3 papers
q-bio.QM2019
RuleVis: Constructing Patterns and Rules for Rule-Based Models
David Abramov, Jasmine Otto, Mahika Dubey +4
We introduce RuleVis, a web-based application for defining and editing "correct-by-construction" executable rules that model biochemical functionality, which can be used to simulat…
cs.GR2017
Dynamic Influence Networks for Rule-based Models
Angus G. Forbes, Andrew Burks, Kristine Lee +4
We introduce the Dynamic Influence Network (DIN), a novel visual analytics technique for representing and analyzing rule-based models of protein-protein interaction networks. Rule-…
q-bio.OT2017
When rule-based models need to count
Pierre Boutillier, Ioana Cristescu
Rule-based modelers dislike direct enumeration of cases when more efficient means of enumeration are available. We present an extension of the Kappa language which attaches to agen…