Standard Analyses & Code Sharing

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Revision as of 18:25, 25 February 2015 by MaryNilsson (talk | contribs) (Agenda for Group Sessions in PhUSE/CSS 2015)
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Working Group Overview

This working group will identify potential standard scripts for data transformations and analyses across and/or within a therapeutic area and exploratory analysis. The goal will be to begin the process of standardizing analyses across the industry, but also include examples of what can be done with a standardized data set. This will be an interactive session using online wiki to create and add input that can be shared openly between industry and regulatory.

Leadership Team

Name Role Organization E-mail
Mary Nilsson Industry Co-lead and Steering Committee Liaison Lilly nilsson_mary_e (at)
Hanming Tu Project Manager Accenture hanming.h.tu (at)
Steve Wilson FDA Liaison FDA Stephen.Wilson (at)
Mat Soukup FDA Liaison FDA mat.soukup (at)

Agenda for Group Sessions in PhUSE/CSS 2015

Sunday Night Working Group Meet & Greet (5 pm - 7 pm) on 3/15/2015
  • Overview of working group (Mary)
  • Overview about Google Code (Hanming)
  • Update on scriptathons (Mike)
  • Update from each projects (Project Leads)
Monday Morning (3/16/2015)
11 am - 12 pm - the whole group
  • Background and Trends (Mat)
  • Overview of WG and Tour of the WG Wiki Pages (Mary)
  • Tour of Repository: structure and Index page (Hanming)
  • Updates for each projects within the working group (Project leads)
Monday Afternoon (3/16/2015) Breakout sessions
Monday 1:30 - 4:30 pm
  • White papers
    • Outlier/shift white paper - Any last comments before finalizing; discuss recommendation to add adjusted percentages to displays
    • Adverse event white paper - Time window for treatment-emergence definition, AEs leading to discontinuation - primary vs multiple reasons in collection and impact on display, when to use time to event, when to use number of events, when to use events per patient year, etc.
  • Platform: qualification process
    • Overview of the qualification process
    • Exercise the qualification process on a pre-selected script
    • Goals of the qualification/scriptathon
      • Clearly define what is qualification process and what means to be qualified.
      • Exercise the qualification process on a selected script
      • Develop other scripts into new phases
      • Qualification is on-going process and the qualified script could be re-qualified for its new version (expanded feature or coverage).
Monday (3/16/2015) Evening Scriptathon
Monday 6:30 pm ~ 11:30 pm
  • Every person will choose one or two scripts to move from its current stage to next stage such as from “D” to “T”
  • At least one or two persons to exercise the whole qualification process on additional script (moving from “C” or “D” to “Q”)
  • Track the progress on a matrix for the status and traceability
Tuesday Morning (3/17/2015) Sessions
8:30 am -12:00 pm
  • 8:30 – 9:00 am: Group Meet
  • 9:00 – 10:00 am: Meet with Therapeutic Area User Guide (TAUG) group on eSHARE
  • 10:00 – 12:00 breakout
    • White papers
      • Hepatotoxicity white paper - feedback on displays recommended in the pre-draft
      • Questionnaire white paper - background on CDISC work and gap this white paper is filling, review some sample displays, recruit volunteers
      • TQT white paper - may not have any topics, but we will allow time to gather feedback on some sample displays if needed
    • Platform will work on creating documentation including tracking matrix
Tuesday Afternoon (3/17/2015) Group Meet
Tuesday 1:00 pm - 2:00 pm
  • wrap up together

Current Projects

  • P01: Look for existing scripts and store them in the repository (Adie Bonwick and Aiyu Li)
    • Ongoing
  • P02: Qualification of scripts in the repository (Dante Di Tommaso; Lina Jørgensen through 2013)
    • Ongoing.
  • P03: Maintain and enhance platform (repository) for sharing scripts (Mike Carniello/Hanming Tu)
  • P04: Legal ownership and issues in open source repository (Sally Cassells)
    • Task completed, creating a summary is planned
  • P05: Create templates and metadata for documenting scripts and coding practices (Jean-Marc Ferran and Eric Sun)
    • Ongoing
  • P07: Implement and further develop communication plan for standard scripts (Dirk Spruck)
    • Ongoing
  • P08: Create white papers providing recommended display and analysis including Table, List and Figure shells (Mary Nilsson)
    • Ongoing

Closed Projects

  • P06: Refine process for creating and editing scripts in Google Code (Kevin Kane)
    • Closed, any remaining tasks moved to Project 03


  1. 09 Oct 2014: Draft 1 of the Adverse Events white paper is available for review until 01 December 2014. This review is a partial draft intended to get initial feedback on the proposed tables and figures. See the [white paper wiki page] for instructions on how to participate in the review.
  2. 09 Oct 2014: Draft 3 of the Outliers/Shifts white paper is available for review until 01 December 2014. This will likely be the last draft sent for review. See the [white paper wiki page] for instructions on how to particpate in the review.
  3. 09 Oct 2014: Version 1 of the Demographics/Disposition/Medications white paper has been finalized and available on (Publications section). The white paper is also available from the [CSS Catalog of Deliverables].
  4. 29 Sep 2014: All Hands Meeting slides File:Standard Script All-Hands meeting2014.pptx
  5. 26 June 2014: Draft White Paper Analyses and Displays Associated with Demographics, Disposition, and Medication in Phase 2-4 Clinical Trials and Integrated Submission Documents is available for review until 8 August 2014.
  6. 25 March 2014: Version 1 of PK white paper is available Analyses and Displays Associated to Non-Compartmental Pharmacokinetics – with a Focus on Clinical Trials.
  7. 18 November 2013: As part of the CSS conference we will host the first ever PhUSE "Script-athon". Find more info here: CSS conference
  8. 10 October 2013: The Central Tendency White Paper has been finalized!
  9. 26 June 2013: Hackathon_notes_20130626 are posted
  10. 01 May 2013: Individual Contributor License Agreement (Draft)
  11. FDA/PhUSE Standard Scripts Agenda (Date Published: March 13, 2013)
  12. The final draft of PhUSE Standard Scripts Update (Date Published: March 1, 2013)
  13. User Guide for Standard Script Repository has been drafted. (Date Published: February 28, 2013)
  14. The first Call for Scripts has been issued and a press release issued.
  15. Google Code has been chosen for our repository.

Group Meetings

Standard Script Group Meeting Minutes
Year 2013 Year 2014 Year 2015

19Mar2013 Platform breakout session
19Mar2013 White Paper Breakout Session
21Aug2013 Co- and Project-Lead Meeting
28Aug2013 Co- and Project-Lead Meeting



Legacy Projects/Information

Development_of_Standard_Scripts_for_Analysis_and_Programming - This contains the legacy working group information.

FDA Disclaimer

FDA comments are an informal communication and represent the individual's best judgment. These comments do not bind or obligate FDA. The contents of this wiki are from the individual contributors and do not necessarily reflect the view and/or policies of the Food and Drug Administration, the employers of the individuals involved or any of their staff.

Disclaimer for Others

Documents and comments provided as part of the PhUSE CSS Working Group efforts represent the individual's best judgment. They do not necessarily reflect the view and/or policies of their company or institution, the employers of the individuals involved or any of their staff.

Note: Individuals participating in PhUSE CSS Working Group discussions on the wiki are responsible for determining whether this disclaimer is sufficient for complying with any relevant procedures from their company or institution.