Loading…
RSEConUK 2019 has ended
The Fourth Conference of Research Software Engineering was held at the University of Birmingham.

Content from all sessions is licensed under a Creative Commons Attribution 2.0 UK: England & Wales License.
Tuesday, September 17 • 12:00 - 12:25
#1B3 - Reproducible Research - Interoperable software for reproducible research

Log in to save this to your schedule and see who's attending!

In most research communities there is not a single, unified software-framework. Instead, researchers are presented with a collection of competing packages from which they pick and choose the functionality that they desire. Interoperability between packages is often poor, with incompatibilities between file formats, hardware, etc. This leads to brittle workflows, poor reproducibility, and lock in to specific software. For the biomolecular simulation community, our solution has been the introduction of an interoperable framework that collects together the core functionality of many packages and exposes it through a simple Python API. By not choosing to reinvent the wheel, we can take advantage of all the fantastic software that has already been written, and can easily plug into new software packages as they appear. Our software can convert between many common molecular file formats and automatically find packages available within the environment on which it is run. I will show how this allows the user to write portable workflow components that can be run with different input, on different environments, and in completely different ways, e.g. command-line, Jupyter notebook, Knime.

Speakers
avatar for Lester Hedges

Lester Hedges

Research Software Engineer, University of Bristol
I am a Research Software Engineer at the University of Bristol where I work as the lead software developer for the CCP-BioSim flagship software project, BioSimSpace. This is a software interoperability layer to allow packages from the biomolecular simulation community to work together... Read More →



Tuesday September 17, 2019 12:00 - 12:25
2. Aston Webb C Block Lecture Theatre Aston Webb Building