13 OPEN PUBLISHING TOOLS TO BOOKMARK NOW

This is part 2 of the 3-part blog series on open science tools. Please click here to read part 1 on 9 Open Science tools that help you with your literature search or here to read part 3 on 6 Open Science tools for analysing your research field.

Open publishing can be hard to navigate. There are a lot of options and the definitions vary widely. Beyond publishing of open-access papers, Open Science strives to make the whole research process transparent, for example by publishing data sets and protocols on their own. 

But how can you identify quality open access journals, find the right repository for your data or preprint, and understand your funder’s requirements for Open Science?  

That’s exactly what we’ll cover in this blog post! I’m introducing you to
13 (!) open publishing tools that you shouldn’t miss. Let’s go:

Publishing in an Open Access journal 

Unfortunately, the rise of open access publishing has encouraged predatory journals to sprawl out. This means that the quality of open access journals varies, and so do their terms of use. Some charge so-called Article Processing Charges, essentially publishing fees, others let authors publish for free. 

I recommend this database to find the right destination for your publication:

Directory of Open Access Journals (DOAJ)

First launched in 2013 at Lund University in Sweden, the DOAJ is an independent database of peer-reviewed open access journals across disciplines that is curated by its community. You can enter keywords or browse subjects to find a suitable open access journal. DOAJ specifies Article Processing Charges and editorial information on peer review, aims & scope and average time between submission and publication. 

Publishing a preprint 

Preprint repositories store preprints, which are openly accessible manuscripts that aren’t peer-reviewed or edited but pre-screened. There exist both multidisciplinary preprint servers and those that focus on a particular research discipline. 

I’ve selected a handful of preprint servers below. For a curated database of Open Access Repositories, please visit OpenDOAR. It’s operated by the UK-based not-for-profit organisation JISC. An extensive list of preprint servers can also be found on Wikipedia. 

>> WATCH NOW <<

arXiv

Launched in 1991, arXiv is the oldest preprint repository and probably doesn’t require much explanation. ArXiv is operated by Cornell University and houses manuscripts in the fields of mathematics, physics, computer science, economics, electrical engineering, quantitative biology and related subjects. 

ChemRxiv 

Compared to physics and mathematics, the preprint tradition in chemistry is young. The preprint server ChemRxiv that accepts papers in catalysis, agricultural chemistry, nanoscience, chemical education and other fields was born only recently, in 2017. ChemRxiv is co-owned and co-operated by chemical societies around the world, the American, German, Chinese, and Japanese Chemical Societies and the Royal Society of Chemistry in the UK. A tempting feature of ChemRxiv is the direct journal transfer feature. This means that you can forward your preprint for submission to certain journals with just a few clicks -- which should save time and patience that is all too often needed for using the submission portals of journals!

bioRxiv and medRxiv

BioRxiv and medRxiv are preprint servers for life science and health science manuscripts, respectively. Both repositories are operated by the not-for-profit Cold Spring Harbor Laboratory and also allow for direct transfer to a large number of journals. 

SSRN 

SSRN is a collection of more than 50 preprint repositories called research networks (RN) across disciplines. For example, you’ll find repositories for architecture (ArchRN), biochemistry (BiochemRN), cognitive science (CSN), ecology (EcoRN), financial planning (FinPlanRN) and nursing (NursingRN). Not exactly famous for their dedication to Open Science, SSRN is run by the publisher Elsevier.

Authorea 

Authorea is a collaborative writing tool that I have introduced you to earlier. You can publicly post your manuscript on the server which can be displayed with interactive figures and hosted data. Authorea is owned by the academic publishing house Wiley.

Publishing protocols, data sets and other research material 

Not only papers are research outputs. You likely produce a lot more material that may be valuable to the scientific community. Some funders and publications also require researchers to store data sets and codes. This is where open access repositories for various research outputs come into play. 

I handpicked a few popular repositories that I think are worth being aware of. If you would like to dive deeper, re3data.org, funded by the German Research Foundation (DFG), provides an extensive database of data repositories in all fields.

protocols.io

All too often, tweaks and details of scientific methods are hard to locate in journal papers or aren’t reported at all. Protocols.io allows you to publish and update any methodological information – be it a protocol for a chemical synthesis, descriptions of a clinical trial or a computational workflow. Once published, you receive a DOI that you can link to the corresponding paper. You can also run your protocols as checklists while performing the research.

Protocols.io is operated by a company. While creating and publishing of protocols as an individual researcher is free (and will remain so according to the company), they charge companies and institutions for licenses. 

Figshare 

On figshare, researchers can share posters, presentations, datasets, videos, code and other research outputs in any file format. Users have 20 GB of free private space, which you can, for example, use to collaborate on a project with your peers. The space for public files is unlimited. As protocols.io, figshare provides a DOI for all published files. The platform is owned by the company Digital Science who provides a number of Open Science tools.

Zenodo

A non-commercial alternative to figshare is Zenodo, which was developed within the EU-funded OpenAire program. Zenodo is an open-access repository for all research material such as data, software, reports and papers. It is hosted and operated by the particle physics research facility CERN but welcomes uploads from any field of research. Uploaded material receives a citeable DOI.

Dryad

Dryad is a non-profit repository for research data sets in any field that correspond to findings published in a paper. You can upload your data in any file format and receive a DOI. Before publication, a team of curators makes sure the uploaded data is useable. Initial funding for Dryad came out of the pockets of the US National Science Foundation, now users are charged when their submissions are accepted.

GitHub

If coding is part of your work, you’ll likely be familiar with GitHub, a platform to host and collaboratively develop software – both privately and publicly. Founded as a startup in 2008, GitHub was acquired by Microsoft in 2018. As of November 2020, the free plan includes 500MB of private and unlimited public storage.

Comparing Open Science policies 

Journals and funding agencies usually have specific policies when it comes to Open Science. But such policies can be time-consuming to find. Here are two services that’ll make your life easier: 

Transpose

Whenever you are considering uploading your manuscript as a preprint, or having a member of your lab help you peer-reviewing a paper, you are probably asking yourself: Is this allowed? Journals’ policies aren’t always easy to find and it’s even harder to compare policies between journals. 

The Transpose database solves this problem: Thanks to crowdsourcing, Transpose lets you search journal policies on open peer review, co-reviewing and preprint policies. This tool draws attention to the fact of just how much journal policies vary and how vague some of them are on the topics of preprints, open peer-review and co-reviewing. 

Sherpa services

The not-for-profit organisation Jisc offers three services that enable authors and institutions to check open access compliance. 

The tool Sherpa Romeo aggregates and analyses the open access policies of journals – similar to the Transpose database described above. Sherpa Juliet lets you search the current policies of funding bodies regarding their requirements on open access publishing and data archiving. Sherpa Fact combines the functionality of Romeo and Juliet and lets you check whether a certain journal complies with the open access policies of your funder.

There you have it: 13 open publishing tools to bookmark now! If you have tried one of the tools, please tell us about your experiences in a comment below. 

And if you can’t get enough when it comes to discovering new tools (yes, I’m a tool-junkie too…), check out these 9 Open Science tools for your literature search or these 19 free tools for scientists. 

>> WATCH NOW <<

ABOUT THE AUTHOR

I’m Dr Anna Clemens, a scientific writing coach and editor. I help scientists to write better papers in less time. I’d love to support you beyond the blog, please click here for more information.

When I’m not at my desk, I’m probably hiking with my dog/assistant Zuza or sipping an oat flat white in one of Prague’s many cosy cafés.

I’d love to connect with you on Twitter (@scientistswrite) and LinkedIn.