Development of Standard Scripts for Analysis and Programming

PhUSE Annual ConferenceOctober 2014Mike Carniello

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Working Group Description

• Goal: Establish a platform for the collaborative development of program code to be used as analytical tools for clinical trial research, reporting, and analysis– Includes recommendations for analyses, tables,

figures, and listings– Process and guidelines for documentation and

management of scripts– Harness data standards whenever feasible

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• Current Leadership– Hanming Tu (Project Management)– Mary Nilsson (Industry co-lead, Steering Committee

Liaison)– Steve Wilson (FDA Liaison)– Mat Soukup (FDA Liaison)– Adrienne Bonwick, Mike Carniello, Sally Cassells,

Jean-Marc Ferran, Aiyu Li, Dirk Spruck, Eric Sun, Dante Di Tommaso (Project leaders)

Working Group Leadership

Vision: Fill the Gap on Analysis Standards

Data Collection Systems

Observed Datasets

Analysis Datasets

Tables, Figures

and Listings

Clinical Data Flow

Trial Design

PRM SDTM ADaM No TFL Stds Exist

Industry

Standards

Alignment

CDASH

TransCelerate (TAs)

Vision: Shared Reusable Code Library (Script Repository)

Focus Areas

• Three Focus Areas, 6 active projects

Script Repository(4 projects)

White Papers on Analyses and Displays

(1 project)

Communications(1 project)

Existing ScriptsQualification StepsPlatformLegal Considerations

Accomplishments

• Script Repository has been created– Google Code chosen as the repository– 3 Scriptathons– 12 scripts exist in the repository, more to come– MIT license chosen– Process guidelines developed– Qualification guidelines developed– First contributed script added to the repository– User-friendly front end developed

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

Script Repository Front End

Accomplishments

• White Papers – 3 finalized– Vital Signs, ECGs, Labs - Central Tendency

• Finalized in October 2013

– Non-Compartmental Pharmacokinetics• Finalized in March 2014

– Demographics, Disposition, and Medications• Finalized October 2014

Accomplishments

• White Papers – 2 just sent for broad review– Vital Signs, ECGs, Labs – Outliers/Shifts– Adverse Events– Comments due 01 December 2014

• White Papers – 2 in progress– Hepatotoxicity– QT Studes

Accomplishments

• Communications

• Continue to build Script Repository– Continue creating code for tables, figures, and listings as outlined in white

papers (including more Scriptathons)– Consider code for SDTM and ADaM development– Look for other existing code – Enhance process and qualification guidelines– Enhance legal documentation

• Continue white paper development– Finalize white papers in progress– Consider additional white papers to develop (Questionnaire data? Additional

safety special topics? Narratives?)

• Communications– Continue presentations at various conferences– Implement other ideas to increase awareness

Plans for Upcoming Year

• Help enhance process and qualification guidelines

• Communications Project – help maintain conference deadlines and links

• White Papers Project – medical writing support

Help Wanted – Working Group

• Script Repository– Actively contribute code– Use the existing code!

• White Papers– Review draft white papers, spread the word to elicit

additional reviewers (include your medical colleagues)– Spread the word on the final white papers– Implement the recommendations!

• Communications– Help spread the word

Help Wanted - General

Interested In Learning More?

• Two posters at this conference• Sign up for the PhUSE working group mailings

– Go to www.phusewiki.org, click “Join a Working Group”, see mailing list instructions, join “CSS-WG-Standard-Scripts”

• Sign up to be a contributor or committer in the Script Repository – Google account required– Send an email to one of the repository maintainers to request

to join the Google Code PhUSE/FDA script repository– Go to repository at https://code.phuse.com and start

interacting

Reference URLs

• PhUSE home: http://phuse.eu/

– Includes final white papers (under Publications)• PhUSE Wiki: www.phusewiki.org

– Includes process and qualifications guidelines, draft white papers

• PhUSE Standard Script Group: http://www.phusewiki.org/wiki/index.php?title=Standard_Scripts

• PhUSE Repository: – http://code.phuse.com– https://code.google.com/p/phuse-scripts/wiki/yml_idx

Q&A