yoyehudi_micklemlab_intermine.pdf (4.5 MB)

Forever in Bluegenes: BlueGenes / InterMine Poster for BOSC 2017

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posted on 19.07.2017 by Yo Yehudi, Inter Mine, Justin Clark-Casey, Daniela Butano

The plight of the computational biologist, or indeed any data scientist, often boils down to data: data may be badly formatted, missing information, hard to access and hard to integrate with other sources. Similarly, user interfaces designed for data analysis may not be easy to use, hindering scientific analysis rather than assisting it.

BlueGenes is designed to facilitate biological data discovery and analysis in a user-friendly and enjoyable way, without requiring that scientists write code or wrangle multiple datasets themselves. Designed as a modern replacement for InterMine’s[1] JSP-powered interface, which traces its origin as far back as 2003, BlueGenes focuses on enhancing user experience using in-page updates, colour-coded data types, and mobile / touch friendliness where possible. Iterative user testing and community feedback is used to enhance usability.

The data available in BlueGenes is sourced via web services from individual InterMine instances, which are typically comprised of multiple high-quality integrated datasets. Using InterMine as a data source allows BlueGenes to source genomic and proteomic data from the array of biological databases worldwide that run InterMine instances, including model organisms such as the mouse, rat, budding yeast, fruit fly, nematode worm, and thale cress as well as cattle, chinese hamster ovary cells, and many plants.

BlueGenes is browser-based and runs client-side. The decoupled architecture separates the user interface from the data server, allowing the same front-end instance to seamlessly switch between InterMine data sources. Whilst the core of BlueGenes is programmed in ClojureScript for rapid iterative prototyping purposes, a plugin architecture is currently under development that will allow data analysis and visualisation tools to be seamlessly integrated in native JavaScript. BlueGenes runs on Re-Frame[2], a ClojureScript library based on React.js.

[1]Smith RN, Aleksic J, Butano D, Carr A, Contrino S, Hu F, Lyne M, Lyne R, Kalderimis A, Rutherford K, Stepan R, Sullivan J, Wakeling M, Watkins X, Micklem G. InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data. Bioinformatics. 28(23):3163-5 (2012)

[2]Thompson, M. Re-Frame: A Reagent Framework For Writing SPAs, in Clojurescript. Zenodo. http://doi.org/10.5281/zenodo.801613 (2015)


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