title: 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.
authors.affiliation: Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland.
authors.forename: Mark A
authors.initials: MA
authors.lastname: Walker
authors.affiliation: Computation Institute, University of Chicago, Argonne National Laboratory, Chicago, Illinois.
authors.forename: Ravi
authors.initials: R
authors.lastname: Madduri
authors.affiliation: Computation Institute, University of Chicago, Argonne National Laboratory, Chicago, Illinois.
authors.forename: Alex
authors.initials: A
authors.lastname: Rodriguez
authors.affiliation: Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland.
authors.forename: Joseph L
authors.initials: JL
authors.lastname: Greenstein
authors.affiliation: Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland. Electronic address: rwinslow@jhu.edu.
authors.forename: Raimond L
authors.initials: RL
authors.lastname: Winslow
mesh_terms: D000818:Animals; D001369:Axons / Q000502:physiology; D002118:Calcium / Q000378:metabolism; D020013:Calcium Signaling; D003198:Computer Simulation; D049832:Decapodiformes; D020407:Internet; D012984:Software
chemical_list: D002118:Calcium