Mass spectronomy-based proteomics

This is a project used to demonstrate the sysnthesis functionality provided by APE.

The use case aims to demonstrate the usefulness of the synthesis approach for solving a workflow discovery problem in bioinformatics. The scenario was demonstrated in [1].

No1 use case describes the 1st Use Case described in the paper, labeled as No. 1.


In order to be able to execute the generated workflows on the machine, the tools have to be annotated accordingly, and the corresponding software should be available.

In order to use the APE library from the command line, simply run the APE-<version>-executable.jar file using command:

java -jar APE-<version>-executable.jar [path_to_ape_configuration_file]

No 1

As an example, if you would download the APE-1.0.2-executable.jar to the root of APE_UseCases repository on your local machine, you could run this demo by executing the following command:

cd ~/git/APE_UseCases
java -jar APE-1.0.1-executable.jar MassSpectometry/No1/ape.configuration

The results of the synthesis would be:

MassSpectometry/No1/solutions.txt - First 100 candidate solutions in textual format
MassSpectometry/No1/Figures/          - Data-flow figures corresponding to the first 10 solutions
MassSpectometry/No1/Executables/  - Executable shell scripts corresponding to the first 6 solutions

Magnus Palmblad, Anna-Lena Lamprecht, Jon Ison, Veit Schwämmle, Automated workflow composition in mass spectrometry-based proteomics, Bioinformatics, Volume 35, Issue 4, 15 February 2019, Pages 656–664,