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DOI: 10.4230/LIPIcs.FSTTCS.2012.276
Graphs, Rewriting and Pathway Reconstruction for Rule-Based Models

Authors: Vincent Danos, Jerome Feret, Walter Fontana, Russell Harmer, Jonathan Hayman, Jean Krivine, Chris Thompson-Walsh, and Glynn Winskel

Published in: LIPIcs, Volume 18, IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2012)

Abstract
In this paper, we introduce a novel way of constructing concise causal histories (pathways) to represent how specified structures are formed during simulation of systems represented by rule-based models. This is founded on a new, clean, graph-based semantics introduced in the first part of this paper for Kappa, a rule-based modelling language that has emerged as a natural description of protein-protein interactions in molecular biology [Bachman 2011]. The semantics is capable of capturing the whole of Kappa, including subtle side-effects on deletion of structure, and its structured presentation provides the basis for the translation of techniques to other models. In particular, we give a notion of trajectory compression, which restricts a trace culminating in the production of a given structure to the actions necessary for the structure to occur. This is central to the reconstruction of biochemical pathways due to the failure of traditional techniques to provide adequately concise causal histories, and we expect it to be applicable in a range of other modelling situations.
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Vincent Danos, Jerome Feret, Walter Fontana, Russell Harmer, Jonathan Hayman, Jean Krivine, Chris Thompson-Walsh, and Glynn Winskel. Graphs, Rewriting and Pathway Reconstruction for Rule-Based Models. In IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2012). Leibniz International Proceedings in Informatics (LIPIcs), Volume 18, pp. 276-288, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2012)

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@InProceedings{danos_et_al:LIPIcs.FSTTCS.2012.276,
  author =	{Danos, Vincent and Feret, Jerome and Fontana, Walter and Harmer, Russell and Hayman, Jonathan and Krivine, Jean and Thompson-Walsh, Chris and Winskel, Glynn},
  title =	{{Graphs, Rewriting and Pathway Reconstruction for Rule-Based Models}},
  booktitle =	{IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2012)},
  pages =	{276--288},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-47-7},
  ISSN =	{1868-8969},
  year =	{2012},
  volume =	{18},
  editor =	{D'Souza, Deepak and Radhakrishnan, Jaikumar and Telikepalli, Kavitha},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSTTCS.2012.276},
  URN =		{urn:nbn:de:0030-drops-38669},
  doi =		{10.4230/LIPIcs.FSTTCS.2012.276},
  annote =	{Keywords: concurrency, rule-based models, graph rewriting, pathways, causality}
}
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