A Software Package for Chemically Inspired Graph Transformation

Jakob L. Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler

doi:10.1007/978-3-319-40530-8_5

A Software Package for Chemically Inspired Graph Transformation

Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler

Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

Abstract

Chemical reaction networks can be automatically generated from graph grammar descriptions, where transformation rules model reaction patterns. Because a molecule graph is connected and reactions in general involve multiple molecules, the transformation must be performed on multisets of graphs. We present a general software package for this type of graph transformation system, which can be used for modelling chemical systems. The package contains a C++ library with algorithms for working with transformation rules in the Double Pushout formalism, e.g., composition of rules and a domain specific language for programming graph language generation. A Python interface makes these features easily accessible. The package also has extensive procedures for automatically visualising not only graphs and transformation rules, but also Double Pushout diagrams and graph languages in form of directed hypergraphs. The software is available as an open source package, and interactive examples can be found on the accompanying webpage.

Original language	English
Title of host publication	Graph Transformation : Proceedings of the 9th International Conference on Graph Transformation
Editors	Rachid Echahed, Mark Minas
Publisher	Springer
Publication date	2016
Pages	73-88
ISBN (Print)	978-3-319-40529-2
ISBN (Electronic)	978-3-319-40530-8
DOIs	https://doi.org/10.1007/978-3-319-40530-8_5
Publication status	Published - 2016
Event	9th International Conference on Graph Transformation - Vienna, Austria Duration: 5. Jul 2016 → 6. Jul 2016 Conference number: 9 https://sites.google.com/site/icgt2016/

Conference

Conference	9th International Conference on Graph Transformation
Number	9
Country/Territory	Austria
City	Vienna
Period	05/07/2016 → 06/07/2016
Internet address	https://sites.google.com/site/icgt2016/

Series	Lecture Notes in Computer Science
Volume	9761
ISSN	0302-9743

Keywords

Chemical graph transformation system
Double Pushout
Graph grammar
Rule composition
Strategy framework

Documents & Links

10.1007/978-3-319-40530-8_5

SDU Link

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1 Conference presentations
1 Talks and presentations in private or public companies

9th International Conference on Graph Transformation
Andersen, J. L. (Speaker)
5. Jul 2016 → 6. Jul 2016
Activity: Talks and presentations › Conference presentations
A Software Package for Chemically Inspired Graph Transformation
Andersen, J. L. (Speaker)
5. Jul 2016
Activity: Talks and presentations › Talks and presentations in private or public companies

Cite this

@inproceedings{bb1f4ba53e2747e5b185da8768769311,

title = "A Software Package for Chemically Inspired Graph Transformation",

abstract = "Chemical reaction networks can be automatically generated from graph grammar descriptions, where transformation rules model reaction patterns. Because a molecule graph is connected and reactions in general involve multiple molecules, the transformation must be performed on multisets of graphs. We present a general software package for this type of graph transformation system, which can be used for modelling chemical systems. The package contains a C++ library with algorithms for working with transformation rules in the Double Pushout formalism, e.g., composition of rules and a domain specific language for programming graph language generation. A Python interface makes these features easily accessible. The package also has extensive procedures for automatically visualising not only graphs and transformation rules, but also Double Pushout diagrams and graph languages in form of directed hypergraphs. The software is available as an open source package, and interactive examples can be found on the accompanying webpage.",

keywords = "Chemical graph transformation system, Double Pushout, Graph grammar, Rule composition, Strategy framework",

author = "Andersen, {Jakob L.} and Christoph Flamm and Daniel Merkle and Stadler, {Peter F.}",

year = "2016",

doi = "10.1007/978-3-319-40530-8_5",

language = "English",

isbn = "978-3-319-40529-2",

series = "Lecture Notes in Computer Science",

publisher = "Springer",

pages = "73--88",

editor = "Rachid Echahed and Mark Minas",

booktitle = "Graph Transformation",

address = "Germany",

note = "9th International Conference on Graph Transformation, ICGT ; Conference date: 05-07-2016 Through 06-07-2016",

url = "https://sites.google.com/site/icgt2016/",

}

Andersen, JL, Flamm, C, Merkle, D & Stadler, PF 2016, A Software Package for Chemically Inspired Graph Transformation. in R Echahed & M Minas (eds), Graph Transformation: Proceedings of the 9th International Conference on Graph Transformation. Springer, Lecture Notes in Computer Science, vol. 9761, pp. 73-88, 9th International Conference on Graph Transformation, Vienna, Austria, 05/07/2016. https://doi.org/10.1007/978-3-319-40530-8_5

A Software Package for Chemically Inspired Graph Transformation. / Andersen, Jakob L.; Flamm, Christoph; Merkle, Daniel et al.
Graph Transformation: Proceedings of the 9th International Conference on Graph Transformation. ed. / Rachid Echahed; Mark Minas. Springer, 2016. p. 73-88 (Lecture Notes in Computer Science, Vol. 9761).

Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

TY - GEN

T1 - A Software Package for Chemically Inspired Graph Transformation

AU - Andersen, Jakob L.

AU - Flamm, Christoph

AU - Merkle, Daniel

AU - Stadler, Peter F.

N1 - Conference code: 9

PY - 2016

Y1 - 2016

N2 - Chemical reaction networks can be automatically generated from graph grammar descriptions, where transformation rules model reaction patterns. Because a molecule graph is connected and reactions in general involve multiple molecules, the transformation must be performed on multisets of graphs. We present a general software package for this type of graph transformation system, which can be used for modelling chemical systems. The package contains a C++ library with algorithms for working with transformation rules in the Double Pushout formalism, e.g., composition of rules and a domain specific language for programming graph language generation. A Python interface makes these features easily accessible. The package also has extensive procedures for automatically visualising not only graphs and transformation rules, but also Double Pushout diagrams and graph languages in form of directed hypergraphs. The software is available as an open source package, and interactive examples can be found on the accompanying webpage.

AB - Chemical reaction networks can be automatically generated from graph grammar descriptions, where transformation rules model reaction patterns. Because a molecule graph is connected and reactions in general involve multiple molecules, the transformation must be performed on multisets of graphs. We present a general software package for this type of graph transformation system, which can be used for modelling chemical systems. The package contains a C++ library with algorithms for working with transformation rules in the Double Pushout formalism, e.g., composition of rules and a domain specific language for programming graph language generation. A Python interface makes these features easily accessible. The package also has extensive procedures for automatically visualising not only graphs and transformation rules, but also Double Pushout diagrams and graph languages in form of directed hypergraphs. The software is available as an open source package, and interactive examples can be found on the accompanying webpage.

KW - Chemical graph transformation system

KW - Double Pushout

KW - Graph grammar

KW - Rule composition

KW - Strategy framework

U2 - 10.1007/978-3-319-40530-8_5

DO - 10.1007/978-3-319-40530-8_5

M3 - Article in proceedings

SN - 978-3-319-40529-2

T3 - Lecture Notes in Computer Science

SP - 73

EP - 88

BT - Graph Transformation

A2 - Echahed, Rachid

A2 - Minas, Mark

PB - Springer

T2 - 9th International Conference on Graph Transformation

Y2 - 5 July 2016 through 6 July 2016

ER -

A Software Package for Chemically Inspired Graph Transformation

Abstract

Conference

Keywords

Documents & Links

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9th International Conference on Graph Transformation

A Software Package for Chemically Inspired Graph Transformation

Cite this