Handbook of theoretical computer science (vol. B)
Artificial Intelligence - Special issue on logical formalizations and commonsense reasoning
Modeling and querying biomolecular interaction networks
Theoretical Computer Science - Special issue: Computational systems biology
Planning for gene regulatory network intervention
IJCAI'07 Proceedings of the 20th international joint conference on Artifical intelligence
The Knowledge Engineering Review
Planning interventions in biological networks
ACM Transactions on Intelligent Systems and Technology (TIST)
Modular-E and the role of elaboration tolerance in solving the qualification problem
Artificial Intelligence
Modelling biological networks by action languages via answer set programming
ICLP'06 Proceedings of the 22nd international conference on Logic Programming
Applications of action languages in cognitive robotics
Correct Reasoning
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In this paper we discuss several representation issues that we came across while modelling molecular interactions in cells of living organisms. One of the issues was that the triggering of events inside cells, an important modelling component, are not necessarily immediate, leading to multiple evolution models in the absence of additional information. Second, often an action or a trigger at one level of granularity of representation can be elaborated and refined. We show the problem that existing representation and modelling formalisms have in dealing with the above issues. We then present an action language which builds up on a previous language, and has the ability to express event ordering knowledge. We show that our language is able to adequately address the above-mentioned issues.