TY - JOUR
T1 - Models and Simulations as a Service
T2 - Exploring the Use of Galaxy for Delivering Computational Models
AU - Walker, Mark A.
AU - Madduri, Ravi
AU - Rodriguez, Alex
AU - Greenstein, Joseph L.
AU - Winslow, Raimond L.
N1 - Publisher Copyright:
© 2016 Biophysical Society.
PY - 2016/3/8
Y1 - 2016/3/8
N2 - 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 Ca2+ 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.
AB - 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 Ca2+ 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.
UR - http://www.scopus.com/inward/record.url?scp=84960929464&partnerID=8YFLogxK
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U2 - 10.1016/j.bpj.2015.12.041
DO - 10.1016/j.bpj.2015.12.041
M3 - Article
C2 - 26958881
AN - SCOPUS:84960929464
SN - 0006-3495
VL - 110
SP - 1038
EP - 1043
JO - Biophysical journal
JF - Biophysical journal
IS - 5
ER -