Welcome to the website for software projects created and maintained by the Computational Omics and Systems Biology Group (Compomics). Below you can find a list of software we have developed, and on the subsequent pages are documentation and links to downloads and source code (hosted on our Github page).

  • colims

    A lims system to automate and expedite proteomics data management, processing and analysis.

  • compomics-utilities

    Open source Java library for computational proteomics

  • dbtoolkit

    Manipulating fasta sequence databases

  • denovogui

    Graphical user interface for de novo sequencing of tandem mass spectra

  • fragmentation-analyzer

    A standalone java tool for analyzing ms/ms fragmentation data.

  • iceLogo

    Next-generation visualization of protein consensus sequences by iceLogo.

  • icelogoserver

    The server edition of the iceLogo tool.

  • jsparklines

    Sparklines for java tables

  • jtraml

    Java implementation of the PSI-MS Transitions Markup Language (TraML) specification.

  • mappi-dat

    analysis and data management tool for high-throughput protein-protein interaction data generated from microarray-MAPPIT system

  • mascotdatfile

    Java API for MS/MS search results by Mascot (Matrix Science).

  • ms-lims

    Mass spectrometry based proteomics information management system.

  • ms2pip_c

    MS2PIP: MS2 Peak Intensity Prediction

  • ols-dialog

    Java front end to the ontology lookup service (OLS)

  • omssa-parser

    Java based parser for OMSSA OMX files

  • pepshell

    Visualization of conformational proteomics data.

  • peptide-shaker

    Interpretation of proteomics identification results

  • pladipus

    Platform for Distributed Proteomics Software

  • pride-asa-pipeline

    Uniform annotation of identified spectra.

  • reporter

    Protein quantification based on reporter ions

  • search-all-assess-subset

    An implementation of the Search All, Asses Subset strategy for FDR estimation in shotgun proteomics.

  • searchgui

    Highly adaptable common interface for proteomics search and de novo engines

  • spectrum_similarity

    Scoring functions to compare MS/MS spectra

  • tabloid-proteome


  • thermo-msf-parser

    Parser and viewer for thermo msf files.

  • ThermoRawFileParser

    Thermo RAW file parser that runs on Linux with mono

  • ThermoRawFileParserGUI

    Graphical user interface for the ThermoRawFileParser

  • xilmass

    An algorithm to identify cross-linked peptides

  • xtandem-parser

    Java based parser for X!Tandem output xml files