Bioinformatics

BioJS – visualising biological data: an interview with F1000Research


Last week we were very pleased to publish the first F1000Research Article Collection. The BioJS collection was initially launched with 12 open source biological visualisation components, one BioJS community article and an overarching editorial. It was very exciting for us to publish this collection based on an open source software initiative which is going from strength to strength. The collection was guest edited by F1000Research Editorial Board member Manuel Corpas of The Genome Analysis Centre (TGAC), UK. So who better than Manny himself to enlighten us about the BioJS project and reveal what’s going on currently, the future plans of the project, and how to become a part of this burgeoning community.

Interview:

Manny, can you tell us a little bit more about BioJS and what the objectives of the initiative are?

Sure. BioJS is an open source community of developers who are concerned with the handling and visualisation of biological data on the web. Institutes like EMBL-EBI and the NCBI are massive hubs of biological data and so they are obviously experts in how to visualise this; for that reason they provide the tools for third parties to use their resources and data. However, there is currently much unnecessary duplication of efforts when third parties want to use these data but have to redevelop their own tools because nothing is available specific to their purposes. To date, there isn’t a standardised way in which biological web visualisation tools should be implemented and shared. BioJS provides a minimum set of guidelines that make it easy for users and developers to reuse, combine and extend existing functionality. Put simply, BioJS is like a set of standard Lego-like pieces for building web applications that display biological data. With BioJS it is now possible to have a centralised place where all available functionality is located and existing components can be reutilised by third parties without having to reinvent the wheel every time.

So what made you decide that publishing the individual components from BioJS would be valuable to the scientific community?

Each BioJS component is a discrete piece of functionality. There are currently 39 components in the BioJS registry that cater for a variety of purposes. A good way to summarise the contribution of a specific BioJS component is through publication. A published article provides the opportunity for wider dissemination of the developed functionality, it enables a further stage of validation through external peer review and it is also a great vehicle for recognition of credit to all those contributing to the development of each component.

BioJS is an Open Source software initiative; does a community effort help improve the bioinformatics tools and software created?

Absolutely. We have seen it with all other major programming languages applied to bioinformatics. JavaScript, being the preeminent language of the web, could not be left out from having its own biologically oriented community. A global community of developers is what makes open source projects thrive. Not only does it allow the sharing of ideas or development, it is a meeting point for like-minded people looking to learn from others and to gain credit for the work they do. Being part of the BioJS community is the way to join this wonderful initiative, and we are very open and very happy to welcome all newcomers!

Why did you choose F1000Research to start an article collection of the BioJS components?

I was actually one of the first authors to publish in the journal with my article: Low budget analysis of Direct-To-Consumer genomic testing familial data, and thus my previous experience with publishing in F1000Research was a really positive one. We felt F1000Research would allow us to have the flexibility we needed to publish our software articles, allowing us to keep the code in the GitHub repository while making the maximum impact by publishing all our initial articles at once. We wanted to have an immediate impact and so the “publish first, review later” model of F1000Researchsuited us particularly well. I knew that publishing the collection at F1000Research would hopefully get us a lot of exposure, especially since our 14 published papers encompass contributions from many leading bioinformatics organisations.

Are there any particular features of F1000Research that the BioJS components can benefit from?

Yes many! As BioJS is an open source initiative, it was only right we published in a fully open access journal. In F1000Research all the components will be accessible to the wider community and all the code/data will be freely available. Each of the components will also be openly peer reviewed enabling the scientific community to help critique and improve them, and by having all the reviews and comments open, it mirrors the community approach that the BioJS registry encourages.

As bioinformaticians we develop and improve tools all the time. F1000Research is unique in that if small updates/patches are made to a component these can be easily documented as there is the ability to update papers to reflect small changes without having to write a completely new article – we can then concentrate on doing more developing rather than writing more manuscripts! F1000Research is quick at publishing articles, so when a new component is added to the registry we can aim to have it published in a matter of days, not weeks or even months.

What do you hope to achieve with BioJS in the next few years?

One of the main reasons why BioJS came to exist was to offer a solution to the wasteful duplication of efforts in biological web development. Not only did we have disparate ways of seeing the same molecular entity, there was also no organised effort to provide support to sharing, development or standardisation. I expect BioJS to become the global place of encounter for all those web developers implementing solutions for biological sciences. I see leading providers of biological data making their visualisation widgets BioJS-compliant and accessible through the BioJS registry. I envisage hundreds of committed developers actively sharing, experimenting and learning from this thriving community. I see training workshops and international BioJS meetings and get-togethers, including local hackathons throughout the major hubs of global technical expertise. Apart from potential additions to other journals, we will carry on publishing articles about BioJS components in this great F1000Research Collection every year.

How can one join the BioJS community?

One good way is to join BioJS’s GitHub portal. Another is to come to one of the many training events that we are providing; to hear about these you can follow our BioJS Twitter account @BiojsLibrary. We also have a Google Group mail list of developers that it is open for anyone to join and/or read: biojs@googlegroups.com. And it goes without saying you are more than welcome to drop me a line and arrange a chat at any time; although I would appreciate this to be during normal UK waking hours! ;-)

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Categories: Bioinformatics, Technology

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