Everpub is an entry for openscienceprize.org. Read The Pitch and join in if you are interested! Read the full proposal.
Participants: Tim Head, Titus Brown, et al.
The proposal is complete, now the work starts! So please contribute.
We propose to make reusability a first-class citizen in computer-aided research by enabling the publication of dynamic and interactive scientific narratives that can be verified, altered, reused, and cited.
A mockup of what a executable paper could look like:
- Combining ideas from
- Useful for researchers from day one.
- Runs locally on your laptop or your lab's cluster.
- Provides a way to automate every step.
- Opinionated.
- Helps setup structure of a research project.
- A toolbox, not a framework.
- Most individual steps already have fantastic solutions out there, people should use them!
- Final step: interactive, re-mixable papers.
Check out issue #14. Introduce yourself and say hello. Though please refrain from having discussion in that issue. Find the most appropriate existing issue and contribute there or create a new one.
Everyone is welcome to contribute. Discussion happens in issues, and changes are handled via pull requests.
You can contribute by filing an issue regarding something you find unclear, needs improving, is missing or is incorrect You can also add an idea of your own. Or you can directly create a pull request with your suggested edits.
As this is about creating a entry for the open science prize, creating the entry should happen in the open as well. Licensing details and a list of contributors can be found in LICENSE.
Watch the repository - this way, you will get email notifications of new conversations. You can do this by clicking on 'Watch' at the top of the repository:
This is an unordered collection of thoughts. Feel free to add to it.
Build a tool that universities/labs/publishers can use to encourage re-use of software and provide a completely new kind of research article, one that is interactive!
- preserving and open access of data is becoming mainstream
- to make sense of data we need lots of documentation and experience
- one source of documentation and experience is the code used to analyse the data in the first place
- sharing code is not enough, code only makes sense in the environment it runs in
- so far very little effort on sharing code and its environment
- adding re-usability/re-producibility as an after thought does not work (misaligned incentives)
- make re-usability a waste product, provide tools that are useful to researchers while developing their analysis pipeline that produce re-usability as a side effect
- bit rot is everywhere, undetected bit rot is a disaster
- periodically and automatically run a subset of analyses to detect bit rot
- researchers use very diverse set of tools, not interested in changing them
- need a flexible system that allows composing
- machine readable environment and entry point allow for completely new kinds of scholarly communication (-> interactive articles)
- simple syste that can be setup at universities or labs or publishers
- lots of problems already solved (sharing -> git(hub), workflow -> make, snakemake, etc), do not reinvent them, instead allow composing of these tools
- do not build a platform that people have to adopt to, or at least reduce the adoption as much as possible and provide benefits to researchers from day one.
- support a model of "bring your own computing", allows users to provide their own computing resources instead of beign tied to host.
- BYOC is inherently flexible in terms of how compute power is provided