Publish your Software Tool article with Gates Open Research

Rapid, open publication to help you get the credit you deserve

Algorithms, code, and software tools are crucial to the discovery process in every field of research, from bioinformatics to digital humanities. At Gates Open Research, we believe that the researchers and software engineers who develop these tools should receive full credit for their work. We also believe that this work should be recognized as part of their research productivity and rewarded as much as traditional research papersThis is where publishing your software tool article comes in.

Software tool articles on Gates Open Research allow you to describe new software you have created to support or conduct research in any field. These articles explore: 

  • Why you developed the software 
  • Details of the code, method, and analysis used 
  • Examples of data input sets 
  • Examples of outputs, and how to interpret these 
  • Tips on how to maximize the tool’s potential 

We also welcome articles describing tools created from existing software, web tools, apps, containers, packages, and workflows

Want to know more? This post on the F1000Research blog is packed with more information about software tools articles

Instructions for authors

Ready to submit your Software Tool article? Take a look at our article guidelines to ensure you've prepared your article correctly.
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About Gates Open Research

Gates Open Research is a fully open access publishing platform, offering rapid publication of articles and other research outputs without editorial bias. All articles benefit from transparent post-publication peer review, and editorial guidance on making source data openly available.

Gates Open Research advocates for transparency and reproducibility in research, and our unique publishing model supports this at every stage. Articles are published rapidly, with post-publication peer review creating an open dialogue between authors and their research community. This generates feedback which can be used to improve the article and develop the author's skills.

Our data and software sharing policy is designed to ensure that research is reproducible. For software tool articles this means the tools themselves should be openly accessible and clearly linked to any appropriate data and results.

Submit now  How it works

Why publish your software tool article on Gates Open Research?

Full credit

Receive full credit and recognition for your work by publishing your software tool article as a separate citable item. 

Interactive figures

Bring your data to life with interactive figures in the body of your article, powered by or via an iFrameInteractive figures can help tell the story of your research by allowing readers to play with different visualizations, zoom in, filter results, and explore the data in detail for themselves.  

Code Ocean 

Embed Code Ocean capsules for in-article code integration and reanalysis. Code Ocean makes it quick and easy for others to re-run your analysis, and even edit your code to see how results differ by changing parameters. Code Ocean supports the reproducibility of science without users needing to install anything on their computer – it all happens within the article. Find out more about Code Ocean capsules in this helpful blog post from F1000Research.

Code syntax highlighting 

Benefit from proper support for code syntax highlighting, so that your code is fully readable in the body of your article. 


Increase the visibility, reach and impact of your research and software through indexing in Scopus and PubMed 


Keep your software tool article up to date by easily publishing new versions whenever you need to share the latest developments in your work. Versions are all individually citable and clearly linked, making it easy for readers to navigate and cite the version they want. 

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Infographic of benefits of publishing a software tool article on F1000Research

Software Tools | Frequently Asked Questions

Got a question about publishing your software tool article on Gates Open Research? We've got you covered.

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.

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

Gates Open Research 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 Gates Open Research?

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.

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 Gates OPen Research 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 and someone will get back to you. There's also an FAQ page on our website which might answer your question. 



Relevant blog posts from F1000Research:

Making reproducibility easier with Code Ocean

Code Ocean makes re-running analyses much (much) easier. Find out more about how to use Code Ocean widget in your article.
Read now

Shining a spotlight on research software

Vicky Hellon introduces the call for papers, and explores the benefits for researchers who publish a software tool article on F1000Research.
Read now

Developing new biomedical software?

This post runs through the key points to consider when it comes to software development, from documentation to licensing.
Read now

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