🔖 Samvera – an open source repository solution for digital content

Bookmarked Samvera - an open source repository solution for digital content (Samvera)
Samvera is a versatile and feature rich repository solution that is being used by institutions worldwide to provide access to their digital content.

📑 We Have Never Been Social | Kathleen Fitzpatrick

Annotated We Have Never Been Social by Kathleen FitzpatrickKathleen Fitzpatrick (Kathleen Fitzpatrick)
So this is where some older paths-not-taken, such as Ted Nelson’s original many-to-many, multidirectional model for hypertext, and some more recent potential paths, such as Herbert van de Sompel’s decentralized, distributed vision for scholarly communication, might come in.  

Herbert van de Sompel sounds familiar but I’m not placing him at the moment. I’ll have to read his work with respect to some of my ideas on academic samizdat.

Thoughts on open notebooks, research, and social media

I remember thinking over a decade ago how valuable it would be if researchers kept open notebooks (aka digital commonplace books) like the one Kimberly Hirsh outlines in her article Dissertating in the Open: Keeping a Public Research Notebook. I’d give my right arm to have a dozen people in research areas I’m interested in doing this very thing!

The best I could hope for back in 2008, and part of why I created the @JohnsHopkins Twitter handle, was that researchers would discover Twitter and be doing the types of things that some of the Johns Hopkins professors outlined in this recent article The Promise and Peril of Academia Wading into Twitter are now finally doing. It seems sad that it has taken over a decade and this article is really only highlighting the bleeding edge of the broader academic scene now. While what they’re doing is a great start, I think they really aren’t going far enough. They aren’t doing their audiences as much service  as they could because there’s only so much that Twitter allows in terms of depth of ideas and expressiveness. It would be far better if they were doing this sort of work from their own websites and more directly interacting with their colleagues on the open web. The only value that Twitter is giving them is a veneer of reach to a broader audience, but they’re also opening themselves up to bigger attacks as is described in the article.

In addition to Kimberly’s example, another related area of potential innovation would be moving the journal clubs run by many research groups and labs online and opening them up. Want to open up science?  Then let’s really do it!  By bookmarking a variety of articles on their own websites, various members could be aggregated to contribute to a larger group, which could then use their own websites with protocols like Webmention or even simple tools like Hypothes.is to guide and participate in larger online conversations to move science communication along at an even faster pace. Greg McVerry and I have experimented in taking some of these tools into the classroom in the past.

If you think about it, arXiv and other preprint servers are really just journal clubs writ large. The problem is that they’re only communicating in one direction by aggregating the initial content, but they’re dramatically failing their audiences in that they aren’t facilitating or aggregating any open discussion around that content. As a result, the largest portion of their true value is still locked away in the individual brains of their readers rather than as commentary or even sentence level highlights and annotations on particular pieces out in the open. Often is the time that I’ll tweet about an interesting article only to receive a (lucky) reply that the results have been debunked, yet that information is almost never disclosed in or around the journal article (especially online) where it certainly belongs. Academic publishers are not only gouging us financially by siloing their content, they’re failing us far worse than most realize.

Another idea: Can’t get a journal of negative results to publish your latest research failure? Why not post a note or article on your own website to help out future researchers? (or even demonstrate to your students that not everything always works out?)

Naturally having aggregation services like indieweb.xyz, building planets, using OPML subscriptions, or the coming wave of feed readers could make a lot of these things easier, but we’re already right on the cusp for people who are willing to take a shot for doing this type of research online on their own websites and out in the open.

Want to try out some of the above? I’m happy to help (gratis) researchers who’d like to experiment in the area to get themselves set up. Just send me a note or give me a call.

👓 UC terminates subscriptions with world’s largest scientific publisher in push for open access to publicly funded research | University of California | Office of the President

Read UC terminates subscriptions with world’s largest scientific publisher in push for open access to publicly funded research (University of California | Office of the President)
As a leader in the global movement toward open access to publicly funded research, the University of California is taking a firm stand by deciding not to renew its subscriptions with Elsevier. Despite months of contract negotiations, Elsevier was unwilling to meet UC’s key goal: securing universal open access to UC research while containing the rapidly escalating costs associated with for-profit journals.

This is some crazy bad-ass news. Almost everyone I know in higher education tweeted this article out today.

Now if only we could get them to all go IndieWeb using a Domain of Their Own and practice academic samizdat

The bookmarking service CiteULike is shutting down on March 30, 2019 after a 15 year run. While some may turn to yet-another-silo or walled garden I highly recommend going IndieWeb and owning all of your own bookmarks on your own website.

I’ve been doing this for several years now and it gives me a lot more control over how much meta data I can add, change, or modify as I see fit. Let me know if I can help you do something similar.

Replied to a tweet by Lior Pachter (Twitter)

Don Zagier’s one sentence proof of Fermat’s theorem on sums of two squares can be found in an archived version via academic samizdat.

Wikipedia also has a slightly longer unpacking of it.

👓 My book, Twitter and Tear Gas, is out! News and Details! | Zeynep Tufekci

Read My book, Twitter and Tear Gas, is out! News and Details! by Zeynep Tufekci (technosociology)
Dear Friends, My book, Twitter and Tear Gas: The Power and Fragility of Networked Protest, is officially out today, as of May 16th! It is published by Yale University Press, and it weaves stories w…

Some news: there will be a free creative commons copy of my book. It will be available as a free PDF download in addition to being sold as a bound book. This is with the hopes that anyone who wants to read it can do so without worrying about the cost. However, this also means that I need to ask that a few people who can afford to do so to please consider purchasing a copy. This is not just so that Yale University Press can do this for more authors, but also because if it is not sold (at least a little bit!) in the initial few weeks, bookstores will not stock it and online algorithms will show it to fewer people. No sales will mean less visibility, and less incentive for publishers to allow other authors creative commons copies.  

I negotiated the creative commons copy with my (wonderful!) publisher Yale University Press because I really wanted to do what I could to share my insights as broadly as I could about social movements and the networked public sphere. If I make a penny more from this book because it sells well by some miracle, I will donate every extra penny to groups supporting refugees, and if I ever meet you in person and you purchased a copy of the book in support, please let me know and I’ll buy the coffee or beer. 😀 This isn’t at all about money for me.

An excellent example of academic samizdat
November 28, 2018 at 11:24AM

Reply to Greg McVerry about academic samizdat pre-print server

Replied to a post by Greg McVerryGreg McVerry (quickthoughts.jgregorymcverry.com)
Then we also make a 12/31/2019 to have published first issue of a academic samizdat POSSE Journal about blogging research from any discipline. I wanna bring back some lightning talks like BlogCon 2003-2006., but first we do the journal.

I like that idea. Perhaps between the models for news.IndieWeb.org and Kicks Condor’s indiweb.xyz, we could create a syndicatable (pre-print) academic journal that allows sorting by top level academic disciplines.

I don’t recall though, are either of them open source, or do we need to re-build by hand?

👓 Mathematics matters | Bits of DNA

Read Mathematics matters by Lior PachterLior Pachter (Bits of DNA)
Six years ago I received an email from a colleague in the mathematics department at UC Berkeley asking me whether he should participate in a study that involved “collecting DNA from the brigh…

Not sure how I had missed this in the brouhaha a few weeks back, but it’s one of the more sober accounts from someone who’s actually got some math background and some reasonable idea about the evolutionary theory involved. It had struck me quite significantly that both Gowers and Tao weighed in as they did given their areas of expertise (or not). Perhaps it was worthwhile simply for the attention they brought? Gowers did specifically at least call out his lack of experience and asked for corrections, though I didn’t have the fortitude to wade through his hundreds of comments–perhaps this stands in part because there was little, if any indication of the background and direct identity of any of the respondents within the thread. As an simple example, while reading the comments on Dr. Pachter’s site, I’m surprised there is very little indication of Nicholas Bray’s standing there as he’s one of Pachter’s students. It would be much nicer if, in fact, Bray had a more fully formed and fleshed out identity there or on his linked Gravatar page which has no detail at all, much less an actual avatar!

This post, Gowers’, and Tao’s are all excellent reasons for a more IndieWeb philosophical approach in academic blogging (and other scientific communication). Many of the respondents/commenters have little, if any, indication of their identities or backgrounds which makes it imminently harder to judge or trust their bonafides within the discussion. Some even chose to remain anonymous and throw bombs. If each of the respondents were commenting (preferably using their real names) on their own websites and using the Webmention protocol, I suspect the discussion would have been richer and more worthwhile by an order of magnitude. Rivin at least had a linked Twitter account with an avatar, though I find it less than useful that his Twitter account is protected, a fact that makes me wonder if he’s only done so recently as a result of fallout from this incident? I do note that it at least appears his Twitter account links to his university website and vice-versa, so there’s a high likelihood that they’re at least the same person.

I’ll also note that a commenter noted that they felt that their reply had been moderated out of existence, something which Lior Pachter certainly has the ability and right to do on his own website, but which could have been mitigated had the commenter posted their reply on their own website and syndicated it to Pachter’s.

Hiding in the comments, which are generally civil and even-tempered, there’s an interesting discussion about academic publishing that could have been its own standalone post. Beyond the science involved (or not) in this entire saga, a lot of the background for the real story is one of process, so this comment was one of my favorite parts.

👓 Top Cancer Researcher Fails to Disclose Corporate Financial Ties in Major Research Journals | New York Times

Read Top Cancer Researcher Fails to Disclose Corporate Financial Ties in Major Research Journals (New York Times)
A senior official at Memorial Sloan Kettering Cancer Center has received millions of dollars in payments from companies that are involved in medical research.

This makes me think that researchers should have a page on their websites (like impressum, about, or other similar pages) that lists all of their potential research conflicts? What to call it? A Disclosure page, a Financial Ties page? It could have a list of current as well as past affiliations, along with dates, and potentially the value amounts paid (which are apparently available publicly in separate filings). In addition to posting their potential conflicts and disclosures on their own websites, researchers could easily cut and paste them into their publications (or at least their students, post docs, fellow researchers, or secretaries could do this when they’re apparently too busy to make a modicum of bother to do it themselves.)

I’m kind of shocked that major publishers like Elsevier are continually saying they add so much value to the chain of publishing they do, yet somehow, in all the major profits they (and others) are making that they don’t do these sorts of checks as a matter of course.

The IndieWeb and Academic Research and Publishing
A microcast with an outline for disrupting academic publishing

#openscience #scholcomm #scicomm #libchat #higherED

https://boffosocko.com/2018/07/28/the-indieweb-and-academic-research-and-publishing/

🎙 The IndieWeb and Academic Research and Publishing

The IndieWeb and Academic Research and Publishing


Running time: 0h 12m 59s | Download (13.9 MB) | Subscribe by RSS | Huffduff

Overview Workflow

Posting

Researcher posts research work to their own website (as bookmarks, reads, likes, favorites, annotations, etc.), they can post their data for others to review, they can post their ultimate publication to their own website.​​​​​​​​

Discovery/Subscription methods

The researcher’s post can webmention an aggregating website similar to the way they would pre-print their research on a server like arXiv.org. The aggregating website can then parse the original and display the title, author(s), publication date, revision date(s), abstract, and even the full paper itself. This aggregator can act as a subscription hub (with WebSub technology) to which other researchers can use to find, discover, and read the original research.

Peer-review

Readers of the original research can then write about, highlight, annotate, and even reply to it on their own websites to effectuate peer-review which then gets sent to the original by way of Webmention technology as well. The work of the peer-reviewers stands in the public as potential work which could be used for possible evaluation for promotion and tenure.

Feedback mechanisms

Readers of original research can post metadata relating to it on their own website including bookmarks, reads, likes, replies, annotations, etc. and send webmentions not only to the original but to the aggregation sites which could aggregate these responses which could also be given point values based on interaction/engagement levels (i.e. bookmarking something as “want to read” is 1 point where as indicating one has read something is 2 points, or that one has replied to something is 4 points  and other publications which officially cite it provide 5 points. Such a scoring system could be used to provide a better citation measure of the overall value of of a research article in a networked world. In general, Webmention could be used to provide a two way audit-able  trail for citations in general and the citation trail can be used in combination with something like the Vouch protocol to prevent gaming the system with spam.

Archiving

Government institutions (like Library of Congress), universities, academic institutions, libraries, and non-profits (like the Internet Archive) can also create and maintain an archival copy of digital and/or printed copies of research for future generations. This would be necessary to guard against the death of researchers and their sites disappearing from the internet so as to provide better longevity.

Show notes

Resources mentioned in the microcast

IndieWeb for Education
IndieWeb for Journalism
Academic samizdat
arXiv.org (an example pre-print server)
Webmention
A Domain of One’s Own
Article on A List Apart: Webmentions: Enabling Better Communication on the Internet

Synidicating to Discovery sites

Examples of similar currently operating sites:
IndieNews (sorts posts by language)
IndieWeb.xyz (sorts posts by category or tag)
 

👓 Scholarly publishing is broken. Here’s how to fix it | Aeon

Read Scholarly publishing is broken. Here’s how to fix it by Jon Tennant (Aeon)
The world of scholarly communication is broken. Giant, corporate publishers with racketeering business practices and profit margins that exceed Apple’s treat life-saving research as a private commodity to be sold at exorbitant profits. Only around 25 per cent of the global corpus of research knowledge is ‘open access’, or accessible to the public for free and without subscription, which is a real impediment to resolving major problems, such as the United Nations’ Sustainable Development Goals.

I agree with much of what he’s saying here, but it’s so dense and talks around the issue so much that it’s simply just another diatribe against the system. While there is a prescriptive portion, we’re going to need a whole lot more in terms of a list of what individuals and institutions should be doing.

So yes, more of the how to fix it piece please.

Kathleen did you own the domain where Planned Obsolescence1 was peer-reviewed? It may be one of the first major examples of book-length online academic samizdat of which I’m aware. Perhaps you know of others which could be documented? I suspect we could help provide additional exemplars and links to other web technology, platforms, plugins, etc. to make this an easier and more commonplace practice.

James Shelley, I’ve noticed your draft efforts2,3 as well. I’m curious if you could take a moment to document them, i.e. what you’re using, how you’ve planned it, etc. to help others as well.

If you’ve already blogged about these in the past, then even links to those could be helpful to others using similar publishing practices in the future. Thoughts on brainstorming, best practices, pros/cons, could be highly useful as the landscape changes.

References

1.
Fitzpatrick K. Planned Obsolescence: Publishing, Technology, and the Future of the Academy. NYU Press. https://amzn.to/2NAfIPF. Published November 1, 2011. Accessed July 23, 2018.
2.
Shelley J. System Thinker Notebook. James Shelley. http://jamesshelley.com/drafts/simple.html. Published July 11, 2018. Accessed July 23, 2018.
3.
Shelley J. On the Simple Life. James Shelley. http://jamesshelley.com/drafts/simple.html. Published July 22, 2018. Accessed July 23, 2018.

I’ve come across many journals (and particularly many talking about Altmetrics1,2) that are supporting the old refback infrastructure and wonder why they haven’t upgraded to implement the more feature rich webmention specification?

I’ve been thinking more lately about how to create a full stack IndieWeb infrastructure to replace the major portions of the academic journal ecosystem which would allow researchers to own their academic papers but still handle some of the discovery piece. Yesterday’s release of indieweb.xyz, which supports categories, reminds me that I’d had an idea a while back that something like IndieNews’ structure could be modified to create a syndication point that could act as an online journal/pre-print server infrastructure for discovery purposes.

A little birdie has told me that there’s about to be a refback renaissance to match the one currently happening with webrings.

References

1.
Akers KG. Introducing altmetrics to the Journal of the Medical Library Association. Journal of the Medical Library Association. http://jmla.mlanet.org/ojs/jmla/article/view/250/403. Published July 3, 2017. Accessed July 2, 2018.
2.
Roemer RC, Borchardt R. Chapter 2. Major Altmetrics Tools. ALA Tech Source. https://journals.ala.org/index.php/ltr/article/view/5746/7187. Published July 1, 2015. Accessed July 2, 2018.