Take on a hands-on marble-run challenge and try to connect different pieces of scientific software. Discover what happens when data does not fit, and why compatible systems, shared standards and infrastructure are important for connected science.
Have a go
A hands-on marble-run challenge where participants attempt to connect disparate pieces of scientific software. Some pieces are missing or do not quite fit, highlighting challenges around data interoperability.
Data interoperability means that the output of one piece of software is not necessarily in the correct format to act as the input to another. The challenge demonstrates the importance of compatible systems, shared standards and infrastructure in enabling connected science.
What's going on?
Hundreds of scientific data formats have evolved over the years, and it is unrealistic to think that researchers will adopt one or a few common formats. In the absence of this ideal situation, it is necessary to convert between formats to connect the software workflow.
Various data-format converters exist, including Open Babel [O’Boyle et al., 2011], c2x [Rutter, 2018] and Atomsk [Hirel, 2015]. Not wishing to reinvent the wheel, the Physical Sciences Data Infrastructure (PSDI) has developed the Data Conversion Service (DCS), which incorporates these three existing converters.
The DCS can be accessed on the web, or as downloadable tools: a Python library, a command-line application and a version of the web application. The downloadable web application can be used without web access. An application programming interface (API) is currently in development.
The DCS adds value by providing a common interface for the individual converters and indicating the likely conversion quality, where known.
To demonstrate the differences between file formats, a Chemical Markup Language file can be converted to a Scalable Vector Graphics file so that the molecule can be visualised.
References
- Pierre Hirel. Atomsk: A tool for manipulating and converting atomic data files. Computer Physics Communications, 197:212–219, 2015.
- Noel M. O’Boyle, Michael Banck, Craig A. James, Chris Morley, Tim Vandermeersch and Geoffrey R. Hutchison. Open Babel: An open chemical toolbox. Journal of Cheminformatics, 3(1):33, 2011.
- Michael J. Rutter. C2x: A tool for visualisation and input preparation for CASTEP and other electronic structure codes. Computer Physics Communications, 225:174–179, 2018.