University of Helsinki Department of Computer Science

Department of Computer Science

Department information


CSBB Software Releases

This page describes software releases by the Computational Systems Biology and Bioinformatics group.

Max-margin Conditional Random Field

MMCRF is a structured classification algorithm for output spaces possessing an associative conditional random field structure. It uses kernelized input, and explicit (non-kernelized) output with graph structure. MMCRF uses conditional gradient optimization to and loopy belief propagation for approximate inference, used in gradient computations and prediction.

MMCRF software package

MMCRF was introduced in:

The method was applied for drug classification task in papers at PGM-2010 and PRIB-2010:


ReTrace is a computational tool for finding branching pathways in genome-scale metabolic networks.


ReMatch is a tool for automating the biochemical nomenclature matching problem encountered in construction of metabolic network models.

Positional Isotopomer Distribution Calculator

Positional Isotopomer Distribution Calculator (PIDC) is a software package that computes a positional isotopomer distribution of the selected atom type of the compound when mass spectra of the compound and its fragments are given.

Fragment Identificator

Fragment Identificator (FiD) is an Windows application for identification of molecular fragments from tandem mass spectrometry data when molecule and spectrum are given.

Pathway Assistant

Pathway Assistant offers tools for metabolic modeling.

Note: Pathway Assistant is offline for now.

String kernels

Implementations of the gappy string kernel algorithm described in the paper by Rousu and Shawe-Taylor are available here:
Previous update: 25.10.2010 - Esa Pitkänen