Symbolic modeling of signal transduction in pathway logic
Proceedings of the 38th conference on Winter simulation
Reasoning about non-immediate triggers in biological networks
Annals of Mathematics and Artificial Intelligence
Integrating answer set programming and constraint logic programming
Annals of Mathematics and Artificial Intelligence
Metabolic Network Expansion with Answer Set Programming
ICLP '09 Proceedings of the 25th International Conference on Logic Programming
ICLP '09 Proceedings of the 25th International Conference on Logic Programming
Issues in reasoning about interaction networks in cells: necessity of event ordering knowledge
AAAI'05 Proceedings of the 20th national conference on Artificial intelligence - Volume 2
Reasoning About Actions for the Management of Urban Wastewater Systems: Preliminary report
Proceedings of the 2009 conference on Artificial Intelligence Research and Development: Proceedings of the 12th International Conference of the Catalan Association for Artificial Intelligence
Reasoning About Actions for the Management of Urban Wastewater Systems: Preliminary report
Proceedings of the 2009 conference on Artificial Intelligence Research and Development: Proceedings of the 12th International Conference of the Catalan Association for Artificial Intelligence
The Knowledge Engineering Review
Supporting decision making in urban wastewater systems using a knowledge-based approach
Environmental Modelling & Software
Modelling gene and protein regulatory networks with Answer Set Programming
International Journal of Data Mining and Bioinformatics
Symmetry-breaking answer set solving
AI Communications - Answer Set Programming
Searching in protein state space
INAP'09 Proceedings of the 18th international conference on Applications of declarative programming and knowledge management
Modelling biological networks by action languages via answer set programming
ICLP'06 Proceedings of the 22nd international conference on Logic Programming
Multiple representations of biological processes
Transactions on Computational Systems Biology VI
Knowledge-based integrative framework for hypothesis formation in biochemical networks
DILS'05 Proceedings of the Second international conference on Data Integration in the Life Sciences
Analyzing pathways using ASP-based approaches
ANB'10 Proceedings of the 4th international conference on Algebraic and Numeric Biology
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Motivation: In this paper we propose to use recent developments in knowledge representation languages and reasoning methodologies for representing and reasoning about signaling networks. Our approach is different from most other qualitative systems biology approaches in that it is based on reasoning (or inferencing) rather than simulation. Some of the advantages of our approach are, we can use recent advances in reasoning with incomplete and partial information to deal with gaps in signal network knowledge; and can perform various kinds of reasoning such as planning, hypothetical reasoning and explaining observations. Results: Using our approach we have developed the system BioSigNet-RR for representation and reasoning about signaling networks. We use a NFκB related signaling pathway to illustrate the kinds of reasoning and representation that our system can currently do. Availability: The system is available on the Web at http://www.public.asu.edu/~cbaral/biosignet