The CombineArchiveWeb application – A web based tool to handle files associated with modelling results

Scharm, Martin; Wendland, Florian; Peters, Martin; Wolfien, Markus; Theile, Tom; Waltemath, Dagmar

doi:10.7287/peerj.preprints.639

Cited by 4 publications

(1 citation statement)

References 2 publications

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“…Users can obtain models and simulations encoded in these formats from repositories such as BioModels ( 24 ) or use tools such as VCell to create models and simulations in these formats. Models and simulations can be packaged into COMBINE archives using tools such as CombineArchiveWeb ( 25 ).…”

Section: Key Featuresmentioning

confidence: 99%

RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats

Shaikh

Marupilla

Wilson

et al. 2021

Nucleic Acids Research

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Comprehensive, predictive computational models have significant potential for science, bioengineering, and medicine. One promising way to achieve more predictive models is to combine submodels of multiple subsystems. To capture the multiple scales of biology, these submodels will likely require multiple modeling frameworks and simulation algorithms. Several community resources are already available for working with many of these frameworks and algorithms. However, the variety and sheer number of these resources make it challenging to find and use appropriate tools for each model, especially for novice modelers and experimentalists. To make these resources easier to use, we developed RunBioSimulations (https://run.biosimulations.org), a single web application for executing a broad range of models. RunBioSimulations leverages community resources, including BioSimulators, a new open registry of simulation tools. These resources currently enable RunBioSimulations to execute nine frameworks and 44 algorithms, and they make RunBioSimulations extensible to additional frameworks and algorithms. RunBioSimulations also provides features for sharing simulations and interactively visualizing their results. We anticipate that RunBioSimulations will foster reproducibility, stimulate collaboration, and ultimately facilitate the creation of more predictive models.

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Section: Key Featuresmentioning

confidence: 99%

RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats

Shaikh

Marupilla

Wilson

et al. 2021

Nucleic Acids Research

View full text Add to dashboard Cite

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Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices

Stanford

Scharm

Dobson

et al. 2019

Methods in Molecular Biology

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runBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats

Shaikh

Marupilla

Wilson

et al. 2021

Preprint

View full text Add to dashboard Cite

Comprehensive, predictive computational models have significant potential for science, bioengineering, and medicine. One promising way to achieve more predictive models is to combine submodels of multiple subsystems. To capture the multiple scales of biology, these submodels will likely require multiple modeling frameworks and simulation algorithms. Several community resources are already available for working with many of these frameworks and algorithms. However, the variety and sheer number of these resources make it challenging to find and use appropriate tools for each model, especially for novice modelers and experimentalists. To make these resources easier to use, we developed runBioSimulations (https://run.biosimulations.org), a single web application for executing a broad range of models. runBioSimulations leverages community resources, including BioSimulators, a new open registry of simulation tools. These resources currently enable runBioSimulations to execute nine frameworks and 44 algorithms, and they make runBioSimulations extensible to additional frameworks and algorithms. runBioSimulations also provides features for sharing simulations and interactively visualizing their results. We anticipate that runBioSimulations will foster reproducibility, stimulate collaboration, and ultimately facilitate the creation of more predictive models.

show abstract

The CombineArchiveWeb application – A web based tool to handle files associated with modelling results

Cited by 4 publications

References 2 publications

RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats

RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats

Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices

runBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats

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