By Michael Markie, F1000 Research.

Two weeks ago F1000Research launched its article collection series with the publication of the BioJS collection, guest edited by F1000Research editorial board member Manuel Corpas from The Genome Analysis Centre (TGAC), UK.

BioJS is an open-source community of developers who are concerned with the handling and visualisation of biological data on the web. Initiated at EMBL-EBI and coordinated by TGAC, it has so far created 39 different software components in a very short space of time. One of the main reasons for building the community was to introduce a standardised way in which biological web visualisation tools should be implemented and shared. BioJS have come up with a centralised registry and a minimum set of guidelines to enable users and developers alike to have the opportunity to reuse, combine and extend the existing functionality. These guidelines have been put into place to minimise the learning curve for developers. Once they know how to build one component, then creating new ones should be straightforward. Once they know how to extend a component, it should be easy for them to extend any other. BioJS provides an open-source community for biologically oriented JavaScript developers to create applications, share code and increase the visibility of their work. I think Manuel Corpas puts it best when explaining the BioJS components as “a set of standard Lego-like pieces for building web applications that display biological data”.

As a publisher dedicated to open science, F1000Research have published 12 selected software components along with the BioJS community article and an overarching editorial. Publication can play a key role in increasing reusability as it enables the software to be disseminated to a much wider audience. At present, there is also an increasing shift towards publishing reproducible computational science, so it is imperative that any software publication facilitates full data and code availability. With the combination of a broader readership and full access to the software, publication can provide a tried and tested path towards meaningful impact.

F1000Research ensures that all the code and related data are freely available from the paper.  A usable copy of the code as it was at the time of publication remains available, with the code being forked into an archival F1000Research space within the same repository used by the authors.  A copy of the code as at the time of publication is also assigned a persistent identifier to eliminate any ambiguity about the code that is described in the article. Additionally, F1000Research ensures the paper includes a link to the author’s own working repository, so that readers of the paper can easily navigate to the latest version of the source code.  By taking these measures users are able to establish the provenance of the code and reuse it easily, hence supporting the reproducibility of the software, which ultimately contributes to making the software more robust. F1000Research also uses open peer review, providing an additional layer of validation for published software articles. Experts from the scientific community are invited to constructively critique the software and lay the foundations for any improvements. Having these reviews, as well as any user comments, open to everyone helps mirror the collaborative approach encouraged by open source initiatives and embraces the open source ‘community’ ethos.

Open-source-software initiatives rely on their vibrant communities to help grow the projects that are being worked on. Publishing source code openly, not only makes work repeatable, but spreads the ideas faster and makes the code better in the long run, since other users can help debug it. For example, BioJS is a global community with contributors from institutions all over the globe, and it is this that has helped it thrive. Manuel mentions that the BioJS community “allows for the sharing of ideas or development, and it is a meeting point for like-minded people looking to learn from others and to gain credit for the work they do”.  We feel it is important that the publication of software mirrors the principles of software developers and communities of openness and sharing.

To find out more about BioJS collection and how to become a part of the community please feel free to read the full interview with Manuel Corpas. And of course if you have software that you feel would benefit from an F1000Research Article Collection of its own or have any software articles you may wish to publish please feel free to get in touch.