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Standard Script All-Hands meeting

Standard Script All-Hands meeting. September 29, 2014. Agenda. Collaboration is the Key – Mat PhUSE CSS Background – Mary Standard Script Group – Hanming Projects P01: Adrienne Bonwick P02: Dante Di Tommaso P03 : Michael Carniello P04 : Sally Cassells

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Standard Script All-Hands meeting

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  1. Standard Script All-Hands meeting September 29, 2014

  2. Agenda • Collaboration is the Key – Mat • PhUSECSS Background – Mary • Standard Script Group – Hanming • Projects • P01: Adrienne Bonwick • P02: Dante Di Tommaso • P03: Michael Carniello • P04: Sally Cassells • P05: Jean-Marc Ferran/Eric Sun • P07: Dirk Spruck • P08: Mary E Nilsson • Upcoming Events - Dirk

  3. In a Silo World Literature/Research Trial Design Data Standardization Double programming Analytics * Code/Tools/Scripts * Software Industry ? ? Literature/Research Trial Design Data Standardization Analytics * Code/Tools/Scripts * Software Academic ? Analytics * Code/Tools/Scripts * Software Literature/Research Trial Design/Actual Trial Data Standardization FDA

  4. In a Integrated World

  5. In a Collaborative World • Create a collaborative environment • Develop analytics repository Note: This Graph is from Mat Soukup, FDA

  6. Collaboration is the Key to Success in the Future • Determining Factors: • Entrepreneurial Spirit • Creativity and Innovation • Cross-cultural Communications • Interpersonal Skills • Information Technology http://2.bp.blogspot.com/-YXUyPEtc5EA/Ur5yCdUdvaI/AAAAAAAAIJE/vT2daLp0b10/s1600/collaboration3.jpg

  7. PhUSE CSS Background • Computational Science Symposium (CSS) Working Groups • 5th year in a Series of Annual Computational Science Meetings established to support the work of FDA’s Center for Drug Evaluation and Research (CDER), Office of Computational Science (OSC) • 3rd Year working with PhUSE (first two were with the DIA) • FDA’s motivation: To work collaboratively with industry, vendors and regulators in a “non-competitive space” to find solutions and advance the computational sciences/technology associated with the development and regulation of new medical products (drugs, biologics, etc.) • Perceived benefits of collaboration and crowd sourcing

  8. PhUse CSS Working Groups

  9. Summary of Standardization • Data Collection Systems • Trial Design • Observed Datasets • Analysis Datasets • Tables, Figures and Listings Clinical Data Flow ? Industry Standards Alignment No TFL Stds Exist SDTM PRM ADaM CDASH TransCelerate (TAs)

  10. Script Repository In the Cloud

  11. Development of Standard Scripts for Analysis and Programming Group was formed during 2012 PhUSE CSS March 2012 meeting Current Leadership Mary Nilsson (Industry co-lead, Steering Committee Liaison) Hanming Tu (Project Management) Steve Wilson (FDA Liaison) Mat Soukup (FDA Liaison) Working Group: Formed in 2012 11

  12. Working Group: Description • Goal: Establish a platform for the collaborative development of specialized program code to be used as analytical tools for the clinical trial research, reporting, and analysis. This includes: • Identification of areas that can benefit from a standard set of analyses • Within a topic area, includes recommendations for analyses, tables and figures • Developing a process and guidelines for documentation and management of scripts • Harness data standards whenever feasible

  13. Working Group: Two Focus Areas • Initially three sub-groups • Sub Group 1: works on developing and prioritizing lists of analysis scripts to be developed • Sub Group 2: works on process for developing, validating and documenting scripts • Sub Group 3: works on technology platform to support script development, testing and documentation. • Two Focus Areas: • White Paper Development: standards, formats, etc. • Repository Platform: platform, process, development, access, validation, etc.

  14. Working Group Repository: Google Code

  15. Working Group: Projects • P01: Look for existing scripts and store them in the repository • Adrienne Bonwick and Aiyu Li • P02: Define qualification steps for scripts in the repository • Dante Di Tommaso • P03: Maintain and enhance platform (repository) for sharing scripts • Mike Carniello/Hanming Tu • P04: Legal ownership and issues in open source repository • Sally Cassells • P05: Create templates and metadata for documenting scripts and coding practices • Jean-Marc Ferran/Eric Sun • P06: Refine process for creating and editing scripts in Google Code • Closed, any remaining tasks moved to Project 03 • P07: Implement and further develop communication plan for standard scripts • Dirk Spruck • P08: Create white papers providing recommended display and analysis including Table, List and Figure shells • Mary Nilsson

  16. Working Group: Accomplishments • Script Repository has been created • Google Code chosen as the repository • Some scripts exist in the repository • MIT license chosen • Process guidelines developed • First FDA Script set added to the repository • Continue calling for additional scripts • White Papers Describing Recommended Analyses, Tables, Figures, and Listings • For common measurements (e.g., safety) • One white paper is complete; 5 others in progress

  17. P01:Adrienne Bonwick and Aiyu Li Remit: • Look for existing scripts and store them in the repository Progress • Received the “Demographics” package from the FDA • Reviewed and updated to work on any PC SAS package using FDA Pilot Data • Provided working instructions • Added to Code Repository • Starting to investigate MAED

  18. Standard Scripts Project 2 2014 - Proposal for Qualification of Standard Scripts

  19. Main Sections • Summary of prior proposal, 2013 • Updated proposal, July 2014

  20. Main Sections • Summary of prior proposal • Concepts, definitions & metadata • Test data considerations • Heavy vs. Light qualification • Updated proposal

  21. Proposal from 2013 • Anyone can submit a script, according to a check list • Categorize scripts by complexity • Complexity: low, medium, high, software • Output: tabulated data, analysis data, table, figure, listing • Metadata for script should indicate • Type of output: tabulated data, analysis data, table, figure, listing • Study design: parallel, crossover, etc • State of qualification: ?

  22. Proposal from 2013 • Test data • Overall project should have minimum test data (SDTM & ADaM) • Scripts can propose new test data, must pass (Data fit? Open CDISC?) • Share program to produce test data, never binary test data • 2 levels of qualification • Light vs. Heavy: according to complexity of script & output • Common elements include • header • adhere to good programming practices • clear scope of script (e.g., study design(s)) • test data matchescope & pass "FDA Data Fit" assessment (Open CDISC?) • documentation available for: usage, inputs, outputs, dependencies

  23. Proposal from 2013 • Heavy qualification • Beta package includes: minimal elements for contribution • Specification & Documentation (could be in pgm header) • Test data (Data Fit? or Open CDISC?) • Tests & Expected results defined • Peer Review: GPP, Specs & Docn reviewed, Tests reproduced • Draft • Write qualification plan, Review tests for completeness/suitability (e.g., Branch testing – are all conditional blocks/combos tested?) • Test • Peer Review: Write qualification report, incl. log/output from tests • Final

  24. Proposal from 2013 • Light qualification • Beta package includes skip if >1 yr production usewithout ERROR • Draftminimal elements for contribution • Specification & Documentation (could be in pgm header) • Test data (Data Fit? or Open CDISC or other, as appropriate) • Tests & Expected results defined • Peer Review: GPP, Specs & Docn reviewed, Tests reproduced • Write qualification plan, Review tests for completeness/suitability (e.g., Branch testing – are all conditional blocks/combos tested?) • Test • Peer Review: Write qualification report, incl. log/output from tests • Final

  25. Proposal through CSS 2104

  26. Main Sections • Summary of prior proposal • Updated proposal • Objectives • Definitions: Qualification, States, Roles • Metadata and Test data • State Transitions

  27. Proposal 2014 - Objectives • For End-users • Clear overview of resources available, incl. purpose & state of each • Inspire confidence from first user experience • Ease-of-use: • clear messaging from scripts • Reproducible results in user's own environment • Consistency of scripts, learning first one makes remaining familiar • Ease of converting users to contributors • For Contributors & Standard Scripts Team • Standardize workflows and checklists • Modularize routine components (e.g., FUTS for dependency checking?) • Automate testing, issue identification (e.g., concept similar to Spotfire/R compatibility) • Centralize & consolidate information & results

  28. Qualification Proposalmeaningful terms in bluehttp://www.phusewiki.org/wiki/index.php?title=File:WG5_P02_Proposal_-_2014.pptx • Qualification Instructions (see embedded template ð) • Certification phase of Qualification applies to new scripts and tests • Confirmation phase applies to updates of existing scripts • States: Contributed, Development, Testing, Qualified • Roles • Contributor: Anyone with appropriate skills & interests • Developer: CSS Working Group 5 volunteer familiar with objectives** • Tester: CSS WG 05 volunteer familiar with objectives** • Environment Tester: Anyone in industry community able to set up automatic test replication in their work environment • Reviewer: Author of white papers, designers of script targets** ** suggests a quick-start onboarding page in CSS Phusewiki

  29. Qualification Proposal • Metadata for scripts should indicate: YML proposal • Whitepaper & output ID uniquely identify the target <Script: Source, Title, Target> • Programming language & version <Language: name, version> • Type of output:<Script: Type> • Study design:<Script: StudyDesign> • State of qualification <Stage>:<Qualification: Stage> • OS is not included, since should be indicated in OS compatibility report • Test Data requirements • available as a program or script (text, not binary) • based on expected standards (SDTM, ADaM) • data requirements clearly & accurately specified for each script • include expected results from these data for defined tests/checks

  30. Qualification Proposal • Transitions"Contributed" is the original State of all scripts • to Development, checklist includes by Developer & Reviewer • R & D confer on suitability of contribution. Suitable starting point?[ may require analysis details, specs, from contributor ] • D reviews components (checklist to be completed) • D works with Contributor to complete minimum components[ including Test Data and Coverage of defined tests ] • D adds standard parameter, dependency checking • D writes Qualification instructions .docx (see template, above) • to Testing, checklist includes by Tester • Review Qualification instructions, consider coverage of tests • Execute Qualification instructions • Work with Developer to complete execution successfully

  31. Qualification Proposal • Transitionscontinued • to Qualified by Tester & Environment Tester & Reviewer • T updates reference test outputs from certification/confirmation • E updates & executes local tests (posting PASS/FAIL results) • R confirms script output matches intention • R confirms qualification process covers important elements and considerations. • R also provides user (rather than technical) feedback? • Achieve "Qualified" state when all tests in all test environments PASS (i.e., match outputs that T has certified and/or confirmed) and that R agrees that target is achieved

  32. Qualification Proposal • Efforts Required • Top priority • Finalize Qualification states, roles, workflow, checklists, and templates • Next priorities • Design test structure in google code • Develop scripts that will allow Environment Testing • Develop general components (e.g. parameter, dependency checking) • Identify Environment Testers based on • Host environment • SAS or R version • Identify opportunities to automate qualification. E.g., • Environment Testers to post results back as machine readable • Script green-light/red-light qualification matrix on Phusewiki

  33. P03:HanmingTu and Mike Carniello Remit: • Maintain and enhance script repository Progress • CSS 2014 Scriptathon work catalogued and displayed (see next slide) • PharmaSUG Scriptathon work to be added to repository • PhUSE 2014 Scriptathon planned What’s next? • Do we use Scriptathons as vehicle for adding code? • Should we spend effort in updating/perfecting what we have? • Scriptathon targets are White Paper displays … should we add SDTM and ADaM scripts as well?

  34. https://code.google.com/p/phuse-scripts/wiki/yml_idx

  35. P04: Legal ownership and issues in the Open Source RepositorySummary 16 Sep 2014

  36. Background • Members of WG5, the PhUSE Standard Script Development group, wanted to ensure that users of posted scripts are protected from any potential claims of ownership from organizations employing individuals who contribute scripts. • The group recommended that a ‘click through’ agreement be obtained from a lawyer and posted on the GoogleCode site. This became P04 for our group.

  37. Assignment March 2013 • Get more scripts in the Script Repository • Networking • Broad Communications • Address any remaining validation, legal, process issues • Finalize first white paper • Goal to finalize within a couple of months • Begin work on the remaining white papers • Looking for more active participants • Goal to be final or near-final by next year

  38. Summary of Next Steps (2013) • The work has now been divided into 8 projects • P01: Look for existing scripts and store them in the repository (Kevin Kane) • P02: Define validation steps for scripts in the repository (LinaJørgensen) • P03: Maintain and enhance platform (repository) for sharing scripts (Hanming Tu) • P04: Legal ownership and issues in open source repository (Kevin Kane/Sally Cassells)

  39. Summary of Next Steps (2013) • 8 projects (cont’d) • P05: Create templates for documenting scripts and coding practices (Jean-Marc Ferran) • P06: Refine process for creating and editing scripts in Google Code (Kevin Kane) • P07: Implement and further develop communication plan for standard scripts (Dirk Spruck) • P08: Create white papers providing recommended display and analysis including Table, List and Figure shells (Mary Nilsson)

  40. Actions for P04 • Sally contacted Chris Decker to request that PhUSE provide a legal contact who could develop the agreement. • Chris provided draft agreement in May 2013 for review. • The agreement is currently posted on the GoogleCode site and in the PhUSE Wiki . The document name is SS 15591982 1 UKGROUPS Harmony Individual Contributor License AgreementDOC.

  41. Issues, Discussions, Decisions • UK vs. US • The Draft Agreement cites UK law rather than US (Section 8). Adding similar clauses for the US would require the services of a US lawyer. • Individually owned tools • Contributor grants full ’worldwide, non exclusive, royalty free, irrevocable license to the IP’. • If tool was developed collaboratively, contributor should get agreement from collaborators before posting. • Click through • Not yet technically click through but contributors can read and agree to the terms.

  42. Next Steps, Recommendations • Investigate possibility of modifying the language in Section 8 to indicate that the agreement applies fully within the US. • Consider a leadership team vote to finalize the draft agreement. • Link to agreement PhUSE Standard Scripts Contributor Agreement

  43. Standard Scripts WG - P05:Jean-Marc Ferran (Qualiance)& Eric Sun (Sanofi) Remit: • Create templates and metadata for documenting scripts and coding practices Progress • Templates for program documentation and user guides created • Next steps: • Document 2 existing scripts from the repository using these and send them for review in order to get more detailed feedback on the structure based on examples • Define metadata for TFL analysis. Link up with Emerging Technology / Analysis metadata WG to see where we can align and re-use each other’s findings

  44. P08: Mary Nilsson Project Description • Create white papers providing recommended displays and analyses including Table, Figure, and Listing shells for clinical trial study reports and summary documents. • The intent is to begin the process of developing industry standards with respect to analysis and reporting for measurements that are common across clinical trials and across therapeutic areas. • Script developers could then create scripts consistent with the recommendations for all to use, improving efficiency and safety signal detection.

  45. Standard Script All-Hands meeting P07 - Communications

  46. Current Activities • Maintain Website with Group Updates • Maintain Conference and Paper Log (update needed) • Distribute News (e.g. PhUSE Newsletter) • Help Preparation of Conference Material • Technical Assistance of White Paper Review • Part of New CSS Communications Group(New CSS Letter Planned) • Backup and Help isNeeded

  47. P08: Mary Nilsson Progress - The following white papers have been finalized: • Analyses and Displays Associated with Measures of Central Tendency – With a Focus on Vitals, ECGs, and Labs in Phase 2-4 Clinical Trials and Integrated Summary Documents (finalized in October 2013) • Analyses and Displays Associated with Non-Compartmental Pharmacokinetics – With a Focus on Clinical Trials (finalized in March 2014) Note: Final white papers can be found on the PhUSEwebsite, Publications section. (www.phuse.eu)

  48. P08: Mary Nilsson Progress - The following white papers are in progress: • Analyses and Displays Associated with Outliers or Shifts from Normal to Abnormal – With a Focus on Vitals, ECGs, and Labs in Phase 2-4 Clinical Trials and Integrated Summary Documents (third draft targeted for public comment in September 2014) • Analyses and Displays Associated with Adverse Events – With a Focus on Phase 2-4 Clinical Trials and Integrated Summary Documents (first draft targeted for public comment in September 2014) • Analyses and Displays Associated with Demographics, Disposition, and Medications – With a Focus on Phase 2-4 Clinical Trials and Integrated Summary Documents (final white paper targeted for October 2014) • Analyses and Displays Associated with Hepatotoxicity – With a Focus on Phase 2-4 Clinical Trials and Integrated Summary Documents (first draft targeted for public comment by the end of 2014) • Analyses and Displays Associated with QT Studies (first draft targeted for public comment by the end of 2014) Note: Draft white papers (where applicable) can be found on the PhUSE Wiki, Development of Standard Scripts Project 08 wiki page (www.phusewiki.org)

  49. P08: Mary Nilsson • How you can help • When a white paper has been finalized, or when a white paper is ready for broad review, please help spread the word within your organization and across your contacts. Please include your medical colleagues. Thanks!

  50. Plans for Upcoming Year • Continue to build Script Repository • Continue creating code for tables and figures as outlined in white papers • Look for other existing code sharing libraries • Continue white paper development • Consider updating the first white paper • Finalize PK white paper this month • Finalize remaining 4 white papers in 2014 • Consider additional white papers to develop • Communications • Presentations at various conferences • Implement other ideas to increase awareness

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