Document your software updates with F1000Research

Posted by Varsha Khodiyar, 22 July 2013

Releasing information in incremental steps is nothing new to software developers, who release updates and patches that add new functionality to existing programmes.  The launch of a new bioinformatics tool is often accompanied by a paper describing the tool for new users.   However, the paper describing the tool will be out of date as soon as a new software update is released but the changes are often not significant enough to warrant a whole new paper.

F1000Research’s system of updating and threading papers makes it easy to include updates about new software releases. To encourage bioinformatics tool developers to try this new way of publishing, we are inviting the submission of software and web tool papers free of charge to F1000Research.  If you have a paper to publish describing your bioinformatics software, you can use the code SOFT13 to submit free of charge before 2014.  So how about providing a threaded publication for your users, which will allow you to update the paper as you improve your software?

Why publish with us?

Some benefits of publishing your software paper with F1000Research:

  • Maximises time spent by developers on developing the software, by reducing the time spent on the equally important (but time consuming) job of disseminating documentation on how to use the tool.
  • Benefits tool users as they only need to read a single paper to gain a full overview of how to use your tool, which will include any recent updates.
  • Provides public documentation of software updates which demonstrates to users that your tool is being maintained and improved.
  • Demonstrates to funding bodies that you are actively disseminating updates to your users.
  • The altmetrics that F1000Research provides for all papers can provide additional evidence to funding bodies that your tool is being used by the research community. As we noticed when reading papers, authors often neglect to cite papers relating to bioinformatics software that they have used.
  • We are providing free submissions for software and web tool papers until the end of the year, including subsequent updates to those papers!


A supporter of this initiative is one of our Advisory Panel members, Alex Bateman of the European Bioinformatics Institute, Hinxton, UK who mentions:

“A real problem for computational biologists is getting updates of their software packages published in journals. Editors and reviewers rarely think that version 2.0 of your software is novel enough to consider another publication. F1000Research‘s innovative approach to allowing authors to publish updated versions of their papers creates a unique opportunity for Bioinformaticians to keep their manuscript up to date with new versions of their software.”

We will be discussing the issues surrounding the peer review of software and web tools in a future post.  In the meantime, developers please post your thoughts below or on twitter  (#SOFT13) and let us know what you think of this new feature to enable article updates to mirror your software/tool updates.

(Laptop image adapted from an image by John Baer)

F1000Research is an original open science publishing platform for life scientists that offers immediate open access publication, transparent post-publication peer review by invited referees, and full data deposition and sharing. F1000Research accepts all scientifically sound articles, including single findings, case reports, protocols, replications, null/negative results, and more traditional articles.

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