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
Cancer miRNA regulatory NetworkThe cancer miRNA regulatory network can be used to identify clinically relevant miRNAs that are candidates for improved diagnostics, prognostics and therapeutics.cancer, miRNA, network Web Application, Software Integration Framework
Cell Phone SimulationIn our cell phone simulation, students have the opportunity to use Cytoscape to model and interrogate the structure and properties of a cell phone network. Cell phone, network, education, cytoscape, simulationVisualization
Chlamy PortalChlamy Portal is a web resource for exploration of Chlamydomonas reingardtii gene regulatory network.Chlamydomonas, network, cmonkey, GRN, EGRINWeb Service, Information Resource
cMonkeycMonkey is a machine learning algorithm and data integration framework which aims to discover co-regulated modules, or bicluster in gene expression profiles.cMonkey, network inference, module, bicluster, gene expressionComputation
cMonkey2Python port of cMonkey, a machine-learning based method for clustering.cMonkey, network inference, module, bicluster, gene expressionComputation
ChromeGooseChromeGoose is a Chrome browser plugin for integration of bioinformatics analysis scripts, visualization tools and desktop and web resources by enabling seamless data exchange between all the components.Chrome, plugin, integration, visualizationSoftware Integration Framework
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
Diatom PortalDiatom Portal’s aim is not only to provide a repository for experimental and computational results, but to be used as an interface to existing resources.T. pseudonana, P. tricornutum, diatom, network, GRNWeb Service, Information Resource
DIRACDifferential Rank Conservation (DIRAC) provides quantitative measures of how network ordering differs within and between phenotypes.
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
EGRINEnvironmental and Gene Regulatory Influence Network for H. salinarumh. salinarum, EGRIN, GRN, networkWeb Service, Information Resource
EGRIN2This website facilitates targeted and exploratory investigation of the EGRIN2.0 model's predictions.EGRIN2, network, cmonkey, inferelator, ensemble, halobacterium, E. coliWeb Service, Information Resource
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
FiregooseThe Firegoose toolbar connects the Gaggle to the web. By downloading and installing this extension into your Firefox browser you can broadcast data between the Gaggle and web resources.Gaggle, Firefox, pluginSoftware Integration Framework
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
Genome BrowserThe Gaggle Genome Browser is an open source software tool for visualizing high-density data plotted against coordinates on the genome. Tiling arrays, ChIP-chip, and high-throughput sequencing are a few potential use-cases. Gaggle, genome browser, tiling arrays, ChIP-chipVisualization
Haloarcula marismortui Genome Annotation DBSearch and retrieve Haloarcula marismortui genome annotationsHaloarcula marismortui, genome, annotationInformation Resource
Halobacterium species NRC-1 Genome Annotation DBSearch and retrieve Halobacterium species NRC-1 genome annotationsHalobacterium salinarum, genome, annotationInformation Resource
Haplotype AnalysisAnalysis Software
InferelatorThe Inferelator is an algorithm for infering predictive regulatory networks from gene expression data.Inferelator, network inference, gene regulatory network, predictive, gene expressionComputation
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
KojakDatabase search algorithm to identify cross-linked peptides from tandem mass spectra.Analysis SoftwareAnalysis, C++, Cross-linking, Protein Interaction, Proteomics
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.
mCADREWe have used mCADRE to reconstruct genome-scale metabolic models for 126 different human tissues and cell types to establish a Tissue-Specific Encyclopedia of Metabolism (TSEM) as a community resource—the largest collection of tissue-specific metabolic models for human to date.
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.miRNA, network, prediction Web Application, Software Integration Framework
mspecLINEWeb ApplicationIntegration, Literature, MS/MS
MTB Network PortalMTB Network portal provides data integration, exploration and analysis tools for exploring the most comprehensive map to date of gene regulation inMycobacterium tuberculosis (MTB)Mycobacterium, omics4tb, tuberculosis, EGRIN, GRNWeb Service, Information Resource
Network PortalNetwork Portal provides analysis and visualization tools for selected gene regulatory networks to aid researchers in biological discovery and hypothesis, cmonkey, inferelator, EGRIN, GRNWeb Services, Information Resource
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
PROMProbabilistic Regulation of Metabolism (PROM) represents the successful integration of a genome scale transcriptional regulatory network with a biochemically detailed metabolic network, bridging two important classes of systems biology models that have rarely been combined quantitatively.
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
Purple Membrane SimulationThis model simulates the biological pathway that produces bacterioRhodopsin in halobacterium. Network, simulation, halobacterium, purple membraneVisualization
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
SNAPRA bioinformatics pipeline for efficient and accurate RNA-seq alignment and analysis.
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
Performs targeted analysis of SWATH-MS data, including automated detection of fragment ion interferences and pursuit of modified peptidesAnalysis softwareSWATH-MS, Proteomics, TPP, Validation
Syntrophy Network PortalNetwork and genome exploration database for syntrophic organisms D. vulgaris and M. maripaludisdesulfovibrio, methanococus, network, enigma, EGRINWeb Service
TF Binding site Database - secure TF Binding site Database transcription factor, database Web Service
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
Tuberculosis Omics PortalThis website serves as a portal for computational modeling program to generate an integrated, predictive gene regulatory network model of host/pathogen interactions by using omics data.mycobacterium, omics4tb, tuberculosis Website
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