Difference between revisions of "Standard Analyses & Code Sharing"

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|Mary Nilsson || Industry Co-lead and Steering Committee Liaison ||Lilly || [mailto:nilsson_mary_e@lilly.com nilsson_mary_e (at) lilly.com]
 
|Mary Nilsson || Industry Co-lead and Steering Committee Liaison ||Lilly || [mailto:nilsson_mary_e@lilly.com nilsson_mary_e (at) lilly.com]
 
|-
 
|-
| Hanming Tu || Project Manager ||Frontage ||[mailto:htu@frontagelab.com htu (at) frontagelab.com]
+
| Hanming Tu || Industry Co-lead and Steering Committee Liaison ||Frontage ||[mailto:htu@frontagelab.com htu (at) frontagelab.com]
 
|-
 
|-
| Mat Soukup|| FDA Liaison || FDA ||[mailto:mat.soukup@fda.hhs.gov mat.soukup (at) fda.hhs.gov]
 
 
|}
 
|}
  
 
= Current Projects =
 
= Current Projects =
  
* [ [[Standard_Script_Index]] ]  [[https://github.com/phuse-org/phuse-scripts/wiki/Simple-Index Simple Index In Github]] - Frond-end User Interface (Hanming Tu)
+
 
* Github: [https://github.com/phuse-org/phuse-scripts Script Repository]
+
{| class="wikitable"
* [[WG5 Project 01|P01 - SDA]]: Script discovery and acquisition (Rebeka M Revis; Alfredo Rojas)
+
|-
* [[WG5 Project 02|P02 - RCD]]: Repository content and delivery (Gustav Bernard; Andrew Miskell; FDA Liaison: Mat Soukup)
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| '''Project || Scope || Recruiting'''
* [[WG5 Project 03|P03 - RGI]]: Repository governance and infrastructure: (Hanming Tu and Mike Carniello)
+
|-
* [[WG5 Project 07|P07 - CPE]]: Communication, Promotion and Education  (Jared Slain and Wendy Dobson)
+
|[[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
* [[WG5 Project 08|P08 - ADW]]: Analysis and Display White papers (Mary Nilsson)
+
|-
* [[WG5 Project 09|P09 - TDF]]: Test Data Factory (Peter Schaefer)
+
| [[Code_Sharing_(Repository)|Code Sharing (Repository)]] (Hanming Tu) || 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
 +
|-
 +
| [[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
 +
|-
 +
| [[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 || FYI
 +
|}
  
 
= News =
 
= News =
 +
# [https://www.phuse.eu/phuse-working-groups PhUSE Deliverables]
 
# 02 May 2017: Mary and Hanming gave a webinar to ASA: [[http://www.phusewiki.org/wiki/images/6/62/PhUSE_20170502_ASAWebinar_v2.pdf ASA presentation]] and [[http://amstat.commpartners.com/se/Meetings/Playback.aspx?meeting.id=779247 Recording]]
 
# 02 May 2017: Mary and Hanming gave a webinar to ASA: [[http://www.phusewiki.org/wiki/images/6/62/PhUSE_20170502_ASAWebinar_v2.pdf ASA presentation]] and [[http://amstat.commpartners.com/se/Meetings/Playback.aspx?meeting.id=779247 Recording]]
 
#February 2017:  The Adverse Events White Paper was finalized.  The final copy is in the PhUSE Deliverables Catalog
 
#February 2017:  The Adverse Events White Paper was finalized.  The final copy is in the PhUSE Deliverables Catalog
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= Conference Records =
 
= Conference Records =
==PhUSE/CSS 2017==
+
[http://www.phusewiki.org/wiki/index.php?title=Standard_Analyses_%26_Code_Sharing_Conference_Materials PhUSE CSS Conferences]
* [http://www.phusewiki.org/wiki/images/b/b8/CSS_2017_Schedule_SACS_draft_v7.pdf PhUSE CSS 2017 Agenda]
 
*  [http://www.phuse.eu/annual-conference.aspx Annual Conference 2017]
 
* Presentations
 
** [http://www.phusewiki.org/wiki/images/2/2d/PhUSE_CSS2017_StandardAnalysesAndCodeSharing_Intro.pdf Background and Vision - Mat Soukup]
 
** [http://www.phusewiki.org/wiki/images/d/d6/PhUSE_CSS2017_StandardAnalysesAndCodeSharing_SundayNight_v3.pdf Working Group Overview - Mary Nilsson/Hanming Tu]
 
** [http://www.phusewiki.org/wiki/images/a/a1/PhUSE_CSS2017_StandardAnalysesAndCodeSharing_ProjectUpdates_v2.pdf Project Updates - All Project Co-leads]
 
** [http://www.phusewiki.org/wiki/images/d/dc/PhUSE_CSS2017_StandardAnalysesAndCodeSharing_ScriptDev.pdf Script Development - Gustav Bernard/Andrew Miskell ]
 
** [http://www.phusewiki.org/wiki/images/8/87/PhUSE_CSS2017_StandardAnalysesAndCodeSharing_JumpStart.pdf JumpStart Scripts - Rebeka Revis]
 
** [http://www.phusewiki.org/wiki/images/8/8b/PhUSE_CSS2017_StandardAnalysesAndCodeSharing_Spotfire.pdf Inter Active Display using Spoffire - Rebeka Revis]
 
** [http://www.phusewiki.org/wiki/images/2/23/PhUSE_CSS2017_ADWandVisualizationsJointMeeting.pptx ADW and Data Visualizations Joint Meeting - Mary Nilsson]
 
** [http://www.phusewiki.org/wiki/images/7/77/PhUSE_CSS2017_ADWandCollectionInstructionsJointMeeting.pptx ADW and Collection Instructions Joint Meeting - Mary Nilsson]
 
** [http://www.phusewiki.org/wiki/images/f/fd/PhUSE_CSS2017_StandardAnalysesAndCodeSharing_Wrapup.pdf Breakup and Wrap-up Sessions]
 
* Posters
 
** [http://www.phusewiki.org/docs/2017_CSS_US/PP14_Final.pdf Standard Analyses and Displays for Common Data in Clinical Trials – The Journey Continues]
 
** [http://www.phusewiki.org/docs/2017_CSS_US/PP17_Final.pdf A User Guide for the PhUSE GitHub Repository]
 
** [http://www.phusewiki.org/docs/2017_CSS_US/PP16_Final.pdf A Contribution to Better Systems – The Test Data Factory (TDF) Project]
 
** [http://www.phusewiki.org/docs/2017_CSS_US/PP18_Final.pdf Reducing Duplicated Effort on Standard Analyses through Collaboration]
 
 
 
==PhUSE/CSS 2016==  
 
 
 
;[http://www.phuse.eu/Single-Day-Events.aspx PhUSE SDE 2016]
 
; PhUSE/CSS 2016 WG Agenda
 
 
 
[[SS_13Mar2016|13Mar2016 Agenda]]<br>
 
 
 
;PhUSE/CSS 2016 Meeting Slides
 
* [http://www.phusewiki.org/wiki/images/2/28/PhUSE_CSS2016SS_Agenda.pdf PhUSE/CSS 2016 Agenda]
 
* [http://www.phusewiki.org/wiki/images/e/ee/PhUSE_CSS2016SS_Motivation.pdf PhUSE/CSS 2016 Motivation]
 
* [http://www.phusewiki.org/wiki/images/b/b7/PhUSE_CSS2016SS_Projects.pdf PhUSE/CSS 2016 Project Updates]
 
* [http://www.phusewiki.org/wiki/images/8/84/PhUSE_CSS2016Git_and_Github.pdf PhUSE/CSS 2016 Git and Github]
 
== [https://www.cdisc.org/events/interchanges CDISC Interchange] ==
 
== [http://www.diaglobal.org/ DIA Global] ==
 
 
 
  
 
= Closed Projects =
 
= Closed Projects =

Latest revision as of 07:27, 22 October 2018


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

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) 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 FYI

News

  1. PhUSE Deliverables
  2. 02 May 2017: Mary and Hanming gave a webinar to ASA: [ASA presentation] and [Recording]
  3. February 2017: The Adverse Events White Paper was finalized. The final copy is in the PhUSE Deliverables Catalog
  4. 25 August 2016: Draft 2 of the Adverse Events white paper is available for review until 14 October 2016. See[white paper wiki page] for instructions on how to participate in the review.
  5. 11 May 2016: We renamed this working group from Development of Standard Scripts for Analysis and Programming to Standard Analyses and Code Sharing.
  6. 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
  7. 27 Aug 2015: All-hands meeting [slides]
  8. 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.
  9. 07 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 [CSS Catalog of Deliverables].
  10. 29 Sep 2014: All Hands Meeting slides File:Standard Script All-Hands meeting2014.pptx
  11. 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.
  12. 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.
  13. 18 November 2013: As part of the CSS conference we will host the first ever PhUSE "Script-athon". Find more info here: CSS conference
  14. 10 October 2013: The Central Tendency White Paper has been finalized!
  15. 26 June 2013: Hackathon_notes_20130626 are posted
  16. 01 May 2013: Individual Contributor License Agreement (Draft)
  17. FDA/PhUSE Standard Scripts Agenda (Date Published: March 13, 2013)
  18. The final draft of PhUSE Standard Scripts Update (Date Published: March 1, 2013)
  19. User Guide for Standard Script Repository has been drafted. (Date Published: February 28, 2013)
  20. The first Call for Scripts has been issued and a press release issued.
  21. GitHub has been chosen for our repository.

Working Group Meeting Minutes

Working Group Meeting Minutes
Year 2013 Year 2014 Year 2015 Year 2016 Year 2017 Year 2018
08Jan2013

16Jan2013
22Jan2013
30Jan2013
06Feb2013
13Feb2013
20Feb2013
27Feb2013
13Mar2013
19Mar2013
19Mar2013
03Apr2013
17Apr2013
01May2013
15May2013
12Jun2013
26Jun2013
10Jul2013
24Jul2013
07Aug2013
21Aug2013
28Aug2013
04Sep2013
18Sep2013
02Oct2013
16Oct2013
30Oct2013
13Nov2013
04Dec2013
18Dec2013

08Jan2014
22Jan2014
05Feb2014
19Feb2014
07Mar2014
17Mar2014Phuse
07Apr2014
16Apr2014
30Apr2014
14May2014
28May2014
11Jun2014
23Jul2014
06Aug2014
03Sep2014
17Sep2014

21Jan2015
19Feb2015
17Mar2015
01Apr2015
29Apr2015
27May2015
15Jul2015
05Aug2015
19Aug2015
16Sep2015
14Oct2015
11Nov2015
09Dec2015

06Jan2016
20Jan2016
27Jan2016
17Feb2016
02Mar2016
13Mar2016 Agenda
06Apr2016
11May2016
01Jun2016
06Jul2016
03Aug2016
07Sep2016
05Oct2016
02Nov2016
07Dec2016

04Jan2017
01Feb2017 CSS Agenda
09Feb2017
01Mar2017
15Mar2017
05Apr2017
03May2017
07June2017
05Jul2017
06Sep2017
04Oct2017
01Nov2017
06Dec2017

03Jan2018
17Jan2018
07Feb2018
21Feb2018
04Apr2018
02May2018
16May2018
20Jun2018
01Aug2018
05Sep2018
03Oct2018


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.

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