BioRxiv: A Preprint Archive for the Life Sciences


I just found out that some of my friends had not yet heard about BioRxiv, the preprint archive for the biological and life science which was launched by Cold Spring Harbor Press last November.

What is the idea behind it? They released a great video yesterday to explain it.

bioRxiv The Preprint Server for Biology

The buzz has reached such influential journals as SCIENCE and NATURE, so you know they are legitimate. This is how they describe themselves.

“bioRxiv (pronounced “bio-archive”) is a free online archive and distribution service for unpublished preprints in the life sciences. It is operated by Cold Spring Harbor Laboratory, a not-for-profit research and educational institution. By posting preprints on bioRxiv, authors are able to make their findings immediately available to the scientific community and receive feedback on draft manuscripts before they are submitted to journals.”

Jon Wilkins gives excellent reasons for participating in his blogpost on Lost in Transcription: open access, speed, normalization, feedback, and “the left side of history.”

Five Reasons Biologists Should Use Preprint Servers

I’d also argue that getting your work out in public view under your own name helps to define your claim to the work, and gives you preemptive identification with the concepts. Not to mention that visibility can lead to or support publication (and there is the absolutely delicious feeling that comes when an editor sees the preprint and asks you to submit your article to their journal).

Just to make it even better, bioRxiv readership and use are included in altmetrics.

This might just make an interesting expansion upon placing your work in Deep Blue, and could also help fulfill some grant requirements for placing work in spaces accessible to the public. Issues to ponder.

Need information on copyright?

copyright symbolThe University Library’s Copyright Office has just announced a series of workshops for faculty and students on copyright.  All workshops will be held in the Faculty Exploratory in the Hatcher Graduate Library.

Can’t go to the workshops?  Use this research guide instead:

Open Access Publications Surge with NIH Mandate

from National Institutes of Health data, posted in the Nature News Blog

In November 2012 the National Institutes of Health announced that in spring 2013 it would be enforcing its 2008 Public Access Policy (PAP) by not awarding non-competing grant continuations to those grantees who were not in compliance with the PAP – that is, with publications resulting from NIH grants submitted to the open access repository, PMC (formerly known as PubMed Central).

Since the announcement, there has been a sizable spike in the number of PMC submissions, and the PAP seems to have a compliance rate now hovering somewhere between 75 and 80%. You can actually download the NIH manuscript submission data as a CVS file, or view monthly statistics here.

A tip of the hat to Kevin Read, NLM Fellow, who first pointed me to this Nature News Blog post.


Is It Time to Quit Honorary Authorship?

"Typewriter," by Simon Child from The Noun Project, CC BY 3.0

Typewriter,” by Simon Child from The Noun Project, CC BY 3.0

A coworker recently sent along an interesting editorial from Science written by Philip Greenland, a professor of preventive medicine at Northwestern University (and the former editor of Archives of Internal Medicine) and Phil B. Fontanarosa, executive editor of the Journal of the American Medical Association, who argue that “honorary authorship must no longer be tolerated.”

Although Greenland & Fontanarosa distinguish between “coercive authorship” and “gift authorship” – senior staff members imposing on publications and tacking on a well-known name to increase the chance of publication/prestige, respectively – they argue that both behaviors exhibit “fraudulent aspects.” Washington University in St. Louis has actually labeled both types as research misconduct and specifically defined what constitutes each type of honorary authorship.

While some institutions are taking initiatives (Harvard, for example, actually has a workshop developed already on “contributorship” and scholarly attribution), overcoming honorary authorship will have to be a collaboration – harnessing the effort of academic institutions, research scientists, publishers, and funders.

#2013SSP: Crosspolinating health sciences libraries and scholarly publishing

SSP 2013


The Society for Scholarly Publishing Annual Meeting has kicked off! Yesterday evening’s keynote speaker was none other than Tim O’Reilly, and what struck me was how much the themes that I ran into at the Medical Library Association conference in Boston resonated in his keynote speech.

Open data in scientific research was one such theme, although I think Tim said it in the most eloquent summary of the dilemma I’ve yet to hear, when discussing the paper that influenced economic austerity measures, and the calculation errors in that set of data: “It is important to also publish data, and not just the conclusions, so that errors can be more easily caught.”

Tim also asked how we can reinvent impact factor in our digital age, which reminded me heavily of Jason Priem’s talk on altmetrics at MLA13 (which I mentioned earlier in the blog). And, of course, no conference would be complete without some discussion on the flawed peer review process, but Tim was succinct in comparing it to the software realm and noting, “distributed peer review works better than picking a few experts.”

Tim included the powerful example of Google’s autonomously driving car, which over the last few years has gotten remarkably better as Google engineers have fed it more data coming from their own Street View sources. The autonomously driving car, Tim said, used to be a book: the road atlas. This comparison absolutely floored me, but I think the comparison is an apt one, with the most important part (relevant to both health sciences libraries, and scholarly publishing): utilizing technology to completely rethink the workflow.

I’m excited to delve into today’s sessions and dive deeper into some of these themes – I’ll report back over the coming days, and you can also follow conference developments through the official hashtag, #2013SSP.

Live from San Francisco, part 1: SF DORA

Image from Jack Dorsey, @Jack

Image from Jack Dorsey, @Jack

This week I am in the wonderful (full disclosure, I’m from there & biased) city of San Francisco to attend the Society for Scholarly Publishing conference. If you’ve ever read anything from the Scholarly Kitchen blog – this is those folks, which is why I’m particularly excited to be in attendance.

I’ll be blogging from the conference, but as I wait for the keynote speaker Tim O’Reilly tonight, to kick off the San Francisco/publishing themed posts, I’m including something that came up recently = on the MEDLIB-L listserv: San Francisco’s Declaration on Research Assessment (DORA).

Although initiated at a December 2012 meeting of the American Society for Cell Biology, the declaration is supposed to be a “worldwide initiative covering all scholarly disciplines”. In actuality, it is a “set of recommendations” to improve the “way in which the output of scientific research is evaluated.”

I was instantly intrigued by this premise, since I’d just heard Jason Priem talk about the hot-button topic at MLA this year: altmetrics, or alternative metrics: different ways to measure impact. In his presentation (the full slide deck is available here),  he spoke about the scientific journal as the cutting edge of scholarly communication tools – in the 17th century. With the proliferation of the web and social media that facilitates peer group connections, he made a convincing point that we need more and different information on impacts than we are getting from peer review and traditional publishing. We should see who our work is reaching, and via what channels – such as on our blogs and Twitter streams. There are many tools to facilitate that (although they are by no means perfect yet) and one explicitly mentioned was his collaboration in creating – which lets you pull in your various digital content (presentations on SlideShare; articles in Mendeley, Tweets linking to papers, papers in PubMed, etc.) and generate a report of impressions, shares, emails, etc.


DORA targets the journal impact factor, pointing out that, “as calculated by Thomson Reuters, was originally created as a tool to help librarians identify journals to purchase, not as a measure of the scientific quality of research in an article.”  DORA then includes 18 recommendations, but themes that run across them include:

  • the need to eliminate the use of journal-based metrics, such as Journal Impact Factors, in funding, appointment, and promotion considerations;
  • the need to assess research on its own merits rather than on the basis of the journal in which the research is published; and
  • the need to capitalize on the opportunities provided by online publication (such as relaxing unnecessary limits on the number of words, figures, and references in articles, and exploring new indicators of significance and impact).

Did I mention the DORA is something you can sign? Read the declaration, voice your thoughts; then if so inclined, join luminary signatures such as Bruce Alberts and diverse organizations such as the Public Library of Science, the American Association for the Advancement of Science, and the Gordon & Betty Moore Foundation.

Hashtags of the Week (HOTW): Stem Cells, Cloning and Publishing, Oh My! (Week of May 20, 2013)

I’m sure most of our readers know that a groundbreaking article was published on May 15th regarding patient specific stem cell cloning. What has come to light since then about the publishing process for the article has been slightly disturbing. First, I looked at the original announcements and information about stem cell research, then I went on to explore issues surrounding science communication and scholarly publishing. It all started (as far as I could tell) with this announcement:

This immediately lead to ethical and policy questions being raised. Many discussions were found on the following hashtags #bioethics, #stemcell, #stemcells, and #cloning.

What we found out this week was that the paper was pushed through the publication process so quickly that some (minor) mistakes were found through post-publication peer review including a manipulated image. These conversations are still unfolding.

This has lent some steam to the conversations that were already focused on the publishing process and its role in research, faculty status, and science communication.

Mendeley + Elsevier – A Marriage Made in Bibliographic Heaven?

Screen Shot 2013-04-23 at 10.36.43 AM

Chances are that by now you’ve heard about Mendeley‘s sale to Elsevier. There had been rumors circulating for some time about the sale, but I heard when they made it official in April – naturally, from a well-informed classmate who heard via Twitter (kudos to @emilyrnlds for the tip).

I thought about posting this in the immediate days after the announcement, but frankly I wanted to see how things would shake out – and naturally, the internet didn’t disappoint.

Twitter users rushed for a pun-filled spin on the issue with #mendelsevier and #mendelete (again, @emilyrnlds led me to those hashtags). But I was curious about some reactions more in-depth than 140 characters, so here’s a round up of what I found:

TL;DR: What does it mean for me?

  • If you’ve got an individual Mendeley account, it’ll still be free
  • You’ll get more (free) storage – 2GB for individual accounts, 5GB for premium and institutional accounts
  • Mendeley will develop an Android app soon to complement it’s iOS usage
  • The API will remain open
  • Do you care about open access/data? That’s not going to fit into a bullet point – so read on:

I anticipated some of the ire from the Mendeley user community due to the dichotomy between Mendeley’s open “hey come look at what your peer group is reading! Collaborate! Innovate!” culture and Elsevier’s rather…controversial business practices; the New Yorker writes Elsevier is:

infamous for restricting the flow of scientific information so it can sell research papers for as much as fifty dollars a piece, generating profit margins of thirty-six per cent and netting the company billions of dollars in revenue annually. The company has fought legislation designed to open up academic research, offered scholars money to file positive reviews, sued libraries for oversharing, and allegedly published fake journals on behalf of the pharmaceuticals industry.

And indeed this seems to fuel the bulk of the user complaints. As part of his response (linked above), David Weinberger writes:

The idea of my reading behaviors adding economic value to a company making huge profits by locking scholarship behind increasingly expensive paywalls is, in a word, repugnant.

And here is where the Scholarly Kitchen blog shines as a beacon of well-balanced online authorship by pointing out the concerns and how, despite the press releases and blog posts and social media chats from Mendelsevier, they avoid

“the question about whether users have the right to openly share copyrighted or licensed content via Mendeley even if they or their institution subscribe (or if there is a CC-BY-NC license associated with the work)…one that ties into the legal risks around this deal and the longevity of Mendeley’s central premise of PDF sharing now that it’s owned by Elsevier.”

Yet, as Kent Anderson (contributing author to Scholarly Kitchen and CEO/publisher of the Journal of Bone & Joint Surgery) points out,

“in the long run, it’s likely better for publishers to see [article usage statistics] under the roof of a company with incentive for respecting copyright, rather than an independent wildcard with no such ties…[since] it’s worth noting that publishers tend to take services at face value, as Connotea and CiteULike were used by many platforms across journals, despite being owned by Nature Publishing Group and supported by Springer, respectively.”

Recognizing that this may not be the most popular opinion, I would like to be cautiously optimistic. I think there could possibly be benefits by having a dedicated system backed by a well-funded company to measure the article-level metrics – which is really where I think the next impact factor is going to come from (Jason Priem, a PhD student at UNC-Chapel Hill will convince you of this in one presentation or less). I had the pleasure of hearing Jason speak at the Medical Library Association conference earlier this month, and naturally in the question portion someone asked about Mendelsevier. For now, I’m sticking with his response (which I won’t quote as I’m paraphrasing and can’t recall the exact wording, but it was something along the lines of): Both companies have said they will preserve Mendeley’s commitment to openness, and that’s what I’ll stick to until I see otherwise.

UMHS, UM Med School, & MLibrary Collaborate to Publish New Book

Read Susan Topol’s full story on the collaboration here.

Book authors autograph copies of ICD Connection at the Young ICD Connection Conference in September, 2012. Image courtesy of Ashley McFarland.

Book authors autograph copies of ICD Connection at the Young ICD Connection Conference in September, 2012. Image courtesy of Ashley McFarland.

From the article:

ICD Connection: Living with an Implantable Cardioverter Defibrillator is a collection of stories that describe what it’s like to live with an ICD—a device that is implanted under the skin to treat life-threatening heart rhythms that can lead to sudden cardiac arrest. The ICD Connection book contains chapters written by ICD patients, family members, and caregivers, and provides perspectives from various ages and backgrounds.

A Mixed Model for Publishing
The project also demonstrated how open and traditional publishing could coincide as a mixed model. [Jasna] Markovac [Senior Advisor for Publishing at the University of Michigan Medical School], who also works closely with Open.Michigan, a U-M initiative that encourages and supports the open sharing of educational resources and research, suggested using a Creative Commons license for the book. [Author Helen] McFarland was glad to support the open sharing philosophy and explains, “I wanted my book to have the broadest impact and reach the largest audience possible, using the open license facilitates this.”

Now Available on Amazon and Open.Michigan
Because it is openly licensed, the complete ICD Connection book, as well as individual chapters, may be downloaded by anyone from the Open.Michigan collection and freely shared with others. It is also available for purchase on Amazon, and an ebook version for the Kindle will be released soon. Since it was made available on Open.Michigan, the complete book was downloaded over 150 times; in addition, individual chapters have been downloaded over 70 times. Fifty copies of the book have been sold on Amazon.

Yahoo! Lecture Series: The End of the Article

The University of California at Irvine’s Geoffrey Bowker will speak at the School of Information about the role of the scientific article as our modern currency of knowledge, and the impeccable growth over the last two centuries of the database as a means of knowledge exploration. Find out more about the talk, and about Dr. Bowker (who also directs Evoke Lab) here.
When: Wednesday, April 10, 2013 from 12 pm – 1 pm
Where: North Quad 2435
This event is sponsored by:
Screen Shot 2013-02-25 at 3.33.10 PM