April 4, 2016 Meeting Notes
From PHUSE Wiki
Meeting minutes of Nonclinical_Script_Assessment_Project
April 29, 2016
|Present||First Name||Last Name||Affiliation|
- Since last meeting, Kevin Snyder supplied an example in GitHub that uses SAS to create HTML output
- Today Kevin and Hanming guided us through the processes needed to use GitHub
- Create account on GitHub site
- Ask hanming (firstname.lastname@example.org) to be a contributor
- Hanming will send an invitation that will come as email from "GitHub"
- If you don't see the invitation link in your email, you can accept the invitation from https://github.com/orgs/phuse-org/invitation
- You can download/clone a whole repository to your computer if you have a client for the repository. You can get either TortoiseSVN (http://blogs.wandisco.com/2011/10/17/how-to-install-tortoisesvn-and-make-your-first-repository-change/) or github desktop (https://desktop.github.com/). See the useful links at https://github.com/phuse-org/phuse-scripts/wiki/Read-Me-First-(Google-Code).
- Read other getting-started information here: https://github.com/phuse-org/phuse-scripts/wiki/Read-Me-First-%28Google-Code%29
- To see a list of contributed scripts
- get into GitHub and select the tab for the Wiki
- Look at the list on the right side and open the link for Simple Index
- When you have contributed a new script, create a YML metadata file so it can be added to the Simple Index
- Copy the metadata file for another script and put in your folder: <script-name>.tar_gz.yml
- Edit the copy to describe your script.
- The changes will appear in the index when Hnming runs his update script.
- Hanming explained that the script status choices are:
- Bill Varady will provide information on converting SAS to R. (R for SAS users)
- Fred Mura will see if he can share their sample SEND data.
- Bill Houser will ask Instem if they can supply their SEND data.
- Bill Houser will add a couple SAS scripts.
- Kevin Snyder is working on getting some scripts for working with PK files
- Everyone should create their GitHub accounts and begin looking at the conventions
- Folder Structure: https://github.com/phuse-org/phuse-scripts/blob/master/folder_structure_proposed.txt
- Name Convention: https://github.com/phuse-org/phuse-scripts/blob/master/naming_conventions_proposed.txt
- Metadata Tags: https://github.com/phuse-org/phuse-scripts/blob/master/MetaData_template.md
- Simple Index: https://github.com/phuse-org/phuse-scripts/wiki/Simple-Index
Agenda for next meeting:
- Discuss questions regarding the current GitHub conventions used by the clinical team.
- Are the status definitions useful and appropriate for us?
- Is it useful to prioritize script ideas? perhpas collecting names of who is willing to write, test, and use them?
- Do we want to create a process to consult with vendors before creating a script to ensure we don't discourage them from creating more useful tools?
- What should we aim for scripting languages (R) and output formats (PDF, HTML, etc)?
- How do we appropriately use the data folder to facilitate script creation and testing?
- We will need scripts to help with getting data in, relationships established, and ready to be processed and analyzed
- SEND to tumor.xpt converter
- Tool to assist in obscuring Test Article Identifiers, Study Numbers, and other sensitive information from SEND datasets