PhUSE Computational Science Working Group Update24 November 2015

Development of Standard Scripts for Analysis and Programming

• Working Group 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

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

CFAST (Therapeutic Areas)

Vision: Shared Reusable Code Library (Script Repository)

Focus Areas

• Three Focus Areas, 5 active projects

Script Repository(3 projects)

Analyses and Display White Papers

(ADW, Mary Nilsson)

Communication, Promotion, Education

(CPE, Dirk Spruck)

Script Discovery and Acquisition (SDA, Adie Bonwick, Aiyu Li)Repository Content and Delivery (RCD, Dante Di Tommaso, Peter Schaefer)Repository Governance and Infrastructure (RGI, Mike Carniello, Hanming Tu)

• Working Group Accomplishments• Script Repository has been created– Started in Google Code, now in GitHub– 5 Scriptathons – Scripts exist in the repository– MIT license chosen– Process guidelines developed– Qualification guidelines developed– User-friendly front end developed

• Working Group Accomplishments• 4 White Papers finalized– Vital Signs, ECGs, Labs - Central Tendency

• Finalized in October 2013, Lead – Mary Nilsson

– Non-Compartmental Pharmacokinetics• Finalized in March 2014, Lead - Francois Vandenhende

– Demographics, Disposition, and Medications• Finalized October 2014, Lead – Simin Baygani

– Vital Signs, ECGs, Labs – Outliers and Shifts• Finalized in September 2015, Lead – Wei Wang

• Deliverables for Public Review• White Paper just went through public review– TQT Studies• Lead - Christos Stylianou

• Upcoming white papers for public review– Adverse Events

• Working on Draft 2 for public review, Lead – Sheryl Treichel

– Hepatotoxicity• Working on Draft 1 for public review, Lead – Terry Walsh

• Goal Between CSS 2015 and CSS 2016

• Create a “full package” for the Vital Signs, ECGs, Labs Central Tendency White Paper• Updated white paper with ADaM specifications• Qualified code for the displays in the white paper• Agreed upon structure for storing scripts• Agreed upon meta-data for scripts

– See the “Boxplot Challenge”• http://

www.phusewiki.org/wiki/index.php?title=WG5_Box_plot_challenge

• Working Group Needs• More project team members• Increased participation in white paper reviews – Help recruit!• Use/reference recommendations in existing final white papers!

– Forward to any existing standards groups– Link to white papers from Statistical Analysis Plans

• Participate in re-usable code development– Write, Test, Qualify, Review, Improve– Sign-up for Scriptathons (e.g., at 2016 CSS)– Participate in the boxplot challenge!

• Keep eyes open for existing scripts that need a public home• Advertise! Advertise! Advertise!

• How to Participate• Sign up for the PhUSE working group mailings– From phusewiki.org, click “Join a Working Group Now”– Standard Scripts Groups

• CSS-WG-Standard-Scripts (Entire Working Group)• CSS-WG-Standard-Scripts-WhitePapers (White Paper Project Team)• CSS-WG-Standard-Scripts-Platform (Script Repository)• CSS-WG-SS-WhitePaperReviewers (Notified when a white paper is

ready for review)

• See wiki pages for each of the projects (www.phusewiki.org)