The thread got started with this question:
- I like the journals that work under the same (or similar) principles of free knowledge projects, a.k.a. open-access journals. I would like to publish some paper regarding to wikis in that kind of OA publications, do you have any recommendation? I found First Monday, which is peer-reviewed and OA, but it is not indexed in ISI. Any more suggestions? -- http://lists.wikimedia.org/pipermail/wiki-research-l/2012-September/002328.html
After that the discussion branched out to include several different topics, some having to do with the pragmatics of making a new journal, some with more philosophical and futuristic ideas about how we want to be doing research. All of these are detailed below.
This page has the following attached subpages:
- A proposal for the visual layout and design of the journal : Wiki Research Ideas/Design
- A list of volunteers for editorial, reviewing and/or "other" tasks : Wiki Research Ideas/Volunteers
- A draft of submission rules : Wiki Research Ideas/Submission rules
- Discussion about the review model to use: Wiki Research Ideas/Review model
- How to support a broad set of research practices with a wiki? Wiki Research Ideas/Research Hub
- A summary of the discussion: Wiki Research Ideas/Summary
- What journals like this are currently available (First Monday, the Journal of Peer Production)
- The value of being indexed by ISI (and how that can be achieved)
- Starting a journal that meets the requirements
- Using a "junior researcher" peer review model (like Law Reviews)
- Getting First Monday indexed in ISI
- pushing WikiSym to the next level (and towards an open license model)
- The fact that there aren't good categories for this sort of work in arXiv/SSRN
- Doing research "the wiki way": let's rethink how academic science works!
- Some demand already for working with WMF on research, from e.g. the Dementia Training Study Centres in Australia
How would a new journal work?
- peer-reviewed, but publish a list of rejected papers and the reviewers comments
- open-access (CC-BY-SA)
- ask always for the datasets and offer them to download, the same for the developed software used in the research
- encourage authors to publish early, publish often (as in free software)
- supported by donations
- maybe join efforts with the Wikimedia Research Newsletter?
- open a wiki (or similar platform) where those who want can write papers in a collaborative and public way.
No matter what, we need :
- indicators of "performance" and/or "excellence" for institutional use
- indicators of "relevance" and/or "searchability" for general public use
For focused discussion about the review model, see Wiki Research Ideas/Review model.
- there’s a community just in this mailing list, and it’s usually easy to find folks to write if you meet the academically-respectable criteria (because folks need publications for grants and tenure etc). But it’s harder to find readers and reviewers and editors.
- the business model? (i.e. this takes time and probably money)
- Counter: An open content journal would be cheap to run. No staff - everything done by volunteers. Hosting - Wikiversity? Meta?
- Does it make sense to work with JoPP ( Starting with a dedicated issue of JOPP seems like a good thing, but going beyond just a special issue)? Questions about their publication standards and review model...
- the JoPP idea: "Once the publication process is launched then yes, normally everything (initial sub, reviews, responses, final paper) is published."
- PLOS bases on Ambra http://www.ambraproject.org/
- the infrastructure to do this is there already with MediaWiki and WMF, but workflow would need some thought 
Getting indexed in ISI
From : See their instruction page: http://ip-science.thomsonreuters.com/mjl/selection/ There is also a list of all journals that *are* indexed, which could be useful: http://ip-science.thomsonreuters.com/mjl/
In short, you request being reviewed and from issue X onwards they check how often an average article from the journal is cited in other ISI journals. If you go above the threshold, you're in. 
Besides timeliness, they also take into consideration international range (given the cosmopolitan composition of the wiki-research mailing list it seems OK) and the originality of research comparing to their usual reviews.
we would have to have a "normal" review process (2-3 double blind reviews), editorial board, many submissions (and rejection rates above 90%, but including major revise and resubmit (R&Rs), that's why R&R is so common). 
So far, it seems fair to begin with a bimestrial of trimestrial rythm of publication : it's long enough to be highly selective and short enough to keep the journal lively.
Rethinking the future of research
Thematic question: What is the quickest way that we would ever want to publish our work? 
A response :
- You have a good project idea someone should do. You publish it.
- You know some people doing interesting work in the area who need x,y,z to tackle such a project, and add that.
- You start a project. You publish a pointer and project name.
- Some collaborators join. You publish names.
- You get a target to take data from, have a meeting, and publish.
- You finalize procedures and start implementing. and publish.
- You get first data. and publish.
- You get context for the data. And publish.
- You find time to look at the data, organize the context, add a summary, and publish.
- You compile a full schedule of data, and run analysis, publishing your error logs and lab notebook pages on the fly.
- You give a paper bag talk with slides (and publish)
- You draft an abstract for peer review (and publish)
- You finish an abstract and submit it for review (a. p.)
- You get feedback from the journal you submitted to (a. p.) and revise (a. p.)
- You get included in a major quarterly Journal, with polish (a. p.)
- You get public commentary, cites, criticism; and make better talk slides (a. p.)
- You add suggestions for your students or others to extend the work in future papers (a. p.)
Cf. "Massively Distributed Authorship of Academic Papers" (Alt.CHI 2012) . (Abstract: Wiki-like or crowdsourcing models of collaboration can provide a number of benefits to academic work. These techniques may engage expertise from different disciplines, and potentially increase productivity. This paper presents a model of massively distributed collaborative authorship of academic papers. This model, developed by a collective of thirty authors, identifies key tools and techniques that would be necessary or useful to the writing process. The process of collaboratively writing this paper was used to discover, negotiate, and document issues in massively authored scholarship. Our work provides the first extensive discussion of the experiential aspects of large-scale collaborative research.)
Some of this cool new stuff could be added to JoPP or a similar journal, e.g. why not have "discussion threads" attached at the bottom of ever paper (including the abstracts of rejected ones) so that readers can, if they wish, continue to discuss the topics with authors, reviewers, and one another?
Note that the community norms for a "research wiki" would be very different from those on Wikipedia. (Maybe requiring different software.) And, indeed, there may be different sets of community norms in different research communities, for example, some researchers wanting to keep their journal submissions (which may possibly be rejected) -- not to mention their research-in-progress -- hidden from prying eyes.
How does research work around Wikimedia now?
Perhaps we should take a closer look at the Research Portal of Wikiversity:
There's also some stuff going on around Meta, including the Wikimedia Research Newsletter:
And there's this, which was sponsored by Wikimedia Germany:
Also, loosely related to research, there's this page for developers:
Further: given the current set of Wikimedia projects (such as Wikiversity), some forms of collaboration between researchers and Wikimedia may already be very attractive. Private organizations frequently spend, say, $50,000 to develop tools and resources for academics, which can quickly disappear if/when funding runs out or people move on or the technology backing them no longer works. By moving to WMF related projects, they can encourage and foster greater collaboration, keep lines of communication more open, better allow the general public to see what they are doing, provide caregivers and others access to better information, etc. 
Support needed, next steps
As the proposals about a journal become more and more specific, it seems more likely that they will happen -- whereas proposals about the laboratory remain somewhat vague and ephemeral. If we want to do more than just hope and dream, then I think we, too, need some specific, do-able proposals.
- One such proposal would be to work closely with the journal, to try to make it, itself, into the "laboratory". For example, this could involve open discussion on published works after publication. That's not rocket science -- it's wiki science!
- Another proposal would be to develop (in practice) some of the specific techniques and workflows that have been described or trialed by e.g. Tomlinson et al. -- in other words, picking some specific research problem, and trying to study it in "the wiki way" ourselves, putting together the infrastructure that we need as we go. We could start by writing a short "literature review" that describes what it might mean to do research "the wiki way".
- One proposal (from me, in the Open Letter quoted below) proposes some very broad cultural shifts, related to but going beyond the Open Access movement. We could take these ideas and subject them to a critique (how realistic are they?). This approaches the question from a "policy" perspective more than a "practice" perspective.
- .... <-- other ideas?
- this Open Letter to Researchers (published earlier on wiki-research-l), which talks about how to get funding for open research
- The homepage of the Free Technology Guild, a nacent project that would help address the "$50K for tools" concern mentioned above.
Related to journals
- The field of "wiki studies" exists but there is no dedicated journal. This is a problem to be solved.
- If the Wikimedia Foundation could support an online journal, this would be a great outcome.
- Bid for funding through a chapter, or through the Grants program (Grants:Index).
- We can consider partnering with an existing journal (such as the Journal of Peer Production), but only if it was fully in line with our goals (including ISI targeting, if we choose so)
Related to the "wiki way of doing research"
- We should pursue broader cultural change in parallel with concrete work on a journal. There is room for cross-over, as contributors to a "Wiki Journal" may also do research in the "Wiki Way".