Which preprint server should I use?

Preprints are rapidly becoming popular in biology as a way to speed up the process of science, get feedback on manuscripts prior to publication, and establish precedence (Desjardins-Proulx et al. 2013). Since biologists are still learning about preprints I regularly get asked which of the available preprint servers to use. Here's the long-form version of my response.

The good news is that you can't go wrong right now. The posting of a preprint and telling people about it is far more important than the particular preprint server you choose. All of the major preprint servers are good choices.Of course you still need to pick one and the best way to do that is to think about the differences between available options. Here's my take on four of the major preprint servers: arXiv, bioRxiv, PeerJ, and figshare.

arXiv

arXiv is the oldest of the science preprint servers. As a result it is the most well established, it is well respected, more people have heard of it than any of the other preprint servers, and there is no risk of it disappearing any time soon. The downside to having been around for a long time is that arXiv is currently missing some features that are increasingly valued on the modern web. In particular there is currently no ability to comment on preprints (though they are working on this) and there are no altmetrics (things like download counts that can indicate how popular a preprint is). The other thing to consider is that arXiv's focus is on the quantitative sciences, which can be both a pro and a con. If you do math, physics, computer science, etc., this is the preprint server for you. If you do biology it depends on the kind of research you do. If your work is quantitative then your research may be seen by folks outside of your discipline working on related quantitative problems. If your work isn't particularly quantitative it won't fit in as well. arXiv allows an array of licenses that can either allow or restrict reuse. In my experience it can take about a week for a preprint to go up on arXiv and the submission process is probably the most difficult of the available options (but it's still far easier than submitting a paper to a journal).

bioRxiv

bioRxiv is the new kid on the block having launched less than a year ago. It has both commenting and altmetrics, but whether it will become as established as arXiv and stick around for a long time remains to be seen. It is explicitly biology focused and accepts research of any kind in the biological sciences. If you're a biologist, this means that you're less likely to reach people outside of biology, but it may be more likely that biology folks come across your work. bioRxiv allows an array of licenses that can either allow or restrict reuse. However, they explicitly override the less open licenses for text mining purposes, so all preprints there can be text-mined. In my experience it can take about a week for a preprint to go up on bioRxiv.

PeerJ Preprints

PeerJ Preprints is another new preprint server that is focused on biology and accepts research from across the biological sciences. Like bioRxiv it has commenting and altmetrics. It is the fastest of the preprint servers, with less than 24 hours from submission to posting in my experience. PeerJ has a strong commitment to open access, so all of it's preprints are licensed with the Creative Commons Attribution License. PeerJ also publishes an open access journal, but you can post preprints to PeerJ Preprints with out submitting them to the journal (and this is very common). If you do decide to submit your manuscript to the PeerJ journal after posting it as a preprint you can do this with a single click and, should it be published, the preprint will be linked to the paper. PeerJ has the most modern infrastructure of any of the preprint servers, which makes for really pleasant submission, reading, and commenting experiences. You can also earn PeerJ reputation points for posting preprints and engaging in discussions about them. PeerJ is the only major preprint server run by a for-profit company. This is only an issue if you plan to submit your paper to a journal that only allows the posting of non-commercial preprints. I only know of only one journal with this restriction, but it is American Naturalist which can be an important journal in some areas of biology.

Figshare

figshare is a place to put any kind of research output including data, figures, slides, and preprints. The benefit of this general approach to archiving research outputs is that you can use figshare to store all kinds of research outputs in the same place. The downside is that because it doesn't focus on preprints people may be less likely to find your manuscript among all of the other research objects. One of the things I like about this broad approach to archiving anything is that I feel comfortable posting that isn't really manuscripts. For example, I post grant proposals there. figshare accepts research from any branch of science and has commenting and altmetrics. There is no delay from submission to posting. Like PeerJ, figshare is a for-profit company and any document posted there will be licensed with the Creative Commons Attribution License.

Those are my thoughts. I have preprints on all three preprint servers + figshare and I've been happy with all three experiences. As I said at the beginning, the most important thing is to help speed up the scientific process by posting your work as preprints. Everything else is just details.

UPDATE: It looks like due to a hiccup with scheduling this post than an early version went out to some folks without the figshare section.

UPDATE: In the comments Richard Sever notes that bioRxiv's preprints are typically posted within 48 hours of submission and that their interpretation of the text mining clause is that this is covered by fair use. See our discussion in the comments for more details.