EPoS-MOL Release 0.9.10

EPoS-MoL

While the official shorthand nomenclature of lipids is a first and important step towards a reporting quality tool, an additional point score reflects the quality of reported data at an even more detailed granularity. Thus, the Empirical Point Score Model for MS-based Lipidomics (EPoS-MoL) is a lipidomics scoring scheme which takes into account all the different layers of analytical information to be obtained by mass spectrometry, chromatography and ion mobility spectrometry and awards scoring points for each of them.

EPoS-MoL is an R-package and also provides a Shiny app for the calculation of the EPoS-MoL score.

Release Notes

v0.9.10

• Fix: updated the eposmol class map table for PIPs and CerIP.

v0.9.9

• First release version of the eposmol R package and associated R Shiny application.
• Provides scoring for the initial set of lipid categories / classes supported by the empirical point score model for ms-based lipidomics.

Installing the package

The package can be installed from GitHub using the following command:

devtools::install_github("lifs-tools/empirical-lipid-ms-score")

If you want to install a particular release version, use the following command:

devtools::install_github("lifs-tools/[email protected]")

in this case for the tag version v0.9.9

Using the package

Please see the package vignette for a detailed description of the package functionality.

vignette("eposmol", package = "eposmol")

Documentation is also available at https://lifs-tools.github.io/empirical-lipid-ms-score/

Accessing the Shiny Webapp

The EpOs-MoL Shiny app can be accessed at the following URL:

https://apps.lifs-tools.org/p/app/eposmol

Running the app from RStudio

In order to load the packages, without the need to build and install it:

devtools::load_all()

You can then use the regular "Run App" button within RStudio to launch the Shiny app.

Alternatively, you can install the package, as shown above, then load it and run:

library(eposmol)
run_eposmol_app()

After that, the app is accessible from your browser. Please check your R console output for the exact URL and port. The following is just an example. The port may be different on your system:

Listening on http://127.0.0.1:6097

Building the Docker image

The Docker image can be built using the following command:

docker build -t eposmol .

If you use buildx, you will need to instruct the image builder to load the created image into the local docker:

docker build --load -t eposmol .

Running the Docker image

The Docker image can be run using the following command:

docker run -p 3838:3838 eposmol

The Shiny app will then be available at http://localhost:3838/eposmol/

Alternatively, you can use the provided compose file to automatically sync local changes during development to the RShiny application. You will need to reload your browser for changes to become effective:

./run.sh

Or use docker compose directly:

docker compose -f docker-compose-eposmol.yml up --watch

The Shiny app will then be available at http://localhost:3838/eposmol/

EPoS-MOL Release 0.9.9

EPoS-MoL

While the official shorthand nomenclature of lipids is a first and important step towards a reporting quality tool, an additional point score reflects the quality of reported data at an even more detailed granularity. Thus, the Empirical Point Score Model for MS-based Lipidomics (EPoS-MoL) is a lipidomics scoring scheme which takes into account all the different layers of analytical information to be obtained by mass spectrometry, chromatography and ion mobility spectrometry and awards scoring points for each of them.

EPoS-MoL is an R-package and also provides a Shiny app for the calculation of the EPoS-MoL score.

Release Notes

v0.9.9

• First release version of the eposmol R package and associated R Shiny application.
• Provides scoring for the initial set of lipid categories / classes supported by the empirical point score model for ms-based lipidomics.

Installing the package

The package can be installed from GitHub using the following command:

devtools::install_github("lifs-tools/empirical-lipid-ms-score")

If you want to install a particular release version, use the following command:

devtools::install_github("lifs-tools/[email protected]")

in this case for the tag version v0.9.9

Using the package

Please see the package vignette for a detailed description of the package functionality.

vignette("eposmol", package = "eposmol")

Documentation is also available at https://lifs-tools.github.io/empirical-lipid-ms-score/

Accessing the Shiny Webapp

The EpOs-MoL Shiny app can be accessed at the following URL:

https://apps.lifs-tools.org/p/app/eposmol

Running the app from RStudio

In order to load the packages, without the need to build and install it:

devtools::load_all()

You can then use the regular "Run App" button within RStudio to launch the Shiny app.

Alternatively, you can install the package, as shown above, then load it and run:

library(eposmol)
run_eposmol_app()

After that, the app is accessible from your browser. Please check your R console output for the exact URL and port. The following is just an example. The port may be different on your system:

Listening on http://127.0.0.1:6097

Building the Docker image

The Docker image can be built using the following command:

docker build -t eposmol .

If you use buildx, you will need to instruct the image builder to load the created image into the local docker:

docker build --load -t eposmol .

Running the Docker image

The Docker image can be run using the following command:

docker run -p 3838:3838 eposmol

The Shiny app will then be available at http://localhost:3838/eposmol/

Alternatively, you can use the provided compose file to automatically sync local changes during development to the RShiny application. You will need to reload your browser for changes to become effective:

./run.sh

Or use docker compose directly:

docker compose -f docker-compose-eposmol.yml up --watch

The Shiny app will then be available at http://localhost:3838/eposmol/