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“bioRxiv (pronounced “bio-archive”) is a free online archive and distribution service for unpublished preprints in the life sciences.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.

#AccessToResearch & More! — Hashtags of the Week (HOTW): (Week of February 3, 2014)


I was pretty excited to see the announcement of the UK Access to Research initiative, a partnership of publishers and libraries across the United Kingdom, which will hopefully extend open access research in ways that may serve as a model for other countries. They made some interesting choices, including requiring people to visit their local library in order to get access.


Why You Should Care About Creative Commons 4.0

Creative Commons by Andres EM  CC BY 2.0

Creative Commons by Andres EM CC BY 2.0

Creative Commons, as many of you know, provides and promotes the sharing of material by creating licenses that allow authors to chose the conditions how their work can be reused. In the science community, Creative Commons is especially important because all scientific research is build on the reuse and re-analysis of other scientific works in an international and interdisciplinary world.

Creative Commons just released CC4 and claims to be the most “globally, legally robust licenses produced by CC to date.” There are many improvements that include internationalization, interoperability and durability, but the most exciting is the advances for data, PSI, science, and education. These exciting advances address the obstacles of adoption of CC by other governments, aka database rights in the EU. According to Puneet Kishor the implications for the change is great:

 That means a database creator in the EU, or any other jurisdiction where SGDR might exist, can use a CC4 license allowing use of the database without the user worrying about violating any database rights. In other words, using CC4 relieves the creator from separately licensing database rights, and it relieves the downstream database user – in particular if located in a region where SGDR apply– from worrying about violating any database rights

If you want to learn more about Creative Commons 4.0 check out this blog post or interview with Puneet Kishor. If you want to learn about applying a Creative Commons license, click here.

Reflecting on The Society for Scholarly Publishing Conference

I spent a glorious bit of time in my hometown of San Francisco attending the Society for Scholarly Publishing’s 35th annual meeting in early June as one of the student travel grant winners. As anyone who’s attended a conference can surely attest, sometimes it is all you can do to take relevant notes, make it to the next session on time, and keep a grasp on the business cards you’re trading – so now that it has been a couple of weeks, I wanted to take the opportunity and reflect on some of the key points as I didn’t have the chance to during the actual conference:

Classroom by

Education by Chris Matthews for The Noun Project, 2012 CC0

MOOCs (if they stick around) are going to be huge for faculty, publishers, and librarians :

The plenary session that kicked off the first full day of conferences focused on massive open online courses (with which the University of Michigan is quite heavily engaged). As I detailed during one of my liveblogging posts during the conference, professors currently undertaking MOOCs are facing notable challenges, including gathering open(ish) content, the time necessary to adapt courses to the online platforms, and measuring the impacts on both student participants and the benefits for professors themselves. Most of the companies involved with MOOCs currently, Coursera, edX, and Udacity, are all just two years old (isn’t that insane?). They, and the entire concept of the MOOC itself, is still very much undergoing an evolutionary process. It is, I think, also an immense opportunity for librarians to get involved with faculty in a very tangible way. We have the expertise on locating sources and instruction – we can leverage it within this context as well.

Diversity is Great, or, Not Everyone Agrees on Open Access:

Open Access LockNormally when I go to a conference, it is comprised of a very specific subset of people – medical librarians, special librarians, etc. – SSP was a departure from that norm, and a very interesting one! I do not have much of an opportunity to interact with vendors or publishers in the course of my daily responsibilities as a University Library Associate at THL, so having publishers, consultants, and librarians at SSP was a bit of a revelation! I had some fascinating conversations with librarians who aren’t as gung-ho about open access as I am, and hearing that not all publishers were entirely against it. We clearly have a long road to travel before there is consensus, but I am hopeful solely to have found that venues like the SSP annual meeting exist, where we can come together and have open communication.

Altmetrics are Cool, But No One’s Got a Handle on them Quite Yet:

Bar graph 2012 by Ben King from The Noun Project, CC0

Bar graph 2012 by Ben King from The Noun Project, CC0

In a theme that very clearly connected my experience at the Medical Library Association conference in May with SSP, altmetrics was again a hot topic. In a very, very broad overview – there are lots of tools that can help look at alternative metrics (such as bookmarks, downloads, tweets, blog posts, etc.), including but not limited to ImpactStory, Plum Analytics, Altmetric [and via Scopus]), but challenges exist in both capturing and analyzing the information efficiently. Not all researchers are convinced they are worthwhile, although that cohort seems to be diminishing. There are concerns about “gaming the metrics,” though buying fake Twitter accounts for example. Then of course there is the larger question of meaning – does a retweet of an article DOI mean the same thing as a download? Does anyone read the paper? These larger conversations all need to be had, but thanks to leaders in the field, like PhD candidate Jason Priem, the movement is gaining traction and those conversations are gaining wider and wider audiences. Follow the conversation online through the #altmetrics hashtag. Also, to tie in the conference and altmetrics, check out this analysis of the #2013ssp Twitter stream.

#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.

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.

Hashtags of the Week (HOTW): Science Online (Week of January 28, 2013)

This week Twitter was abuzz with news from the Science Online Conference (#scio13).  As the tweet above says, this annual conference began in 2007 to bring together science bloggers and their readers and has grown ever since.  The schedule is chosen in an “unconference” style and facilitated through the use of a wiki.  For those who aren’t familiar, an unconference is a conference in which participant feedback is used to determine topics centered around a theme.  The conference is also being broadcast online and has viewing parties around the world.  We’ll highlight some tweets from the conference as well as hashtags spinning off or related to conference tweets.


As you might expect, a conference that was started by science bloggers also populates the hashtag #ScienceBlogging

There was also quite a bit of chatter about data publication and #OpenAccess coming out of the conference.



#SciOut is about science and outreach moving beyond press releases.

#SciSummary focuses on the vagaries of science visualization and publishing.

NIHPAP Compliance Changes

A new notice, NOT-OD-12-160, was posted last week by the National Institutes of Health in regards to compliance with the NIH Public Access Policy that explictly states:

….Since 2008, compliance with the NIH public access policy has been a statutory requirement and a term and condition of all grant awards and cooperative agreements. NIH and its awardees have developed increasingly effective ways to track and report compliance with the public access policy.  To this end, NIH has provided outreach and worked to assist applicants with understanding the policy.  However, there is a need to improve grantee compliance.

Upcoming Process Change:
With this Notice, NIH informs grantees that in Spring, 2013, at the earliest, NIH will delay processing of non-competing continuation grant awards if publications arising from that award are not in compliance with the NIH public access policy.  The award will not be processed until recipients have demonstrated compliance.  This change will take effect in tandem with NIH requiring the use of the Research Performance Progress Report (RPPRs) for all Streamlined Non-competing Award Process (SNAP) and Fellowship awards in the Spring of 2013 (see NIH NOT-OD-12-142).

NIH will simultaneously implement the procedural change outlined below to facilitate public access reporting in paper progress reports (PHS 2590) submitted on or after this ‘to be announced’ spring date…

The Taubman Health Sciences Library provides a research guide to assist you with compliance requirements at:


What is Open Access?

Open Access (OA) Week has passed, but we like to encourage people to continue to learn and understand the concept.  OA can be confusing, and so PhD Comics has partnered with The Scholarly Publishing & Academic Resources Coalition (SPARC) to produce a video,  What is Open Access?, to help us all understand it better…

An OA definition supported by SPARC is the one from The Budapest Open Access Initiative and reads as follow: “By open access, we mean its immediate, free availability on the public internet, permitting any users to read, download, copy, distribute, print, search or link to the full text of these articles, crawl them for indexing, pass them as data to software or use them for any other lawful purpose…”

You know that OA is my soapbox issue.  I believe that information is the single most empowering commodity on the face of this earth.  Making it available to everyone regardless of race, religion, socioeconomic status or any other characteristic you can think to name here can only be a good thing…  So it’s worth knowing more about how to make information available to everyone.  My two cents.



Open Access Week at UM

The MLibrary Open Access Week Committee invites you to celebrate the 6th annual Open Access Week, October 22 – October 26.  All events take place in the Hatcher Graduate Library Gallery.  Refreshments will be served.

OA Week Lightning Talks, Monday, October 22, 1:30 – 3:00 pm

Hear brief talks on Open Michigan, Federal Research Public Access Act: FRPAA, Opening Access to Your Data: Why It’s Good, Why It’s Different, and What You Can Do, and more!

What’s in it for You?  The U-M Copyright Policy (Standard Practice Guide 601.28), Tuesday, October 23, 9:30 – 10:30 am, Melissa Levine, Lead Copyright Officer, MPublishing, and Jack Bernard, Associate General Counsel, Office of the Vice President and General Counsel

Your scholarly work is important and worthy of long-term preservation. The U-M’s new copyright policy – recently updated for the first time in many years – charges the university with that preservation responsibility. Learn how the new policy aff ects your publishing, and why it serves as a foundation for a campus-wide open access policy.

Using HathiTrust for Education and Research, Tuesday, October 23, 3:00 – 4:00 pm, Angelina Zaytsev, Project Librarian for HathiTrust

Interested in learning how to use HathiTrust in your research and class work? Topics include an overview of content, search, collection building, understanding copyright statements and usage restrictions, text mining and data analysis, and upcoming initiatives of the HathiTrust Research Center.