Nov 10, 2016 Meeting Notes
From PHUSE Wiki
Meeting minutes of Nonclinical_Script_Assessment_Project
Oct 27, 2016
|Present||First Name||Last Name||Affiliation|
|Yes||Peter||Scaefer||Validated Cloud Applications|
Action Items from previous process meetings:
- We should reach out to Pinnacle 21 to join us - Bill sent email Aug 17, 2016 and Sept 22 asking if they would be interested in in joining us. - Tony will ask Mike to see if he is communicating with Max at Pinnacle 21.
- Their experience would help us
- They could benefit from our contributions
- Bill Houser will create list of principles that we agree to as general practice.- not done yet.
- Kevin Snyder found that to analyze the PDS data we need to look at PCTPTNUM to get the hour after dose, but this doesn't work with the Instem dataset. For the Instem script we need PCELTM and PCRFTDTC. He suggested it would probably be worth enabling the script to work with either dataset.
- We discussed if we should preserve the SEND values or modify them as we prepare the information for analysis. We concluded that we should preserve the SEND values and copy or transform them to variables we use for analysis.
- As we proceed, we agreed to try to create generalized functions in a library. (concept similar to Unix commands in that they are simple and can be combined in powerful ways).
- New Function Idea: create a function that will pull rows from a .xpt file that match a subjects defined by a characteristic in another .xpt file (e.g., get the body weight data from only male animals)
- All should try to the TK analysis script with our private data to see what we can learn.
Notes from previous coding meetings:
- We should each try the script on our own data and share the results
- Stephen tried and encountered an error reading the xpt file. There are multiple analytes in his data, but the data frame only had one analyte.
- Kevin has successfully used it on a study with multiple analytes.
- Stephen will try some more.
- Kevin showed the Krona plotting tool for browsing hierarchical data: https://github.com/marbl/Krona/wiki
- The team began a collaborative in-meeting project to write an R script that can pull data from control animals.
- Hanming volunteered to integrate a parameter file (using .yml format) into one of the scripts.
Previous Meeting Notes:
- Bob Friedman contributed an R script that can convert an excel template of a TS domain into an .xtp file.
- Hanming contributed a function that can download a single .xpt file and represent it as a dataframe in R.
- The team contributed further together in writing the R script that can pull data from control animals.
- Bob Friedman talked through his CreateTsXPT.R script.
- Peter Schaefer presented his Test Data Factory Project.
- Bob volunteered to talk through a clinical R script that he has contributed in the past.
- Peter (or perhaps a representative from his PhUSE project) will begin attending our meetings on a regular basis.
- Peter will consider the possibility of generating test data sets for toxicokinetics data in accordance with the SEND standard with the goal of identifying all of the different ways that this data could be "correctly" encoded and determining whether a universal analysis routine could be performed successfully across all possible interpretations of the standard.