Why I chose figshare for my homeless manuscript

I’m sure all scientists have one – a folder with unfinished manuscripts, or ones that were finished but never found homes. In my case, the folder has manuscripts as old as 6 years and as recent as a few months. But there was one manuscript in particular that I just couldn’t let go. It was work from my dissertation, which is probably one of the reasons I felt so attached to it. I’d invested many hours (some of them while pregnant and far too big to be sitting at an electrophysiology rig) gathering those recordings. In my completely biased opinion, they were beautiful, interesting, and deserved to do more than sit buried in a 300+ page dissertation that few people would ever read.

The problem is there are gaps in the work. We were unable to fully characterize one of the genetic manipulations we were using, leaving doubts about the precise effects on the cells in which it was expressed. There are also a lot of open questions. Some of the results were unexpected and the underlying mechanisms merited further exploration. Additional experiments could have ruled out certain possibilities. But then life happened. I had a baby, graduated, moved away. I wrote up what I had, but with the obvious gaps, the manuscript seemed unpublishable in mainstream journals. I knew what reviewers were going to say and I had no satisfying answers to give them. I no longer had access to the equipment required to do experiments, so collecting more data was out of the question. The manuscript sat in my folder collecting digital dust. For the next two years, I would occasionally read over it again and I always arrived at the same two conclusions: (1) that it included interesting data that deserved to be seen, and (2) that it would not pass peer review in a mainstream journal. So, it was either archive it, or find a non-conventional way to get the work out.

This last week, inspired in part by a recent post by Zen Faulkes @DoctorZen explaining why he published a paper on his blog, I decided that I had to put the work out in some form or another. I considered publishing it on my blog, but since my blog is not well-established, I felt I needed something more visible. I began to debate the pros and cons of posting my manuscript on either arXiv or figshare, and opened it up for discussion on Twitter. Thanks to Bala Iyengar @balapagos, P Desjardins-Proulx @phdpqc, and @figshare who contributed to the discussion and provided information that helped me make my decision. In the end, I’ve decided to go with figshare. Here are just some of the reasons why:

Figshare accepts all file formats. In answer to my query about whether figshare accepts tex files in particular, @figshare tweeted:

figshare_1

 

 

 

I responded that I think this flexibility and utility gives figshare an advantage over competitors like arXiv, which are more restrictive in the file types they accept. According to their website, arXiv accepts only LaTeX, PDF, Postscript, or HTML for text submissions, and only PS/EPS, JPEG, GIF, PNG, or PDF (if using LaTeX) for figures. Now, I’m a LaTeX gal. I prepare almost all my documents, presentations, and posters in LaTeX. So, I have no problem submitting in one of the file formats specified. In addition, @phdpqc tweeted:

phdpqc_1

 

 

 

I couldn’t agree more on the need to be saved from MS Word, and it is definitely a plus that arXiv provides LaTeX source code. But figshare loses no points here. As already mentioned, they accept tex files, too. I also like the fact that no matter what format I may have for supplementary materials, be it figures in another format, videos, spreadsheets, code, etc., figshare will take it. In addition, figshare allows you to upload all of your research outputs, even if they don’t come as part of a full-fledged manuscript. In contrast, arXiv only accepts materials that are linked to a manuscript submission.

Materials are available on figshare immediately after upload. I think this is what @balapagos had in mind when tweeting:

balapagos_1

 

 

 

In contrast, submissions have to go through moderation on arXiv before they are posted. I had the impression from arXiv’s site that this process might take some time, but @phdpqc commented:

phdpqc_2

 

 

 

Ok, 48 hours. Not so bad. Still, having been on the other side of the lab bench, spinning your wheels for any number of days because you didn’t know the experiment had already been done (or failed) can be frustrating. And even if I didn’t mind the delay, there’s something else about arXiv’s moderation that bothers me. On their site it says, “The arXiv moderators are experts in their fields and in the types of submissions that are appropriate for their subject classifications. They evaluate based on the content of the submission. arXiv moderators may recommend reclassification or removal of a submission”. At the risk of sounding less than humble here, I am an expert in my research and I think I know best how it should be classified. On figshare, there is no moderation process that reclassifies or removes my research materials (unless, of course, they contain something completely inappropriate). I decide what to upload, what categories to place it in, and what tags to put on my submission.

Figshare gives my research a Digital Object Identifier (DOI). This has a number of advantages, including making the work easily citable. arXiv allows you to add a DOI if your article is published elsewhere and given one, but does not automatically give one to your submission. In addition, as mentioned above, arXiv only allows submission of manuscripts, which means ‘orphan’ research outputs such as figures not part of a manuscript, posters, grant applications, etc. cannot get any type of citable link on arXiv. On figshare, all materials receive their own DOI, making them citable units in their own right.

Figshare does not require me to be endorsed to submit. For me, this was the real kicker. arXiv has a system by which authors submitting for the first time, and particularly those who do not have a university affiliation, must be endorsed by another arXiv user before they can submit. The argument is, “endorsement…will verify that arXiv contributors belong [to] the scientific community”. Since I don’t currently have a university affiliation and this would be my first time submitting to arXiv, I would be required to find an endorser. I have friends and colleagues who submit to arXiv and could endorse me. But that’s not the point. First, this process would be yet another delay, in addition to moderation, in the dissemination of my research. True, the delay would likely be negligible, but it is still a delay. Second, I object to this endorsement system on conceptual grounds. Just because I do not have a current university affiliation,  does that make me less a part of the scientific community? In the current job market, there are many ‘floating academics’ like myself who do not have an affiliation. In the computational sciences, there are also many researchers who work as programmers in companies and do research in their own time. Is there research less trustable because they don’t work at a university? Furthermore, the growing rate of high-profile retractions shows that simply belonging to the scientific community in the form of a university affiliation is no guarantee that the research is of good quality. arXiv says, “people who fail to get endorsement are still free to post articles on their web site or to submit their publications to peer-reviewed journals”. Or, they can post them to figshare without worrying about an endorsement from another scientist.

Don’t get me wrong, I like arXiv. Any site where people can post their science and people can read it for free is a good thing. But I’ve decided that the better home for my manuscript is figshare. All that remains is to do some final editing before I upload it. In the end, what am I hoping to get out of this? I know that it is unlikely I will get many citations. I’m also under no illusions that this manuscript will help me get that tenure track position I’ve been searching for. Unfortunately, most search committees will not consider this a ‘real’ publication. In fact, there are many who would say I am wasting my time preparing this manuscript (or even writing this post) when I could be working on papers that have a chance of getting published in peer-reviewed journals. Maybe they’re right. But this is important to me. I believe strongly in open science and that research, no matter the gaps or open questions it leaves, does people more good when it gets seen. Ultimately, people will have to evaluate for themselves what contribution, if any, my manuscript makes. I am hoping at the very least that it gives others ideas that they can build on in their own research. And if nothing else, it will be one more manuscript I can move out of the homeless folder.

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19 Comments

  1. This almost sounds like a return to the original days of scientific publication when Liebniz and Kepler and the like would send letters out to their circle of friends. This had the double effect of establishing primacy, and of inviting comment from peers. One might call it something like, Oh I don’t know, peer review. It can only be a healthy development.

    1. I think this relates to what Tim Gowers calls the “unit of discourse” (see this great video sent to me by @balapagos http://youtu.be/YrhVH3jU6nY). When scientists such as Leibniz and Clarke were corresponding, the unit of discourse was usually longer than a face-to-face conversation but shorter than a full-fledged manuscript or book. They also tended to write as the ideas were evolving, with the result that more of the scientific process was visible. Tim Gowers and others argue that in blogging science something similar happens, where the unit of discourse is somewhere between conversation and journal article. People can articulate their ideas in real time and respond to others in real time. I am hoping that such a discussion will ensue after I post my manuscript, which is another reason for getting it out there. Peers can only review my work if they can read it!

    1. Thanks! I’ll keep you posted. I’m also following with interest the responses to you posting your paper on your blog. I’m curious, have the responses been what you expected, or have there been any surprises (pleasant or otherwise)?

      1. Time for an update. In the couple of months since I’ve done this, there was more interest in that I tried publishing a paper on my blog than I ever anticipated. And most of the reaction to my explanation of why I did this was positive.

        1. Thanks for the update! I’m very encouraged to hear you’ve had such positive feedback. I hope this indicates a more general shift in thinking about what constitutes a valuable research output.

  2. Great post! It’s true that figshare has many advantages over arXIv, including the tag system, being able to upload anything, no need for endorsers (I’m an endorser for arXiv’s q-bio.PE section), and it is arguably in a better position to evolve than arXiv. The biggest practical advantage of arXiv is that, since it’s devoted exclusively to manuscripts, it can easily be tracked by services such as Google Scholar. That being said, perhaps the solution is for such services to track more content than just articles.

    ohh, I made the word “soul” appears on a neurophysiologist’s website 😛

    1. Thanks! I agree that figshare is in a better position to evolve than arXiv, and I think the key here is that it *wants* to evolve. As @figshare told me on Twitter (using that very word!), “we’re really trying to evolve based on feedback of academics.”. As I said, I like arXiv, but I don’t get the impression from their site that they are looking to evolve much. They seem to be happy with the setup they have, and for many academics their setup works very well. But I think arXiv would be even better if it allowed for more flexibility and more features. As for article tracking, it may be easier for Google Scholar to track articles from sites that only include this type of research output. But I did a quick search using titles of articles I found on figshare, and they do come up on Google Scholar. So, it seems to have no problem tracking them. As to your last point, I think it would be great if these services tracked more than just articles. It really is time more people started recognizing that scientific contributions come in more forms than just journal articles. Fortunately, figshare does recognize that and I’m hoping that others will soon follow suit.

  3. Interesting stuff. I recently found myself in a very similar position with a manuscript that had started life as a chapter of my dissertation, and ended up posting it on arXiv.

    I agree that FigShare is an excellent option, but for the record the main reason I went the other way is track-record: arXiv has been around, doing a superb and reliable job, for more than twenty years, and that makes me confident that it will still be around, in essentially it’s current form, in another twenty. Now it’s quite possible that FigShare will also be with us in 20 years, and that in that time it will have evolved into something much better than arXiv; but it still has that to prove.

    Regarding the delays at arXiv: my paper had already been in limbo for three years (since my dissertation was successfully viva’d), so an additional four or five days didn’t feel like a problem. The checks that arXiv imposes — requiring an endorser, scanning the submission — are very lightweight, and intended only to ensure that what gets deposited is a scientific paper. It’s nice that arXiv doesn’t feel the need to do this yet; perhaps when it’s a big and recognised as arXiv, that will have to change.

    Finally, on reclassification: my arXiv paper was reclassified by q-bio.OT (Other Quantitative Biology) to q-bio.TO (Tissues and Organs) with a cross-list to q-bio.PE (Populations and Evolution). I’m in favour of that. I went with “Other” just because I wasn’t familiar with how arXiv interprets its biology classifications, and it’s to my advantage that someone who is familiar with their classification put my work where it better fits.

    So all in all, I am really happy with how my choice of arXiv is working out. I hope you’ll be equally happy with FigShare (which I may well use for other projects in the future, especially for sets of specimen photos).

    1. Thanks for your comment! I’ve heard from several people arguing in favor of figshare, so it’s great to finally hear someone make the case for arXiv. I’m encouraged to hear that your experience with arXiv was a positive one and that the checks they require weren’t a limiting factor in getting your work out there. It will be interesting to see how figshare deals with the issue of filtering as submission volume increases (which I’m sure it will). I’m sure it will be a challenge, but I certainly hope they keep their current submission policies.

      It’s true that, at present, arXiv wins hands down as far as track-record, and I can certainly understand choosing a preprint server that has proven itself. But I think there in lies a dilemma for researchers. We want to put our work in reliable places that we’re confident are going to stick around. But great startups need our support, too. I realize some researchers may think it too risky, but we can use our submissions as votes of confidence that the new venture is going to successful. And the more researchers who take that risk and submit, the more likely it *will* be successful. I really think figshare has developed something great that has the potential to be around for a long time.

      But in the end, the most important thing is not where people post their preprints or author versions, but just that they post them somewhere where people can read them for free and build on the work. For that reason, I really liked your recent post encouraging all scientists to put their work on preprint servers. And congratulations on your arXiv article (great title, by the way!). I’m glad you found a good home for your manuscript.

      1. “In the end, the most important thing is not where people post their preprints or author versions, but just that they post them somewhere where people can read them for free and build on the work.”

        Amen!

    1. That’s great! It seems to me that figshare is gaining popularity with academics. Soon, hopefully the scientific community at large will stop considering these research outputs as “trash bin” material, and see them as the valuable contributions they are.

  4. Hi, I am always wondering what the PIs are saying to this self-publishing pratice. I know from my PhD time there were many, who felt the work of students was their own and would protect it. Sometimes they even FORBIT publishing for miscellaneous reasons. What is your experience with this? Klara

    1. Thanks for your comment, Klara. It is unfortunate (and wrong, in my opinion) that many PIs do view students’ work as belonging to them and seek to control how it is disseminated. I think it is very important that students know their rights, which is why I recently wrote a series of posts on this subject. You can access them here, here, and here. I have seen PIs attempt to forbid their students from publishing, especially self-publishing, saying things like, “the value of online, non-reviewed, publication remains unclear in the view of many scientists”. Many are still reluctant to move away from the traditional publishing model, despite its many flaws. The way I see it, research is always more valuable when it is out in the open, and there is a growing movement towards open science. I hope that sooner rather than later we’ll see the majority of scientists coming around to this view.

  5. 一声巨响响起,陈力纹丝不动。体内却被反震力绞了个天翻地覆。虚幻的手掌凹陷都没有产生,仿佛刚刚的一切只是幻觉,它依然在前进,直接抓住了被震成重伤的陈力。
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