Pathway Logic — Publications

Papers

"Explaining response to drugs using Pathway Logic." by Carolyn Talcott and Merrill Knapp. In Computational Methods in Systems Biology, 2017.
"The Pathway Logic Formal Modeling System: Diverse views of a formal representation of signal transduction." by Carolyn Talcott. In Workshop on Formal Methods in Bioinformatics and Biomedicine, 2016.
"Inferring Executable Models from Formalized Experimental Evidence" by Vivek Nigam, Robin Donaldson, Merrill Knapp, Tim McCarthy and Carolyn Talcott. In Computational Methods in Systems Biology, 2015.
"Applications of Pathway Logic Modeling to Target Identification" by Anupama Panikkar, Merrill Knapp, Huaiyu Mi, Dave Anderson, Krishna Kodukula, Amit K. Galande and Carolyn Talcott. In Formal Modeling: Actors, Open Systems, Biological Systems, 2011.
"Understanding Signalling Networks as Collections of Signal Transduction Pathways" by Robin Donaldson, Carolyn Talcott, Merrill Knapp, and Muffy Calder. In Computational Methods in Systems Biology, 2010.
"Symbolic Systems Biology and Pathway Logic" by Patrick. D. Lincoln and Carolyn Talcott. A chapter of Symbolic Systems Biology, 2010.
"Integrated analysis of breast cancer cell lines reveals unique signaling pathways" by L.M. Heiser et.al. In Genome Biology 2009.
Pathway Logic by Carolyn Talcott. Presented at the 8th International School on Formal Methods for the Design of Computer, Communication, and Software Systems.
Analyzing a Discrete Model of Aplysia Central Pattern Generator by Ashish Tiwari, and Carolyn Talcott. In Computational Methods in Systems Biology, 2008.
Quantitative and Probabilistic Modeling in Pathway Logic by Alessandro Abate, Yu Bai, Nathalie Sznajder, Carolyn Talcott, and Ashish Tiwari. In the IEEE proceedings of the 7th International Symposium on Bioinformatics and Bioengineering, 2007.
Executable Symbolic Models of Neural Processes by Sriram M Iyengar, Carolyn Talcott, Riccardo Mozzachiodi, Enrico Cataldo and Douglas A Baxter in Network Tools and Applications in Biology, NETTAB07.
Analyzing Pathways using SAT-based Approaches by Ashish Tiwari, Carolyn Talcott, Merrill Knapp, Patrick Lincoln and Keith Laderoute in Algebraic Biology 2007.
Formal Executable Models of Cell Signaling Primitives by Carolyn Talcott in 2nd International Symposium On Leveraging Applications of Formal Methods, Verification and Validation ISOLA06
Symbolic Modeling of Signal Transduction in Pathway Logic by Carolyn Talcott. From Proceedings of the 2006 Winter Simulation Conference. December, 2006.
Multiple Representations of Biological Processes by Carolyn Talcott and David L. Dill. From Transactions on Computational Systems Biology. 2006.
The Pathway Logic Assistant by Carolyn Talcott and David L. Dill. In proceedings of Computational Methods in Systems Biology, March 2005. (The Petri net representation of Pathway Logic models.)
IOP--The Interoperability Platform & IMaude--an Interactive Extension of Maude by Ian Mason and Carolyn Talcott. From Workshop on Rewriting Logic and Applications, March 2004. (The basis for the Pathway Logic Assistant. A revised version for journal sumission is here.)
Pathway Logic Modeling of Protein Functional Domains in Signal Transduction by Carolyn Talcott and Steven Eker and Merrill Knapp and Patrick Lincoln and Keith Laderoute. From Proceedings of the Pacific Symposium on Biocomputing. January, 2004.
Pathway Logic: Executable Models of Biological Networks by Steven Eker, Merrill Knapp, Keith Laderoute, Patrick Lincoln, and Carolyn Talcott. From Fourth International Workshop on Rewriting Logic and Its Applications (WRLA'2002). Elsevier. 2002.
Pathway Logic: Symbolic Analysis of Biological Signaling by Steven Eker and Merrill Knapp and Keith Laderoute and Patrick Lincoln and Jose Meseguer and Kemal Sonmez. From Proceedings of the Pacific Symposium on Biocomputing. January, 2002. Pages 400-412.

For your convenience, you can download a BibTeX file containing these references.

Posters and Presentations

"The Pathway Logic Formal Modeling System: Diverse views of a formal representation of signal transduction." Presented by Carolyn Talcott at the Workshop on Formal Methods in Bioinformatics and Biomedicine. Shenzhen China, December 2016.
"Datum Logic: A Formal Executable Semantics for Experimental Evidence." Presented by Carolyn Talcott at the AMS session on Applications of Logic, Model Theory, and Theoretical Computer Science to Systems Biology. Seattle January 2016.
"Challenges in formal reasoning about signaling networks." Presented by Carolyn Talcott at the Simons Institute Workshop on Dynamic Biological Modeling: Abstractions, Algorithms & Logic, August 2015.
"Construction of A Pathway Logic Model of Intracellular Signal Transduction" by Merrill Knapp, Tim McCarthy, Carolyn Talcott Poster presented at the DARPA BigMechanism KickOff, July 2014.
"Pathway Logic. Symbolic Systems Biology. Using formal systems and and reasoning tools to understand how things work and why things don’t work" Presented by Carolyn Talcott at the Stanford Systems Biology Seminar, Dec 2013.
"Datums: a knowledge base and representation system for experimental findings concerning cellular response to stimuli" By Merrill Knapp, Tim McCarthy, Carolyn Talcott. Poster presented at Bio-X Interdisciplinary Initiatives Symposium, Monday, August 26th, 2013
"Symbolic Systems Biology: Using Formal Methods Tools to Model Biological Processes" Invited talk at Centre for Computational and Systems Biology (CoSBI), Trento, Italy, May 2009.
"PATHWAY LOGIC: Formal Methods for Biology" Invited talk at Fundamentals of Software Engineering: Theory and Practice (FSEN), Kish Iran, April, 2009.
"Symbolic systems biology and Pathway Logic" Presented at San Jose State University, September 2008.
"Pathway Logic models of sleep-wake behavior" Presented to several DoD agencies, May 2008.
"Overview of Pathway Logic and some applications" Presented January 2008 at the SRI Center for Computational Biology seminar series.
"An Egf Signalling Map in Pathway Logic" poster presented, along with the appendix, at the NIH NGMS-NCI project meeting 07 June 13, Cambridge, Massachusetts. [Abstract].
"Using Pathway Logic to Integrate Signal Transduction and Gene Expression Data" (TLR signaling) poster presented at the BioSciences Review June 5-8, 2006, Hunt Valley, MD (sponsered by DTRA, USAMRMD and USAMRICD). [Abstract].
"Using Pathway Logic to Integrate Signal Transduction and Gene Expression Data" (Egf Signaling) poster presented at Computational Methods in Systems Biology, Trento, Italy 18-19 October, 2006. [Abstract].
"Executable Symbolic Modeling of Neural Processes" poster presented at Computational Methods in Systems Biology, Trento, Italy 18-19 October, 2006 and Winter Simulation Conference Monterey, California, 3-6 December, 2006 [Abstract].
"Using Pathway Logic to Integrate Signal Transduction and Gene Expression Data" poster presented at IEEE Computer Society Bioinformatics Conference (CSB2006). [Abstract]
Talk at ISB, December 2005. (This talk has more demo screen shots than the Inria talk, and less details about the modeling formalism and related formal modeling approaches.)
Talk at Inria Roquencourt, October 2005.
Pathway Logic overview and Poster, May 2005, at IEEE Computer Society Bioinformatics Conference (CSB2005).
Poster presentation at IEEE Computer Society Bioinformatics Conference (CSB2003).
Poster presentation at the Protein Phosphorylation Workshop, Asilomar, December 2003.
Promotional presentation, September 2003.
Talk at the 4th International Workshop on Rewriting Logic and Its Applications (WRLA), 2002.

Tutorials

Applications of Rewriting Logic in Biology tutorial presented at the RISC Summer School, July 5-6, 2007, Castle Hagenberg, Hagenberg, Austria: