2016
DOI: 10.1101/074138
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Automated Visualization of Rule-based Models

Abstract: Frameworks such as BioNetGen, Kappa and Simmune use "reaction rules" to specify biochemical interactions compactly, where each rule specifies a mechanism such as binding or phosphorylation and its structural requirements. Current rule-based models of signaling pathways have tens to hundreds of rules, and these numbers are expected to increase as more molecule types and pathways are added. Visual representations are critical for conveying rule-based models, but current approaches to show rules and interactions … Show more

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Cited by 3 publications
(5 citation statements)
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“…Taking advantage of the PySB interface to BioNetGen, we also incorporated (1) compact rule visualization, (2) atom-rule graph, and (3) tunable compression pipeline as implemented by Sekar et al. (Sekar et al., 2017) into the PyViPR workflow to enable a more thorough and complete visualization of large rule-based models.…”
Section: Resultsmentioning
confidence: 99%
See 2 more Smart Citations
“…Taking advantage of the PySB interface to BioNetGen, we also incorporated (1) compact rule visualization, (2) atom-rule graph, and (3) tunable compression pipeline as implemented by Sekar et al. (Sekar et al., 2017) into the PyViPR workflow to enable a more thorough and complete visualization of large rule-based models.…”
Section: Resultsmentioning
confidence: 99%
“…Various tools for visualization of rule-based models have also been published. These include Simmune (Cheng et al., 2014), BioNetGen (Smith et al., 2012, Sekar et al., 2017), rxncon (Tiger et al., 2012), Virtual Cell (Vasilescu et al, 2018), and Kappa (Boutillier et al., 2018). All of these tools take advantage of the structured definition of molecules and rules to generate intelligible visualizations of large models.…”
Section: Discussionmentioning
confidence: 99%
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“…Within this context, a very fertile ecosystem of computational tools for modeling cellular biochemistry has flourished (Bartocci and Lio, 2016;Gillespie, 1977a).There are now also approaches that enable scientists who are not computational experts themselves to translate their hypotheses about cellular signaling mechanisms into formal models in compact and intuitive ways; these include using textual rules (Faeder, 2011; Harris et al, Maus et al, 2011) or iconographic symbols (Schaff et al, 2016;Sekar et al, 2017;Zhang et al, 2013) to specify molecular interactions. Based on those specifications, the tools generate the resulting computational representations of the signaling networks and allow modelers to easily modify their assumptions to explore the consequences of such simulated manipulations on cellular behavior.…”
Section: Introductionmentioning
confidence: 99%
“…Smith et al's RuleBender [31] provides a visual interface for simulating, visualizing, and editing rules in the BioNetGen Language [19]. More recently, Sekar et al [29] introduce an alternative representation of rules that includes a "tunable compression pipeline" to generate more compact layouts. RuleVis visualizes patterns and rules written in the Kappa language, and also facilitates the interactive construction of new rules via a visual interface, leveraging a user's visual intuition when generating Kappa expressions.…”
Section: Introductionmentioning
confidence: 99%