README.md
In ipb-halle/MetFamily: MetFamily: Discovering Regulated Metabolite Families in Untargeted Metabolomics Studies
MetFamily
Understanding metabolism is fundamental in biomedical and plant research and the identification and quantification of thousands of metabolites by mass spectrometry in modern metabolomics is a prerequisite for elucidating this area. However, the identification of metabolites is a major bottleneck in traditional approaches hampering advances. Here, we present a novel approach for the untargeted discovery of metabolite families offering a bird's eye view of metabolic regulation in comparative metabolomics. We implemented the presented methodology in the easy-to-use web application MetFamily to enable the analysis of comprehensive metabolomics studies for all researchers worldwide. MetFamily is available under http://msbi.ipb-halle.de/MetFamily/.
Docker images
The image sneumann/metfamily-base contains all dependencies
for the MetFamily web application.
Building the container(s)
Build via docker build -t sneumann/metfamily-base -f Dockerfile-base .
The image sneumann/metfamily is built on top and contains
the actual MetFamily code and web application.
Build via docker build -t sneumann/metfamily .
The build of the metfamily-base image https://hub.docker.com/r/sneumann/metfamily-base is triggerd whenever in the master branch a tag basechange-<date> e.g. basechange-20190804 is specified.
Running from a container
To run the resulting container, start with
docker run --rm -p 3838:3838 sneumann/metfamily:latest
and point your browser to http://localhost:3838/
Developing and debugging in a container
If you want to develop and debug stuff, you can build a container
on top of metfamily:latest that has an added rstudio server.
First build using docker build -t metfamily-rstudio -f Dockerfile-rstudio .
and then run via docker run -it --rm -p 8787:8787 metfamily-rstudio:latest.
CAVEAT: the Dockerfile-rstudio specifies a fixed user/password combo
of rstudio:rstudio. Do not use in Production !
You can also pass a local directory with checked out MetFamily git tree
via the docker run -v argument.
Running locally with MetFamily R Package
After installing the MetFamily R package and its dependencies, you can
library(MetFamily)
runApp(system.file("MetFamily", package="MetFamily"))
Running through Kubernetes
At IPB we are running MetFamily inside a Kubernetes cluster.
Please contact us for questions.
ipb-halle/MetFamily documentation built on Oct. 13, 2024, 7:03 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
MetFamily
Understanding metabolism is fundamental in biomedical and plant research and the identification and quantification of thousands of metabolites by mass spectrometry in modern metabolomics is a prerequisite for elucidating this area. However, the identification of metabolites is a major bottleneck in traditional approaches hampering advances. Here, we present a novel approach for the untargeted discovery of metabolite families offering a bird's eye view of metabolic regulation in comparative metabolomics. We implemented the presented methodology in the easy-to-use web application MetFamily to enable the analysis of comprehensive metabolomics studies for all researchers worldwide. MetFamily is available under http://msbi.ipb-halle.de/MetFamily/.
Docker images
The image sneumann/metfamily-base contains all dependencies
for the MetFamily web application.
Building the container(s)
Build via docker build -t sneumann/metfamily-base -f Dockerfile-base .
The image sneumann/metfamily is built on top and contains
the actual MetFamily code and web application.
Build via docker build -t sneumann/metfamily .
The build of the metfamily-base image https://hub.docker.com/r/sneumann/metfamily-base is triggerd whenever in the master branch a tag basechange-<date> e.g. basechange-20190804 is specified.
Running from a container
To run the resulting container, start with
docker run --rm -p 3838:3838 sneumann/metfamily:latest
and point your browser to http://localhost:3838/
Developing and debugging in a container
If you want to develop and debug stuff, you can build a container
on top of metfamily:latest that has an added rstudio server.
First build using docker build -t metfamily-rstudio -f Dockerfile-rstudio .
and then run via docker run -it --rm -p 8787:8787 metfamily-rstudio:latest.
CAVEAT: the Dockerfile-rstudio specifies a fixed user/password combo
of rstudio:rstudio. Do not use in Production !
You can also pass a local directory with checked out MetFamily git tree
via the docker run -v argument.
Running locally with MetFamily R Package
After installing the MetFamily R package and its dependencies, you can
library(MetFamily)
runApp(system.file("MetFamily", package="MetFamily"))
Running through Kubernetes
At IPB we are running MetFamily inside a Kubernetes cluster. Please contact us for questions.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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