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Models and Simulations as a Service: Exploring the Use of Galaxy for Delivering Computational Models.

ABSTRACT: We describe the ways in which Galaxy, a web-based reproducible research platform, can be used for web-based sharing of complex computational models. Galaxy allows users to seamlessly customize and run simulations on cloud computing resources, a concept we refer to as Models and Simulations as a Service (MaSS). To illustrate this application of Galaxy, we have developed a tool suite for simulating a high spatial-resolution model of the cardiac Ca(2+) spark that requires supercomputing resources for execution. We also present tools for simulating models encoded in the SBML and CellML model description languages, thus demonstrating how Galaxy's reproducible research features can be leveraged by existing technologies. Finally, we demonstrate how the Galaxy workflow editor can be used to compose integrative models from constituent submodules. This work represents an important novel approach, to our knowledge, to making computational simulations more accessible to the broader scientific community.

SUBMITTER: Walker MA

PROVIDER: S-EPMC4788737 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature

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Models and Simulations as a Service: Exploring the Use of Galaxy for Delivering Computational Models.

Walker Mark A MA Madduri Ravi R Rodriguez Alex A Greenstein Joseph L JL Winslow Raimond L RL

Biophysical journal 20160301 5

We describe the ways in which Galaxy, a web-based reproducible research platform, can be used for web-based sharing of complex computational models. Galaxy allows users to seamlessly customize and run simulations on cloud computing resources, a concept we refer to as Models and Simulations as a Service (MaSS). To illustrate this application of Galaxy, we have developed a tool suite for simulating a high spatial-resolution model of the cardiac Ca(2+) spark that requires supercomputing resources f ...[more]

PMID: 26958881

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Dataset Information

Models and Simulations as a Service: Exploring the Use of Galaxy for Delivering Computational Models.

Publications

Models and Simulations as a Service: Exploring the Use of Galaxy for Delivering Computational Models.

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