Open access is not only a form of publishing such that research papers become available to the large public free of charge, it also refers to a trend in science that the act of doing research becomes more open and transparent. Collected or generated research data as well as procedures are published alongside a research paper.
Increasingly, scientific results are generated by numerical manipulation of data that were already collected, and may involve simulation experiments that are entirely carried out computationally. Reproducibility of research findings, the ability to repeat experimental procedures and confirm previously found results, is at the heart of the scientific method. As opposed to the collection of experimental data in labs or nature, computational experiments lend themselves very well for reproduction. Some of the reasons why scientists do not publish data and computational procedures that allow reproduction will be hard to change, e.g. privacy concerns in the data, fear for embarrassment or of losing a competitive advantage. Others reasons however involve technical aspects, and include the lack of standard procedures to publish such information and the lack of benefits after publishing them. We aim to resolve these two technical aspects.
We propose a system that supports the evolution of scientific publications from static papers into dynamic, executable research documents and aim for the main aspects of open access: improving the exchange of, facilitating productive access to, and simplifying reuse of research results that are published over the internet.
Building on existing open standards and software, this project develops standards and tools for executable research documents, and will demonstrate and evaluate these, initially focusing on the geosciences domains. Building on recent advances in mainstream IT, o2r envisions a new architecture for storing, executing and interacting with the original analysis environment alongside the corresponding research data and manuscript. o2r bridges the gaps between long-term archiving, practical geoscientific research, and publication media.
For Open Science and reproducible research, we see not alternative to Open Source software. All scripts, code, and libraries supporting a computational analysis must be open for scrutiny by fellow scientists. We publish current code online, instead of holding back until publication of a paper, to profit from interaction with the Free and Open Source Software (FOSS) community. Even the software of supported workflows (i.e. R) and underlying technologies (i.e. Docker) are published under FOSS principles. Already in the project proposal, we set a clear agenda on the question of software licenses:
All software developed by project staff will be distributed under a permissive open source license that allows reuse, modification and integration in commercial systems (e.g., Apache 2.0). Development happens openly at GitHub and all developments are visible directly instead of after the end of the project.
This is the o2r team and supporting university staff in alphabetical order.
The o2r project is connected to external partners since its inception, and the group has been extended since then. They come from different disciplines and regularly enrich discussions with their insights. These are the partners in alphabetical order.
This project Opening Reproducible Research (see also Offene Reproduzierbare Forschung @ DFG GEPRIS) is funded by the German Research Foundation (Deutsche Forschungsgemeinschaft, DFG) under project numbers PE 1632/10-1, KR 3930/3-1 and TR 864/6-1.