# 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 was introduced in:

- J. Rousu, C. Saunders, S. Szedmak, and J. Shawe-Taylor. Efficient algorithms for max-margin structured classification. Predicting Structured Data, pages 105-129, 2007.

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

- Hongyu Su, Markus Heinonen, Juho Rousu. Multilabel Classification of Drug-like Molecules via Max-Margin Conditional Random Fields. Probabilistic Graphical Models, 2010. [Dataset]
- Hongyu Su, Markus Heinonen, Juho Rousu. Structured Output Prediction of Anti-Cancer Drug Activity. Pattern Recognition in Bioinformatics 2010. Lecture notes in bioinformatics, 2010. [Dataset]

## ReTrace

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

## ReMatch

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:- A MATLAB code is available from here
- kernlab stringkernel package contains a C++ implementation of the algorithm by Martin Kober

*Previous update: 25.10.2010 - Esa Pitkänen*