BioJavaScript (BioJS; http://biojs.net/) was set up to meet a need for an open source library of reusable components to visualize and analyse biological data on the web (Figure 1; Corpas et al., 2014). These components are discrete modules that can be reused, extended and combined to meet a particular visualization need. Unlike proprietary (or closed-source) systems, which are typically distributed as ‘executable’ files under restrictive licenses, open source software projects make their source code freely available under a permissive license (Millington, 2012; Balch, et al., 2015). This allows other users to modify, extend and re-distribute the software with few restrictions and at no cost to other users.

Figure 1

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However, the fact that the community is allowed and encouraged to contribute to an open source software project is no guarantee that they will contribute. It is certainly not a sufficient condition for ensuring sustainability: repositories of open source software such as GitHub (https://github.com) and SourceForge (http://sourceforge.net) are littered with abandoned projects that have failed to gain the support needed to survive beyond the originator's initial enthusiasm and/or funding.

In the case of BioJS we were acutely aware of the need to gain buy-in from the community for two reasons:

1. To fulfil the vision of a suite of tools capable of displaying diverse biological data requires expertise and capacity that is well beyond that of any individual group of developers working in isolation.

2. To encourage users to spend time integrating BioJS tools into their websites and applications, the project has to have, and be seen to have, a potential lifespan far beyond that of its initial funding.

Predicting the success of projects is hard, and there is nothing in the nature of open source initiatives that makes this any easier. There have been attempts to quantify success in open source software (see, e.g., the metrics proposed by Crowston et al., 2003), but these have gained little traction. More useful, we feel, have been articles that provide pragmatic advice to would-be open software developers, such as ‘Ten simple rules for the open development of scientific software’ (Prlic and Procter, 2012). Rather than repeating or re-working the general-purpose recommendations of others, here we describe what we have learned from the BioJS project.

BioJS was initially developed in 2012 through a collaboration between the European Bioinformatics Institute (EMBL-EBI) and The Genome Analysis Centre (TGAC). The project began as a set of individual graphical components deposited in a bespoke online registry. Since then it has expanded into a community of 41 code contributors spread across four continents, a Google Group forum with more than 150 members (https://groups.google.com/forum/#!forum/biojs), and 15 published papers (as of May 2015). The project's first paper, published in 2013 (Gomez, et al., 2013), has been cited 31 times to date.

The BioJS registry (http://biojs.io) offers a modern platform for fast and customizable access to components. The registry provides a centralized resource where deposited components can be discovered, tested and downloaded at the push of a button. BioJS components are organized as packages. This modular approach reduces duplication of effort and has been used by other projects, such as BioGem (Bonnal, et al., 2012). Several recognized projects and institutions have already shown commitment to BioJS by utilizing and developing components: examples of this include PredictProtein (Yachdav et al., 2014), CATH (Sillitoe et al., 2013), Genome3D (Lewis et al., 2013), Reactome (Croft et al., 2014), Expression Atlas (Petryszak et al., 2014), Ensembl (Cunningham et al., 2015), InterMine (Smith et al., 2012), PolyMarker (Ramirez-Gonzalez et al., 2015) and the TGAC Browser (http://browser.tgac.ac.uk).

In this section we discuss the factors that, we believe, have played an important role in the growth of the BioJS open source community.

None of the points raised above are unique to BioJS as there are a number of other open source software projects in the life sciences. For instance, Cytoscape.js (http://js.cytoscape.org), an open source community developing a web-based viewer for the Cytoscape network viewer (Shannon, et al., 2003), is also mostly decentralized, being organized through some simple rules and with a community of contributors from both the public and private sectors. These contributors add new features to the library and discuss new feature ideas and bug reports. However, code contributions (i.e., pull requests) do require centralized review before merging into the main codebase.

The Galaxy project (Giardine, et al., 2005; Blankenberg, et al., 2010; Goecks, et al., 2010) is making advanced bioinformatics software accessible to biologists by directly providing an intuitive web interface to these applications. The Galaxy software enables the reproduction of computational research workflows by capturing and organizing the pipeline's layout and components into re-runnable protocols. The project also makes use of public collaboration tools to coordinate code contributions with the development community, and it maintains a dedicated portal (https://biostar.usegalaxy.org/) to communicate and support its user base. Like BioJS, the Galaxy core framework can be easily extended by plugins of all kinds, and the Galaxy core team offers the Galaxy ToolShed to distribute and share all these extensions in an App-Store like fashion. The annual Galaxy Community Conference (GCC) also attracts more than 200 participants and offers a variety of workshops and a hackathon.

The Bionode project (http://www.bionode.io) aims to provide modular, scalable and highly reusable tools for bioinformatics analysis. The community that surrounds this project is mainly composed of bioinformaticians and JavaScript (Node.js) developers who dedicate their time either as a hobby or because they need to add a feature (or fix a bug) for their own projects. Bionode is very open to any kind of contribution and does not enforce too many rules or governance to the community.

Life science open source communities have their own special peculiarities and motivations. We have presented a compilation of experiences that, in our view, have helped BioJS to become a robust international project within a relatively short period of time. Apart from fostering the right skills and technical experience to develop BioJS, we have established formal means to reward contributors, to keep the community members motivated, and to increase our impact. If used with care and fairness, recognition can be a powerful lever with which to build communities. We believe that some of the lessons we have learned and the practices we have established will help others to build similarly robust open source projects and communities.

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Author details

1. Guy Yachdav

   Bioinformatik, Technische Universität München, Garching, Germany

   Contribution

   GY, Conception and design, Drafting or revising the article

   For correspondence

   gyachdav@bio-sof.com

   Competing interests

   The authors declare that no competing interests exist.

2. Tatyana Goldberg

   Bioinformatik, Technische Universität München, Garching, Germany

   Contribution

   TG, Conception and design, Drafting or revising the article

   Competing interests

   The authors declare that no competing interests exist.

3. Sebastian Wilzbach

   Bioinformatik, Technische Universität München, Garching, Germany

   Contribution

   SW, Contributed unpublished essential data or reagents

   Competing interests

   The authors declare that no competing interests exist.

4. David Dao

   Bioinformatik, Technische Universität München, Garching, Germany

   Contribution

   DD, Contributed unpublished essential data or reagents

   Competing interests

   The authors declare that no competing interests exist.

5. Iris Shih

   Bioinformatik, Technische Universität München, Garching, Germany

   Contribution

   IS, Contributed unpublished essential data or reagents

   Competing interests

   The authors declare that no competing interests exist.

6. Saket Choudhary

   Molecular and Computational Biology, University of Southern California, Los Angeles, United States

   Contribution

   SC, Contributed unpublished essential data or reagents

   Competing interests

   The authors declare that no competing interests exist.

   "This ORCID iD identifies the author of this article:" 0000-0001-5202-7633

7. Steve Crouch

   Web and Internet Science, University of Southampton, Southampton, United Kingdom

   Contribution

   SC, Drafting or revising the article

   Competing interests

   The authors declare that no competing interests exist.

8. Max Franz

   Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada

   Contribution

   MF, Drafting or revising the article

   Competing interests

   The authors declare that no competing interests exist.

9. Alexander García

   Linkingdata I/O LLC, Austin, United States

   Contribution

   AG, Drafting or revising the article

   Competing interests

   The authors declare that no competing interests exist.

10. Leyla J García

    European Molecular Biology Laboratory-European Bioinformatics Institute, Cambridge, United Kingdom

    Contribution

    LJG, Drafting or revising the article, Contributed unpublished essential data or reagents

    Competing interests

    The authors declare that no competing interests exist.

11. Björn A Grüning

    Bioinformatics Group, Department of Computer Science and Centre for Biological Systems Analysis, University of Freiburg, Freiburg, Germany

    Contribution

    BAG, Contributed unpublished essential data or reagents

    Competing interests

    The authors declare that no competing interests exist.

    "This ORCID iD identifies the author of this article:" 0000-0002-3079-6586

12. Devasena Inupakutika

    Web and Internet Science, University of Southampton, Southampton, United Kingdom

    Contribution

    DI, Drafting or revising the article, Contributed unpublished essential data or reagents

    Competing interests

    The authors declare that no competing interests exist.

13. Ian Sillitoe

    Institute of Structure and Molecular Biology, University College London, London, United Kingdom

    Contribution

    IS, Contributed unpublished essential data or reagents

    Competing interests

    The authors declare that no competing interests exist.

14. Anil S Thanki

    The Genome Analysis Centre, Norwich, United Kingdom

    Contribution

    AST, Contributed unpublished essential data or reagents

    Competing interests

    The authors declare that no competing interests exist.

15. Bruno Vieira

    School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom

    Contribution

    BV, Contributed unpublished essential data or reagents

    Competing interests

    The authors declare that no competing interests exist.

    "This ORCID iD identifies the author of this article:" 0000-0002-4878-6431

16. José M Villaveces

    Max Planck Institute of Biochemistry, Planegg, Germany

    Contribution

    JMV, Contributed unpublished essential data or reagents

    Competing interests

    The authors declare that no competing interests exist.

17. Maria V Schneider

    The Genome Analysis Centre, Norwich, United Kingdom

    Contribution

    MVS, Contributed unpublished essential data or reagents

    Competing interests

    The authors declare that no competing interests exist.

18. Suzanna Lewis

    Lawrence Berkeley National Laboratory, Berkeley, United States

    Contribution

    SL, Contributed unpublished essential data or reagents

    Competing interests

    The authors declare that no competing interests exist.

19. Steve Pettifer

    School of Computer Science, The University of Manchester, Manchester, United Kingdom

    Contribution

    SP, Drafting or revising the article

    Competing interests

    The authors declare that no competing interests exist.

20. Burkhard Rost

    Bioinformatik, Technische Universität München, Garching, Germany

    Contribution

    BR, Drafting or revising the article

    Competing interests

    The authors declare that no competing interests exist.

21. Manuel Corpas

    The Genome Analysis Centre, Norwich, United Kingdom

    Contribution

    MC, Conception and design, Drafting or revising the article

    For correspondence

    manuel.corpas@tgac.ac.uk

    Competing interests

    The authors declare that no competing interests exist.

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