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27th October 2016
Wibo Pipping – The Hyve
Glowing bear
A modern user interface for tranSMART using the
REST API
2
Agenda/Overview
● IMI Translocation
● Principles for the new UI
● Glowing bear
○ Design
○ Current status
○ Roadmap
● Questions
IMI Translocation
New drugs 4 bad bugs
4
Translocation
● Part of the IMI antimicrobial resistance programme
● Integrate existing knowledge
○ Preclinical data
○ Clinical data
● Extend the REST API
5
Translocation - Role in project
6
Translocation - features
● Extended tranSMART REST API
● Improved R client
○ Reduced data download overhead
○ Extended constraints for data download
● Started work on new UI - Glowing bear
7
Translocation - New UI
● cBioPortal inspired
● Utilizes the REST API
● Well received
● Use cases provided by
● tranSMART community
Principles
Current UI and glowing bear
9
Current tranSMART UI
● User experience:
○ Outdated look and feel
○ Steep learning curve
○ Feedback not always clear
10
Current tranSMART UI
● Technological debt:
○ Old fashioned server architecture
○ No separation of concerns
○ No test coverage
Currentcodequality→
Time to implement new feature →
11
Glowing bear - Goals
● Replace old UI for all common use cases
● Improve cohort selection to improve usability
● Improve user experience
● Leverage new functionality and improved REST API
build in 17.1 project
○ Longitudinal data
○ Modifier support
○ Cross study support
○ Data linking to third parties (i.e. Arvados)
12
Principles
● Responsive
○ Feedback to the user
● Informative
○ Insight into what data the user has
● Intuitive
○ Gradual learning curve
○ Low threshold to start
13
Responsive
● Feedback
○ Early
○ Correct location
○ Clear
14
Informative
● Insight in what the data has to offer
○ Ranges and distributions
○ Update figures when selecting data
● Maintain information flow through the system
15
Intuitive
● Flatten learning curve
● Lower threshold for new users
● Dynamic transition from simple to more complex use
cases
16
Glowing bear - design part 1
● Interactive dynamic web application
○ cBioPortal inspired
● Separation of concerns
○ Modular system
○ Separate back-end and front-end
TranSMART
CoreDB + CoreAPI
REST API
Glowing bear
● Processing power
● long running jobs
● data storage
17
Glowing bear - design part 2
● Separation of concerns
○ Also in the front-end itself
● Plugin architecture
○ SmartR
○ Genome browser?
○ …. ?
● Why?
○ Simplify development and maintenance
Glowing bear
SmartR
Plugin X
18
Glowing bear - design part 3
● Produced code has to have tests
○ Avoid regressions
○ Maintain quality of the product
● Current UI code base has a 0.00% test coverage
19
Recent additions
● Improved cohort selection
○ Supports up to 2 cohorts
○ Cohort grid
● Save and retrieve cohorts
● Plugin architecture
○ SmartR support
● Searching on study level
● metadata
Glowing bear
In development and Roadmap
21
Currently in development
● Data export
○ Adjusting REST API for support
● Longitudinal data
● Improved study selection
● File linking
● Cross study support
● Improve smartR workflow
● Extend searching concepts/metadata
● Frontpage - study changes statistics
● Advanced visualisations
● Notebook support
22
Planned roadmap - features
23
Planned roadmap
● Longitudinal data
○ Waiting for 17.1 Backend implementation
○ Support temporal relations in data queries
○ UI component in design phase
● Improve smartR workflow
24
Planned roadmap
● Improved study selection
○ Controlled vocabulary
○ Genes
● Frontpage - study changes statistics
○ Recently loaded studies
25
Planned roadmap
● File linking
○ Arvados
● Cross study support
● Extend searching concepts/metadata
○ Searching on concepts
● Advanced visualisations
○ Line graphs with data transformation
● Notebook support
○ Adding custom analysis
26
Want to contribute/test?
● Get in touch with us to become a tester/developer or
adopt a feature:
○ office@thehyve.nl
○ wibo@thehyve.nl
○ sjoerd@thehyve.nl
Questions
Glowing bear

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Glowing bear

  • 1. 27th October 2016 Wibo Pipping – The Hyve Glowing bear A modern user interface for tranSMART using the REST API
  • 2. 2 Agenda/Overview ● IMI Translocation ● Principles for the new UI ● Glowing bear ○ Design ○ Current status ○ Roadmap ● Questions
  • 4. 4 Translocation ● Part of the IMI antimicrobial resistance programme ● Integrate existing knowledge ○ Preclinical data ○ Clinical data ● Extend the REST API
  • 6. 6 Translocation - features ● Extended tranSMART REST API ● Improved R client ○ Reduced data download overhead ○ Extended constraints for data download ● Started work on new UI - Glowing bear
  • 7. 7 Translocation - New UI ● cBioPortal inspired ● Utilizes the REST API ● Well received ● Use cases provided by ● tranSMART community
  • 9. 9 Current tranSMART UI ● User experience: ○ Outdated look and feel ○ Steep learning curve ○ Feedback not always clear
  • 10. 10 Current tranSMART UI ● Technological debt: ○ Old fashioned server architecture ○ No separation of concerns ○ No test coverage Currentcodequality→ Time to implement new feature →
  • 11. 11 Glowing bear - Goals ● Replace old UI for all common use cases ● Improve cohort selection to improve usability ● Improve user experience ● Leverage new functionality and improved REST API build in 17.1 project ○ Longitudinal data ○ Modifier support ○ Cross study support ○ Data linking to third parties (i.e. Arvados)
  • 12. 12 Principles ● Responsive ○ Feedback to the user ● Informative ○ Insight into what data the user has ● Intuitive ○ Gradual learning curve ○ Low threshold to start
  • 13. 13 Responsive ● Feedback ○ Early ○ Correct location ○ Clear
  • 14. 14 Informative ● Insight in what the data has to offer ○ Ranges and distributions ○ Update figures when selecting data ● Maintain information flow through the system
  • 15. 15 Intuitive ● Flatten learning curve ● Lower threshold for new users ● Dynamic transition from simple to more complex use cases
  • 16. 16 Glowing bear - design part 1 ● Interactive dynamic web application ○ cBioPortal inspired ● Separation of concerns ○ Modular system ○ Separate back-end and front-end TranSMART CoreDB + CoreAPI REST API Glowing bear ● Processing power ● long running jobs ● data storage
  • 17. 17 Glowing bear - design part 2 ● Separation of concerns ○ Also in the front-end itself ● Plugin architecture ○ SmartR ○ Genome browser? ○ …. ? ● Why? ○ Simplify development and maintenance Glowing bear SmartR Plugin X
  • 18. 18 Glowing bear - design part 3 ● Produced code has to have tests ○ Avoid regressions ○ Maintain quality of the product ● Current UI code base has a 0.00% test coverage
  • 19. 19 Recent additions ● Improved cohort selection ○ Supports up to 2 cohorts ○ Cohort grid ● Save and retrieve cohorts ● Plugin architecture ○ SmartR support ● Searching on study level ● metadata
  • 21. 21 Currently in development ● Data export ○ Adjusting REST API for support
  • 22. ● Longitudinal data ● Improved study selection ● File linking ● Cross study support ● Improve smartR workflow ● Extend searching concepts/metadata ● Frontpage - study changes statistics ● Advanced visualisations ● Notebook support 22 Planned roadmap - features
  • 23. 23 Planned roadmap ● Longitudinal data ○ Waiting for 17.1 Backend implementation ○ Support temporal relations in data queries ○ UI component in design phase ● Improve smartR workflow
  • 24. 24 Planned roadmap ● Improved study selection ○ Controlled vocabulary ○ Genes ● Frontpage - study changes statistics ○ Recently loaded studies
  • 25. 25 Planned roadmap ● File linking ○ Arvados ● Cross study support ● Extend searching concepts/metadata ○ Searching on concepts ● Advanced visualisations ○ Line graphs with data transformation ● Notebook support ○ Adding custom analysis
  • 26. 26 Want to contribute/test? ● Get in touch with us to become a tester/developer or adopt a feature: ○ office@thehyve.nl ○ wibo@thehyve.nl ○ sjoerd@thehyve.nl