Software Philosophies
How do we design and distribute software in a way that maximally encourages OARR? This is, undoubtedly, a dauntingly broad area. It can cover software engineering philsophies, distribution tools, ecosystems approaches, ideas on version control, and a whole slew of related thoughts and practices. This overlaps with several other sections, but also includes a subset of ideas which seem not to cleanly fit with any other area.
Virtualization
- VMs are Bad for RR (C T Brown): blog
- VMs don't allow remixing
- Greg Wilson, "VMs are PDF's for software": tweet
- Konrad Hinsen: more on VM's being bad: blog
- Bill Howe: "...the point is that publishing a VM is trivial, while making your code portable and reusable for others is not. I think if everyone published a VM associated with their paper, which incurs essentially zero extra effort, we'd be in a better state than we are today. You're holding out for the utopia of everyone becoming linux hackers."
Manifestos and Platforms
- Software Sustainability Institute: manifesto
- Kitware (open source, training, etc): page
- Small tools manifesto for bioinformatics: manifesto
- Requirements for Bionode modules template
- Docker
- Dynamic figures blog
Other
- My views about Science blog
- Thoughts on Reproducibility of Open Scientific Software blog
- Discovery of Scientific Software blog
- Stodden: runmycode.org: page
- Dissemination of platform for executing published code, gen results