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RuleBender specifications


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


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Publication for RuleBender

RuleBender citations


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

PMCID: 5860782
PMID: 29518071
DOI: 10.1371/journal.pcbi.1006022

[…] 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, and may be applied […]


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

PMCID: 4977479
PMID: 27490268
DOI: 10.1186/s12918-016-0294-z

[…] of kf2 that σ for any value of kf2 greater than 0.40 molecule −1s−1 would be too high to be acceptable., 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 […]


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

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

[…] (). we adopt this approach so that models written using the conventions that we describe here do not require modification of the modelling software, kasim ( and rulebender (), that is their primary target., we use the language’s comment delimiter followed by the ‘^’ character to denote annotations in the textual representation of rule-based languages. kappa […]


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

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

[…] 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 […]


Modeling the Effect of APC Truncation on Destruction Complex Function in Colorectal Cancer Cells

PMCID: 3784502
PMID: 24086117
DOI: 10.1371/journal.pcbi.1003217

[…] supporting information for the base model () and its variants (, , , , , , , ). bngl is compatible with bionetgen , , a software tool for rule-based modeling, and a number of other tools, such as rulebender , an interface for bionetgen. in addition to parameter values and initial data, each model-specification included molecule type definitions and rules. molecule type definitions delimit […]


Programming biological models in Python using PySB

PMCID: 3588907
PMID: 23423320
DOI: 10.1038/msb.2013.1

[…] models but are unwieldy to use with rule-based or programmatic approaches because models must be exported and imported using sbml (; ). at the same time, rule-based model editors such as rulebender for bngl () and rulestudio for kappa ( facilitate development of rule-based models but do not incorporate tools for data analysis, parameter […]

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

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