(595b) Expanding Molecular Simulation Use By Data/Code Sharing in Scientific Publishing
- Conference: AIChE Annual Meeting
- Year: 2016
- Proceeding: 2016 AIChE Annual Meeting
- Group: Computational Molecular Science and Engineering Forum
- Time: Wednesday, November 16, 2016 - 3:45pm-4:05pm
We have developed a new approach to writing scientific documents that enables the direct inclusion of human-readable, and machine-addressable data and code in the narrative text. In this talk we will illustrate the approach by example from papers [1,2] we have recently published using the approach. We will show examples of how we use this approach to document molecular simulation results, and how other researchers can see what we have done, and reuse the code/data from the published manuscripts for new purposes. We show that the combination of an extensible editor (Emacs) with a lightweight markup language (org-mode) provides a remarkable solution to data sharing and research reproducibility issues. This combination enables the documentation of experimental setup, data generation, and analysis in a single document, and subsequent export of a scientific manuscript that is suitable for submission to most journals. When coupled with external data repositories, the approach enables sharing of large or complex data sets that cannot easily be captured in a manuscript.
1. Kitchin, John R., Data Sharing in Surface Science, Surface Science, in press (2015). doi:10.1016/j.susc.2015.05.007.
2. Kitchin, John R., Examples of Effective Data Sharing in Scientific Publishing, ACS Catalysis, 5(6), pp. 3894-3899 (2015). doi:10.1021/acscatal.5b00538.