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.


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.


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


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


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.

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

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

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

Corra is a single, user-friendly, informatic framework, that is simple to use and fully customizable, for the enabling of LC-MS-based quantitative proteomic workflows of any size, able to guide the user seamlessly from MS data generation, through data processing, visualization, and statistical an

Analysis Software Analysis, MS1, Proteomics, Validation
iProphet Analysis Software C++, MS/MS, Peptides, Proteomics, TPP, Validation

It has been noted [1] that only a handful of a protein’s possible tryptic peptides are consistently observed in proteomics experiments. We denote these consistently observed peptides to be proteotypic peptides.

Analysis Software MS/MS, Peptides, Proteomics, Proteotypic