Java Proteomic Library

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.

In order to share code and ease maintenance, we developed a proteomic library in Java (Java Proteomic Library for JPL) of objects and routines commonly used in proteomics. The JPL is an on-going open-source project providing classes for the analysis of mass spectrometry proteomic data and enabling rapid bioinformatics application development in the Java programming language.

It is composed of several modules. The library contains APIs for manipulating basic biological objects such as peptide or protein sequences, post- translational modifications and mass spectra. It provides objects for protein digestion and peptide fragmentation taking into account various ion types and modifications.

It also supplies readers and writers and support different standard data file formats (fasta, mgf, mz(X)ML, dta, sptxt or msp).

JPL is a unit testing driven project and requires Java JDK 5 or higher.

2014/03/28

The JPL project is no longer updated and maintained. It has evolved after being completely reengineered and upgraded. The new project is available at http://mzjava.expasy.org.

2012/01/24

New version of tool Liberator.

2012/01/17

New release 1.0.