A publication model that aligns with the key open source software principles Michael L. Markiea, Varsha K. Khodiyara, Rebecca N. Lawrencea

a F1000Research, Faculty of 1000, Middlesex House, 34–42 Cleveland St, London W1T 4LB, UK

F1000Research.com | research@f1000.com | @f1000research | facebook.com/F1000Research

INTRODUCTION

Open source software in the life sciences is often published in scientific journals to share it with relevant users, as well as to gain formal academic credit for the work. However, traditional ‘static’ journals are restricted in how they can disseminate software articles, and currently publishing a permanent formal record of a piece of software is like trying to fit a square peg in a round hole.

Here, we describe F1000Research’s open science publication model which better reflects and supports the requirements of open source software and provides clear benefits for both software developers and scientific researchers.

ARTICLE COLLECTIONS

Open source software projects are made up of several components, tools and applications. F1000Research has recently worked with two such flourishing projects: BioJS (www.ebi.ac.uk/Tools/biojs/registry) and Cytoscape Apps (apps.cytoscape.org) to create dedicated article collections for each project.

F1000Research article collections collate all the project articles onto a single personalised, searchable landing page, which allows the collection as a whole to be cited. Each article within a collection can also be cited independently as required. These collections are edited by the project leaders who actively participate in helping to promote, shape and grow the collection. This central hub for related articles is similar to having a dedicated micro journal, allowing users to easily discover relevant papers as well as potentially identify collaborative groups.

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Cytoscape Apps

CONCLUSION

F1000Research is an ideal publishing venue for open source software developers who would like their work to be formally published and peer reviewed in as open a manner as possible. If you have life science software that you would like to publish, or an idea for an article collection, please get in touch.

REPRODUCIBILITY

When software code is open source it is important that the related data is freely available from an article. The F1000Research publishing model enables the provenance of the code to be clearly ascertained by including a standardised software availability section in each article, to facilitate both reuse and citation of any published code.

F1000Research provides a link to the executable software/program, as well as to the author’s own working repository, so that readers can easily navigate to both the software and the latest version of the source code. F1000Research also forks an archival copy of the code as it was at the time of publication to remove ambiguity about the code described in the article. A persistent identifier is also added to the code through the archiving of an additional copy of the code and any associated files in the repository Zenodo. Finally, details of the software licence chosen by the author are included in the accompanying article.

All these steps help to ensure that the full provenance of all source code published in F1000Research articles is clearly traceable, thus increasing the reproducibility of the research based on the published code.

2 UPDATING DOCUMENTATION

Traditionally published software articles often become obsolete soon after publication, as new software updates are developed and released. These software updates are often not significant enough to warrant a whole new paper, which means the most recent developments remain undocumented for a sustained period of time.

F1000Research allows papers to be published in synch with the way in which software is developed. Published and peer-reviewed articles can be updated with any relevant changes enabling the article to continue to match the software. Article versions are individually citable and cross-linked, with a short summary of the main updates clearly documented at the top of the article. This publishing model enables developers to provide the most up-to-date information for users of their life science software.

1 OPEN PEER REVIEW AND OPEN COMMUNITIES

Open source software initiatives rely on collaborative and dynamic communities to help expand projects and ideas. Each piece of software published in F1000Research is published immediately (following a rapid internal check) and then openly peer reviewed by invited experts from the scientific community enabling them to contribute and constructively critique the work, which then lays the foundations for improvements in the quality of the code.

Open reviews with named referees, enables software developers to communicate directly with the reviewers to discuss the software. Along with user comments, publication in F1000Research therefore embraces the open source ‘community’ ethos. A completely open process makes work repeatable and spreads ideas faster which in turn helps improve the code, and subsequent research, for the long run.

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FINAL SUBMISSION TO PUBLICATION : DAYS

Article Submission In-house Pre-Publication

Check

Publication + Data Repository

Open Refereeing + User Commenting

Article Revision Indexing

1 SOFTWARE ACCESS URL link to where the software/program can be downloaded and/or used.

2 LATEST SOURCE CODE URL link to the authors most up-to-date source code on a Version Control System (VCS) such as GitHub, BitBucket and SourceForge.

3 SOURCE CODE AS AT THE TIME OF PUBLICATION URL link to a copy of the author’s source code forked from the author’s VCS repository at the time of publication of this paper.

4 ARCHIVED SOURCE CODE AS AT THE TIME OF PUBLICATION Persistent DOI link to F1000Research’s archival space within Zenodo. The source code should be cited using this DOI.

5 SOFTWARE LICENCE The licence under which the software has been published.

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