Save the date: participative Bay Area OA week event for Generation Open

Join us as we join forces with ScienceOpen, ZappyLab and My Science Work (and others to be announced) to celebrate OA with a participative event at Open Access Week in the Bay Area.

A core group initiated by Liz Allen (ScienceOpen), including Lenny Teytelman (ZappyLab), Laurence Bianchini (My Science Work), Peter Binfield and Georgina Gurnhill (PeerJ), brainstormed what our ideal OA week event would look like.

We agreed that we wanted to avoid a traditional format and so we settled on:

- Moderated un-conference where the audience talks and asks questions

- Simple event theme, we picked “#OpenAccess – it’s up to all of us

- “Lightning talks” that anyone can give, 5 image slides in 5 minutes

- Time to chat and mingle over a drink and something to eat

- Ideally, a cool venue with great views (and Disabled Access)

As a group we feel that the program below achieves our vision. We ran it past our academic partners UCSF Library (Anneliese Taylor), UAW post-doc union (Felicia Goldsmith) and they liked it too. Now all we need is for you all to save the date and make this an event to remember.

Date: Thursday, October 23rd, 2014

Venue: SkyDeck, Berkeley (one of the first research university startup accelerators)

Time: 6.00 pm – 8.30 pm

Theme: #OpenAccess – it’s up to all of us

Format (suitable for global cloning!):

  1. 8 mins – relax with a drink, a snack and “What is OA?” video by Jorge Cham (PhD Comics), Nick Shockey (Right to Research) and Jonathan Eisen (UCD)
  2. 10 minutes – un-conference OA topic selection by audience
  3. 20 minutes – topic discussion with moderation (your host for the evening, Lenny!)
  4. 10 minutes – grab another drink (alcoholic or non), stave off hunger with nibbles
  5. 40 minutes – lightning talks, “#OpenAccess – it’s up to all of us”
  6. Last 30 minutes or so – greeting old friends and making some new ones

In the coming weeks, we’ll be letting you know where to send your lightning talks and the deadline for doing so. We will be recording them for social media too - so anyone not able to attend in person can listen in. Look out for the Eventbrite too so you can RSVP.

Finally, in the spirit of “the more the merrier” other OA Publishers and Academic Partners who want to participate are welcome to email Liz.  


Is today’s science where the software industry was in the 70s?

Today there are literally billions of apps that you can download to your smartphone anywhere in the world and start using in seconds. Imagine a totally different world though, one where in order to use an App you had to buy a new phone each time or spend weeks developing it yourself. This was more or less the state of the computing world up until the 1980s. 

There’s a recent blog post called “The Myth of the Fall" regarding open source software. In it the argument is made that up to the 70s/early 80s it was all proprietary software, and that’s because the differing architectures made it impossible for a software program to be compatible with more than one computer - what we call "portability." It was as if in order to use the same software you first had to first translate it into the specific language that a particular computer could "speak." Reusing programs, one of the key benefits to open source, just wasn’t practical. Progress was cumbersome.

It took decades for dedicated individuals to engineer the hardware architectures needed for software portability and just as long for communities to adopt the common standards to make it possible. Once that was established, then open source software such as the Unix operating system could flourish and now the world literally runs on open source - and you can download countless apps to your phone. (Some nice parallels to the billions of years of evolution it took to get past single-cell organisms and into the multi-cellular explosion once it did happen)

Could it be that our science today, and in particular scholarly publishing, is where we were at with software in the 1970s? Software had to battle with incompatible computer hardware in the 70s, and in science we have cultural practices and business models that limit the reuse and dissemination of scholarly knowledge. Paywall publishers continue to lobby against Open Access, much like the 1970s IBM tried to convince us that personal computers weren’t needed - until Apple showed us what could be done with them. The result is that we aren’t making as much progress as we might otherwise achieve. Academic publishing today is like the non-portable software we had 30 years ago. That’s slowly changing though.

The Open Access movement today is to scientific progress as Open Source software was to the information technology explosion that began in the 1980s. And as common hardware architectures greased the wheels for open source to thrive, so do today’s emerging reproducibility and data availability initiatives hint towards a budding scientific explosion. Government and funding agency mandates for Open Access are also greasing those wheels, so that science is more “portable” and accessible to a larger audience.

Our mission at PeerJ is to efficiently publish the world’s knowledge, so that we can tackle this century’s greatest challenges. It’s going to take a modern update to how we think about doing science and publishing to achieve this. Because of that mission we don’t view PeerJ as a publisher in the traditional sense and you’ll continue to see us marching to the beat of a 21st century drum. Our job is to grease the wheels of science by getting scholarly knowledge (of any size) out there as far and as cheap as possible - with a few carrots thrown in for motivation. The software industry is a model we can all take a good look at and have confidence in for what is possible when “Open” is embraced. 


Interview with an Author - Todd Vision

This week is Open Access week, and we thought it would be interesting to talk with Todd Vision, the senior author on our recent publication “Data reuse and the open data citation advantage”. This article, was originally submitted as our first ever PeerJ PrePrint and the PeerJ version was published three weeks ago and has subsequently attracted quite a bit of interest in the scientific community. image

Todd Vision is in the Department of Biology at the University of North Carolina at Chapel Hill and has been the Associate Director for Informatics at NESCent (the National Evolutionary Synthesis Center) since 2006. His research spans evolutionary genetics, computational biology, data science and scholarly communication. He is a co-founder of Dryad, a widely used repository for data underlying biological and medical publications.

PJ: Tell us a bit about the research you published with us, and what is the ‘Take Home Message’ of your article?

This is part of a larger effort to gather evidence on the costs and benefits of making research data accessible and reusable, particular for the data producers themselves. We focused one of the potential motivators for data producers, namely how much additional credit they receive in the form of increased article citations for depositing the data reported the article to a public repository.

One take home message is there is a nontrivial benefit to data producers for making data openly available, and it is increasing over time. Another is that the reuse by others of openly available gene expression data accounts for well more than half of its total usage in the literature, and that this proportion is also on the increase. The implications for policy makers are, we think, pretty self-evident.

PJ: What challenges did you face while doing this research?

The biggest challenge was simply getting machine access to the literature, both to query the citation data and to mine the full text of articles for data accession numbers. At the time we conducted this study, the only option for querying citation data with a list of PubMed IDs was Scopus. Unfortunately, this wasn’t available to us through our institutions, and Elsevier declined to provide us individual access despite our willingness to pay. Heather [Piwowar, first author of the article] tried to use the British Library’s walk-in access during a trip overseas, but the restrictions imposed by the library were not designed for the digital world, and made the exercise impractical. It would have required her to manually type in ten thousand PubMed identifiers one by one. She eventually obtained access to Scopus through an arrangement with Canada’s National Research Library, but even that had its Kafka-esque elements, since she needed to be fingerprinted to obtain a police clearance certificate first. Once she had access, getting the data out of Scopus was very laborious, because she compiled these citation data before Elsevier made the current API available. A study of the scientific literature on this scale is difficult to pull off without the ability to automate the search, either with an API or access to the source data.

Another challenge is that we didn’t (and still don’t) have access to mine the full text of all the scientific articles that might be mentioning these datasets. For that reason, the second part of the study was restricted to the subset of articles available from PubMedCentral. This means we had to extrapolate our estimates, or rely on minimum estimates, for a number of the core results. Even though our university library pays for a subscription that enables humans to read these articles, there is a layer of legal fog that prevents academic researchers from writing software that reads the articles. At one point, multiple Elsevier executives were on the phone with Heather to discuss granting her full-text access to the articles they publish. But the legal negotiations were too slow to be of much help for this study, and at any rate it was only one publisher. There are precious few academics with the time, determination and expertise to negotiate bilateral agreements with all the relevant publishers, and to do it afresh every time there is some new study that requires full text access.

So, we are very happy that publishing our own article as Open Access in PeerJ isn’t contributing another brick in this access wall for future researchers.

PJ: So far, did you get any comments from colleagues about the results you have published with us?

We have been getting an encouraging stream of attention and feedback on this work since it was posted as a PeerJ Preprint in April. In fact, I suspect that the availability of the preprint is the reason the article has managed to start receiving citations already, even though it has been published for less than three weeks.

PJ: PeerJ encourages Authors to make their review comments visible. Why did you choose to reproduce the complete peer-review history of your article?

A lot of expert time goes into reviews, and often the dialog between the authors, the reviewers and the editor adds valuable context that does not get fully surfaced in the paper. I find that writing reviews knowing that they will be made public motivates me to be as constructive as I can. If reviewers wish to stay anonymous, that is still an option - and note that one of the two did in this case. Furthermore, if reviewers wish to make sensitive comments, they always have the option of sharing those privately with the editor. Actually, I’m not sure anymore what purpose is served by having the content of the reviews kept secret by default!

PJ: You received some great media coverage for your article. How was that process? Did the fact that we are an Open Access publisher help with exposure at all?

It’s a fairly involved paper, with lots of different quantitative analyses, including 11 figures and tables. Distilling that down to a few key points for a wider audience has been an interesting and fun challenge, and it has shifted my own thinking about which results are most important and why.

Some of the pieces I have seen were clearly based on the PeerJ press release, but in others you can tell that the reporter went to get additional material from the article itself. It stands to reason that reporters are more likely to do that for an Open Access article like this one.

PJ: With our new Q&A feature, you’ve already had the chance to answer a few questions about your paper. Could you comment on that?

We had one questioner, who asked both ‘did you think of this?’ and ‘where can I learn more about this?’ kinds of questions. Since we, as authors, don’t have an infallible crystal ball that lets us know where readers will want to delve deeper, I think it’s great to allow readers and authors to continue the dialog after publication. It feels like being in a very dispersed, asynchronous journal club, except everyone involved is really interested and has actually read the paper. And the authors can respond if someone thinks they’ve found a fatal flaw! The way that has been implemented in the website, marked in the margin for the relevant section of the manuscript, is very nice.

PJ: Anything else you would like to talk about?

One interesting piece of backstory is the source of the introductory paragraph. Heather felt that she opened the introduction well in a paper she published on the same topic in 2007, and was disinclined to reword the same ideas just for the sake of it. The rationale is that since the introduction section is supposed to restate ideas from the literature anyway, there’s not much point in putting them in new, and potentially inferior, words. So we convinced ourselves to just include the passage verbatim. But then it wasn’t clear whether or how to attribute the passage in order to avoid concerns of self-plagiarism. In the end, we simply stated the source in the acknowledgements. That should be noncontroversial, since these were, after all, one of the author’s own words and the original paper was Open Access. But it did cause some mild unease during review, so we appreciate that PeerJ allowed us, as authors, to make the final call.

Another interesting aspect of the paper is that it was written under version control in a way that all the analyses in the paper, including tables and figures, can be updated just by modifying and replacing the data and recompiling the thing. We used Knitr with embedded R code and data, and had all the files versioned on GitHub. After it was published we put the final snapshot into Dryad, so anyone interested in reusing the data or analysis is free to do so. We’d be delighted if others end up use our source files as a template for figuring out how to write their own reproducible papers.

 PJ: Thank you for your time. We are pleased to have published this paper, which clearly contributes important new information in the open access debate.

If you would like to experience the future of publishing for yourself, then submit now to PeerJ.


Alleged deletion of comments on new Elsevier video - is that innovating?

A new video showing on YouTube that was produced by Elsevier aims to promote how “Open” most of it journals really are. It’s actually a decent explainer video about the basics of Open Access and how many of Elsevier’s journals meet Open Access requirements from funding bodies. A few details of course were left out, for example failing to explain what hybrid journals are and the controversy of “double dipping”, or the fact that not all Elsevier journals offer the same CC licensing, etc. 

The main concern, as shown in this Twitter conversation, is that Elsevier is selective in which comments it allows on its blogs, videos, etc. As pointed out in that thread by John Wilbanks, who was previously at Creative Commons, one should either turn off comments altogether, or allow all of them (save for obvious spam/abuse of course).  


Now, there is no universal law that states a company must abide by the commenting “netiquette” described by Wilbanks. What the alleged removal of comments (in this case mentioning other Open Access options besides Elsevier) suggests however, is that there is a disconnect between what some companies say and what they do. You cannot proclaim to be innovative, but not understand or follow the norms of the Internet, which is to say allowing comments fair and square, even if it means competing journals are mentioned.

Removing comments is a prudent short-term business tactic, but it won’t help in the long-term. It suggests a lack of innovation and desire to have a real conversation for improving Open Access options available to researchers.  


Hack4ac - A London Hackday to celebrate CC-BY

RSVP for the event here or learn more about it on the Hack4ac website.

PeerJ is teaming up with eLife to present a day of hacking, with further sponsorship from PLOS, Digital ScienceAmazon Web Services (giving away major AWS credits) and SkillsMatter

Hack4ac, that’s pronounced “Hack - for - Ack” (ac = academia), is taking place on the 6th of July in London to make use of openly licensed materials and Open Source code to build new tools and to teach interested academics the basics of programming.

Kicking off the event is Mark Thorley, chair of RCUK Research Outputs, who will be giving a few brief remarks on the importance of CC-BY licences. In addition, many in the London area who are major contributors to all things Open Access have already registered to attend

The motivation for the event was two-fold. First, there is no question any longer of the importance and growing acceptance of Open Access and open licenses when it comes to academic literature. With this growth we now have the opportunity to further demonstrate value by working together on new tools to digest, filter, discover, and explore that data and content. Many people are just now learning about Open Access and this is an opportunity to show them how important it is to advancing science. 

A secondary motivation for the event is to bring in academics and others who may not have a background in hacking or programming, but wish to learn. It can often be intimidating to join hackdays or know where to get started, but at the same time learning to program or design tools can benefit anyone in their projects and careers. This is a chance to feel comfortable about being new to something. We warmly welcome all to this event. Programming on the day is not a requirement, and in fact most hack events involve people with different sets of skills who work together to build better tools. 

We’re looking forward to hacking with you!

Space is limited, so RSVP for the event now or learn more about it on the Hack4ac website.