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B Temperton - The Bioinformatics Testing Consortium

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Presentation at BOSC2012 by B Temperton - The Bioinformatics Testing Consortium

Presentation at BOSC2012 by B Temperton - The Bioinformatics Testing Consortium

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  • 1. The Bioinformatics Testing Consortium:Improving Bioinformatics software one manuscript at a timeBetter Science through Superior Software - Titus BrownBen TempertonGiovannoni LabDepartment of MicrobiologyOregon State Universitybtemperton@gmail.com@bentemperton
  • 2. Bioinformatics - Dealing with the data deluge Data problem identified
  • 3. Bioinformatics - Dealing with the data deluge Data problem identified Software written to analyze data
  • 4. Bioinformatics - Dealing with the data deluge Data problem identified Software written to analyze data Solution published and shared
  • 5. Bioinformatics - Dealing with the data deluge Data problem identified Software written to analyze data Solution published and shared
  • 6. The Problem - Insufficient codebase quality checks• Software is released having been tested only by those who wrote it
  • 7. The Problem - Insufficient codebase quality checks• Software is released having been tested only by those who wrote it
  • 8. The Problem - Insufficient codebase quality checks• Software is released having been tested only by those who wrote it• Software rarely checked as part of the manuscript review process
  • 9. Not a new problem in IT Developer ‘Client’ Unit testing Integration testing System testingUser Acceptance testing
  • 10. Not a new problem in IT Developer Tester ‘Client’ Unit testing Integration testing System testing User Acceptance testing
  • 11. Not a new problem in IT Developer Tester ‘Client’ Unit testing Integration testing Installs System testing Runs User Acceptance testing Meets Requirements
  • 12. Not a new problem in IT Developer Tester ‘Client’ Unit testing Integration testing Installs System testing Runs User Acceptance testing Meets Requirements
  • 13. Not a new problem in Science - Peer Review Manuscript Peer Review: Improving quality for free*! * not free
  • 14. The Bioinformatics Testing ConsortiumDeveloper places code in Does it compile?Open Source Repository Does it run? and registers project Testers run through standard Does the test data output match? tests ... Testers assigned to project by BTC Minimum Developer fixes bugs/issues BTC standards met? NO YES BTC APPROVED Testers raise bugs/issues in discussion with developer
  • 15. Who Benefits?• New Users • Reduced activation energy when using BTC-approved software • Compulsory inclusion of a test data set with known results
  • 16. Who Benefits?• New Users • Reduced activation energy when using BTC-approved software • Compulsory inclusion of a test data set with known results• Developers • Rapid awareness of issues • Bugs raised in a consistent manner with enough details to replicate
  • 17. Who Benefits?• New Users • Reduced activation energy when using BTC-approved software • Compulsory inclusion of a test data set with known results• Developers • Rapid awareness of issues • Bugs raised in a consistent manner with enough details to replicate• BTC Testers • Using students as testers teaches standards in early career
  • 18. Who Benefits?• New Users • Reduced activation energy when using BTC-approved software • Compulsory inclusion of a test data set with known results• Developers • Rapid awareness of issues • Bugs raised in a consistent manner with enough details to replicate• BTC Testers • Using students as testers teaches standards in early career• Journal Editors • Assurance that software described in a manuscript is fit-for-purpose and key analyses can be reproduced
  • 19. What’s Needed? Feedback
  • 20. What’s Needed? Feedback Participation
  • 21. What’s Needed? Feedback Participation Test Cases
  • 22. What’s Needed? Feedback Participation Test Cases @BioTestConsort
  • 23. With thanks to:Iddo Friedberg Stephen J. GiovannoniJ. Cameron Thrash Bank BeszteriJonathan EisenPascale Gaudet Jason StajichTitus Brown Hilmar LappCameron NeylonChris Sullivan