Software Resources and Downloads

Title Description Category Tags
DNA Microarray Data Processing

This website provides a set of software tools to quantitate, process, and combine data from a set of experiments performed with a two-color DNA microarray.


The need for appropriate statistical methods for coping with error in DNA microarray measurements is widely recognized.

MAGMA Multiobjective Analyzer for Genetic Marker Acquisition

A genetic mapping project, typically implemented during a search for genes responsible for a disease, requires the acquisition of a set of data from each of a large number of individuals. This data set includes the values of multiple genetic markers.


VisQuick is a Javascript library utilizing the Protovis project to provide configurable, interactive, informative data exploration tools.


Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.


Fastbreak is a set of python scripts implementing an O(n) algorithm for detecting translocations and other genetic structural variants from aligned mate pair sequence data in SAM/BAM format.


RF-ACE is an efficient implementation of a robust machine learning algorithm for uncovering multivariate associations from large and diverse data sets.

Golem (Go Launch on Every Machine)

Golem (Go Launch on Every Machine) is a light weight system for distributing analysis across processes and machines using web technologies and core features of the Go language.

Distributed Computing

The Adaptive Data Management Service Architecture provides web applications and services, and defines REST APIs to facilitate rapid application development.

Web Services
PIPE2 (Protein Information and Property Explorer) Web Application GO, Protein list, Visualization

A web service for enhanced P-value estimation in permutation tests

Web Application

ProbTF is a web server that enables the analysis of DNA sequences using mouse-specific position weight matrices from the TRANSFAC™ database.

Web Application

Pubcrawl is an application that combines literature based semantic distances with protein domain interactions to dynamically create network topologies of terms.

Web Application
Proteomics Toolkit Web Application Java, MS/MS, Proteomics

DoDoMa is a tool that automatically identifies transcription factors with matching DNA binding domains, and returns all associated position weight matrix (PWM).

Web Application
mspecLINE Web Application Integration, Literature, MS/MS
Trans-Proteomic Pipeline

The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.

Analysis Software C++, MS/MS, Proteomics, TPP, Validation

PeptideProphet is a tool for generating statistical validation of MS/MS search engines' spectra-to-peptide sequence assignments. This tool was orginally develped at the SPC, part of the ISB. PeptideProphet is now a core part of the Trans-Proteomic Pipeline software distrubtion.

Analysis Software C++, MS/MS, Proteomics, PSM, TPP, Validation
ATAQS (Automated and Targeted Analysis with Quantitative SRM)

As a complement to the well-established discovery proteomic methods, targeted mass spectrometry based on SRM is becoming an important tool for the generation of reproducible, sensitive and quantitatively accurate data from biological samples.

Analysis Software Analysis, Proteomics, SRM, Validation

ProteinProphet is a tool for generating probablities for protein identifications based on MS/MS data. ProteinProphet makes use of results from PeptideProphet, which produces validation results for peptide sequence identifications.

Analysis Software C++, MS/MS, Proteins, Proteomics, TPP, Validation