Software Tools – F1000 Research

What is a software tool article?

It’s an article  describing a novel software tool which has been developed for research, for example an algorithm, code, container, docker, web-app or workflow. Software tool articles explain the rationale for the tool’s development, details of the code used to build it, examples of suitable input data sets, and examples of the outputs from the tool (and how to interpret these).

What if I didn’t create the original software?

That’s fine! We also welcome articles which describe tools created from existing software, web tools, apps, containers, packages, and workflows.

How do I write a software tool article?

See our Instructions for Authors for specific guidance on what to include in your article.

How much does it cost to publish a Software Tool Article on F1000Research?

F1000Research charges an Article Processing Charge (APC) for all articles. You can find out more about these costs here.

Why are software tools a separate article type from traditional research articles?

F1000Research publish a range of article types, allowing researchers credit for all their different research outputs. Software tools are often included as a footnote, or part of the methods section of a traditional research article, so offering software tools as a separate article type allows the software engineer to get sufficient credit for their work. It also provides space to describe the software tool fully (with no word limits) and increases the discoverability of the software itself. Software tool articles can be cited in the methods section of ‘traditional’ research articles.

Do I need to make the source code open if I’m publishing on F1000Research?

Yes. We require a software availability section to be completed in the manuscript. GitHub links are accepted however we also require a permanent archived version, stored somewhere like Zenodo. You can find out more about how software fits into our Open Data Policy in our brand new resource hub, Understanding Open Data.

Do you publish tools that use proprietary software?

Software used as part of an article must be open access or an open access alternative must be provided. Additionally, code used or created must be compatible with an open-source programming language or an open alternative provided. If the article does not meet this criteria, it may be rejected at the discretion of the F1000Research editorial team.

Do you accept tex files?

Unfortunately not, however you can submit via our Overleaf template. We will do any pre-publication check edits in Overleaf and return to you where you can address any changes there.

Do you support Jupyter notebooks?

Unfortunately we do not currently support Jupyter notebooks, however we can host these through an iFrame.

I have a question which isn’t answered here – how do I get in touch?

Drop us an email on [email protected] and someone will get back to you. There’s also an FAQ page on our website which might answer your question.