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RuleBender specifications

Information


Unique identifier OMICS_06967
Name RuleBender
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Medium
Stability Stable
Maintained Yes

Versioning


No version available

Publication for RuleBender

RuleBender citations

 (10)
library_books

Stoichiometric balance of protein copy numbers is measurable and functionally significant in a protein protein interaction network for yeast endocytosis

2018
PLoS Comput Biol
PMCID: 5860782
PMID: 29518071
DOI: 10.1371/journal.pcbi.1006022

[…] D,mean,2(11) where f = 10,000 (weak misinteractions, corresponding to an energy gap of ~9.21) or 1,000 (stronger misinteractions, energy gap of ~6.91)Network maps were generated using Cytoscape[] and RuleBender[]. Plots were generated in MATLAB. C++ code for the network balancing algorithm SBOPN is available at https://github.com/mjohn218/StoichiometricBalance, and may be applied to any interface- […]

library_books

Extending rule based methods to model molecular geometry and 3D model resolution

2016
BMC Syst Biol
PMCID: 4977479
PMID: 27490268
DOI: 10.1186/s12918-016-0294-z

[…] The rule-based model is specified using the BioNetGen language [] and implemented with the RuleBender program []. RuleBender generates the ODEs associated with the binding rules and tracks the aggregates that are formed as the IgE receptors bind to the Pen a 1 molecules in an ODE simulation […]

library_books

Annotation of rule based models with formal semantics to enable creation, analysis, reuse and visualization

2015
Bioinformatics
PMCID: 4803388
PMID: 26559508
DOI: 10.1093/bioinformatics/btv660

[…] e entities in this format inherit the annotation property from the standard SBML and can therefore include RDF annotations. Such SBML models can thus be imported or exported by tools such as KaSim or RuleBender in the future, avoiding the loss of any biological information. Extensions of rule-based models such as MetaKappa makes possible to define rules using abstract agents and allowing agent inh […]

library_books

Visinets: A Web Based Pathway Modeling and Dynamic Visualization Tool

2015
PLoS One
PMCID: 4447416
PMID: 26020230
DOI: 10.1371/journal.pone.0123773

[…] oposed [, ], they were not developed into fully user-friendly and graphically oriented software packages. There are few software packages available that are user-friendly (e.g., Cell Collective [] or RuleBender []) but they are using other modeling methods such as rule-based modeling and/or Boolean algebra and thus having their own limitations. Other known tools such as Cytoscape or Ingenuity Path […]

library_books

Computational Analysis of an Autophagy/Translation Switch Based on Mutual Inhibition of MTORC1 and ULK1

2015
PLoS One
PMCID: 4356596
PMID: 25761126
DOI: 10.1371/journal.pone.0116550

[…] as then used to numerically integrate the ODEs, using default settings. The steps described above were performed automatically by BioNetGen and invoked using point-and-click commands available within RuleBender [], which provides a graphical user interface for accessing BioNetGen’s capabilities.Each one-dimensional bifurcation analysis was performed numerically as follows. We added a rule to the m […]

library_books

MOSBIE: a tool for comparison and analysis of rule based biochemical models

2014
BMC Bioinformatics
PMCID: 4261755
PMID: 25253680
DOI: 10.1186/1471-2105-15-316

[…] , with 32- and 64-bit releases available for Windows, Linux, and Mac OS X. The system uses Java, Rich Client Platform (RCP), Perl, and Prefuse libraries. MOSBIE is implemented as a perspective in the RuleBender interface for rule-based modeling [, ]; the RuleBender release includes the BioNetGen software [] as well as NFsim, which is an additional simulator that allows for efficient simulation of […]

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RuleBender institution(s)
Department of Computer Science, University of Pittsburgh, PA, USA

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