B Temperton - The Bioinformatics Testing Consortium

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B Temperton - The Bioinformatics Testing Consortium

  1. 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. 2. Bioinformatics - Dealing with the data deluge Data problem identified
  3. 3. Bioinformatics - Dealing with the data deluge Data problem identified Software written to analyze data
  4. 4. Bioinformatics - Dealing with the data deluge Data problem identified Software written to analyze data Solution published and shared
  5. 5. Bioinformatics - Dealing with the data deluge Data problem identified Software written to analyze data Solution published and shared
  6. 6. The Problem - Insufficient codebase quality checks• Software is released having been tested only by those who wrote it
  7. 7. The Problem - Insufficient codebase quality checks• Software is released having been tested only by those who wrote it
  8. 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. 9. Not a new problem in IT Developer ‘Client’ Unit testing Integration testing System testingUser Acceptance testing
  10. 10. Not a new problem in IT Developer Tester ‘Client’ Unit testing Integration testing System testing User Acceptance testing
  11. 11. Not a new problem in IT Developer Tester ‘Client’ Unit testing Integration testing Installs System testing Runs User Acceptance testing Meets Requirements
  12. 12. Not a new problem in IT Developer Tester ‘Client’ Unit testing Integration testing Installs System testing Runs User Acceptance testing Meets Requirements
  13. 13. Not a new problem in Science - Peer Review Manuscript Peer Review: Improving quality for free*! * not free
  14. 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. 15. Who Benefits?• New Users • Reduced activation energy when using BTC-approved software • Compulsory inclusion of a test data set with known results
  16. 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. 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. 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. 19. What’s Needed? Feedback
  20. 20. What’s Needed? Feedback Participation
  21. 21. What’s Needed? Feedback Participation Test Cases
  22. 22. What’s Needed? Feedback Participation Test Cases @BioTestConsort
  23. 23. With thanks to:Iddo Friedberg Stephen J. GiovannoniJ. Cameron Thrash Bank BeszteriJonathan EisenPascale Gaudet Jason StajichTitus Brown Hilmar LappCameron NeylonChris Sullivan

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