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gastro-docker: Analyze 13C Breath Test and MRI gastric emptying

Author: Dieter Menne, Menne Biomed Consulting, Tübingen in cooperation with University Hospital of Zürich

The gastro-docker container allows you to compute fits to gastric emptying time series, or to 13C time series from a web interface without installation hassles if your institution allows you to install Docker.

On Github:
https://github.com/dmenne/gastro-docker

On Docker Hub:
https://hub.docker.com/r/dmenne/gastro-docker/

On Docker Cloud to check build details:
https://cloud.docker.com/app/dmenne/repository/docker/dmenne/gastro-docker/general

  • Analyze Gastric Emptying time series from MRI or from scintigraphy using package gastempt.
  • 13C breath test data for gastric emptying using packages breathtestshiny, breathtestcore and breathteststan. Fitting works already for single curves and for studies, tabular reporting is available.
  • We welcome your feedback on report formats and your experience with not-so-well-behaved time series, especially those with multiple peaks.

How to run

  • Install Docker. For Windows, you can get the installer from the Docker store.
  • Linux users know how to install Docker anyway.
  • Docker works best on Windows 10 Professsional where it can be run as a native application; on earlier Windows 64-bit versions, it requires the Oracle Virtual Box which is automatically installed. For installation details, see here.
  • Docker should have at least 2 GB of memory; on Windows, use Settings from the Docker tray icon. If you want to compile Docker yourself, at least 4 GB are required; expect strange error messages if you do not provide sufficient RAM.
  • From the command line, enter the following:
docker run --name gastro-docker  -p 8787:8787 -p 3838:3838 -d dmenne/gastro-docker
  • The first startup needs some time because 3 GB of applications are downloaded. Subsequent startups require only a few seconds.
  • Connect to the apps with your browser: localhost:3838.
  • To interact with the exposed functions via R code, you can connect to RStudio server with localhost:8787.
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