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

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

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

Automated Statistical Analysis on Protein Ratio (ASAPRatio) accurately calculates the relative abundances of proteins and the corresponding confidence intervals from ICAT-type ESI-LC/MS data.

Analysis Software C++, MS/MS, Proteomics, Quantification, TPP
Haplotype Analysis Analysis Software

Libra is a module within the trans-proteomic pipeline to perform quantification on MS/MS spectra that have isobaric multi-reagent labeled peptides. More specifically, at ISB we use Libra on MS/MS spectra of iTRAQ labeled samples; it can also be used on TMT labeled samples.

Analysis Software C++, MS/MS, Proteomics, Quantification, TPP
Kaviar (queryable database of known variants)

(~Known VARiants) is a very simple tool for answering a very specific question:
What variants have been reported already for a given specific genomic location?

Analysis Software Database