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Wibo Pipping

Wibo Pipping

Data Scientist

@TheHyveNL

translocationAt the tranSMART Foundation Annual Meeting in La Jolla, CA, we presented the new User Interface for tranSMART that The Hyve is developing as part of IMI Translocation under the working name Glowing Bear.

Glowing Bear is a web based UI which is built on top of the tranSMART REST API. When we started with the design of the UI we wanted to make sure it would be more informative, intuitive and responsive than the current tranSMART UI.

The basic cohort selection functionality should not need extensive documentation and training to start using. Graphs produced should provide the user with up to date information and at all times display the number of patients or subjects in the selected cohort.

In addition to these user centric principles we wanted to make sure the UI would be maintainable and extendable for developers and future contributors. To this end we included a testing framework and documentation of the code.

The cohort selection functionality including the possibility to combine two graphs to generate a boxplot, scatterplot or heatmap

The cohort selection functionality including the possibility to combine two graphs to generate a boxplot, scatterplot or heatmap

The main goals of the Glowing Bear UI are to:

  • Leverage the new 17.1 REST API improvements which include longitudinal data support, modifier support and cross-study data linking
  • Improve cohort selection to improve usability
  • Replace the old UI for all common use cases.

During the last six months the UI has seen great progress with new functionality coming in regularly. During this time the ability to load and save selected cohorts, support for selecting up to two cohorts, searching on study level metadata and inclusion of SmartR were realised.

On the side of maintainability the plugin architecture was designed and implemented with SmartR being the first plugin to make use of this. Additionally, the unit test coverage of the code has increased from around 30% to 70% and in the time between the annual meeting and the release of this blog post has increased to 90%.

screen-shot-2016-12-06-at-14-11-21

Creating two or more patient cohorts

screen-shot-2016-12-06-at-14-13-39

Integration with the popular tranSMART plugin for interactive data analysis SmartR

The glowing bear UI can be found here: transmart-gb.thehyve.net, to play around with the UI please contact us for login credentials at office@thehyve.nl.

Glowing Bear road map

The road map for Glowing Bear is a combination from requirements set at the start and feedback received from the tranSMART community (Sanofi, Pfizer, TraIT/BBMRI). Work is currently ongoing on data export and porting the Glowing Bear to 17.1 to start longitudinal data support. Improvements and features were taken up after the first demos and user tests. Currently we are looking for people to try out the UI, give feedback or adopt a feature.  The following features are on the roadmap:

Future feature Funded?
Data export Partly
Longitudinal data Partly
Improved study search No
File linking No
Cross study support No
Frontpage No
Extended search (concepts/metadata) No
Improved SmartR workflow No
Advanced visualisations No
Analytics notebook support No
SmartR-notebook conversion No

 

Presentation by Wibo Pipping on tranSMART Glowing Bear at the tranSMART Foundation Annual Meeting 2016

 

Slides available here:

 

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Wibo Pipping

Data Scientist

@TheHyveNL