PhUSE SS Update20130318

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Development of Standard Scripts for Analysis and Programming

18 March 2013

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 tables and figures
    • Developing a process and guidelines for documentation and management of scripts
    • Harness data standards whenever feasible
  • Leadership
    • Hanming Tu (Project Management)
    • Scott Getzin (Steering Committee Liaison)
    • Steve Wilson (FDA co-lead)
    • Mat Soukup (FDA co-lead)
    • Mary Nilsson (Industry co-lead)

Summary of Accomplishments

  • Script Repository has been created
    • Google Code chosen
    • Some scripts exist on repository
    • Call for additional scripts issued last month
    • MIT license chosen
    • Process guidelines developed
  • White Papers Describing Recommended Tables, Figures, and Listings
    • For common measurements (e.g., safety)
    • One white paper is nearing completion; 5 others planned

Google Code Platform

  • Google Code Repository
    • Google Code provides a free collaborative development environment for open source projects.
    • Project hosting on Google Code provides the tools necessary for engineers to work together to build, and maintain open source software.
    • Each project comes with its own member controls, Subversion/Mercurial/Git repository, issue tracker, wiki pages, and downloads section.
  • Roles in the repository
    • Require: Google Account email address. Each person must have already created a Google Account with that email address.
    • Project owners: may make any change to this project.
    • Project committers: may work in the project, but may not reconfigure it. In FDA/PhUSE project, a committer shall take some duties in the repository and shall take ownership for at least one script and shall guide and recruit developers to develop the script and document milestones of the script advancements.
    • Project contributors: start with the same permissions as non-members, but their role in the project is visible. A contributor shall take at least one duty in the repository and may participate at development of a script.
    • Additional permissions can be granted to committers and contributors on the project's people sub-tab.

Phuse tortoiseSVN commit.JPG

Team Member Recognition

We would like to recognize the following members for their contributions:

  • Evaluated 3 technology platforms for the repository based on requirements developed in March 2012
  • Performed ‘proof of concept’ tests
  • Evaluated UI tools and developed self-training materials for the Wiki.
Mike Carniello - Takaeda
Mike Carniello.JPG
Ian Fleming – D-Wise
Ian Fleming.JPG
Sam Tamioka - Sunovian
Sam Tamioka.JPG

Summary of Next Steps

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 (Lina Jørgensen)
  • P03: Maintain and enhance platform (repository) for sharing scripts (Hanming Tu)
  • P04: Legal ownership and issues in open source repository (Kevin Kane/Sally Cassells)
  • 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)

Last revision by Htu,03/1/2013