58 citations · 112 across the 14 of their papers we have counts for
3 papers · 1 filter
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…
Combinatorial protein-protein interactions on a polymerizing scaffold
Andrés Ortiz-Muñoz, Héctor F. Medina-Abarca, Walter Fontana
Scaffold proteins organize cellular processes by bringing signaling molecules into interaction, sometimes by forming large signalosomes. Several of these scaffolds are known to pol…
Interactions between Causal Structures in Graph Rewriting Systems
Ioana Cristescu, Walter Fontana, Jean Krivine
Graph rewrite formalisms are a powerful approach to modeling complex molecular systems. They capture the intrinsic concurrency of molecular interactions, thereby enabling a formal…