsterdam, The Netherlands, The Netherlands},
	Author = {Phillips, Iain and Ulidowski, Irek},
	Doi = {10.1016/j.entcs.2007.08.018},
	Issn = {1571-0661},
	Issue_Date = {October, 2007},
	Journal = {Electron. Notes Theor. Comput. Sci.},
	Keywords = {Reversible computation, hereditary history-preserving bisimulation, labelled transition systems, prime event structures},
	Number = {1},
	Numpages = {16},
	Pages = {93--108},
	Publisher = {Elsevier Science Publishers B. V.},
	Title = {Reversibility and Models for Concurrency},
	Url = {http://dx.doi.org/10.1016/j.entcs.2007.08.018},
	Volume = {192},
	Year = {2007},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.entcs.2007.08.018}}

@incollection{danoscausality,
	Author = {Danos, Vincent and Feret, J\'{e}r\^{o}me and Fontana, Walter and Harmer, Russell and Krivine, Jean},
	Booktitle = {CONCUR 2007 - Concurrency Theory},
	Editor = {Caires, Lu{\'\i}s and Vasconcelos, Vasco T.},
	Isbn = {978-3-540-74406-1},
	Language = {English},
	Pages = {17--41},
	Publisher = {Springer},
	Series = {Lecture Notes in Computer Science},
	Title = {Rule-Based Modelling of Cellular Signalling},
	Volume = {4703},
	Year = {2007},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/978-3-540-74407-8_3}}

@article{sugarrules,
	Doi = {10.1021/jo01037a001},
	Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jo01037a001},
	Journal = {The Journal of Organic Chemistry},
	Number = {2},
	Pages = {281--291},
	Title = {Rules of Carbohydrate Nomenclature},
	Url = {http://pubs.acs.org/doi/abs/10.1021/jo01037a001},
	Volume = {28},
	Year = {1963},
	Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jo01037a001},
	Bdsk-Url-2 = {http://dx.doi.org/10.1021/jo01037a001}}

@book{BaetenBook,
	Author = {Josef C. M. Baeten and W. Peter Weijland},
	Isbn = {0521400430},
	Publisher = {Cambridge University Press},
	Title = {Process Algebra (Cambridge Tracts in Theoretical Computer Science 18)},
	Year = {1990}}

@book{ACPBook,
	Author = {Wan Fokkink},
	Isbn = {354066579X},
	Publisher = {Springer},
	Title = {Introduction to Process Algebra},
	Year = {2000}}

@incollection{irekconcur2013,
	Author = {Phillips, Iain and Ulidowski, Irek},
	Booktitle = {CONCUR 2013 - Concurrency Theory},
	Doi = {10.1007/978-3-642-40184-8_22},
	Editor = {D'Argenio, Pedro R. and Melgratti, Hern{\'a}n},
	Isbn = {978-3-642-40183-1},
	Language = {English},
	Pages = {303--318},
	Publisher = {Springer},
	Series = {Lecture Notes in Computer Science},
	Title = {Reversibility and Asymmetric Conflict in Event Structures},
	Url = {http://dx.doi.org/10.1007/978-3-642-40184-8_22},
	Volume = {8052},
	Year = {2013},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/978-3-642-40184-8_22}}

@inproceedings{Uli92,
	Author = {Irek Ulidowski},
	Booktitle = {Proceedings of the 7th Annual IEEE Symposium on Logic in Computer Science},
	Pages = {148--159},
	Publisher = {IEEE},
	Title = {Equivalences on Observable Processes},
	Year = 1992}

@incollection{irek2014,
	Author = {Ulidowski, Irek and Phillips, Iain and Yuen, Shoji},
	Booktitle = {Reversible Computation, 6th International Conference, RC 2014},
	Doi = {10.1007/978-3-319-08494-7_1},
	Editor = {Yamashita, Shigeru and Minato, Shin-ichi},
	Isbn = {978-3-319-08493-0},
	Language = {English},
	Pages = {1--14},
	Publisher = {Springer},
	Series = {Lecture Notes in Computer Science},
	Title = {Concurrency and Reversibility},
	Url = {http://dx.doi.org/10.1007/978-3-319-08494-7_1},
	Volume = {8507},
	Year = {2014},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/978-3-319-08494-7_1}}

@inproceedings{PhillipsUlidowski06,
	Author = {Ian Phillips and Irek Ulidowski},
	Booktitle = {Proceedings of 9th International Conference on Foundations of Software Science and Computation Structures, {FOSSACS} 2006},
	Pages = {246--260},
	Publisher = {Springer},
	Series = {Lecture Notes in Computer Science},
	Title = {Reversing algebraic process calculi},
	Volume = 3921,
	Year = 2006}

@incollection{Lanese_controllingreversibility,
	Author = {Lanese, Ivan and Mezzina, Claudio Antares and Schmitt, Alan and Stefani, Jean-Bernard},
	Booktitle = {CONCUR 2011 - Concurrency Theory},
	Doi = {10.1007/978-3-642-23217-6_20},
	Editor = {Katoen, Joost-Pieter and K{\"o}nig, Barbara},
	Isbn = {978-3-642-23216-9},
	Language = {English},
	Pages = {297--311},
	Publisher = {Springer},
	Series = {Lecture Notes in Computer Science},
	Title = {Controlling Reversibility in Higher-Order Pi},
	Url = {http://dx.doi.org/10.1007/978-3-642-23217-6_20},
	Volume = {6901},
	Year = {2011},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/978-3-642-23217-6_20}}

@incollection{Lanese_controlled,
	Author = {Lanese, Ivan and Mezzina, Claudio Antares and Stefani, Jean-Bernard},
	Booktitle = {Reversible Computation, 4th International Workshop, RC 2012},
	Doi = {10.1007/978-3-642-36315-3_19},
	Editor = {Gl{\"u}ck, Robert and Yokoyama, Tetsuo},
	Isbn = {978-3-642-36314-6},
	Language = {English},
	Pages = {233--240},
	Publisher = {Springer},
	Series = {Lecture Notes in Computer Science},
	Title = {Controlled Reversibility and Compensations},
	Url = {http://dx.doi.org/10.1007/978-3-642-36315-3_19},
	Volume = {7581},
	Year = {2013},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/978-3-642-36315-3_19}}

@inproceedings{CKV13,
	Author = {Ioana Cristescu and Jean Krivine and Daniele Varacca},
	Booktitle = {28th Annual ACM/IEEE Symposium on Logic in Computer Science},
	Pages = {388--397},
	Publisher = {IEEE Computer Society},
	Title = {A Compositional Semantics for the Reversible p-Calculus},
	Year = {2013}}

@inproceedings{LaneseMS10,
	Author = {Ivan Lanese and Claudio Antares Mezzina and Jean-Bernhard Stefani},
	Booktitle = {CONCUR 2010 - Concurrency Theory},
editor = {Paul Gastin and Fran{\c{c}}ois Laroussinie},
	Pages = {478--493},
	Publisher = {Springer},
	Series = {Lecture Notes in Computer Science},
	Title = {Reversing Higher-Order Pi},
	Volume = {6269},
	Year = {2010}}

@incollection{merevcomp2015,
	Author = {Kuhn, Stefan and Ulidowski, Irek},
	Booktitle = {Reversible Computation, 7th International Conference, RC 2015},
	Doi = {10.1007/978-3-319-20860-2_19},
	Editor = {Krivine, Jean and Stefani, Jean-Bernard},
	Isbn = {978-3-319-20859-6},
	Keywords = {Reversible process calculi; Out-of-causal order reversibility; Local reversibility; Modelling of chemical reactions},
	Language = {English},
	Pages = {279--284},
	Publisher = {Springer},
	Series = {Lecture Notes in Computer Science},
	Title = {Towards Modelling of Local Reversibility},
	Url = {http://dx.doi.org/10.1007/978-3-319-20860-2_19},
	Volume = {9138},
	Year = {2015},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/978-3-319-20860-2_19}}

@incollection{merevcomp2018,
	Author = {Kuhn, Stefan},
	Booktitle = {Reversible Computation, 10th International Conference, RC 2018},
	Editor = {Karri, Jarko and Ulidowski, Irek},
	Language = {English},
	Pages = {123--129},
	Publisher = {Springer},
	Series = {Lecture Notes in Computer Science},
	Title = {Simulation of Base Excision Repair in the Calculus of Covalent Bonding},
	Volume = {11106},
	Year = {2018}}

@article{KUHN201818,
	Author = {Stefan Kuhn and Irek Ulidowski},
	Doi = {https://doi.org/10.1016/j.scico.2017.09.008},
	Issn = {0167-6423},
	Journal = {Science of Computer Programming},
	Keywords = {Reversible process calculi, Local reversibility, Modelling of biochemical reactions},
	Number = {Supplement C},
	Pages = {18--47},
	Title = {Local reversibility in a Calculus of Covalent Bonding},
	Url = {http://www.sciencedirect.com/science/article/pii/S016764231730196X},
	Volume = {151},
	Year = {2018},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S016764231730196X},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.scico.2017.09.008}}

@inproceedings{Cardelli:2011:RS:2037509.2037529,
	Acmid = {2037529},
	Address = {New York, NY, USA},
	Author = {Cardelli, Luca and Laneve, Cosimo},
	Booktitle = {Proceedings of the 9th International Conference on Computational Methods in Systems Biology},
	Doi = {10.1145/2037509.2037529},
	Isbn = {978-1-4503-0817-5},
	Location = {Paris, France},
	Numpages = {10},
	Pages = {131--140},
	Publisher = {ACM},
	Series = {Lecture Notes in Computer Science},
	Title = {Reversible Structures},
	Url = {http://doi.acm.org/10.1145/2037509.2037529},
	Volume = {3082},
	Year = {2011},
	Bdsk-Url-1 = {http://doi.acm.org/10.1145/2037509.2037529},
	Bdsk-Url-2 = {http://dx.doi.org/10.1145/2037509.2037529}}

@book{metalcatalysis,
	Author = {Calderazzo, Fausto and Carmona, Daniel and Catellani, Marta and Brintzinger, Hans and Clerici, Mario G and Dwyer, Catherine and Fink, Gerhard and Fraile, Jose and Haynes, Anthony and Howard, Philip and Morris, George and Oro, Luis A and Ricci, Marco and Strukul, Giorgio and Sunley, Glenn},
	Doi = {10.1039/9781847555328},
	Editor = {Chiusoli, Gian Paolo and Maitlis, Peter M},
	Isbn = {978-0-85404-862-5},
	Pages = {P001--290},
	Publisher = {The Royal Society of Chemistry},
	Title = {Metal-catalysis in Industrial Organic Processes},
	Url = {http://dx.doi.org/10.1039/9781847555328},
	Year = {2006},
	Bdsk-Url-1 = {http://dx.doi.org/10.1039/9781847555328}}

@inproceedings{Koehler2014,
	Address = {Cham},
	Author = {K{\"o}hler, Agnes and Krivine, Jean and Vidmar, Jakob},
	Booktitle = {Computational Methods in Systems Biology: 12th International Conference, CMSB 2014},
	Doi = {10.1007/978-3-319-12982-2_13},
	Editor = {Mendes, Pedro and Dada, Joseph O. and Smallbone, Kieran},
	Isbn = {978-3-319-12982-2},
	Pages = {173--195},
	Publisher = {Springer},
	Title = {A Rule-Based Model of Base Excision Repair},
	Url = {http://dx.doi.org/10.1007/978-3-319-12982-2_13},
	Year = {2014},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/978-3-319-12982-2_13}}

@inproceedings{BaroukhAsthma,
	Author = {Baroukh, Caroline and Rowe, Anthony and Guo, Yike},
	Booktitle = {2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops},
	Doi = {10.1109/BIBMW.2010.5703802},
	Pages = {217--222},
	Publisher = {IEEE},
	Title = {Process calculi for systems biology and applications in severe asthma},
	Url = {http://dx.doi.org/10.1109/BIBMW.2010.5703802},
	Year = {2010},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/BIBMW.2010.5703802}}

@misc{jgrapht,
	Author = {JGraphT},
	Note = {\url{http://www.jgrapht.org}. Accessed 11-July-2016},
	Title = {JGraphT website},
	Url = {http://www.jgrapht.org},
	Year = {2016},
	Bdsk-Url-1 = {http://www.jgrapht.org}}

@misc{kappadna,
	Author = {Jean Krivine},
	Note = {\url{https://www.irif.fr/~jkrivine/homepage/Teaching_files/TP-DNA.pdf}. Accessed 11-November-2017},
	Title = {Kappa project: DNA repair},
	Url = {https://www.irif.fr/~jkrivine/homepage/Teaching_files/TP-DNA.pdf},
	Year = {2017},
	Bdsk-Url-1 = {https://www.irif.fr/~jkrivine/homepage/Teaching_files/TP-DNA.pdf}}

@article{higham,
	Author = {Desmond J. Higham},
	Doi = {10.1137/060666457},
	Eprint = {http://dx.doi.org/10.1137/060666457},
	Journal = {SIAM Review},
	Number = {2},
	Pages = {347--368},
	Title = {Modeling and Simulating Chemical Reactions},
	Url = {http://dx.doi.org/10.1137/060666457},
	Volume = {50},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1137/060666457}}

@inproceedings{CardelliMobileAmbients,
	Acmid = {759638},
	Address = {London, UK},
	Author = {Cardelli, Luca and Gordon, Andrew D.},
	Booktitle = {Proceedings of the First International Conference on Foundations of Software Science and Computation Structure},
	Isbn = {3-540-64300-1},
	Numpages = {16},
	Pages = {140--155},
	Publisher = {Springer},
	Series = {FOSSACS '98},
	Title = {Mobile Ambients},
	Url = {http://dl.acm.org/citation.cfm?id=646790.759638},
	Year = {1998},
	Bdsk-Url-1 = {http://dl.acm.org/citation.cfm?id=646790.759638}}

@inbook{ProjectiveBrane,
	Address = {Berlin, Heidelberg},
	Author = {Danos, Vincent and Pradalier, Sylvain},
	Booktitle = {Computational Methods in Systems Biology: International Conference CMSB 2004, Paris, France, May 26-28, 2004, Revised Selected Papers},
	Doi = {10.1007/978-3-540-25974-9_11},
	Editor = {Danos, Vincent and Schachter, Vincent},
	Isbn = {978-3-540-25974-9},
	Pages = {134--148},
	Publisher = {Springer},
	Series = {Lecture Notes in Computer Science},
	Title = {Projective Brane Calculus},
	Url = {http://dx.doi.org/10.1007/978-3-540-25974-9_11},
	Volume = {3082},
	Year = {2005},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/978-3-540-25974-9_11}}

@inbook{Cristescu2016,
	Address = {Cham},
	Author = {Cristescu, Ioana and Krivine, Jean and Varacca, Daniele},
	Booktitle = {Reversible Computation: 8th International Conference, RC 2016},
	Doi = {10.1007/978-3-319-40578-0_1},
	Editor = {Devitt, Simon and Lanese, Ivan},
	Isbn = {978-3-319-40578-0},
	Pages = {3--19},
	Publisher = {Springer},
	Series = {Lecture Notes in Computer Science},
	Title = {Rigid Families for the Reversible $\pi$-Calculus},
	Url = {http://dx.doi.org/10.1007/978-3-319-40578-0_1},
	Volume = {9720},
	Year = {2016},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/978-3-319-40578-0_1}}

@incollection{PlotkinLBS,
	Acmid = {2172314},
	Address = {Berlin, Heidelberg},
	Author = {Pedersen, Michael and Plotkin, Gordon D.},
	Booktitle = {Transactions on Computational Systems Biology XII},
	Editor = {Priami, Corrado and Breitling, Rainer and Gilbert, David and Heiner, Monika and Uhrmacher, Adelinde M.},
	Isbn = {3-642-11711-2, 978-3-642-11711-4},
	Keywords = {Petri nets, coloured Petri nets, combinatorial explosion, continuous time Markov chains, large-scale, nondeterminism, ordinary differential equations, parametrised modules, subtyping},
	Numpages = {69},
	Pages = {77--145},
	Publisher = {Springer},
	Title = {A Language for Biochemical Systems: Design and Formal Specification},
	Url = {http://dl.acm.org/citation.cfm?id=2172311.2172314},
	Year = {2010},
	Bdsk-Url-1 = {http://dl.acm.org/citation.cfm?id=2172311.2172314}}

@inbook{PlotkinCCS,
	Address = {Berlin, Heidelberg},
	Author = {Plotkin, Gordon D.},
	Booktitle = {In Search of Elegance in the Theory and Practice of Computation: Essays Dedicated to Peter Buneman},
	Doi = {10.1007/978-3-642-41660-6_24},
	Editor = {Tannen, Val and Wong, Limsoon and Libkin, Leonid and Fan, Wenfei and Tan, Wang-Chiew and Fourman, Michael},
	Isbn = {978-3-642-41660-6},
	Pages = {445--465},
	Publisher = {Springer},
	Title = {A Calculus of Chemical Systems},
	Url = {http://dx.doi.org/10.1007/978-3-642-41660-6_24},
	Year = {2013},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/978-3-642-41660-6_24}}

@techreport{fontana,
	Address = {IIASA, Laxenburg, Austria},
	Author = {W. Fontana and L.W. Buss},
	Publisher = {WP-96-027},
	Title = {The Barrier of Objects: From Dynamical Systems to Bounded Organizations},
	Type = {{IIASA} Working Paper},
	Url = {http://pure.iiasa.ac.at/4999/},
	Year = {1996},
	Bdsk-Url-1 = {http://pure.iiasa.ac.at/4999/}}

@article{Gillespie,
	Author = {Daniel T. Gillespie},
	Doi = {10.1021/j100540a008},
	Eprint = {http://dx.doi.org/10.1021/j100540a008},
	Journal = {The Journal of Physical Chemistry},
	Number = {25},
	Pages = {2340--2361},
	Title = {Exact stochastic simulation of coupled chemical reactions},
	Url = {http://dx.doi.org/10.1021/j100540a008},
	Volume = {81},
	Year = {1977},
	Bdsk-Url-1 = {http://dx.doi.org/10.1021/j100540a008}}

@article{biocham,
	Author = {Fran{\c{c}}ois Fages and Sylvain Soliman and Nathalie Chabrier-Rivier},
	Journal = {Journal of Biological Physics and Chemistry},
	Pages = {64--73},
	Title = {Modelling and querying interaction networks in the biochemical abstract machine 
		{BIOCHAM}},
	Volume = {4},
	Year = {2004}}

@article{cham,
	Abstract = {We introduce a new kind of abstract machine based on the chemical metaphor used in the Γ language of Ban{\^a}tre and Le M{\'e}tayer. States of a machine are chemical solutions where floating molecules can interact according to reaction rules. Solutions can be stratified by encapsulating subsolutions within membranes that force reactions to occur locally. We illustrate the use of this model by describing the operational semantics of the TCCS and CCS process calculi and of the fragment of Milner, Parrow and Walker's Calculus of Mobile Processes used by Milner to encode the lambda-calculus. We also give ideas on how to extract a higher-order concurrent λ-calculus out of the basic concepts of the chemical abstract machine.},
	Author = {R. De Nicola and U. Montanari and G{\'e}rard Berry and G{\'e}rard Boudol},
	Doi = {http://dx.doi.org/10.1016/0304-3975(92)90185-I},
	Issn = {0304-3975},
	Journal = {Theoretical Computer Science},
	Number = {1},
	Pages = {217--248},
	Title = {The chemical abstract machine},
	Url = {http://www.sciencedirect.com/science/article/pii/030439759290185I},
	Volume = {96},
	Year = {1992},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/030439759290185I},
	Bdsk-Url-2 = {http://dx.doi.org/10.1016/0304-3975(92)90185-I}}

@inbook{Winskel1987,
	Address = {Berlin, Heidelberg},
	Author = {Winskel, Glynn},
	Booktitle = {Petri Nets: Applications and Relationships to Other Models of Concurrency: Advances in Petri Nets 1986, Part II Proceedings of an Advanced Course Bad Honnef, 8.--19. September 1986},
	Doi = {10.1007/3-540-17906-2_31},
	Editor = {Brauer, Wilfried and Reisig, Wolfgang and Rozenberg, Grzegorz},
	Isbn = {978-3-540-47926-0},
	Pages = {325--392},
	Publisher = {Springer},
	Series = {Lecture Notes in Computer Science},
	Title = {Event structures},
	Url = {http://dx.doi.org/10.1007/3-540-17906-2_31},
	Volume = {8052},
	Year = {1987},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/3-540-17906-2_31}}

@inproceedings{kappacausal,
	Address = {Dagstuhl, Germany},
	Annote = {Keywords: concurrency, rule-based models, graph rewriting, pathways, causality},
	Author = {Vincent Danos and Jerome Feret and Walter Fontana and Russell Harmer and Jonathan Hayman and Jean Krivine and Chris Thompson-Walsh and Glynn Winskel},
	Booktitle = {IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2012)},
	Doi = {http://dx.doi.org/10.4230/LIPIcs.FSTTCS.2012.276},
	Editor = {Deepak D'Souza and Telikepalli Kavitha and Jaikumar Radhakrishnan},
	Isbn = {978-3-939897-47-7},
	Issn = {1868-8969},
	Pages = {276--288},
	Publisher = {Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
	Series = {Leibniz International Proceedings in Informatics (LIPIcs)},
	Title = {{Graphs, Rewriting and Pathway Reconstruction for Rule-Based Models}},
	Url = {http://drops.dagstuhl.de/opus/volltexte/2012/3866},
	Urn = {urn:nbn:de:0030-drops-38669},
	Volume = {18},
	Year = {2012},
	Bdsk-Url-1 = {http://drops.dagstuhl.de/opus/volltexte/2012/3866},
	Bdsk-Url-2 = {http://dx.doi.org/10.4230/LIPIcs.FSTTCS.2012.276}}

@article{sbml,
	Abstract = {Motivation: Molecular biotechnology now makes it possible to build
elaborate systems models, but the systems biology community needs
information standards if models are to be shared, evaluated and developed
cooperatively.Results: We summarize the Systems Biology Markup Language (SBML)
Level 1, a free, open, XML-based format for representing biochemical
reaction networks.  SBML is a software-independent language for describing
models common to research in many areas of computational biology, including
cell signaling pathways, metabolic pathways, gene regulation, and others.Availability: The specification of SBML Level 1 is freely
available from http://www.sbml.org/Contact: sysbio-team@caltech.edu
        
      },
	Author = {Hucka, Michael and Finney, Andrew and Sauro, Herbert and Bolouri, Hamid and Doyle, John and Kitano, Hiroaki and others},
	Doi = {10.1093/bioinformatics/btg015},
	Eprint = {http://bioinformatics.oxfordjournals.org/content/19/4/524.full.pdf+html},
	Journal = {Bioinformatics},
	Number = {4},
	Pages = {524--531},
	Title = {The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models},
	Url = {http://bioinformatics.oxfordjournals.org/content/19/4/524.abstract},
	Volume = {19},
	Year = {2003},
	Bdsk-Url-1 = {http://bioinformatics.oxfordjournals.org/content/19/4/524.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1093/bioinformatics/btg015}}

@misc{kasim,
	Author = {Pierre Boutillier and J{\'e}r{\^o}me Feret and Jean Krivine and L{\'y} Kim Quy{\^e}n},
	Note = {\url{http://dev.executableknowledge.org/docs/KaSim-manual-master/KaSim_manual.htm}. Accessed: 2-September-2016},
	Title = {KaSim \& KaSa reference manual (release 3.90)}}

@book{claydon,
	Author = {Claydon, Jonathan and Greeves, Nick and Warren, Stuart and Wothers, Peter},
	Edition = {1st},
	Isbn = {9780198503460},
	Publisher = {Oxford University Press},
	Title = {Organic Chemistry},
	Year = {2001}}

@incollection{Cleaveland2001711,
	Abstract = {Abstract This chapter surveys the semantic ramifications of extending traditional process algebras with notions of priority that allow some transitions to be given precedence over others. The need for these enriched formalisms arises when one wishes to model system features such as interrupts, prioritized choice, or real-time behavior. Approaches to priority in process algebras can be classified according to whether the induced notion of pre-emption on transitions is global or local and whether priorities are static or dynamic. Early work in the area concentrated on global pre-emption and static priorities and led to formalisms for modeling interrupts and aspects of real-time, such as maximal progress, in centralized computing environments. More recent research has investigated localized notions of pre-emption in which the distribution of systems is taken into account, as well as dynamic priority approaches. The latter allows priority values to change as systems evolve and enables an efficient encoding of real-time semantics. Technically, this chapter studies the different models of priorities by presenting extensions of Milner's Calculus of Communicating Systems (CCS) with static and dynamic priority as well as with notions of global and local pre-emption. For each extension, the operational semantics of \{CCS\} is modified appropriately, behavioral theories based on strong and weak bisimulation are given, and related approaches for other process-algebraic settings are discussed. },
	Address = {Amsterdam},
	Author = {Rance Cleaveland and Gerald L{\"o}ttgen and V. Natarajan},
	Booktitle = {Handbook of Process Algebra},
	Chapter = {12},
	Doi = {https://doi.org/10.1016/B978-044482830-9/50030-8},
	Editor = {Bergstra, Jan A. and Ponse, Alban and Smolka, Scott Allen},
	Isbn = {978-0-444-82830-9},
	Pages = {711--765},
	Publisher = {Elsevier Science},
	Title = {Priority in Process Algebra},
	Url = {http://www.sciencedirect.com/science/article/pii/B9780444828309500308},
	Year = {2001},
	Bdsk-File-1 = {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},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/B9780444828309500308},
	Bdsk-Url-2 = {https://doi.org/10.1016/B978-044482830-9/50030-8}}

@incollection{KU16,
	Author = {Kuhn, Stefan and Ulidowski, Irek},
	Booktitle = {Reversible Computation, 8th International Conference, RC 2016},
	Doi = {10.1007/978-3-319-40578-0_2},
	Editor = {Devitt, Simon and Lanese, Ivan},
	Isbn = {978-3-319-40578-0},
	Language = {English},
	Pages = {20--35},
	Publisher = {Springer},
	Series = {Lecture Notes in Computer Science},
	Title = {A Calculus for Local Reversibility},
	Volume = {9720},
	Year = {2016},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/978-3-319-40578-0_2}}

@article{Lanese14,
	Author = {Ivan Lanese and Claudio Antares Mezzina and Francesco Tiezzi},
	Bibsource = {dblp computer science bibliography, https://dblp.org},
	Biburl = {https://dblp.org/rec/bib/journals/eatcs/Lanese14},
	Journal = {Bulletin of the {EATCS}},
	Timestamp = {Wed, 19 Nov 2014 17:04:43 +0100},
	Title = {Causal-Consistent Reversibility},
	Url = {http://eatcs.org/beatcs/index.php/beatcs/article/view/305},
	Volume = {114},
	Year = {2014},
	Bdsk-Url-1 = {http://eatcs.org/beatcs/index.php/beatcs/article/view/305}}

@article{mousavi,
	Abstract = {Structured Operational Semantics (SOS) is a popular method for defining semantics by means of transition rules. An important feature of SOS rules is negative premises, which are crucial in the definitions of such phenomena as priority mechanisms and time-outs. However, the inclusion of negative premises in SOS rules also introduces doubts as to the preferred meaning of SOS specifications. Orderings on SOS rules were proposed by Phillips and Ulidowski as an alternative to negative premises. Apart from the definition of the semantics of positive GSOS rules with orderings, the meaning of more general types of SOS rules with orderings has not been studied hitherto. This paper presents several candidates for the meaning of general SOS rules with orderings and discusses their conformance to our intuition for such rules. We take two general frameworks (rule formats) for SOS with negative premises and SOS with orderings, and present semantics-preserving translations between them with respect to our preferred notion of semantics. Thanks to our semantics-preserving translation, we take existing congruence meta-results for strong bisimilarity from the setting of SOS with negative premises into the setting of SOS with orderings. We further compare the expressiveness of rule formats for SOS with orderings and SOS with negative premises. The paper contains also many examples that illustrate the benefits of SOS with orderings and the properties of the presented definitions of meaning.},
	Author = {MohammadReza Mousavi and Iain Phillips and Michel A. Reniers and Irek Ulidowski},
	Doi = {http://dx.doi.org/10.1016/j.ic.2007.11.008},
	Issn = {0890-5401},
	Journal = {Information and Computation},
	Number = {2},
	Pages = {85--119},
	Title = {Semantics and expressiveness of ordered {SOS}},
	Url = {http://www.sciencedirect.com/science/article/pii/S0890540108001247},
	Volume = {207},
	Year = {2009},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0890540108001247},
	Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.ic.2007.11.008}}

@article{irek2002,
	Abstract = {We present a general and uniform method for defining structural operational semantics (SOS) of process operators by traditional Plotkin-style transition rules equipped with orderings. This new feature allows one to control the order of application of rules when deriving transitions of process terms. Our method is powerful enough to deal with rules with negative premises and copying. We show that rules with orderings, called ordered SOS rules, have the same expressive power as GSOS rules. We identify several classes of process languages with operators defined by rules with and without orderings in the setting with silent actions and divergence. We prove that branching bisimulation and eager bisimulation relations are preserved by all operators in process languages in the relevant classes.},
	Author = {Irek Ulidowski and Iain Phillips},
	Doi = {http://dx.doi.org/10.1006/inco.2002.3161},
	Issn = {0890-5401},
	Journal = {Information and Computation},
	Number = {1},
	Pages = {180--213},
	Title = {Ordered {SOS} Process Languages for Branching and Eager Bisimulations},
	Url = {http://www.sciencedirect.com/science/article/pii/S0890540102931615},
	Volume = {178},
	Year = {2002},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0890540102931615},
	Bdsk-Url-2 = {http://dx.doi.org/10.1006/inco.2002.3161}}

@book{pepa,
	Author = {Hillston, Jane},
	Collection = {Distinguished Dissertations in Computer Science},
	Doi = {10.1017/CBO9780511569951},
	Place = {Cambridge},
	Publisher = {Cambridge University Press},
	Series = {Distinguished Dissertations in Computer Science},
	Title = {A Compositional Approach to Performance Modelling},
	Year = {1996},
	Bdsk-Url-1 = {http://dx.doi.org/10.1017/CBO9780511569951}}

@article{Lymphocyte,
	Abstract = { This article presents a stochastic model of lymphocyte recruitment in inflamed brain microvessels. Recent studies about the inflammatory process of the brain that leads to multiple sclerosis have revealed that lymphocyte extravasation is a sequence of dynamical states, mediated by partially overlapped interactions of different adhesion molecules and activation factors. This study's model of lymphocyte recruitment is based on process algebras for mobile systems. The biochemical system is modelled as a set of concurrent processes of the biochemical stochastic π-calculus. Processes are driven by suitable probability distributions that quantitatively describe the rates and the times at which reactions to simulations occur. The results of the model reproduce, within the estimated experimental errors, the functional behavior of the data obtained from laboratory measurements. },
	Author = {Paolo Lecca and Corrado Priami and P. Quaglia and B. Rossi and C. Laudanna and G. Constantin},
	Doi = {10.1177/0037549704045800},
	Eprint = {https://doi.org/10.1177/0037549704045800},
	Journal = {SIMULATION},
	Number = {6},
	Pages = {273--288},
	Title = {A Stochastic Process Algebra Approach to Simulation of Autoreactive Lymphocyte Recruitment},
	Url = {https://doi.org/10.1177/0037549704045800},
	Volume = {80},
	Year = {2004},
	Bdsk-Url-1 = {https://doi.org/10.1177/0037549704045800},
	Bdsk-Url-2 = {http://dx.doi.org/10.1177/0037549704045800}}

@article{eros,
	Author = {H{\"o}llering, Robert and Gasteiger, Johann and Steinhauer, Larissa and Schulz, Klaus-Peter and Herwig, Achim},
	Doi = {10.1021/ci990433p},
	Eprint = {http://dx.doi.org/10.1021/ci990433p},
	Journal = {Journal of Chemical Information and Computer Sciences},
	Number = {2},
	Pages = {482--494},
	Title = {Simulation of Organic Reactions: From the Degradation of Chemicals to Combinatorial Synthesis},
	Url = {http://dx.doi.org/10.1021/ci990433p},
	Volume = {40},
	Year = {2000},
	Bdsk-Url-1 = {http://dx.doi.org/10.1021/ci990433p}}

@article{rna,
	Author = {Federica Ciocchetta and Jane Hillston and Martin Kos and David Tollervey},
	Doi = {https://doi.org/10.1016/j.tcs.2008.07.012},
	Issn = {0304-3975},
	Journal = {Theoretical Computer Science},
	Keywords = {Parameter estimation},
	Number = {1},
	Pages = {41--54},
	Title = {Modelling co-transcriptional cleavage in the synthesis of yeast pre-rRNA},
	Url = {http://www.sciencedirect.com/science/article/pii/S0304397508005045},
	Volume = {408},
	Year = {2008},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0304397508005045},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.tcs.2008.07.012}}

@article{eco1,
	Author = {Sumpter, David J. and Blanchard, Guy B. and Broomhead, David S.},
	Journal = {Bulletin of Mathematical Biology},
	Number = {5},
	Pages = {951--980},
	Title = {{{A}nts and agents: a process algebra approach to modelling ant colony behaviour}},
	Volume = {63},
	Year = {2001}}

@article{eco2,
	Author = {Sumpter, David J. and Broomhead, David S.},
	Journal = {Proceedings of the Royal Society B: Biological Sciences},
	Number = {1470},
	Pages = {925--932},
	Title = {{{R}elating individual behaviour to population dynamics}},
	Volume = {268},
	Year = {2001}}

@article{eco3,
	Author = {Sumpter, David J. and Broomhead, David S.},
	Journal = {Journal of Theoretical Biology},
	Number = {1},
	Pages = {1--14},
	Title = {{{S}hape and dynamics of thermoregulating honey bee clusters}},
	Volume = {204},
	Year = {2000}}

@article{beeepidemics,
	Author = {Sumpter, David J. and Martin, Stephen J.},
	Doi = {10.1111/j.1365-2656.2004.00776.x},
	Issn = {1365-2656},
	Journal = {Journal of Animal Ecology},
	Keywords = {collective resistance, honey bee, mathematical model, Varroa, virus dynamics},
	Number = {1},
	Pages = {51--63},
	Publisher = {Blackwell Science Ltd},
	Title = {The dynamics of virus epidemics in Varroa-infested honey bee colonies},
	Url = {http://dx.doi.org/10.1111/j.1365-2656.2004.00776.x},
	Volume = {73},
	Year = {2004},
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1365-2656.2004.00776.x}}

@article{hivepidemics,
	Author = {Chris McCaig and Rachel Norman and Carron Shankland},
	Doi = {https://doi.org/10.1016/j.tcs.2010.09.024},
	Issn = {0304-3975},
	Journal = {Theoretical Computer Science},
	Keywords = {Semantics},
	Number = {17},
	Pages = {1557--1580},
	Title = {From individuals to populations: A mean field semantics for process algebra},
	Url = {http://www.sciencedirect.com/science/article/pii/S0304397510005037},
	Volume = {412},
	Year = {2011},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0304397510005037},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.tcs.2010.09.024}}

@inbook{Guerriero2009,
	Abstract = {Several approaches have been proposed to model biological systems by means of the formal techniques and tools available in computer science. To mention just a few of them, some representations are inspired by Petri nets theory and others by stochastic processes.},
	Address = {Berlin, Heidelberg},
	Author = {Guerriero, Maria Luisa and Prandi, Davide and Priami, Corrado and Quaglia, Paola},
	Booktitle = {Algorithmic Bioprocesses},
	Doi = {10.1007/978-3-540-88869-7_23},
	Editor = {Condon, Anne and Harel, David and Kok, Joost N. and Salomaa, Arto and Winfree, Erik},
	Isbn = {978-3-540-88869-7},
	Pages = {463--486},
	Publisher = {Springer},
	Title = {Process Calculi Abstractions for Biology},
	Url = {https://doi.org/10.1007/978-3-540-88869-7_23},
	Year = {2009},
	Bdsk-Url-1 = {https://doi.org/10.1007/978-3-540-88869-7_23},
	Bdsk-Url-2 = {http://dx.doi.org/10.1007/978-3-540-88869-7_23}}

@inbook{Calder2006,
	Abstract = {This paper examines the influence of the Raf Kinase Inhibitor Protein (RKIP) on the Extracellular signal Regulated Kinase (ERK) signalling pathway [5] through modelling in a Markovian process algebra, PEPA [11]. Two models of the system are presented, a reagent-centric view and a pathway-centric view. The models capture functionality at the level of subpathway, rather than at a molecular level. Each model affords a different perspective of the pathway and analysis. We demonstrate the two models to be formally equivalent using the timing-aware bisimulation defined over PEPA models and discuss the biological significance.},
	Address = {Berlin, Heidelberg},
	Author = {Calder, Muffy and Gilmore, Stephen and Hillston, Jane},
	Booktitle = {Transactions on Computational Systems Biology VII},
	Doi = {10.1007/11905455_1},
	Editor = {Priami, Corrado and Ing{\'o}lfsd{\'o}ttir, Anna and Mishra, Bud and Riis Nielson, Hanne},
	Isbn = {978-3-540-48839-2},
	Pages = {1--23},
	Publisher = {Springer},
	Title = {Modelling the Influence of RKIP on the {ERK} Signalling Pathway Using the Stochastic Process Algebra PEPA},
	Url = {https://doi.org/10.1007/11905455_1},
	Year = {2006},
	Bdsk-Url-1 = {https://doi.org/10.1007/11905455_1},
	Bdsk-Url-2 = {http://dx.doi.org/10.1007/11905455_1}}

@incollection{Kuttler:2006:GRP:2172228.2172230,
	Acmid = {2172230},
	Address = {Berlin, Heidelberg},
	Author = {Kuttler, C{\'e}line and Niehren, Joachim},
	Booktitle = {Transactions on Computational Systems Biology VII},
	Editor = {Priami, Corrado and Ing\'{o}lfsd\'{o}ttir, Anna and Mishra, Bud and Riis Nielson, Hanne},
	Isbn = {3-540-48837-5, 978-3-540-48837-8},
	Numpages = {32},
	Pages = {24--55},
	Publisher = {Springer},
	Title = {Gene Regulation in the Pi Calculus: Simulating Cooperativity at the Lambda Switch},
	Url = {http://dl.acm.org/citation.cfm?id=2172228.2172230},
	Year = {2006},
	Bdsk-Url-1 = {http://dl.acm.org/citation.cfm?id=2172228.2172230}}

@inbook{Maurin2009,
	Abstract = {In this paper, we address the problem of modeling biological regulatory networks thanks to the stochastic $\pi$-calculus. We propose a method which extends a logical method, that is the approach of Ren{\'e} Thomas. By introducing temporal and stochastic aspects there, we make our formalism closer to biological reality. We then use the SPiM stochastic simulator to illustrate the practical interests of this description. The application example concerns the behaviors of four interacting genes involved in the $\lambda$-phage. Interesting results are emerging from the simulations. First, it confirms knowledge of the regulation phenomena. In addition, experiments with different values of the delay parameters give some precious hints of a tendency either for the lytic phase or to the lysogenic phase.},
	Address = {Berlin, Heidelberg},
	Author = {Maurin, Myl{\`e}ne and Magnin, Morgan and Roux, Olivier},
	Booktitle = {Bioinformatics and Computational Biology: First International Conference, BICoB 2009},
	Doi = {10.1007/978-3-642-00727-9_27},
	Editor = {Rajasekaran, Sanguthevar},
	Isbn = {978-3-642-00727-9},
	Pages = {282--294},
	Publisher = {Springer},
	Title = {Modeling of Genetic Regulatory Network in Stochastic $\pi$-Calculus},
	Url = {https://doi.org/10.1007/978-3-642-00727-9_27},
	Year = {2009},
	Bdsk-Url-1 = {https://doi.org/10.1007/978-3-642-00727-9_27},
	Bdsk-Url-2 = {http://dx.doi.org/10.1007/978-3-642-00727-9_27}}

@article{CARAVAGNA201226,
	Author = {Giulio Caravagna and Jane Hillston},
	Doi = {https://doi.org/10.1016/j.tcs.2011.11.028},
	Issn = {0304-3975},
	Journal = {Theoretical Computer Science},
	Keywords = {DDEs},
	Number = {Supplement C},
	Pages = {26--49},
	Title = {Bio-PEPAd: A non-Markovian extension of Bio-PEPA},
	Url = {http://www.sciencedirect.com/science/article/pii/S0304397511009479},
	Volume = {419},
	Year = {2012},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0304397511009479},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.tcs.2011.11.028}}

@article{pmid25252105,
	Author = {Schormann, Norbert and Ricciardi, Robert and Chattopadhyay, Debasish},
	Journal = {Protein Science},
	Number = {12},
	Pages = {1667--1685},
	Title = {{{U}racil-{D}{N}{A} glycosylases-structural and functional perspectives on an essential family of {D}{N}{A} repair enzymes}},
	Volume = {23},
	Year = {2014}}

@article{plotkinsos,
	Author = {Gordon D. Plotkin},
	Bibsource = {dblp computer science bibliography, http://dblp.org},
	Biburl = {http://dblp.org/rec/bib/journals/jlp/Plotkin04a},
	Journal = {The Journal of Logic and Algebraic Programming},
	Pages = {17--139},
	Timestamp = {Mon, 21 Feb 2005 12:50:35 +0100},
	Title = {A structural approach to operational semantics},
	Volume = {60--61},
	Year = {2004}}

@article{BANATRE199055,
	Author = {Jean-Pierre Ban{\^a}tre and Daniel Le M{\'e}tayer},
	Doi = {https://doi.org/10.1016/0167-6423(90)90044-E},
	Issn = {0167-6423},
	Journal = {Science of Computer Programming},
	Number = {1},
	Pages = {55--77},
	Title = {The gamma model and its discipline of programming},
	Url = {http://www.sciencedirect.com/science/article/pii/016764239090044E},
	Volume = {15},
	Year = {1990},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/016764239090044E},
	Bdsk-Url-2 = {https://doi.org/10.1016/0167-6423(90)90044-E}}

@inbook{Fages2008,
	Abstract = {Biologists use diagrams to represent interactions between molecular species, and on the computer, diagrammatic notations are also employed in interactive maps. These diagrams are fundamentally of two types: reaction graphs and activation/inhibition graphs. In this tutorial, we study these graphs with formal methods originating from programming theory. We consider systems of biochemical reactions with kinetic expressions, as written in the Systems Biology Markup Language (SBML), and interpreted in the Biochemical Abstract Machine (Biocham) at different levels of abstraction, by either an asynchronous boolean transition system, a continuous time Markov chain, or a system of Ordinary Differential Equations over molecular concentrations. We show that under general conditions satisfied in practice, the activation/inhibition graph is independent of the precise kinetic expressions, and is computable in linear time in the number of reactions. Then we consider the formalization of the biological properties of systems, as observed in experiments, in temporal logics. We show that these logics are expressive enough to capture semi-qualitative semi-quantitative properties of the boolean and differential semantics of reaction models, and that model-checking techniques can be used to validate a model w.r.t. its temporal specification, complete it, and search for kinetic parameter values. We illustrate this modelling method with examples on the MAPK signalling cascade, and on Kohn's map of the mammalian cell cycle.},
	Address = {Berlin, Heidelberg},
	Author = {Fages, Fran{\c{c}}ois and Soliman, Sylvain},
	Booktitle = {Formal Methods for Computational Systems Biology: 8th International School on Formal Methods for the Design of Computer, Communication, and Software Systems, SFM 2008, Advanced Lectures},
	Doi = {10.1007/978-3-540-68894-5_3},
	Editor = {Bernardo, Marco and Degano, Pierpaolo and Zavattaro, Gianluigi},
	Isbn = {978-3-540-68894-5},
	Pages = {54--80},
	Publisher = {Springer},
	Series = {Lecture Notes in Computer Science},
	Title = {Formal Cell Biology in Biocham},
	Url = {https://doi.org/10.1007/978-3-540-68894-5_3},
	Volume = {5016},
	Year = {2008},
	Bdsk-Url-1 = {https://doi.org/10.1007/978-3-540-68894-5_3},
	Bdsk-Url-2 = {http://dx.doi.org/10.1007/978-3-540-68894-5_3}}

@misc{biochamsoftware,
	Note = {\url{https://lifeware.inria.fr/biocham/}. Accessed 3-November-2017},
	Title = {The Biochemical Abstract Machine BIOCHAM 3},
	Url = {https://lifeware.inria.fr/biocham/},
	Year = {2017},
	Bdsk-Url-1 = {https://lifeware.inria.fr/biocham/}}

@book{kinetics,
	Author = {Smart, Lesley},
	Doi = {10.1039/9781847557803},
	Editor = {Mortimer, Micheal and Taylor, Peter},
	Isbn = {978-0-85404-670-6},
	Pages = {X001-X004},
	Publisher = {The Royal Society of Chemistry},
	Series = {The Molecular World},
	Title = {Chemical Kinetics and Mechanism},
	Url = {http://dx.doi.org/10.1039/9781847557803},
	Year = {2002},
	Bdsk-Url-1 = {http://dx.doi.org/10.1039/9781847557803}}

@book{lewars,
	Author = {Lewars, Errol G.},
	Edition = {3rd},
	Publisher = {Springer},
	Subtitle = {Introduction to the Theory and Applications of Molecular and Quantum Mechanics},
	Title = {Computational Chemistry},
	Year = {2016}}

@article{pmid12353013,
	Author = {Aviv Regev and Ehud Shapiro},
	Journal = {Nature},
	Number = {6905},
	Pages = {343},
	Title = {{{C}ells as computation}},
	Volume = {419},
	Year = {2002}}

@misc{goldbook,
	Author = {Miloslav Nic and Jiri Jirat and Bedrich Kosata},
	Note = {\url{https://goldbook.iupac.org/}. Accessed 12-December-2017},
	Title = {IUPAC Compendium of Chemical Terminology (Gold Book)},
	Url = {https://goldbook.iupac.org/},
	Year = {Release 2.3.3b, 2017-03-27},
	Bdsk-Url-1 = {https://goldbook.iupac.org/}}

@misc{formaldehydeindustrial,
	Author = {Department of Chemistry, University of York, Centre for Industry Education Collaboration},
	Note = {\url{http://www.essentialchemicalindustry.org/chemicals/methanal.html}. Accessed 22-January-2018},
	Title = {The Essential Chemical Industry - online. Methanal (Formaldehyde)},
	Url = {http://www.essentialchemicalindustry.org/chemicals/methanal.html},
	Year = {2016},
	Bdsk-Url-1 = {http://www.essentialchemicalindustry.org/chemicals/methanal.html}}

@book{chang,
	Author = {Raymond Chang and Ken Goldsby},
	Ion = {7th},
	Publisher = {McGraw-Hill},
	Title = {General Chemistry. The Essential Concepts},
	Year = {2014}}

@article{pmid3894502,
	Author = {Fox, Cecil H. and Johnson, Frank B. and Whiting, John and Roller, Peter P.},
	Journal = {Journal of Histochemistry and Cytochemistry},
	Number = {8},
	Pages = {845--853},
	Title = {{{F}ormaldehyde fixation}},
	Volume = {33},
	Year = {1985}}

@book{kemp,
	Author = {William Kemp},
	Edition = {4th},
	Publisher = {Macmillan},
	Title = {NMR in Chemistry. A Multinuclear Introduction},
	Year = {1995}}

@misc{xomdom,
	Author = {Bill Venners},
	Note = {\url{https://www.artima.com/intv/dom.html}. Accessed 1-July-2018},
	Title = {The Good, the Bad, and the DOM},
	Url = {https://www.artima.com/intv/dom.html},
	Year = {2018},
	Bdsk-Url-1 = {https://www.artima.com/intv/dom.html}}

@misc{cwb,
	Author = {Perdita Stevens},
	Note = {\url{http://homepages.inf.ed.ac.uk/perdita/cwb/}. Accessed 25-June-2018},
	Title = {The Edinburgh Concurrency Workbench},
	Url = {http://homepages.inf.ed.ac.uk/perdita/cwb/},
	Year = {2018},
	Bdsk-Url-1 = {http://homepages.inf.ed.ac.uk/perdita/cwb/}}

@misc{prob,
	Author = {ProB},
	Note = {\url{https://www3.hhu.de/stups/prob/index.php/Main_Page}. Accessed 25-June-2018},
	Title = {The ProB Animator and Model Checker},
	Url = {https://www3.hhu.de/stups/prob/index.php/Main_Page},
	Year = {2018},
	Bdsk-Url-1 = {https://www3.hhu.de/stups/prob/index.php/Main_Page}}

@misc{maude,
	Author = {Maude},
	Note = {\url{http://maude.cs.illinois.edu/}. Accessed 25-June-2018},
	Title = {The Maude System},
	Url = {http://maude.cs.illinois.edu/},
	Year = {2018},
	Bdsk-Url-1 = {http://maude.cs.illinois.edu/}}

@misc{mxgraph,
	Author = {mxGraph},
	Note = {\url{https://jgraph.github.io/mxgraph/}. Accessed 5-May-2018},
	Title = {mxGraph website},
	Url = {https://jgraph.github.io/mxgraph/},
	Year = {2018},
	Bdsk-Url-1 = {https://jgraph.github.io/mxgraph/}}

@misc{xom,
	Author = {XOM},
	Note = {\url{https://xom.nu/}. Accessed 5-May-2018},
	Title = {XOM website},
	Url = {https://xom.nu/},
	Year = {2018},
	Bdsk-Url-1 = {https://xom.nu/}}

@misc{junit,
	Author = {JUnit},
	Note = {\url{https://junit.org/}. Accessed 12-May-2018},
	Title = {JUnit website},
	Url = {https://junit.org/},
	Year = {2018},
	Bdsk-Url-1 = {https://junit.org/}}

@misc{wg3soar,
	Author = {Matthias Soeken, Nabila Abdessaied, Pawel Kerntopf, Claudio Moraga, Krzysztof Podlaski, Robert Wille},
	Note = {\url{https://github.com/COST-IC1405/wg3-soar-report/blob/master/README.md}. Accessed 22-Nov-2018},
	Title = {COST Action IC1405: Reversible Computation - Extending Horizons of Computing. State of the Art Report Working Group 3: Reversible logic synthesis},
	Url = {https://github.com/COST-IC1405/wg3-soar-report/blob/master/README.md},
	Year = {2018},
	Bdsk-File-1 = {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},
	Bdsk-Url-1 = {https://github.com/COST-IC1405/wg3-soar-report/blob/master/README.md}}

@article{VF2,
	Author = {Luigi P. Cordella and Pasquale Foggia and Carlo Sansone and Mario Vento},
	Doi = {10.1109/TPAMI.2004.75},
	Issn = {0162-8828},
	Journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	Keywords = {computational complexity;graph theory;pattern matching;graph isomorphism algorithm;graphs matching;spatial complexity;subgraph isomorphism;technical drawings;Algorithm design and analysis;Application software;NP-complete problem;Pattern analysis;Pattern matching;Pattern recognition;Performance analysis;Performance evaluation;Relational databases;Testing;Index Terms- Graph-subgraph isomorphism;attributed relational graphs.;large graphs;Algorithms;Artificial Intelligence;Cluster Analysis;Computer Graphics;Image Enhancement;Image Interpretation, Computer-Assisted;Imaging, Three-Dimensional;Information Storage and Retrieval;Numerical Analysis, Computer-Assisted;Pattern Recognition, Automated;Reproducibility of Results;Sensitivity and Specificity;Signal Processing, Computer-Assisted;Subtraction Technique},
	Number = {10},
	Pages = {1367-1372},
	Title = {A (sub)graph isomorphism algorithm for matching large graphs},
	Volume = {26},
	Year = {2004},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2004.75}}

@article{lecerf,
	Author = {Yves Lecerf},
	Journal = {Comptes Rendus Hebdomadaires des S{\'e}ances de l'Acad{\'e}mie des Sciences},
	Pages = {2597-26},
	Title = {Machines de Turing r{\'e}eversibles},
	Volume = {257},
	Year = {1963}}

@article{1057537,
	Author = {David A. Huffman},
	Doi = {10.1109/TIT.1959.1057537},
	Issn = {0096-1000},
	Journal = {IRE Transactions on Information Theory},
	Keywords = {Sequential machines;Transducers;Nonlinear equations;Laboratories;Circuit synthesis;Circuit noise;Combinational circuits;Research and development},
	Number = {5},
	Pages = {41-59},
	Title = {Canonical forms for information-lossless finite-state logical machines},
	Volume = {5},
	Year = {1959},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TIT.1959.1057537}}

@article{5392446,
	Author = {Rolf Landauer},
	Doi = {10.1147/rd.53.0183},
	Issn = {0018-8646},
	Journal = {IBM Journal of Research and Development},
	Number = {3},
	Pages = {183-191},
	Title = {Irreversibility and Heat Generation in the Computing Process},
	Volume = {5},
	Year = {1961},
	Bdsk-Url-1 = {http://dx.doi.org/10.1147/rd.53.0183}}

@book{gof,
	Author = {Erich Gamma, John Vlissides, Ralph Johnson, Richard Helm},
	Edition = {1st},
	Publisher = {Pearson},
	Subtitle = {Elements of Reusable Object-Oriented Software},
	Title = {Design Patterns},
	Year = {1994}}

@inproceedings{isomorphisms,
	Acmid = {2448946},
	Author = {Lee, Jinsoo and Han, Wook-Shin and Kasperovics, Romans and Lee, Jeong-Hoon},
	Booktitle = {Proceedings of the 39th international conference on Very Large Data Bases},
	Location = {Trento, Italy},
	Numpages = {12},
	Pages = {133--144},
	Publisher = {VLDB Endowment},
	Series = {PVLDB'13},
	Title = {An in-depth comparison of subgraph isomorphism algorithms in graph databases},
	Url = {http://dl.acm.org/citation.cfm?id=2448936.2448946},
	Year = {2013},
	Bdsk-Url-1 = {http://dl.acm.org/citation.cfm?id=2448936.2448946}}

@inproceedings{Yokoyama:2007:RPL:1244381.1244404,
	Acmid = {1244404},
	Address = {New York, NY, USA},
	Author = {Yokoyama, Tetsuo and Gl\"{u}ck, Robert},
	Booktitle = {Proceedings of the 2007 ACM SIGPLAN Symposium on Partial Evaluation and Semantics-based Program Manipulation},
	Doi = {10.1145/1244381.1244404},
	Isbn = {978-1-59593-620-2},
	Keywords = {Janus, non-standard interpreter hierarchy, program inversion, reversible computing, reversible programming language, self-interpreter},
	Location = {Nice, France},
	Numpages = {10},
	Pages = {144--153},
	Publisher = {ACM},
	Series = {PEPM '07},
	Title = {A Reversible Programming Language and Its Invertible Self-interpreter},
	Url = {http://doi.acm.org/10.1145/1244381.1244404},
	Year = {2007},
	Bdsk-Url-1 = {http://doi.acm.org/10.1145/1244381.1244404},
	Bdsk-Url-2 = {http://dx.doi.org/10.1145/1244381.1244404}}

@inproceedings{10.1007/978-3-642-19805-2_4,
	Abstract = {Reversible computing is the study of computation models that exhibit both forward and backward determinism. Understanding the fundamental properties of such models is not only relevant for reversible programming, but has also been found important in other fields, e.g., bidirectional model transformation, program transformations such as inversion, and general static prediction of program properties.},
	Address = {Berlin, Heidelberg},
	Author = {Axelsen, Holger Bock and Gl{\"u}ck, Robert},
	Booktitle = {Foundations of Software Science and Computational Structures},
	Editor = {Hofmann, Martin},
	Isbn = {978-3-642-19805-2},
	Pages = {42--56},
	Publisher = {Springer Berlin Heidelberg},
	Title = {What Do Reversible Programs Compute?},
	Year = {2011}}

@article{MATOS20032063,
	Abstract = {Very simple reversible programming languages can be useful for the study of reversible transformations. For this purpose we define simple reversible language (SRL), a very simple reversible language, and analyse its properties. The language SRL is similar to the ``loop'' languages that have been used by several authors to characterise the set of primitive recursive functions. There are, however, important differences: SRL has domain Z instead of N and only reversible programs can be written in SRL. The reversibility of linear homogeneous SRL programs is related to the fact that the corresponding set of matrices has the algebraic structure of a group. We show that such programs implement exactly the linear transformations corresponding to the group of integer positive modular matrices, while in ESRL, an extended version of SRL, the set of transformations that can be implemented by linear homogeneous programs corresponds exactly to the group of integer modular matrices.},
	Author = {Armando B. Matos},
	Doi = {https://doi.org/10.1016/S0304-3975(02)00486-3},
	Issn = {0304-3975},
	Journal = {Theoretical Computer Science},
	Keywords = {Loop languages, Group of modular matrices, Reversibility},
	Number = {3},
	Pages = {2063 - 2074},
	Title = {Linear programs in a simple reversible language},
	Url = {http://www.sciencedirect.com/science/article/pii/S0304397502004863},
	Volume = {290},
	Year = {2003},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0304397502004863},
	Bdsk-Url-2 = {https://doi.org/10.1016/S0304-3975(02)00486-3}}

@phdthesis{Frank:1999:REC:930275,
	Address = {Cambridge, MA, USA},
	Author = {Frank, Michael P.},
	Note = {AAI0800784},
	Publisher = {Massachusetts Institute of Technology},
	Title = {Reversibility for Efficient Computing},
	Year = {1999}}

@article{Leeman:1986:FAU:5001.5005,
	Acmid = {5005},
	Address = {New York, NY, USA},
	Author = {Leeman,Jr., George B.},
	Doi = {10.1145/5001.5005},
	Issn = {0164-0925},
	Issue_Date = {Jan. 1986},
	Journal = {ACM Trans. Program. Lang. Syst.},
	Number = {1},
	Numpages = {38},
	Pages = {50--87},
	Publisher = {ACM},
	Title = {A Formal Approach to Undo Operations in Programming Languages},
	Url = {http://doi.acm.org/10.1145/5001.5005},
	Volume = {8},
	Year = {1986},
	Bdsk-Url-1 = {http://doi.acm.org/10.1145/5001.5005},
	Bdsk-Url-2 = {http://dx.doi.org/10.1145/5001.5005}}

@inproceedings{EPTCS276.7,
	Author = {Hoey, James and Ulidowski, Irek and Yuen, Shoji},
	Booktitle = {{\rm Proceedings Combined 25th International Workshop on} Expressiveness in Concurrency {\rm and 15th Workshop on} Structural Operational Semantics, {\rm Beijing, China, September 3, 2018}},
	Doi = {10.4204/EPTCS.276.7},
	Editor = {P\'erez, Jorge A. and Tini, Simone},
	Pages = {69-86},
	Publisher = {Open Publishing Association},
	Series = {Electronic Proceedings in Theoretical Computer Science},
	Title = {Reversing Parallel Programs with Blocks and Procedures},
	Volume = {276},
	Year = {2018},
	Bdsk-Url-1 = {http://dx.doi.org/10.4204/EPTCS.276.7}}

@inproceedings{EPTCS255.4,
	Author = {Hoey, James and Ulidowski, Irek and Yuen, Shoji},
	Booktitle = {{\rm Proceedings Combined 24th International Workshop on} Expressiveness in Concurrency {\rm and 14th Workshop on} Structural Operational Semantics, {\rm Berlin, Germany, 4th September 2017}},
	Doi = {10.4204/EPTCS.255.4},
	Editor = {Peters, Kirstin and Tini, Simone},
	Pages = {51-66},
	Publisher = {Open Publishing Association},
	Series = {Electronic Proceedings in Theoretical Computer Science},
	Title = {Reversing Imperative Parallel Programs},
	Volume = {255},
	Year = {2017},
	Bdsk-Url-1 = {http://dx.doi.org/10.4204/EPTCS.255.4}}

@article{Bennett:1973:LRC:1664562.1664568,
	Acmid = {1664568},
	Address = {Riverton, NJ, USA},
	Author = {Bennett, C. H.},
	Doi = {10.1147/rd.176.0525},
	Issn = {0018-8646},
	Issue_Date = {November 1973},
	Journal = {IBM J. Res. Dev.},
	Number = {6},
	Numpages = {8},
	Pages = {525--532},
	Publisher = {IBM Corp.},
	Title = {Logical Reversibility of Computation},
	Url = {http://dx.doi.org/10.1147/rd.176.0525},
	Volume = {17},
	Year = {1973},
	Bdsk-Url-1 = {http://dx.doi.org/10.1147/rd.176.0525}}

@article{DBLP:journals/jca/MorrisonU16,
	Author = {Daniel Morrison and Irek Ulidowski},
	Bibsource = {dblp computer science bibliography, https://dblp.org},
	Biburl = {https://dblp.org/rec/bib/journals/jca/MorrisonU16},
	Journal = {J. Cellular Automata},
	Number = {1-2},
	Pages = {101--120},
	Timestamp = {Wed, 28 Sep 2016 19:54:27 +0200},
	Title = {Direction-Reversible Self-Timed Cellular Automata for Delay-Insensitive Circuits},
	Url = {http://www.oldcitypublishing.com/journals/jca-home/jca-issue-contents/jca-volume-12-number-1-2-2016/jca-12-1-2-p-101-120/},
	Volume = {12},
	Year = {2016},
	Bdsk-Url-1 = {http://www.oldcitypublishing.com/journals/jca-home/jca-issue-contents/jca-volume-12-number-1-2-2016/jca-12-1-2-p-101-120/}}

@article{BARYLSKA201848,
	Doi = {https://doi.org/10.1016/j.scico.2017.10.008},
	Issn = {0167-6423},
	Journal = {Science of Computer Programming},
	Keywords = {Petri net, Reversibility, Reversible computation, Decidability},
	Note = {Special issue of the 8th Conference on Reversible Computation (RC 2016)},
	Pages = {48 - 60},
	Title = {Reversible computation vs. reversibility in Petri nets},
	Url = {http://www.sciencedirect.com/science/article/pii/S0167642317302204},
	Volume = {151},
	Year = {2018},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0167642317302204},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.scico.2017.10.008}}

@inproceedings{10.1007/978-3-319-99498-7_6,
	Author = {Philippou, Anna and Psara, Kyriaki},
	Booktitle = {Reversible Computation},
	Editor = {Kari, Jarkko and Ulidowski, Irek},
	Isbn = {978-3-319-99498-7},
	Pages = {84--101},
	Publisher = {Springer International Publishing},
	Title = {Reversible Computation in {P}etri Nets},
	Year = {2018}}

@inproceedings{10.1007/978-3-642-36315-3_8,
	Address = {Berlin, Heidelberg},
	Author = {Schultz, Ulrik Pagh},
	Booktitle = {Reversible Computation},
	Editor = {Gl{\"u}ck, Robert and Yokoyama, Tetsuo},
	Isbn = {978-3-642-36315-3},
	Pages = {97--111},
	Publisher = {Springer Berlin Heidelberg},
	Title = {Towards a General-Purpose, Reversible Language for Controlling Self-reconfigurable Robots},
	Year = {2013}}

@inproceedings{DBLP:conf/rc/SchultzLEA15,
	Author = {Ulrik Pagh Schultz and Johan Sund Laursen and Lars{-}Peter Ellekilde and Holger Bock Axelsen},
	Bibsource = {dblp computer science bibliography, https://dblp.org},
	Biburl = {https://dblp.org/rec/bib/conf/rc/SchultzLEA15},
	Booktitle = {Reversible Computation - 7th International Conference, {RC} 2015, Grenoble, France, July 16-17, 2015, Proceedings},
	Crossref = {DBLP:conf/rc/2015},
	Doi = {10.1007/978-3-319-20860-2\_7},
	Pages = {111--126},
	Timestamp = {Fri, 02 Nov 2018 09:40:46 +0100},
	Title = {Towards a Domain-Specific Language for Reversible Assembly Sequences},
	Url = {https://doi.org/10.1007/978-3-319-20860-2\_7},
	Year = {2015},
	Bdsk-Url-1 = {https://doi.org/10.1007/978-3-319-20860-2%5C_7},
	Bdsk-Url-2 = {http://dx.doi.org/10.1007/978-3-319-20860-2%5C_7}}

@inproceedings{10.1007/978-3-319-59936-6_5,
	Address = {Cham},
	Author = {Haulund, Tue and Mogensen, Torben {\AE}gidius and Gl{\"u}ck, Robert},
	Booktitle = {Reversible Computation},
	Editor = {Phillips, Iain and Rahaman, Hafizur},
	Isbn = {978-3-319-59936-6},
	Pages = {66--73},
	Publisher = {Springer International Publishing},
	Title = {Implementing Reversible Object-Oriented Language Features on Reversible Machines},
	Year = {2017}}

@misc{undodb,
	Author = {UndoDB},
	Note = {\url{https://undo.io/}. Accessed 22-Nov-2018},
	Title = {UndoDB website},
	Url = {https://undo.io/},
	Year = {2018},
	Bdsk-Url-1 = {https://undo.io/}}

@inproceedings{6338149,
	Author = {Jakob Engblom},
	Booktitle = {Proceedings of the 2012 System, Software, SoC and Silicon Debug Conference},
	Issn = {2114-3684},
	Keywords = {digital simulation;program debugging;reverse engineering;reverse debugging;program failure;reverse execution;Wind River Simics;Debugging;Instruction sets;Instruments;Hardware;History;Software Debugging;Computer Simulation;Review;Computing History},
	Pages = {1-6},
	Title = {A review of reverse debugging},
	Year = {2012}}

@inproceedings{EPTCS222.5,
	Author = {Dezani-Ciancaglini, Mariangiola and Giannini, Paola},
	Booktitle = {{\rm Proceedings Combined 23rd International Workshop on} Expressiveness in Concurrency {\rm and 13th Workshop on} Structural Operational Semantics, {\rm Qu\'ebec City, Canada, 22nd August 2016}},
	Doi = {10.4204/EPTCS.222.5},
	Editor = {Gebler, Daniel and Peters, Kirstin},
	Pages = {60-74},
	Publisher = {Open Publishing Association},
	Series = {Electronic Proceedings in Theoretical Computer Science},
	Title = {Reversible Multiparty Sessions with Checkpoints},
	Volume = {222},
	Year = {2016},
	Bdsk-Url-1 = {http://dx.doi.org/10.4204/EPTCS.222.5}}

@inproceedings{Mutyam:2001:PSM:648057.744279,
	Acmid = {744279},
	Address = {Berlin, Heidelberg},
	Author = {Mutyam, Madhu and Krithivasan, Kamala},
	Booktitle = {Proceedings of the Third International Conference on Machines, Computations, and Universality},
	Isbn = {3-540-42121-1},
	Numpages = {12},
	Pages = {276--287},
	Publisher = {Springer-Verlag},
	Series = {MCU '01},
	Title = {P Systems with Membrane Creation: Universality and Efficiency},
	Url = {http://dl.acm.org/citation.cfm?id=648057.744279},
	Year = {2001},
	Bdsk-Url-1 = {http://dl.acm.org/citation.cfm?id=648057.744279}}

@inproceedings{DBLP:conf/csp/VirbitskaiteG18,
	Author = {Irina Virbitskaite and Nataliya Gribovskaya},
	Bibsource = {dblp computer science bibliography, https://dblp.org},
	Biburl = {https://dblp.org/rec/bib/conf/csp/VirbitskaiteG18},
	Booktitle = {Proceedings of the 27th International Workshop on Concurrency, Specification and Programming, Berlin, Germany, September 24-26, 2018.},
	Crossref = {DBLP:conf/csp/2018},
	Timestamp = {Sun, 11 Nov 2018 18:29:44 +0100},
	Title = {Preserving Behavior in Transition Systems from Event Structure Models},
	Url = {http://ceur-ws.org/Vol-2240/paper13.pdf},
	Year = {2018},
	Bdsk-Url-1 = {http://ceur-ws.org/Vol-2240/paper13.pdf}}

@inproceedings{nominallogic,
	Author = {Murdoch {Gabbay} and Andrew {Pitts}},
	Booktitle = {Proceedings. 14th Symposium on Logic in Computer Science (Cat. No. PR00158)},
	Doi = {10.1109/LICS.1999.782617},
	Issn = {1043-6871},
	Keywords = {set theory;inference mechanisms;formal languages;formal logic;abstract syntax;binders;Fraenkel-Mostowski permutation model;set theory;FM-sets;meta-logics;reasoning;formal systems;name binding;/spl alpha/-conversion;capture avoiding substitution;object-level syntax module;algebraic data types;Laboratories;Reactive power;Set theory;Computer languages;Machinery;Concrete;Proposals;Algorithm design and analysis},
	Pages = {214-224},
	Title = {A new approach to abstract syntax involving binders},
	Year = {1999},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/LICS.1999.782617}}

@article{CIMINI2012103,
	Abstract = {Plotkinʼs style of Structural Operational Semantics (SOS) has become a de facto standard in giving operational semantics to formalisms and process calculi. In many such formalisms and calculi, the concepts of names, variables and binders are essential ingredients. In this paper, we propose a formal framework for dealing with names in SOS. The framework is based on the Nominal Logic of Gabbay and Pitts and hence is called Nominal SOS. We define nominal bisimilarity, an adaptation of the notion of bisimilarity that is aware of binding. We provide evidence of the expressiveness of the framework by formulating the early π-calculus and Abramskyʼs lazy λ-calculus within Nominal SOS. For both calculi we establish the operational correspondence with the original calculi. Moreover, in the context of the π-calculus, we prove that nominal bisimilarity coincides with Sangiorgiʼs open bisimilarity and in the context of the λ-calculus we prove that nominal bisimilarity coincides with Abramskyʼs applicative bisimilarity.},
	Author = {Matteo Cimini and MohammadReza Mousavi and Michel A. Reniers and Murdoch J. Gabbay},
	Doi = {https://doi.org/10.1016/j.entcs.2012.08.008},
	Issn = {1571-0661},
	Journal = {Electronic Notes in Theoretical Computer Science},
	Keywords = {SOS, Nominal SOS, Nominal calculi, -calculus, -calculus},
	Note = {Proceedings of the 28th Conference on the Mathematical Foundations of Programming Semantics (MFPS XXVIII)},
	Pages = {103 - 116},
	Title = {Nominal SOS},
	Url = {http://www.sciencedirect.com/science/article/pii/S1571066112000382},
	Volume = {286},
	Year = {2012},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S1571066112000382},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.entcs.2012.08.008}}

@inbook{Csoernyei2008,
	Abstract = {Lambda calculus ($\lambda$-calculus) is one of the most well-known formal models of computer science. It is the basis for functional programming like Turing machines are the foundation of imperative programming. These two systems are equivalent and both can be used to formulate and investigate fundamental questions about solvability and computability.},
	Address = {Berlin, Heidelberg},
	Author = {Cs{\"o}rnyei, Zolt{\'a}n and D{\'e}vai, Gergely},
	Booktitle = {Central European Functional Programming School: Second Summer School, CEFP 2007, Cluj-Napoca, Romania, June 23-30, 2007, Revised Selected Lectures},
	Doi = {10.1007/978-3-540-88059-2_3},
	Editor = {Horv{\'a}th, Zolt{\'a}n and Plasmeijer, Rinus and So{\'o}s, Anna and Zs{\'o}k, Vikt{\'o}ria},
	Isbn = {978-3-540-88059-2},
	Pages = {87--111},
	Publisher = {Springer Berlin Heidelberg},
	Title = {An Introduction to the Lambda Calculus},
	Url = {https://doi.org/10.1007/978-3-540-88059-2_3},
	Year = {2008},
	Bdsk-Url-1 = {https://doi.org/10.1007/978-3-540-88059-2_3},
	Bdsk-Url-2 = {http://dx.doi.org/10.1007/978-3-540-88059-2_3}}

@article{NaCo18,
	Abstract = {We present the bonding calculus, a calculus in which it is easy to handle covalent bonds between molecules. Our purpose is to use bonding calculus to model the dynamics of the interactions in biochemical systems. We provide an operational semantics by means of a transition system, and use a known software platform to both simulate the chemical reactions described naturally in bonding calculus and verify their specific properties.},
	Author = {Aman, Bogdan and Ciobanu, Gabriel},
	Day = {01},
	Doi = {10.1007/s11047-018-9709-7},
	Issn = {1572-9796},
	Journal = {Natural Computing},
	Number = {4},
	Pages = {823--832},
	Title = {Bonding calculus},
	Url = {https://doi.org/10.1007/s11047-018-9709-7},
	Volume = {17},
	Year = {2018},
	Bdsk-Url-1 = {https://doi.org/10.1007/s11047-018-9709-7},
	Bdsk-Url-2 = {http://dx.doi.org/10.1007/s11047-018-9709-7}}

@InProceedings{10.1007/978-3-319-99498-7_8,
author="Kuhn, Stefan",
editor="Kari, Jarkko
and Ulidowski, Irek",
title="Simulation of Base Excision Repair in the Calculus of Covalent Bonding",
booktitle="Reversible Computation",
year="2018",
publisher="Springer International Publishing",
address="Cham",
pages="123--129",
abstract="In previous papers we have introduced a new process calculus inspired by chemical reactions, called the Calculus of Covalent Bonding. The key feature of the calculus was a new prefix operator of the form (s; b), where doing of action b triggers undoing of one of the actions in s. Because of this connection between doing and undoing of actions (or forming and breaking of bonds in a chemical modelling) we called this local reversibility. We have shown that our calculus enables out-of-causal order reversibility. In this paper we demonstrate the Base Excision Repair of DNA, a high-level biological example, using our calculus. We also introduce a software which allows us to check the syntax of processes and to simulate their execution.",
isbn="978-3-319-99498-7"
}