Discuss what we will consider a GPF
Executable Papers
Elsevier carried out an [ Executable Papers Challenge].
The Case of the Tuberculosis Drugome
This is a case where the workflow was made explicit and published as linked open data in RDF (i.e., accessible Web objects in the Semantic Web). The data were assigned DOIs, as was the workflow.
- the original "drugome" paper
- the web site that describes how that paper was reproduced
- detailed documentation of the drugome method
- a publication that reports on that work.
What is a Geoscience Paper of the Future?
In the future, scientists will use tools to generate GPFs routinely. As scientists do their work, those tools will be documenting the work and all the associated digital objects (data, software, etc) so that when it comes time to publish a paper everything will be easily documented and included. Today, several research tools exist for working in this way, but not for every lab environment.
In the future, publishers will accept submissions that do not just contain PDF but also data, software, and other digital objects relevant to the research. Today, many journals accept datasets together with papers, some journals accept software and software papers, but no journal includes the full details of the data, software, workflow, and visualizations of a paper.
In the future, readers of papers will be able to interact with the paper document, modify its figures to explore the data, reproduce the results, run the method with new data. Today, readers simply get a static paper, and even if the data is available they have to download it and analyze it themselves.
In the future, data producers and software developers will get credit for the work that they do because all publications that build on their work will acknowledge their work through citations. Today, there is limited credit and reward for those that create data and software.
A GPF paper includes:
- data: documented, in a public repository, and cited with DOIs
- software: documented, in a public repository, and cited with DOIs
- workflow is explicitly documented, possibly in a shared repository and given a DOI
- figures/visualizations are generated by explicit code and included in that workflow
