figshare

Recently I have started using figshare to share some figures I've created a while back and that perhaps otherwise would have never seen the light of day. I am certainly not the only one having stuff in the drawer because we never got to finish a manuscript or get to a few more experiments. Another phenomenon playing into this is also widespread and has been named the file drawer effect. Many studies in a given area of research may have been conducted but never reported, because we all have the tendency to not publish negative or inconclusive results. 

There is an open source solution to this available and it doesn't cost you anything aside from a couple of minutes to upload your data. figshare allows researchers to publish research outputs in an easily citable, sharable and discoverable manner. All file formats can be published, including videos and datasets. There is no peer review process, and researchers are actually encouraged to publish null results, avoiding the file drawer effect. figshare uses creative commons licensing and provides you with a DOI and a QR code for every file you've uploaded. Categories and tagging support easy access as well

I have just started using it and I really like this way of sharing results openly. Not only is it a home for all the used (of course the ones published should be up as well) and unused figures but also a great resource when it comes to preparing lectures, courses, and talks. There are some great resources for teachers out there but not as many for university educators.

And most importantly it is real open access. In case you haven't heard of figshare, please check it out and start sharing.

Open Access, seriously (2)

Let's continue with the open access theme...

(2) Do not do ANY work for non open access journals. 

This includes reviewing, suggesting reviewers, etc. Let's assume a bunch of people have made the conscious decision to stop submitting their work to non-open access journals. What impact would that actually have on the publishers? Frankly, not a big immediate one unless we're assuming a massive migration to open access journals. That is rather unlikely and therefore, everyone should consider step two: stop all other work for those journals, i.e. decline to review articles for them, don't even make suggestions for alternative reviewers, and do not serve on the editorial board. Yes - ignore the emails!

For those who feel uneasy to publish exclusively open access but still are skeptical of the traditional publishing market this might be a good starting point and if done by many it probably hurts even more. Why is that?

All these jobs are done on a voluntary basis. Peer review is an essential part of scientific publishing and when done right it helps to improve publications and also prevents bad science from getting any attention. At least that's the theory and most often it works. All journals need our expertise in order to assess the quality and scientific integrity of a publication and we are all happily provide it free of charge. We even volunteer some of our time to serve as editors thereby essentially relieving publishers from at least one management level in their company. As good and important this community driven review process is there is no real return of investment for me as editor or reviewer aside from providing service to the community. Don't get me wrong here, I am not arguing for paid services as this would bring up costs even more. But, for a moment just picture this scenario - you serve as a volunteer for a local sports club or as I do, for a choral organisation. My time and efforts are spend to support the members of the organisation by enabling the group to do more for its members but certainly not to increase revenue. That's why I am not volunteering for a company which would gain the benefit of reduced expenses and higher profit if I did. 

I am not an economist but this business model seems to be flawed as it relies very strongly on other peoples good will. Instead of changing it over time to make it more self-sustaining it looks like the publishing companies kept building on it and over the years they started to push more and more responsibilities towards authors, reviewers, and editors. An example are ever growing rule sets for formatting (length, line spacing, fonts, citations...). We even had to learn to include DOI's for some journals. In any other branch of publishing this is the job of the publishing company. In our little world it is a requirement for submission (and rejection for that matter). I hope nobody believes that these things are intended to help reviewers or editors. They are not! Actually it is a nuisance to pay attention to this instead of focusing solely on content. I wouldn't mind if it would help to bring down the costs for us authors and our institutions but this doesn't seem to be the case. On the contrary with increased outsourcing subscriptions paradoxically went up. I wonder whether prices will climb again when all of a sudden all reviewers and editors resign and move to open access journals. For once some companies would face the true costs of publishing and the real hardship other sectors in the industry are already going through.

For my part I feel much better to provide my service as reviewer and editor for an open access journal. I still devote a part of my time to do service to the scientific community - as we all should - but I think I am doing the right thing to set us up for the future of scientific publishing.

Open Access, seriously (1)

Last week I had talked about open access and the tribute to Aaron Swartz  through the #PDFTribute movement. I also had announced that I plan to change my habits and consequently publish and review exclusively in fully open access journals from now on - or use my blog as an outlet. This was mainly triggered by a post by Jonathan Eisen in which he showed a list of things one can do to really support open access. I know that some of them are perceived as not so easy to follow through especially by those of us that are not in a tenured position yet. That might be true but I thought it would be a good idea to go through them one by one and provide my ideas to make such a shift perhaps more desirable. The first suggestion in the list of ten is perhaps the one that has the most immediate impact but it is also the most controversial as there is so much anxiety connected to it.

(1) Only publish in fully open access journals.

Let's first clarify what is meant with fully open access journals. Full open access content is easily accessible online, available to anyone free of charge, and available for re-use without restriction except that attribution be given to the source. Especially the latter is not always given although authors are usually charged for open access options. Some publishers e.g. have adopted a business model through which authors pay for immediate publication on the Internet but the publisher nonetheless keeps commercial reuse rights for itself. This is not full open access! 

If you want to make sure you publish with the right journals and what your options are when it comes to full open access have a look at the Directory of Open Access Journals.

Make no mistake - open access costs money. Authors are charged for publications. Your paper won't be published out of the sheer goodness of the hearts of the publishers. With open access also came a shift of expenses. In the traditional publishing system authors didn't have to pay as publishers were making their profit by charging for subscriptions or per view of an article. The average scientist at a larger university was able to enjoy the advantages of institutional subscriptions for a multitude of journals without the need to budget for the costs. In the worst case they were part of the overhead already taken away. However, researchers at institutions with lower budgets had no access whatsoever and they perhaps still constitute the majority on our planet. Furthermore, the interested public was excluded as well although most of the research is financed with tax payers money. One particular field in my line of research is actually very bad when it comes to accessibility of research publications - taxonomy. Most descriptions, even the more recent ones, appear either in some exotic journals nobody has access to, or more and more they are published online in Zootaxa. Unfortunately, this journal is anything but open access (although they offer that option to authors at proof stage for a fee). They are the biggest player in the field and many species descriptions are published there but only a fraction of the scientists have access to them because they can't afford a subscription and neither can their institution. Species descriptions in particular should be considered common good and as such accessible to everyone without having to pay any fee. By the way, there is an open access alternative for taxonomists (ZooKeys).

Most open access journals charge at the other end and the fees vary greatly. This puts authors under considerable pressure as this is an expense they need to cover through their budget. However, I do see a good chance that often that can be included in grant proposals as separate line item. Most funding agencies are aware of the shift in the publication market and some actually expect grantees to publish exclusively open access. My experience with that is consistently positive and I always justified the additional costs with the need for open access. Also there are new models for fees in the works - one good example is a membership approach for authors such as in PeerJ.

That leaves us with the omnipresent impact factor argument. I know, the open access idea is rather young and certainly not fully established in our scientific circles. As a consequence impact factors are low to medium. If you want to make a big splash à la Science or Nature you won't stand a chance with open access although in recent years especially the press has been paying a lot of attention to journals such as PLoSONE or the ones from the BMC series. But do we really need to publish in big journals at all cost? Do we really need an impact factor and all related indices to assess the performance of a researcher? Is it really necessary that search committees at universities use these indices or just the fact that somebody has published in a high profile journal as selection criterion?

The internet has changed a lot for that matter and modern web tools provide better and perhaps more objective metrics. From my point of view the number of times one of my articles has been cited is of less value than the actual number of times it has been accessed over a given time. The first value provides a measure of how often my work was recognized by my colleagues but the second one tells me how many people in general found it interesting enough to download it. For example in less than half a year my blog has been accessed by more people than all my papers have been cited altogether in the last 10 years. None of these metrics provides any indication of the quality of my research. Like it or not if you want to know how good my work really is you have to read my publications.

What it comes down to is what we want for our little precious study. Is it more important to present it to as many people as possible, researchers and non-researchers alike or will we continue to try to place it in one of the big ones with ridiculously high rejection and subscription rates, or do we want to have it bedded comfortably in a more specialized journal read by a handful of like minded colleagues?

I made my decision in favor of accessibility because I think it will work for me and not damaging my career (and I am not tenured or even tenure track!). I am convinced that the world of science will eventually change to open access and it is about time to join the crowd.

Here you find Part 2 of the series.

#PDFTribute

You might have heard of the tragic death of Aaron Swartz a software developer and internet activist. Swartz co-authored the first RSS specifications at the age of 14 and was co-owner of Reddit. Later he also focused on sociology, civic awareness and activism and was a strong advocate for open access in general. He committed suicide at the age of 26 and was found dead in his apartment last Friday.

In July 2011, Swartz was indicted on federal charges of gaining illegal access to JSTOR, a subscription-only service for distributing scientific and literary journals, and downloading 4.8 million articles and documents, nearly the entire library. The pending charges were potential penalties of up to 35 years in prison and $1 million in fines and many believe that these and the pressure build up by prosecutorial overreach is what eventually killed him.

Apparently he had struggled with depression for a while already. Depression is a very serious and unfortunately underestimated problem. It is not "just a phase" that people go through. It won't go away without proper treatment and can lead to a number of other serious problems if it is not dealt with properly.

Although I don't believe in any conspiracy theories out there and I find it exaggerating to make others responsible for someones suicidal death, I can fully understand that a person with chronic depression facing disproportional charges for something meant positive doesn't see any other way out of this dilemma. That is the tragic in this story which eventually took the life of a bright mind that had already accomplished so much for the cause of open access in all its forms.

As a reaction to Aaron Swartz's death supporters responded with an effort called #pdftribute to promote open access. In a tribute to him, researchers have begun posting pdf's to Twitter to honor his campaign for open access. 

I have long pondered if I should join them and post my pdf's elsewhere but I think many are already public as I tried to publish and review as much as possible open access for years. There is also the growing ResearchGate which is home to quite a few pdf's but in all honesty this won't get us anywhere but to serve as a tribute. What we need is a change of publishing attitude. Researchers should exclusively publish open access. Jonathan Eisen has assembled a great list of things we can to do to really support open access on his Tree of life blog. I intend to change my habits accordingly and consequently publish and review only in real open access journals from now on - or simply here in my blog.

However such paradigm shifts also require a change in attitude if it comes to valuing a scientists work. Search committees and funding agencies have to stop looking for high impact factor publications but more for open access contributions. After all it is mostly tax payers money that pays us. We owe it to them to make our research accessible instead of wasting some of it to pay for insanely high subscription fees. We just need to start with it. #pdftribute could serve as a good starting point for such a movement but it is sad to realize that again it needed such a tragedy to get the ball rolling.

PeerJ

When I recently did my little number crunching exercise I was also looking at the percentage of DNA Barcoding papers that have been published in open access journals. Among the major ones was of course PLoSONE but there were also a few others that have papers available without subscription fees. However, it only amounts to a total of 12% of the publications that are available to everyone. In turn that means that about 88% of all DNA Barcoding papers are not available to every researcher on the planet. I find that very frustrating as I thought that especially in this new field there is more inclusiveness!

In 2006 Marguerite Holloway published an article in Conservation in Practice in which she tried to capture the innovative thinking behind the at that time very new method called DNA Barcoding. The title was "Democratizing Taxonomy" referring to Dan Janzen and Winnie Hallwachs who believe passionately that greater access to knowledge and technology will transform the future of conservation. I've heard this term from Dan in various of his talks and I am always reminded of it when it comes to publishing as researchers do not live in a free publishing world. This is especially true for all of us in early phases of our careers where an insufficient measure (impact factor) is dictating where to publish. The result is that many researchers, maybe even the majority, have no access to a lot of what we've published over the last 10 years just because they or their institution can't afford the often ridiculously high subscription fees. That's a shame!

The more happy I am to announce the birth of a new journal with a new business model of open access publishing. PeerJ is a new multidisciplinary open access journal that announced today the first formal call for papers. Unique among academic publishers, PeerJ provides authors with low cost lifetime memberships giving them the rights to publish their papers freely thereafter. A basic membership plan is only $99 that would give an author the right to publish once a year for the rest of their life. That seems reasonable and compared to some of the usual fees of other open access journals it is very cheap. Access to the articles is of course free!

Open access publishing

I am a great supporter of open access publishing in science. It's great to see that more and more DNA Barcoding papers are published in open access journals, and I try to support this as much as possible e.g. by being an editor in PLoS ONE and encouraging colleagues and students to use such journals in favor of the traditional ones.

Yesterday, one of my favorite sites for fun and humor related to work  - PHD Comics released an animated cartoon explaining everything around open access publishing and why one would do it. The cartoon is build around phone interviews with two prominent advocates for open access publishing - Nick Shockey and Jonathan Eisen. 

I think it is a little masterpiece worth leaving your work aside for 8 1/2 minutes.