BioSimSpace – filling the gaps between molecular simulation codes
Host institution: University of Manchester
Start: Wednesday, 27 June 2018 @ 15:00
End: Wednesday, 27 June 2018 @ 16:00
Scientific topic: Molecular modelling, Molecular dynamics, WorkflowsTarget audience:
BioSimSpace is a flagship software project from the CCP-BioSim and HEC-BioSim biomolecular modelling communities. The project aims to make it easier for researchers to develop, share and re-use biomolecular simulation workflow nodes. The software problem in our community is that we have lots of different pieces of software that are all incompatible and are not interoperable.
This forces the community to hand-write small scripts for converting between different file formats, or to generate different software input files. The resulting scripts are specific for the software and task performed, leading to the community generating lots of bespoke and brittle workflows.
BioSimSpace solves this problem by providing an interoperability layer between the major molecular simulation packages. In effect, BioSimSpace provides the shims that fill in the gaps between codes. BioSimSpace Python scripts can be run from the command line, used as workflow nodes in packages such as Knime, or run on the cloud as Jupyter notebooks.
In this talk, we will show how BioSimSpace has been implemented, will talk about its capabilities and our future plans, and will demonstrate some BioSimSpace workflow nodes running on the cloud.
Keywords: GROMACS, Python, KNIME, Jupyter notebookExternal resources: