https://github.com/ipb-halle/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/.
https://github.com/ipb-halle/metfamily

analysis annotation comprehensive-metabolomics-studies mass-spectrometry metabolites

Last synced: 12 days ago
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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/.

• Host: GitHub
• URL: https://github.com/ipb-halle/metfamily
• Owner: ipb-halle
• License: gpl-3.0
• Created: 2016-03-23T13:08:11.000Z (almost 9 years ago)
• Default Branch: master
• Last Pushed: 2024-11-07T12:24:15.000Z (about 2 months ago)
• Last Synced: 2024-11-07T12:30:26.863Z (about 2 months ago)
• Topics: analysis, annotation, comprehensive-metabolomics-studies, mass-spectrometry, metabolites
• Language: R
• Size: 40 MB
• Stars: 10
• Watchers: 11
• Forks: 7
• Open Issues: 33
• Metadata Files:
  • Readme: README.md
  • Changelog: NEWS
  • License: LICENSE

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# 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-` 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.