The Proteome Informatics Group (PIG) at the Swiss Institute of Bioinformatics (SIB) is involved in the development of proteomics applications and services mainly available at ExPASy server.

MzJava is an on-going open-source project providing classes for the analysis of mass spectrometry data and enabling rapid bioinformatics application development in the Java programming language.


To allow modular development the project has been split into separate repositories. The parent repository is mzjava and there are separate repositories for mzjava-core, mzjava-proteomics and mzjava-glycomics.

To set up the project cd to the directory in which the project is to be cloned and execute the following commands

git clone                #replacing me with your git user name
cd mzjava
git clone           #replacing me with your git user name
git clone     #replacing me with your git user name
git clone      #replacing me with your git user name

Contribution guidelines

To contribute to the MzJava project follow the forking workflow. More details can be found on this page and video.

During the review of the pull requests the code will be run through SonarQube. The rules that we use can be found on our public SonarQube server

To set up forks of the repositories required for MzJava