corinalogan/cuttingedgeoajournal

This was a plan until Peer Community In came along. Now this repo is an archive of a conversation and resources for a 100% OA overlay journal on general science (or broader) that only publishes reproducible manuscripts with open, editorial-managed post-publication peer review, CC-BY, selects based on validity (not subjective impact), no APCs, and keeps up with modern publishing by incorporating new open practices as they're invented. Owned/run by NGO and/or the researchers themselves.

cuttingedgeoajournal's Issues

Journal name and scope

Is it a general science journal? Or broader? (I love inclusivity!) Is too broad going to be too overwhelming in terms of website management/hosting space?

Interesting reading

Given that there are so many links going around, maybe make a collection here.

Reproducible documents/containers

• Statistical Analyses and Reproducible Research

Higher level thinking

• Envisioning the Scientific Paper of the Future
  • from a series of talks at CalTech

Please add in the comments!

How to publish reproducible manuscripts?

From the initial conversation on twitter: https://twitter.com/LoganCorina/status/872833978495115264

@gmbecker: Depending on what you mean, ensuring/enforcing that manuscripts are actually reproducible is really hard in general case. I know about dynamic docs. (subject of my thesis, in fact), but an Rmd/Rnw isn't reproducible by itself, see http://biostats.bepress.com/bioconductor/paper2/ …
Red files don't include data and the exact versions of packages used by original authors, so while u have code, u may not be able to run it.

@chartgerink: well if data are publicly available you can download the data based on a doi so you can ensure provenance and replicate with just rmd.

@lgatto: Yes, if... but the Rmd as such doesn't guarantee it. As it doesn't guarantee that the required software is available. But Rmd + good practice goes a long way to enable reasonable repro in many cases, I think. I am testing submission and handling Rmds with @F1000Research (should submit in a couple of weeks). Will let you know.

@chartgerink: I am amazed with Rmd and the HTMLs it turns out, I can imagine building on that would provide a good way to start. Using Rnotebooks would be even better (show/hide code user). Implement plugins (pubpeer,hypothesis). Easy to include notice of dependencies in manuscript (what I do now already; e.g. last page http://bit.ly/2s8zMlD). absolute direct reproducibility not feasible (nor doable), what we need to know is limits of. With Rmd (example) we can do much. my thoughts on this: automate version testing, determine dependencies upon sharing, look at other versions producing same or diff result. subsequently, we can produce crosstable that actually indicates when results differ from the original. How they differ is something dif.

The website that is the face of the journal + posts the peer review history

Who is the web host? Who creates and updates the website? Who writes up the initial mission/description/code of conduct of the journal?

The publishing platform

Free open source options =
Open Journal Systems (developed by universities, https://pkp.sfu.ca/ojs/)
@elifesciences Continuum (https://github.com/elifesciences/elife-continuum-documentation), now called Libero https://libero.pub/products/libero-publisher/

(Initial conversation on twitter: https://twitter.com/LoganCorina/status/872833978495115264)

Who does what?