Difference between revisions of "Nonclinical Script Assessment Project"

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=== Working Pages ===
=== Working Pages ===

Revision as of 12:29, 26 June 2018

Welcome to the site for the "Nonclinical Script Assessment Project" group.

This page describes high-level project management details on the group, including purpose, milestones, attendees, and so on. We are part of the FDA/PhUSE Computational Sciences Nonclinical Working Group. Learn more about the larger working group at Nonclinical Topics Working Group.

Project Overview

Identified Need/Challenge

Analysis scripts for SEND data would be valuable tools. Can existing clinical scripts repository be used to help develop nonclinical scripts? What data processing steps are helpful to prepare SEND data for analysis?

Project Scope

To collaboratively develop analysis scripts based on SEND data.

Plan Ideas

1) Review outputs from the SEND for Analysis and Histopathology Visualization groups to identify possible scripts for development
2) Develop an R package to support SEND data processing for analysis.
3) Create an R shiny app to export the domain data merged with the groupSEND in CSV format
4) Building on what we learned creating the Body Weight Gain Analysis script, create LB visualization and other domains.
5) expanding the parsedata package to handle ISO 8601 duration helping us understand how to create a package
6) Statistical summary of a study to help answer: is the data complete?


March 2017 -- March 2018

1) Developed a Body Weight Gain Analysis script using the BW domain
2) Create a function to transform common ISO 8601 duration formats to units of seconds
3) Publish status of project at PhUSE CSS March 2018


1) Web conferences: every two weeks
2) PhUSE Wiki: ad hoc

Participation Needs

The team was established at the PhUSE CSS March 2016.

Call for participation!

What is the commitment?

  • Time (minimum of 1 hour every 2-3 weeks for team meetings, up to 3 hours / month)
  • Expected to contribute, not just be a spectator
  • Contribution of viewpoints and content
  • Wiki - creating/reviewing page content

If you would like to participate, please contact the co-leads for this group:
william.houser@bms.com or kevin.snyder@fda.hhs.gov

Work Group Participants


  • Atul Mishra, Pfizer
  • Anthony Fata, SNBL
  • Bill Houser, BMS
  • Drashtti Vasant, Bayer
  • Elaine Thompson, FDA
  • Fred Mura, PDS
  • Hanming Tu, Frontage Lab
  • Jarad Slain, MPI Research
  • Kevin Snyder, FDA
  • Kevin Cahill, EPL
  • Bill Varady, Boehringer Ingelheim
  • Bob Friedman, Xybion

Conference Calls and Minutes

Our meetings are scheduled every other Thursday at 10am Eastern continuing from Jan 4, 2018

To join one of our regular meetings: 1. Dial into the conference:

  Dial-in Number: (515) 604-9803 - United States
  Access Code: 986154
  International Dial-in Numbers: https://www.freeconferencecall.com/wall/houser/#international

2. Join the online meeting:

  Online Meeting Link: https://join.freeconferencecall.com/houser
  Online Meeting ID: houser

Meeting Minutes

April 1, 2016 Meeting Notes
April 29, 2016 Meeting Notes
May 12, 2016 Meeting Notes
May 26, 2016 Meeting Notes
June 9, 2016 Meeting Notes
June 23, 2016 Meeting Notes (meeting with vendors)
June 30, 2016 Meeting Notes
July 14, 2016 Meeting Notes
Aug 4, 2016 Meeting Notes
Aug 18, 2016 Meeting Notes
Sept 1, 2016 Meeting Notes
Sept 22, 2016 Meeting Notes
Oct 13, 2016 Meeting Notes
Oct 27, 2016 Meeting Notes
Nov 10, 2016 Meeting Notes
Dec 8, 2016 Meeting Notes
Jan 5, 2017 Meeting Notes
Jan 19, 2017 Meeting Notes
Feb 16, 2017 Meeting Notes
Mar 2, 2017 Meeting Notes
Mar 16, 2017 Meeting Notes
Mar 30, 2017 Meeting Notes
Apr 13, 2017 Meeting Notes
Apr 27, 2017 Meeting Notes
May 11, 2017 Meeting Notes
May 25, 2017 Meeting Notes
Jun 8, 2017 Meeting Notes
Jun 22, 2017 Meeting Notes
Jul 6, 2017 Meeting Notes
Jul 20, 2017 Meeting Notes
Aug 3, 2017 Meeting Notes
Aug 17, 2017 Meeting Notes
Aug 31, 2017 Meeting Notes
Sep 28, 2017 Meeting Notes
Oct 12, 2017 Meeting Notes
Oct 26, 2017 Meeting Notes
Nov 9, 2017 Meeting Notes
Dec 7, 2017 Meeting Notes
Dec 21, 2017 Meeting Notes
Jan 4, 2018 Meeting Notes
Jan 18, 2018 Meeting Notes
Feb 1, 2018 Meeting Notes
Feb 15, 2018 Meeting Notes
Mar 15, 2018 Meeting Notes
Mar 29, 2018 Meeting Notes
May 3, 2018 Meeting Notes
May 17, 2018 Meeting Notes
June 11, 2018 Meeting Notes

Project Design Notes



File:Converter tools between xpt and csv.docx

Working Pages

List of Scripts

Reference Material

Getting GitHub script repository access for contributors

Coding Standards:

PhUSE group focused on Good Programming Practices: http://www.phusewiki.org/wiki/index.php?title=Good_Programming_Practice

Learning R for SAS programmers

  1. R FOR SAS AND SPSS USERS - https://science.nature.nps.gov/im/datamgmt/statistics/r/documents/r_for_sas_spss_users.pdf
  2. SASxport Users Guide - https://cran.r-project.org/web/packages/SASxport/SASxport.pdf
  3. R for SAS programmers: It’s different, but friendly - http://www.lexjansen.com/phuse/2014/ad/AD04.pdf

More R Resources

  1. Cheat Sheets for R Concepts and Packages - https://www.rstudio.com/resources/cheatsheets/
  2. Using R for Data Analysis and Graphics - https://cran.r-project.org/doc/contrib/usingR.pdf