Software Resources and Downloads

Title Description Category Tags

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

Web Services

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
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

BioFabric uses a novel network presentation method that represents nodes as horizontal line segments, one per row.

Network Analysis, Visualization
BioSap (Blast Integrated Oligonucleotide Selection Accelerator Package)

The advent of custom designed oligonucleotide microarrays made possible by recent advancements in ink-jet microarray synthesis technology, provides the opportunity to quickly iterate through different microarray experiments.

Analysis Software C++, Oligo Design

BioTapestry is an interactive tool for building, visualizing, and simulating genetic regulatory networks.

Analysis Software Visualization

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

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.

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.


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

Web Application

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

Web Application

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.


The practice of systems biology depends upon many software tools, operating on many kinds of data from many different sources. The Gaggle is a framework for exchanging data between independently developed software tools and databases to enable interactive exploration of systems biology data.

Software Integration Framework Database, Software
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
Haplotype Analysis Analysis Software
Host-Pathogen Network Portal

This website serves as a portal for computational modeling program to generate an integrated, predictive gene regulatory network model of host/pathogen interactions.

Software Integration Framework Database, Integration, Software
Inheritance State Block Analysis Analysis Software
iProphet Analysis Software C++, MS/MS, Peptides, Proteomics, TPP, Validation
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

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