AddamaThe Adaptive Data Management Service Architecture provides web applications and services, and defines REST APIs to facilitate rapid application development.Web Services
ASAPRatioAutomated 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 SoftwareC++, 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 SoftwareAnalysis, Proteomics, SRM, Validation
BioFabricBioFabric uses a novel network presentation method that represents nodes as horizontal line segments, one per row.NetworkAnalysis, 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 SoftwareC++, Oligo Design
BioTapestryBioTapestry is an interactive tool for building, visualizing, and simulating genetic regulatory networks.Analysis SoftwareVisualization
CorraCorra 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 anAnalysis SoftwareAnalysis, MS1, Proteomics, Validation
CytoscapeCytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.Visualization
DNA Microarray Data ProcessingThis 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.
DoDoMaDoDoMa is a tool that automatically identifies transcription factors with matching DNA binding domains, and returns all associated position weight matrix (PWM).Web Application
EPEPTA web service for enhanced P-value estimation in permutation testsWeb Application
FastbreakFastbreak 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.Computation
GaggleThe 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 FrameworkDatabase, 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 AnalysisAnalysis Software
Host-Pathogen Network PortalThis website serves as a portal for computational modeling program to generate an integrated, predictive gene regulatory network model of host/pathogen interactions.Software Integration FrameworkDatabase, Integration, Software
Inheritance State Block AnalysisAnalysis Software
iProphetAnalysis SoftwareC++, 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 SoftwareDatabase
LibraLibra 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 SoftwareC++, MS/MS, Proteomics, Quantification, TPP
MAGMA Multiobjective Analyzer for Genetic Marker AcquisitionA 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.
miRvestigator FrameworkThe miRvestigator framework is designed to take as input a list of co-expressed genes and will return the most likely miRNA regulating these genes.Software Integration FrameworkDatabase, Software
mspecLINEWeb ApplicationIntegration, Literature, MS/MS
PASSEL (PeptideAtlas SRM Experiment Library)The PeptideAtlas SRM Experiment Library (PASSEL) is a component of the PeptideAtlas project that is designed to enable submission, dissemination, and reuse of SRM experimental results from analysis of biological samples.Information ResourceDatabase, Proteomics, Public Resource, SRM, Transitions
PeptideAtlasPeptideAtlas is a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments.Information ResourceDatabase, MS/MS, Proteomics, Public Resource
PeptideProphetPeptideProphet 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 SoftwareC++, MS/MS, Proteomics, PSM, TPP, Validation
PeptideSieveIt 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 SoftwareMS/MS, Peptides, Proteomics, Proteotypic
PhosphoPepPhospoPep version 2.0 is a project to support systems biology signaling research by providing interactive interrogation of MS-derived phosphorylation data from 4 different organisms.Information ResourceDatabase, MS/MS, Phosphoproteomics, Proteomics, Public Resource
PIPE2 (Protein Information and Property Explorer)Web ApplicationGO, Protein list, Visualization
ProbTFProbTF is a web server that enables the analysis of DNA sequences using mouse-specific position weight matrices from the TRANSFAC™ database.Web Application
ProteinProphetProteinProphet 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 SoftwareC++, MS/MS, Proteins, Proteomics, TPP, Validation
Proteomics ToolkitWeb ApplicationJava, MS/MS, Proteomics
PubcrawlPubcrawl is an application that combines literature based semantic distances with protein domain interactions to dynamically create network topologies of terms.Web Application
RF-ACERF-ACE is an efficient implementation of a robust machine learning algorithm for uncovering multivariate associations from large and diverse data sets.Computation
SBEAMS (Systems Biology Experiment Analysis Manangement System)In order to better support the data being generated by local microarray, proteomics, macroarray, and other experiments, we are developing and using SBEAMS (Systems Biology Experiment Analysis Management System), a framework for collecting, storing, and accessing data produced by these andData ManagementLIMS, Multi-Omics, Perl
SpectraSTSpectraST (short for “Spectra Search Tool” and rhymes with “contrast”) is a spectral library building and searching tool designed primarily for shotgun proteomics applications.Analysis SoftwareC++, MS/MS, Proteomics, Spectral library search, TPP
SRMAtlas The SRMAtlas is a compendium of targeted proteomics assays to detect and quantify proteins in complex proteome digests by mass spectrometry.Information ResourceDatabase, Proteomics, Public Resource, SRM, Transitions
The GESTALT WorkbenchLarge amounts of ‘raw’ genomic sequence data already exist and continue to grow exponentially. Many tools are available for automated analysis of these data by comparison to known sequences or by pattern recognition.Analysis SoftwareAnalysis, Modeling
Trans-Proteomic PipelineThe Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.Analysis SoftwareC++, MS/MS, Proteomics, TPP, Validation
UniPepUnipep is a project to provide access to proteomics data from the Serum Biomarker group at the Swiss Federal Institute of Technology (ETH) in Zurich Switzerland, and the Institute for Systems Biology (Information ResourceDatabase, MS/MS, N-glycocapture, Proteomics, Public Resource
VERA and SAMThe need for appropriate statistical methods for coping with error in DNA microarray measurements is widely recognized.
VisQuickVisQuick is a Javascript library utilizing the Protovis project to provide configurable, interactive, informative data exploration tools.Visualization