Difference between revisions of "Standard Analyses & Code Sharing"

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= Working Group Overview =
 
= 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.
 
  
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{| class="wikitable"
 +
|-
 +
|  Name/Vision/Goals || Presentation 
 +
|-
 +
|
 +
;Name:
 +
* Standard Analyses and Code Sharing (formerly Development of Standard Scripts for Analysis and Programming)
 +
;Vision:
 +
* Leverage crowd-sourcing to improve the content and implementation of analyses for medical research, leading to better data interpretations and increased efficiency in the clinical drug development and review processes.
 +
;Goals:
 +
# Establish and maintain a publicly available repository for storing program code to be used as analytical tools for medical research.
 +
# Where gaps exist, develop recommendations for analyses and displays in areas that could benefit from crowd-sourcing.
 +
# Where gaps exist, develop code for recommended analyses and displays that could benefit from crowd-sourcing (to reside in the repository).
 +
||
 
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= Leadership Team =
 
= Leadership Team =
 +
 +
{| class="wikitable" style="width:100%"
 +
|-
 +
| '''Name''' || '''Role''' || '''Organization'''|| '''E-mail'''
 +
|-
 +
|Mary Nilsson || Industry Co-lead and Steering Committee Liaison ||Lilly || [mailto:nilsson_mary_e@lilly.com nilsson_mary_e (at) lilly.com]
 +
|-
 +
| Hanming Tu || Industry Co-lead and Steering Committee Liaison ||Frontage ||[mailto:htu@frontagelab.com htu (at) frontagelab.com]
 +
|-
 +
| Wendy Dobson || PHUSE Project Manager || PHUSE || Wendy@phuse.eu
 +
|}
 +
 +
= Current Projects =
 +
  
 
{| class="wikitable"
 
{| class="wikitable"
 
|-
 
|-
! Name !! Role !! Organization!! E-mail
+
| '''Project || Scope || Recruiting'''
 
|-
 
|-
|Mary Nilsson || Industry Co-lead and Steering Committee Liaison ||Lilly || [mailto:nilsson_mary_e@lilly.com nilsson_mary_e (at) lilly.com]
+
|[[WG5_Project_08|Analysis and Display White papers]] (Mary Nilsson) || This project includes the development of white papers that provide recommended Tables, Figures, and Listings for clinical trial study reports and submission documents. The intent is to begin the process of developing industry standards with respect to analysis and reporting for measurements that are common across clinical trials and across therapeutic areas. Script developers could then create scripts consistent with the recommendations for all to use, improving efficiency and safety signal detection. || Yes
 
|-
 
|-
| Hanming Tu || Project Manager ||Accenture ||[mailto:hanming.h.tu@accenture.com hanming.h.tu (at) accenture.com]
+
| [[Code_Sharing_(Repository)|Code Sharing (Repository)]] (Hanming Tu, Bob Friedman, Gustav Bernard) || Establish and maintain a collaboration platform for leveraging crowd-sourcing to improve the content and implementation of analyses for medical research and leading to better data interpretations and increased efficiency in the clinical drug development and review processes. || Yes
 
|-
 
|-
| Steve Wilson|| FDA Liaison || FDA ||[mailto:Stephen.Wilson@fda.hhs.gov Stephen.Wilson (at) fda.hhs.gov]
+
| [[WG5_Project_07|Communication, Promotion and Education]]  (Jared Slain and Wendy Dobson) || The success of working group “Standard Analyses and Code Sharing” relies on the acceptance, input, feedback and further development from/by the user community. A main priority will be to develop a Communication Plan that conceptualizes efficient ways to communicate working group progress and results, e.g. white papers, and the call for scripts. It will define target groups, timing, communication channels, and the presentation. || Yes
 
|-
 
|-
| Mat Soukup|| FDA Liaison || FDA ||[mailto:mat.soukup@fda.hhs.gov mat.soukup (at) fda.hhs.gov]
+
| [[Best Practices for Quality Control and Validation]] (Maria Dalton and Jane Marrer) || Quality and accuracy is essential in the health and life sciences industries. Patients and regulators must be able to trust analyses of clinical data. This paper will provide an in-depth review of best practices for robust quality control. The scope of the paper will be quality control of analysis programming of clinical data in health and life sciences organisations. It is applicable to the organisations who produce analyses of clinical data, including Contract Research Organisations. The paper will not discuss oversight of outsourced programming || Yes
 +
|-
 +
| [[Good_Programming_Practice_in_Macro_Development|GPP in Macro Development]] (Ninan Luke) || Macros provide an effective way to automate and reuse code in a standard and consistent manner across SAS programs. This ability to reuse code means that the use of GPP is particularly important in macro code and we think that there is a need to develop a consensus and document good programming prairies specifically for macro programming. || Yes
 +
|-
 +
| [[WG5_Project_09|Test Data Factory]] (Peter Schaefer) || Several CS Projects develop and specify medical research methods, features, or processes, and some even create software components or subsystems for common tasks in drug development. As part of these efforts, a variety of SDTM or ADaM test datasets are required. The typical fallback position of project teams is to use data from the CDISC pilot project and/or anonymized study data that are provided by project team members. The Test Data Factory project aims at providing test data formatted in SDTM and ADaM that support a more systematic and comprehensive testing of these concepts and scripts. || Yes
 +
|-
 +
| [https://www.phusewiki.org/wiki/index.php?title=Standard_Analyses_%27Deliverables_%26_Key_Links%27 Key Links] || Previously published deliverables & News || FYI
 
|}
 
|}
  
= Current Projects =
+
== Small tasks that Working Group members can help with ==
 +
*CPE project - Help with entering conferences and due dates for abstract submissions
 +
*CPE project - After a presentation is given, add the ppt and pdf versions to the wiki
 +
 
 +
=Working Group Meeting Minutes=
 +
Starting in 2019, meeting minutes are kept in [https://phuse.teamworkpm.net/#projects/336388/notebooks Teamwork] instead of the Wiki which is accessible to Project Members only<br>
 +
<br>
 +
Previous minutes can be found [[Archived_Meeting_Minutes|here]]
  
* [ [[Standard_Script_Index]] ]  [[https://github.com/phuse-org/phuse-scripts/wiki/Simple-Index Simple Index In Github]] - Frond-end User Interface (Hanming Tu)
+
= Conference Records =
* [[WG5 Project 01|P01 - SDA]]: Script discovery and acquisition (Adrienne Bonwick and Aiyu Li)
+
[http://www.phusewiki.org/wiki/index.php?title=Standard_Analyses_%26_Code_Sharing_Conference_Materials PhUSE CSS Conferences]
* [[WG5 Project 02|P02 - RCD]]: Repository content and delivery (Dante Di Tommaso and Peter Schaefer)
 
** Central tendency package: target – March 13, 2016 
 
* [[WG5 Project 03|P03 - RGI]]: Repository governance and infrastructure: (Mike Carniello and Chris Butler)
 
* [[WG5 Project 07|P07 - CPE]]: Communication, Promotion and Education  (Dirk Spruck)
 
* [[WG5 Project 08|P08 - ADW]]: Analysis and Display White papers (Mary Nilsson)
 
  
 
= Closed Projects =
 
= Closed Projects =
Line 43: Line 81:
 
* [[WG5 Project 06|P06]]: Refine process for creating and editing scripts in Google Code              (Kevin Kane)
 
* [[WG5 Project 06|P06]]: Refine process for creating and editing scripts in Google Code              (Kevin Kane)
 
**Closed, any remaining tasks moved to Project 03
 
**Closed, any remaining tasks moved to Project 03
 
= News =
 
#10 Sep 2015: Final white paper version 1.0 of white paper on Outliers or Shifts from Normal to Abnormal: [[File:CS WhitePaper OutliersShifts v1.0.pdf]]
 
#27 Aug 2015: All-hands meeting [[http://www.phusewiki.org/wiki/images/5/5d/Standard_Script_All-Hands_meeting2015_v3.pdf slides]]
 
#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 [[http://www.phusewiki.org/wiki/index.php?title=SS_P08_Adverse_Events_White_Paper white paper wiki page]] for instructions on how to participate in the review. 
 
#09 Oct 2014: Version 1 of the Demographics/Disposition/Medications white paper has been finalized and available on www.phuse.eu (Publications section).  The white paper is also available from the [[http://www.phuse.eu/CSS-deliverables.aspx CSS Catalog of Deliverables]].
 
#29 Sep 2014: All Hands Meeting slides [[file:Standard_Script_All-Hands_meeting2014.pptx]]
 
#26 June 2014: Draft White Paper [[media:CSS_WhitePaper_DemoDispMed_draft3.docx|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.
 
#25 March 2014: Version 1 of PK white paper is available [[media:PhUSE_CSS_WhitePaper_PK_final_25March2014.pdf|Analyses and Displays Associated to Non-Compartmental Pharmacokinetics – with a Focus on Clinical Trials]].
 
#18 November 2013: As part of the CSS conference we will host the first ever PhUSE "Script-athon". Find more info here: [http://www.phuse.eu/css CSS conference]
 
#10 October 2013: The [http://www.phusewiki.org/wiki/images/4/48/CSS_WhitePaper_CentralTendency_v1.0.pdf Central Tendency White Paper] has been finalized!
 
#26 June 2013: [[Hackathon_notes_20130626]] are posted
 
#01 May 2013: [[SS_15591982_1_UKGROUPS_Harmony Individual Contributor License AgreementDOC|Individual Contributor License Agreement (Draft)]]
 
# [[Phuse_SS_Agenda20130318|FDA/PhUSE Standard Scripts Agenda]] (Date Published: March 13, 2013)
 
# The final draft of [[PhUSE_SS_Update20130318|PhUSE Standard Scripts Update]] (Date Published: March 1, 2013)
 
# [[User Guide for Standard Script Repository]] has been drafted.  (Date Published: February 28, 2013)
 
# The [[First Call For Scripts|first Call for Scripts]] has been issued and a [[Press Release for Call for Scripts 1|press release]] issued.
 
# [https://github.com/phuse-org/phuse-scripts/ GitHub] has been chosen for our repository.
 
 
= Group Meetings =
 
== Working Group PhUSE/CSS 2016 Agenda==
 
; Conference Date and Location
 
March 13~15, 2016
 
Silver Spring Civic Center
 
Silver Spring, Maryland, USA
 
 
; 3/13/2016 Sunday Night: Working Group Overview  (5:00 - 7:00 pm)
 
* 5:15~6:15 Working Group Introduction
 
** 10 minute presentation (Mary/Hanming)
 
** Need to prepare 5~8 slides
 
 
; 3/14/2016 Monday
 
* Monday 11:00 am - 12 pm - the whole group
 
** Background and Motivation (Steve/Mat)
 
** Mary: Overview of the WG
 
** Updates from three focus areas
 
*** Whitepaper Update (Mary)
 
*** Repository Update (Mike/Dante/Adie)
 
*** Communication (Dirk)
 
 
 
==Working Group Meeting Minutes==
 
{| border="1" class="wikitable"
 
|+ Standard Script Group Meeting Minutes
 
! Year 2013
 
! Year 2014
 
! Year 2015
 
! Year 2016
 
|-
 
|[[WG5_08Jan2013|08Jan2013]]<br>
 
[[WG5_16Jan2013|16Jan2013]]<br>
 
[[WG5_22Jan2013|22Jan2013]]<br>
 
[[WG5_30Jan2013|30Jan2013]]<br>
 
[[WG5_06Feb2013|06Feb2013]]<br>
 
[[WG5_13Feb2013|13Feb2013]]  <br>
 
[[Media:20Feb2013.docx|20Feb2013]]<br>
 
[[WG5_27Feb2013|27Feb2013]]<br>
 
[[WG5_13Mar2013|13Mar2013]]<br>
 
[[SS_19Mar2013|19Mar2013 Platform breakout session]]<br>
 
[[19Mar2013 White Paper Breakout Session|19Mar2013 White Paper Breakout Session]]<br>
 
[[SS_03Apr2013|03Apr2013]]<br>
 
[[SS_17Apr2013|17Apr2013]]<br>
 
[[SS_01May2013|01May2013]]<br>
 
[[SS_15May2013|15May2013]]<br>
 
[[SS_12Jun2013|12Jun2013]]<br>
 
[[SS_26Jun2013|26Jun2013]]<br>
 
[[SS_10Jul2013|10Jul2013]]<br>
 
[[SS_24Jul2013|24Jul2013]]<br>
 
[[SS_07Aug2013|07Aug2013]]<br>
 
[[SS_21Aug2013|21Aug2013 Co- and Project-Lead Meeting]]<br>
 
[[SS_28Aug2013|28Aug2013 Co- and Project-Lead Meeting]]<br>
 
[[SS_04Sep2013|04Sep2013]]<br>
 
[[SS_18Sep2013|18Sep2013]]<br>
 
[[SS_02Oct2013|02Oct2013]]<br>
 
[[SS_16Oct2013|16Oct2013]]<br>
 
[[SS_30Oct2013|30Oct2013]]<br>
 
[[SS_13Nov2013|13Nov2013]]<br>
 
[[SS_04Dec2013|04Dec2013]]<br>
 
[[SS_18Dec2013|18Dec2013]]<br>
 
|
 
[[SS_08Jan2014|08Jan2014]]<br>
 
[[SS_22Jan2014|22Jan2014]]<br>
 
[[SS_05Feb2014|05Feb2014]]<br>
 
[[SS_19Feb2014|19Feb2014]]<br>
 
[[SS_07Mar2014|07Mar2014]]<br>
 
[[SS_17Mar2014Phuse|17Mar2014Phuse]]<br>
 
[[SS_02Apr2014|07Apr2014]]<br>
 
[[SS_16Apr2014|16Apr2014]]<br>
 
[[SS_30Apr2014|30Apr2014]]<br>
 
[[SS_14May2014|14May2014]]<br>
 
[[SS_28May2014|28May2014]]<br>
 
[[SS_11Jun2014|11Jun2014]]<br>
 
[[SS_23Jul2014|23Jul2014]]<br>
 
[[SS_06AUG2014|06Aug2014]]<br>
 
[[SS_02SEP2014|03Sep2014]]<br>
 
[[SS_17SEP2014|17Sep2014]]<br>
 
|
 
[[SS_21JAN2015|21Jan2015]]<br>
 
[[SS_19FEB2015|19Feb2015]]<br>
 
[[SS_17Mar2015|17Mar2015 Phuse2015CSS]]<br>
 
[[SS_01Apr2015|01Apr2015]]<br>
 
[[SS_29Apr2015|29Apr2015]]<br>
 
[[SS_27May2015|27May2015]]<br>
 
[[SS_15Jul2015|15Jul2015]]<br>
 
[[SS_05Aug2015|05Aug2015]]<br>
 
[[SS_19Aug2015|19Aug2015]]<br>
 
[[SS_16Sep2015|16Sep2015]]<br>
 
[[SS_14Oct2015|14Oct2015]]<br>
 
[[SS_11Nov2015|11Nov2015]]<br>
 
[[SS_09Dec2015|09Dec2015]]<br>
 
|
 
[[SS_06Jan2016|06Jan2016]]<br>
 
[[SS_20Jan2016|20Jan2016]]<br>
 
[[SS_27Jan2016|27Jan2016]]<br>
 
|}
 
 
<inputbox>
 
type=create
 
buttonlabel=Create new Minutes
 
preload=Template:WG5Minutes
 
</inputbox>
 
  
 
= Legacy Projects/Information =
 
= Legacy Projects/Information =
  
 
''[[Development_of_Standard_Scripts_for_Analysis_and_Programming]]'' - This contains the legacy working group information.
 
''[[Development_of_Standard_Scripts_for_Analysis_and_Programming]]'' - This contains the legacy working group information.
 
  
 
= FDA Disclaimer =
 
= FDA Disclaimer =
Line 174: Line 90:
  
 
= Disclaimer for Others =
 
= 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.  
+
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.
+
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.

Latest revision as of 09:32, 5 September 2019


Working Group Overview

Name/Vision/Goals Presentation
Name
  • Standard Analyses and Code Sharing (formerly Development of Standard Scripts for Analysis and Programming)
Vision
  • Leverage crowd-sourcing to improve the content and implementation of analyses for medical research, leading to better data interpretations and increased efficiency in the clinical drug development and review processes.
Goals
  1. Establish and maintain a publicly available repository for storing program code to be used as analytical tools for medical research.
  2. Where gaps exist, develop recommendations for analyses and displays in areas that could benefit from crowd-sourcing.
  3. Where gaps exist, develop code for recommended analyses and displays that could benefit from crowd-sourcing (to reside in the repository).


Leadership Team

Name Role Organization E-mail
Mary Nilsson Industry Co-lead and Steering Committee Liaison Lilly nilsson_mary_e (at) lilly.com
Hanming Tu Industry Co-lead and Steering Committee Liaison Frontage htu (at) frontagelab.com
Wendy Dobson PHUSE Project Manager PHUSE Wendy@phuse.eu

Current Projects

Project Scope Recruiting
Analysis and Display White papers (Mary Nilsson) This project includes the development of white papers that provide recommended Tables, Figures, and Listings for clinical trial study reports and submission documents. The intent is to begin the process of developing industry standards with respect to analysis and reporting for measurements that are common across clinical trials and across therapeutic areas. Script developers could then create scripts consistent with the recommendations for all to use, improving efficiency and safety signal detection. Yes
Code Sharing (Repository) (Hanming Tu, Bob Friedman, Gustav Bernard) Establish and maintain a collaboration platform for leveraging crowd-sourcing to improve the content and implementation of analyses for medical research and leading to better data interpretations and increased efficiency in the clinical drug development and review processes. Yes
Communication, Promotion and Education (Jared Slain and Wendy Dobson) The success of working group “Standard Analyses and Code Sharing” relies on the acceptance, input, feedback and further development from/by the user community. A main priority will be to develop a Communication Plan that conceptualizes efficient ways to communicate working group progress and results, e.g. white papers, and the call for scripts. It will define target groups, timing, communication channels, and the presentation. Yes
Best Practices for Quality Control and Validation (Maria Dalton and Jane Marrer) Quality and accuracy is essential in the health and life sciences industries. Patients and regulators must be able to trust analyses of clinical data. This paper will provide an in-depth review of best practices for robust quality control. The scope of the paper will be quality control of analysis programming of clinical data in health and life sciences organisations. It is applicable to the organisations who produce analyses of clinical data, including Contract Research Organisations. The paper will not discuss oversight of outsourced programming Yes
GPP in Macro Development (Ninan Luke) Macros provide an effective way to automate and reuse code in a standard and consistent manner across SAS programs. This ability to reuse code means that the use of GPP is particularly important in macro code and we think that there is a need to develop a consensus and document good programming prairies specifically for macro programming. Yes
Test Data Factory (Peter Schaefer) Several CS Projects develop and specify medical research methods, features, or processes, and some even create software components or subsystems for common tasks in drug development. As part of these efforts, a variety of SDTM or ADaM test datasets are required. The typical fallback position of project teams is to use data from the CDISC pilot project and/or anonymized study data that are provided by project team members. The Test Data Factory project aims at providing test data formatted in SDTM and ADaM that support a more systematic and comprehensive testing of these concepts and scripts. Yes
Key Links Previously published deliverables & News FYI

Small tasks that Working Group members can help with

  • CPE project - Help with entering conferences and due dates for abstract submissions
  • CPE project - After a presentation is given, add the ppt and pdf versions to the wiki

Working Group Meeting Minutes

Starting in 2019, meeting minutes are kept in Teamwork instead of the Wiki which is accessible to Project Members only

Previous minutes can be found here

Conference Records

PhUSE CSS Conferences

Closed Projects

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

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.