about this paperpresentation abstract bibitemdownloadsbook chapter (on HAL) editor link |
Rule-based modelling is an effective way of handling the explosive combinatorics of biological networks. The use of partial objects in describing molecular interactions means that only the necessary conditions for a rule are specified and not the complete chemical entities taking part in a reaction. This leads to descriptions that are easier to set up and more compact. Networks of substantial scale can be described without having to reduce the combinatorics of the system—as other approaches must.
An important aspect of the rule-based approach is its agility, as one can easily modify rules to incorporate new knowledge, or test different assumptions. A special and rather frequent case is when one wishes to replace a rule with ones imposing stronger conditions. This process is called refinement and we approach it in this study both from the practical and the theoretical point of view.
@inbook{ecsb:2009, Author = {Elaine Murphy and Vincent Danos and Jerome Feret and Jean Krivine and Russell Harmer}, Chapter = {Rule Based Modelling and Model Refinement}, Editor = {Huma Lodhi and Stephen Muggleton}, series = {Wiley Book Series on Bioinformatics}, publisher = {John Wiley & Sons, Inc.}, Title = {Elements of Computational Systems Biology}, Year = {2010}} }