Difference between revisions of "PHUSE Wiki"

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== Welcome ==
<!--------------------------------------Main heading----------------------------------------->
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This is the wiki home of the working group that is developing tools to support development and contributions of analysis scripts and programs.
{| id="mainpage-welcome-box" style="width:100%; background:#ffffff; border:2px solid #000000;"
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== White Paper ==
| style="width:30%; text-align:left; white-space:nowrap; color:#000;" |
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<span style="background-color:orange">
<div style="font-size:150%; border:none; margin:0; padding:.1em; color:#0097FF;">Welcome to the [[File:Phuse135.jpg|link=http://www.phuse.eu ]] Wiki</div>
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<big><big>''Notice'':  Draft white paper on Tables, Flags and Listings associated with central tendency open for comments</big></big>
<div style="font-size:100%;color:#ff8c00">Currently {{NUMBEROFUSERS}} users are helping to<br />
+
</span><br />
<big> '''''Share, Contribute and Advance'''''</big> clinical informatics.</div>
 
  
| style="width:15%;font-size:90%" |
 
'''[[FDA_Working_Groups|FDA Working Groups]]'''<br />
 
[[Image:icon-wgs.jpg|left|bottom|100px|link=FDA_Working_Groups|alt=]]&nbsp;
 
  
 +
'''[[Media:FDA_PhUSE_WhitePaper_CentralTendency_DRAFT2_ForReview_29Oct2012.docx|Click Here! Central tendency TFLs white paper draft (2nd draft)]]'''<br />
  
| style="width:15%;font-size:90%;" |
 
  
'''[[Annual_Conference|Annual Conference Budapest]]'''<br />
+
Please provide comments in the '''[[Talk:Development_of_Standard_Scripts_for_Analysis_and_Programming|Discussion Tab]]''' of the Working Group wiki by 14 December 2012.  Please provide only content-related comments and suggested references, and not formatting, spelling, or typographical error comments. 
[[Image:icon-conf.jpg|left|bottom|100px|link=Annual_Conference|alt=]]&nbsp;
+
With each comment, please provide the document section number.
  
 +
We realize the Discussion tab might not be an ideal method for providing and receiving comments.  Alternative methods are being assessed and may be available for future reviews.
  
| style="width:15%;font-size:90%;" |
+
== Script Development Platform ==
 +
Working group 5 are pleased to announce that the initial platform for sharing and developing scripts (SAS, R, S+, STATA etc) is up and running at the following location:
  
'''[[Good_Programming_Practice_Steering_Board|Good Programming Practice]]'''<br />
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* http://code.google.com/p/phuse-scripts
[[Image:icon-gpp.jpg|left|bottom|100px|link=Good_Programming_Practice_Steering_Board|alt=]]&nbsp;
 
  
 +
Some team members have set up Tortoise SVN which provides a GUI for working with GoogleCode in a windows environment.  The GoogleCode site is configured to use the MIT License.
 +
 +
Progress report on script sharing platform by Mike Carniello
 +
[[Platform for Standard Script Development: Progress as of September 18 2012]]
 +
 +
== Script Documentation ==
 +
We are working on creating templates for specification and user guide documentation.  Initial draft documents ready for review are here:
 +
 +
[[File:User_Guide_template.docx]]<br>
 +
[[File:Requirements Specifications template.doc]]<br>
 +
 +
We are hoping to use the Good Programming Practice processes being developed by a seperate PhUSE group.
 +
 +
== Validating Scripts ==
 +
Here are the slides from the FDA workshop in march 2012 from subgroup 2, working on defining the process of creating and validating slides:
 +
 +
[[File:WG5_Subgroup_2_slides_v2.pptx]]
 +
 +
Similar slides were presented to PSDM (Pharmaceutical Statistics and Data Management), a Dutch network group of statisticians, clinical programmers and data managers working in and for the pharmaceutical industry. The aim of the PSDM is to facilitate professional conduct and development of its members and to provide a platform for the exchange of expertise and ideas by organizing scientific meetings, workshops and courses in the Netherlands.  The slides were a personal reflection from Kevin Kane of his experiences at the conference:
 +
 +
[[File:FDA_CSS_PhUSE_initiative.pptx]]
 +
 +
The subgroup have started working on adding more details to the process of validating scripts.  Here is the initial document for review:
 +
 +
[[File:FDA_Scrips.ppt]]
 +
 +
== Mission  ==
 +
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:  Co-Leads ==
 +
{| class="wikitable"
 +
| Mary Nilsson || Eli Lilly || mnilsson@lilly.com
 +
|-
 +
| Sally Cassells || Next Step || sally.cassells@gmail.com
 +
|-
 +
| Hanming Tu || Octagon Research || HTu@OCTAGONRESEARCH.com
 +
|-
 +
| Kevin Kane || Phastar || kevink@phastar.co.uk
 +
|-
 +
| Joy Li || FDA - CDER || Joy.Li@fda.hhs.gov
 +
|-
 +
| Mat Soukup || FDA - CDER || mat.soukup@fda.hhs.gov
 
|}
 
|}
  
All content on this wiki is non-binding. All content expresses opinions of users and not necessarily that of their employer nor PhUSE.  See our [[PhUSEWiki:General_disclaimer|Disclaimers]] page.
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Steering Committee Liaison: Scott Getzin    sgetzin@lilly.com
{| border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"
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|-
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.
|valign="top" style="border:1px solid #000000; background-color:#ffffff; width:50%;" |
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<!-----------------------------What is this place------------------------------>
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== Conference Calls and Minutes ==
<div style="background:#E5F6FF; border-bottom:3px solid #939AAC; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">What is this place?</div>
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<!-- Add links to your Minutes pages by creating the page from the box and adding the name here. -->
The PhUSE Wiki is an [http://www.phuse.eu PhUSE]/FDA/Industry collaboration to provide a medium to share information specifically relating to clinical trial informatics.  The wiki has three main goals:<br />
+
[[WG5 11JAN2012]]<br>
#To support the [[FDA Working Groups|FDA Computational Science Center Working Groups]] by creating an online collaboration environment.
+
[[WG5 22FEB2012]] <br>
#To support the sharing of statistical and informatics software code (SAS,R etc).
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[[WG5 14MAR2012]] <br>
#To serve as a medium to share information related to software programming and processes for pharmaceutical, biotech, CRO, medical device and health care programmers.
+
[[WG5 Subgroup1 F2F March 19-20 2012]]<br>
<div style="border-bottom:3px solid #939AAC; padding:0.4em 1em 0.3em;">
+
[[File:WG5_subgroup_2_TC_7_Nov_12.docx]]<br>
</div>
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[[WG5 Subgroup3 F2F March 19-20]]<br>
<!--------------------------------What Can I do here?---------------------------------->
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[[WG5 Subgroup3 TC June 7]]<br>
<div style="background:#E5F6FF; border-bottom:1px solid #939AAC; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">What can I do here?</div>
+
[[Discussion Club: FDA/PhUSE CSS Working Group 5 Update Budapest 2012]]<br>
Well that depends who you are.  If you are an  '''[[FDA Working Groups|FDA Working Group member you can click here]]''' to access your specific working group.  If you are '''[[Annual_Conference|authoring a wiki for the Budapest Conference you can click here]]'''.Otherwise, if you have something to share, enter the title of your page into the box below.  If you are looking for something, use the search below or at the top right of this page.
 
<br /><br />
 
Start by  '''[[Special:UserLogin|creating a User account]]'''. In order to keep this Wiki transparent for all users it would be great if you could '''use your real name as your user name'''. Note that you also need to create a User account if you are a PhUSE member. '''Your PhUSE login details do not work here.''' It might also be good to familiarize yourself with the '''[[Help|wiki language]]'''.  After that, you are welcome to add, edit, read, and discuss anything in this wiki.  If you have questions, please '''[mailto:wikiadmin@phusewiki.org contact us]''' .  Interested, but don't know which topic to tackle?  Check out the '''[[Special:WantedPages|Wanted]]''' pages.  Make someone's day by answering their question.
 
<div style="border-bottom:1px solid #939AAC; padding:0.4em 1em 0.3em;">
 
</div>
 
  
<!----------------------------------------Recent Changes------------------------------------------->
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[[WG5 DDMONYYYY]](template)
<div style="background:#E5F6FF; border-top:2px solid #4A3C3B; border-bottom:2px solid #4A3C3B; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Recent Changes</div>
 
{{Special:RecentChanges/days=2,limit=25,hideminor}}
 
<div style="padding:0.4em 1em 0.3em;">
 
</div>
 
  
  
|style="padding:0 0.5em;"|
 
|style="background:#F9FDFF; border:1px solid #243B79; vertical-align:top; width:50%;" |
 
<!-------------------------Add New Wiki Page---------------------------------->
 
<div style="background:#E5F6FF; border-bottom:2px solid #4A3C3B; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Add a new wiki page</div>
 
 
<inputbox>
 
<inputbox>
 
type=create
 
type=create
buttonlabel=Add new Wiki!
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buttonlabel=Create new Minutes
 +
preload=Template:WG5Minutes
 
</inputbox>
 
</inputbox>
<div style="border-bottom:1px solid #F9FDFF; padding:0.4em 1em 0.3em;">
 
  
</div>
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== Approach ==
<!----------------------------------------News Updates------------------------------------------->
+
[[FDA/PhUSE WG5 Subgroup1B]]
<div style="background:#E5F6FF; border-top:2px solid #4A3C3B; border-bottom:2px solid #4A3C3B; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">News</div>
 
  
'''[[Wiki_Updates_May_2012|READ ME MAY 2012 - UPDATES TO WIKI FUNCTIONALITY]]'''
+
== Charter ==
 +
[[WG5 Charter]]
 +
==Scope==
  
[[Image:PhUSECSS2013.jpg|500x500px|link=https://www.phuse.eu/PhUSE-Conference-2013-Registration.aspx]] '''Register Now!'''
 
  
'''[http://www.phusewiki.org/wiki/index.php?title=Development_of_Standard_Scripts_for_Analysis_and_Programming Draft White Paper on Central Tendency TFL open for comments]''' <br />
+
===Example Scripts: Current and Future State===
  
'''[http://dij.sagepub.com/content/early/2012/08/09/0092861512456839 Join FDA/PhUSE Working Groups to Help Harness the Power of Computational Science published in the Drug Information Journal]''' <br />
+
Script Example - Posted: March 14, 2012:
  
[[Image:Banner_SDE.jpg|500x500px|link=http://www.phuse.eu/Single-Day-Events.aspx]]
+
[http://www.phusewiki.org/wiki/images/c/ca/WG5_-_Example_Overview.pptx  Example Overview Presentation]
'''[http://www.phuse.eu/One-Day-Events2012home.aspx See if a Single Day Event is coming to your area]'''<br />
 
  
[[Image:Brussels_Banner_.jpg|500x500px|link=http://www.phuse.eu/annual-conference.aspx |caption]] [[Indications|'''Patient Centricity: New Wiki for Indications''']]
+
[http://www.phusewiki.org/wiki/images/c/ce/WG5_-_Current_State_Example.zip  Current State Example Files]
  
'''[http://www.phusewiki.org/wiki/index.php?title=Category:PhUSE_Budapest_2012 Budapest 2012 Wikis ]''' <br />
+
[http://www.phusewiki.org/wiki/images/6/6d/WG5_-_Future_State_Example.zip  Future State Example Files]
  
</div>
+
.
 +
==Draft Call for Scripts==
 +
Here is draft text that is under review.  It is planned to send this out to the statistical computing community before the March 2013 conference:
  
 +
First Call for Scripts
  
 +
The Computational Science Center of the FDA in combination with the Pharmaceutical Users Software Exchange (www.phuse.eu), have a new project to create an open source repository for scripts (tools, computer programs, resources) to help manage, summarise, explore, analyse and report clinical trial data.  The scripts can be in any computer language (e.g. R/SAS/S+/STATA/C++/java).<br>
 +
We would like to invite you and your organisation to get involved in this project, by considering whether you could add any scripts to the repository.  Ask yourself the following two questions:<br>
 +
# Do you or your organisation have existing scripts that could be shared with the statistical computing community, that could help increase the efficiency of clinical trials?
 +
# Do you or your organisation have the time and/or resource to create new scripts?
 +
It is hoped that in the future, the repository will be the home to an extensive variety of tools and resources that can be used in medical research.  We are continuing to work to develop standards and processes relating to validation, so that scripts may be flagged as validated in the system.  Additionally, we hope that the development of scripts may build on existing CDISC standards, and may also be used as a catalyst to standardise the way we report clinical trials data.<br>
 +
Once scripts are added into the system, they can be enhanced and improved by the statistical computing community.  Issues with scripts can be tracked and fixed by the community of users.  All scripts will be available publicly without any cost.<br>
 +
Finally, there are obvious advantage of having scripts that could be used both in the drug development process as well as by regulators in the review and approval process.  We look forward to interacting with you in the script repository.<br>
  
|}
 
  
 +
==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==
 +
Working drafts and comments provided as part of the FDA/PhUSE Working Group efforts are informal communications and 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 FDA/PhUSE 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.
  
----
+
---
 
Last revision by {{REVISIONUSER}},{{REVISIONMONTH}}/{{REVISIONDAY}}/{{REVISIONYEAR}}
 
Last revision by {{REVISIONUSER}},{{REVISIONMONTH}}/{{REVISIONDAY}}/{{REVISIONYEAR}}
 +
 +
[[Category:WG5]]
 +
[[Category:Standard Scripts]]
 +
[[Category:FDA Working Groups]]
 +
 +
 +
<!-- Use one of the following Categories based on your WG: Data Validation ; Site Selection ; Data Integration ; Data Conversion ; CDISC Implementation; Standard Scripts ; Non-Clinical >

Revision as of 04:00, 16 January 2013


Welcome

This is the wiki home of the working group that is developing tools to support development and contributions of analysis scripts and programs.

White Paper

Notice: Draft white paper on Tables, Flags and Listings associated with central tendency open for comments


Click Here! Central tendency TFLs white paper draft (2nd draft)


Please provide comments in the Discussion Tab of the Working Group wiki by 14 December 2012. Please provide only content-related comments and suggested references, and not formatting, spelling, or typographical error comments. With each comment, please provide the document section number.

We realize the Discussion tab might not be an ideal method for providing and receiving comments. Alternative methods are being assessed and may be available for future reviews.

Script Development Platform

Working group 5 are pleased to announce that the initial platform for sharing and developing scripts (SAS, R, S+, STATA etc) is up and running at the following location:

Some team members have set up Tortoise SVN which provides a GUI for working with GoogleCode in a windows environment. The GoogleCode site is configured to use the MIT License.

Progress report on script sharing platform by Mike Carniello Platform for Standard Script Development: Progress as of September 18 2012

Script Documentation

We are working on creating templates for specification and user guide documentation. Initial draft documents ready for review are here:

File:User Guide template.docx
File:Requirements Specifications template.doc

We are hoping to use the Good Programming Practice processes being developed by a seperate PhUSE group.

Validating Scripts

Here are the slides from the FDA workshop in march 2012 from subgroup 2, working on defining the process of creating and validating slides:

File:WG5 Subgroup 2 slides v2.pptx

Similar slides were presented to PSDM (Pharmaceutical Statistics and Data Management), a Dutch network group of statisticians, clinical programmers and data managers working in and for the pharmaceutical industry. The aim of the PSDM is to facilitate professional conduct and development of its members and to provide a platform for the exchange of expertise and ideas by organizing scientific meetings, workshops and courses in the Netherlands. The slides were a personal reflection from Kevin Kane of his experiences at the conference:

File:FDA CSS PhUSE initiative.pptx

The subgroup have started working on adding more details to the process of validating scripts. Here is the initial document for review:

File:FDA Scrips.ppt

Mission

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: Co-Leads

Mary Nilsson Eli Lilly mnilsson@lilly.com
Sally Cassells Next Step sally.cassells@gmail.com
Hanming Tu Octagon Research HTu@OCTAGONRESEARCH.com
Kevin Kane Phastar kevink@phastar.co.uk
Joy Li FDA - CDER Joy.Li@fda.hhs.gov
Mat Soukup FDA - CDER mat.soukup@fda.hhs.gov

Steering Committee Liaison: Scott Getzin sgetzin@lilly.com

.

Conference Calls and Minutes

WG5 11JAN2012
WG5 22FEB2012
WG5 14MAR2012
WG5 Subgroup1 F2F March 19-20 2012
File:WG5 subgroup 2 TC 7 Nov 12.docx
WG5 Subgroup3 F2F March 19-20
WG5 Subgroup3 TC June 7
Discussion Club: FDA/PhUSE CSS Working Group 5 Update Budapest 2012

WG5 DDMONYYYY(template)



Approach

FDA/PhUSE WG5 Subgroup1B

Charter

WG5 Charter

Scope

Example Scripts: Current and Future State

Script Example - Posted: March 14, 2012:

Example Overview Presentation

Current State Example Files

Future State Example Files

.

Draft Call for Scripts

Here is draft text that is under review. It is planned to send this out to the statistical computing community before the March 2013 conference:

First Call for Scripts

The Computational Science Center of the FDA in combination with the Pharmaceutical Users Software Exchange (www.phuse.eu), have a new project to create an open source repository for scripts (tools, computer programs, resources) to help manage, summarise, explore, analyse and report clinical trial data. The scripts can be in any computer language (e.g. R/SAS/S+/STATA/C++/java).
We would like to invite you and your organisation to get involved in this project, by considering whether you could add any scripts to the repository. Ask yourself the following two questions:

  1. Do you or your organisation have existing scripts that could be shared with the statistical computing community, that could help increase the efficiency of clinical trials?
  2. Do you or your organisation have the time and/or resource to create new scripts?

It is hoped that in the future, the repository will be the home to an extensive variety of tools and resources that can be used in medical research. We are continuing to work to develop standards and processes relating to validation, so that scripts may be flagged as validated in the system. Additionally, we hope that the development of scripts may build on existing CDISC standards, and may also be used as a catalyst to standardise the way we report clinical trials data.
Once scripts are added into the system, they can be enhanced and improved by the statistical computing community. Issues with scripts can be tracked and fixed by the community of users. All scripts will be available publicly without any cost.
Finally, there are obvious advantage of having scripts that could be used both in the drug development process as well as by regulators in the review and approval process. We look forward to interacting with you in the script repository.


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

Working drafts and comments provided as part of the FDA/PhUSE Working Group efforts are informal communications and 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 FDA/PhUSE 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.

--- Last revision by Kevin Kane,01/16/2013