Methodologies of how to publish your methods, not technical details. Technical details are under scientific computation workflow, and under build/pipelines tools The painful process of journals and article validation is under academic publishing.
This is coupled closely with build tools.
Actually existing open notebook tools
See Scientific workbooks as well as scientific computation workflow.
Docker is designed for reproducible deployment which makes it an approximate fit for reproducible research. See docker for reproducible research.
Sundry data sharing ideas
See Data sharing.
Collaboration – general
For the first time, researchers, engineers, developers and scientists can upload code and data in any open source programming language and link working code in a computational environment with the associated article for free. We assign a Digital Object Identifier (DOI) to the algorithm, providing correct attribution and a connection to the published research.
The platform provides open access to the published software code and data to view and download for everyone for free. But the real treat is that users can execute all published code without installing anything on their personal computer. Everything runs in the cloud on CPUs or GPUs according to the user needs. We make it easy to change parameters, modify the code, upload data, run it again, and see how the results change.
The also ran a workshop on this.