%% Pathway Logic references (in chronological order)

@InProceedings{Eker+2002a,
  author = 	 {Steven Eker and Merrill Knapp and Keith Laderoute and Patrick Lincoln and Jos\'{e} Meseguer and Kemal Sonmez},
  title = 	 {{Pathway Logic}: Symbolic Analysis of Biological Signaling},
  booktitle = 	 {Proceedings of the Pacific Symposium on Biocomputing},
  pages = 	 {400--412},
  year = 	 {2002},
  month = 	 {January},
}

@InProceedings{Eker+2002b,
  author = 	 {Steven Eker and Merrill Knapp and Keith Laderoute and Patrick Lincoln and Carolyn Talcott},
  title = 	 {{Pathway Logic}: Executable Models of Biological Networks},
  booktitle = 	 {Proceedings of Fourth International Workshop on Rewriting Logic and Its Applications (WRLA)},
  year = 	 {2002},
}

@InProceedings{Talcott+2004,
  author = 	 {Carolyn Talcott and Steven Eker and Merrill Knapp and Patrick Lincoln and Keith Laderoute},
  title = 	 {Pathway Logic Modeling of Protein Functional Domains in Signal Transduction},
  booktitle = 	 {Proceedings of the Pacific Symposium on Biocomputing},
  pages = 	 {568--580},
  year = 	 {2004},
  month = 	 {January},
}

@InProceedings{MasonTalcott2004,
  author = 	 {Ian Mason and Carolyn Talcott},
  title = 	 {{IOP} -- The Interoperability Platform \& {IMaude} -- an Interactive Extension of Maude},
  booktitle = 	 {Proceedings of International Workshop on Rewriting Logic and Its Applications (WRLA)},
  year = 	 {2004},
  month = 	 {March},
}

@InProceedings{TalcottDill2005,
  author = 	 {Carolyn Talcott and David L. Dill},
  title = 	 {The Pathway Logic Assistant},
  booktitle = 	 {Proceedings of the Workshop Computational Methods in Systems Biology (CMSB)},
  year = 	 {2005},
  month = 	 {March},
}

@article{talcott-dill-05cmsb-jrnl,
  title = {Multiple Representations of Biological Processes},
  author = {Carolyn Talcott and David L. Dill},
  journal = {Transactions on Computational Systems Biology},
  editor = {Gordin Plotkin},
  year = {2006},
  publisher = {Springer},
  abstract = {This paper describes representations of biological processes based on Rewriting Logic and Petri net formalisms and mappings between these representations used in the Pathway Logic Assistant. The mappings are shown to preserve properties of interest. In addition a relevant subnet transformation is defined, that specializes a Petri net model to a specific query to reduce the number of transitions that must be considered when answering the query.   The transformation is shown to preserve the query in the sense that no answers are lost.},
  keywords = {signal transduction, biological process, Pathway Logic, Rewriting Logic, Petri Net},
}

@inproceedings{talcott-06wsc,
  title = {Symbolic Modeling of Signal Transduction in Pathway Logic},
  author = {Carolyn Talcott},
  booktitle = {2006 Winter Simulation Conference},
  editor = {L. F. Perrone and F. P. Wieland and J. Liu and B. G. Lawson and  D. M. Nicol and R. M. Fujimoto},
  year = {2006},
  month = {December},
  abstract = {Pathway Logic is a step towards a vision of symbolic systems biology. It is an approach to modeling cellular processes based on formal methods. In particular, formal executable models of processes such as signal transduction, metabolic pathways, and immune system cell-cell signaling are developed using the rewriting logic language Maude and a variety of formal tools are used to query these models. An important objective of Pathway logic is to reflect the ways that biologists think about problems using informal models, and to provide bench biologists with tools for computing with and analyzing these models that are natural. In this paper we describe the Pathway Logic approach to the modeling and analysis of signal transduction, and the use of the Pathway Logic Assistant tool to browse and query these models. The Rac1 signaling pathway is used to illustrate the concepts.},
  keywords = {Pathway Logic, signal transduction, symbolic, formal executable model}
}

@misc{pl-06csb,
  title ={Using Pathway Logic to Integrate Signal Transduction and Gene Expression Data},
  author = {L. Briesemeister and L. Heiser and M. Knapp and K. Laderoute and A. Poggio and P. Spellman and C. Talcott and J. Gray},
  year = {2006},
  note = {poster presented at CSB06},
}

@inproceedings{talcott-06isola,
author = {Carolyn Talcott},
title = {Formal Executable Models of Cell Signaling Primitives},
booktitle = {2nd International Symposium On Leveraging Applications of Formal Methods, Verification and Validation {ISOLA06}},
year = 2006,
editor = {Tiziana Margaria and Anna Philippou and Bernhard Steffen},
pages = {303--307},
keywords = {coordination, composition, distributed object reflection,
goal, autonomy,policy},
}


@inproceedings{tiwari-etal-07ab,
author = {Ashish Tiwari and Carolyn Talcott and Merrill Knapp and Patrick Lincoln 
and Keith Laderoute},
title = {Analyzing Pathways using SAT-based Approaches},
booktitle = {Algebraic Biology 2007},
year = 2007,
editor = {Hirokazu Anai and Katsuhisa Horimoto and Temur Kutsia},
series = {LNCS},
volume = 4545,
pages = {155--169},
keywords = {coordination, composition, distributed object reflection,
goal, autonomy,policy},
}

@inproceedings{baxter-etal-07nettab,
title = {Executable Symbolic Models of Neural Processes},
author = {Sriram M Iyengar and  Carolyn Talcott and  Riccardo 
          Mozzachiodi and  Enrico Cataldo and  Douglas A Baxter},
booktitle = {Network Tools and Applications in Biology {NETTAB07}},
year = 2007,
keywords = {coordination, composition, distributed object reflection,
goal, autonomy,policy},
}