BioJS collection of open-access visualisation tools released

Posted by a.hay on 13 February 2014 - 2:11pm

A new collection of visualisation tools for representing biological information is now available thanks to TGAC, EMBL-EBI and F1000Research.

TGAC’s BioJS collection, published today by the journal F1000Research, comprises 14 open-access articles detailing the functionality, design, implementation and potential applications for a suite of open-source, JavaScript software components contributed by developers all over the world. The collection marks a significant step towards improving the way scientists can visualise biological data.

Data visualisations help researchers generate hypotheses and translate them into knowledge. Now, for the first time, developers can freely access a central software library for sharing standardised, community-approved JavaScript tools for visualising biological information. BioJS, an open-source, community-based project, has a modular, structured design that is ideal for scientists working in data-intensive research. The BioJS community, initiated at EMBL-EBI and coordinated by TGAC, has enabled the creation of 39 different software components in a very short time. Its new collection, like the community itself, provides a valuable resource for disseminating knowledge swiftly.

Manuel Corpas, Guest Editor of the F1000Research BioJS collection, and Project Leader for Plant and Animal Genomes at TGAC, said: “There are many websites out there that try to give people new ways to visualise biological data that might originate with providers like EMBL-EBI or the NCBI. For users, for the scientists, it’s important that the software behind those visualisations is held to an agreed standard. It ensures a level of quality, and more importantly it makes it much, much easier to compare things and draw interesting parallels.”

Rafael Jimenez, formerly Senior Software Developer at EMBL-EBI and now Chief Technical Officer of ELIXIR, added: “The BioJS project started in the Proteomics Services team with the idea to reuse graphical representations within EMBL-EBI. Today BioJS encompasses a vibrant and wider bioinformatics community that has converged on best practises and a common architecture. People who have created a new tool can submit it to BioJS, where the community can share the development. Once it’s in the library, it’s much easier for people to discover it.”

Henning Hermjakob, Team Leader for Proteomics Services at EMBL-EBI, emphasises the dual benefit of the project, said: “For software engineers, BioJS means more efficient development, for users it provides a recognition effect by standardising the way information is presented across multiple resources.”

Steven Newhouse, Head of Technical Services at EMBL-EBI, said: “The growing adoption and development of BioJS components and the supporting community, such as those provided by TGAC, will allow us to improve the user experience when browsing the community data held at EMBL-EBI.”

The BioJS community provides a range of freely available, open-access functionalities. They have set up a registry that sets categories, provides installation instructions and testing facilities and collates the source code for all components. These are available at the main TGAC resources page.

Each associated component article in the F1000Research collection is about two pages long and follows a structure describing its design and implementation, a use case, and potential applications for the component. A carefully selected set of components has been chosen for the launch of this article collection and other BioJS components are encouraged to join the growing collection.  

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