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01/12/2022
Representing catalytic mechanisms with rule composition
Reaction mechanisms are often presented as sequences of elementary steps...
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08/09/2021
Cayley Graphs of Semigroups Applied to Atom Tracking in Chemistry
While atom tracking with isotope-labeled compounds is an essential and s...
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02/05/2021
Graph Transformation for Enzymatic Mechanisms
Motivation: The design of enzymes is as challenging as it is consequenti...
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11/12/2019
RuleVis: Constructing Patterns and Rules for Rule-Based Models
We introduce RuleVis, a web-based application for defining and editing "...
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01/03/2019
Interactions between Causal Structures in Graph Rewriting Systems
Graph rewrite formalisms are a powerful approach to modeling complex mol...
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11/02/2017
Dynamic Influence Networks for Rule-based Models
We introduce the Dynamic Influence Network (DIN), a novel visual analyti...
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03/03/2016