| Title | Description | Category | Tags |
|---|---|---|---|
| ASAPRatio | 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 | 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 | BioTapestry is an interactive tool for building, visualizing, and simulating genetic regulatory networks. | Analysis Software | Visualization |
| Cancer miRNA regulatory Network | The 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 Simulation | In 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, simulation | Visualization |
| Chlamy Portal | Chlamy Portal is a web resource for exploration of Chlamydomonas reingardtii gene regulatory network. | Chlamydomonas, network, cmonkey, GRN, EGRIN | Web Service, Information Resource |
| cMonkey | cMonkey 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 expression | Computation |
| cMonkey2 | Python port of cMonkey, a machine-learning based method for clustering. | cMonkey, network inference, module, bicluster, gene expression | Computation |
| ISB-CGC | Access, explore and analyze large-scale cancer data through the Google Cloud with ISB-CGC. ISB's Cancer Gateway to the Cloud is a resource of the NIH Cancer Data Research Commons. | Cloud Software Platform | Cancer Data, Cancer Research, Cloud Computing, Google Cloud, Resource, Software Platform |
| Corra | 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 | 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. | Visualization | |
| Diatom Portal | Diatom 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, GRN | Web Service, Information Resource |
| DIRAC | Differential Rank Conservation (DIRAC) provides quantitative measures of how network ordering differs within and between phenotypes. | ||
| 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 | DoDoMa is a tool that automatically identifies transcription factors with matching DNA binding domains, and returns all associated position weight matrix (PWM). | Web Application | |
| EGRIN | Environmental and Gene Regulatory Influence Network for H. salinarum | h. salinarum, EGRIN, GRN, network | Web Service, Information Resource |
| EGRIN2 | This website facilitates targeted and exploratory investigation of the EGRIN2.0 model's predictions. | EGRIN2, network, cmonkey, inferelator, ensemble, halobacterium, E. coli | Web Service, Information Resource |
| EPEPT | A web service for enhanced P-value estimation in permutation tests | Web Application | |
| Fastbreak | 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. | Computation | |
| Genome Fingerprints | Genome fingerprints enable ultrafast comparison of personal genomes. | Analysis Software | Computation, Genomics, Analysis, Privacy |
| Genotype Fingerprints | Genotype fingerprints enable fast and private comparison of genetic testing results for research and direct-to-consumer applications. | Analysis Software | Computation, Genomics, Analysis, Privacy |
| Halobacterium species NRC-1 Genome Annotation DB | Search and retrieve Halobacterium species NRC-1 genome annotations | Halobacterium salinarum, genome, annotation | Information Resource |
| Inferelator | The Inferelator is an algorithm for infering predictive regulatory networks from gene expression data. | Inferelator, network inference, gene regulatory network, predictive, gene expression | Computation |
| 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 |
| Kojak | Database search algorithm to identify cross-linked peptides from tandem mass spectra. | Analysis Software | Analysis, C++, Cross-linking, Protein Interaction, Proteomics |
| Libra | 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 |
| 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. | ||
| mCADRE | We 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 Framework | The 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 |
| mspecLINE | Web Application | Integration, Literature, MS/MS | |
| MTB Network Portal | MTB 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, GRN | Web Service, Information Resource |
| Network Portal | Network Portal provides analysis and visualization tools for selected gene regulatory networks to aid researchers in biological discovery and hypothesis development. | network, cmonkey, inferelator, EGRIN, GRN | Web 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 Resource | Database, Proteomics, Public Resource, SRM, Transitions |
| PeptideAtlas | PeptideAtlas is a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. | Information Resource | Database, MS/MS, Proteomics, Public Resource |
| PeptideProphet | PeptideProphet is a tool for generating statistical validation of MS/MS search engines’ spectra-to-peptide sequence assignments. This tool was originally develped at the SPC, part of the ISB. PeptideProphet is now a core part of the Trans-Proteomic Pipeline software distrubtion. | Analysis Software | C++, MS/MS, Proteomics, PSM, TPP, Validation |
| PeptideSieve | 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 |
| PhosphoPep | PhospoPep 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 Resource | Database, MS/MS, Phosphoproteomics, Proteomics, Public Resource |
| PROM | Probabilistic 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. | ||
| ProteinProphet | 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 |
| Proteomics Toolkit | Web Application | Java, MS/MS, Proteomics | |
| Purple Membrane Simulation | This model simulates the biological pathway that produces bacterioRhodopsin in halobacterium. | Network, simulation, halobacterium, purple membrane | Visualization |
| RF-ACE | RF-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 and | Data Management | LIMS, Multi-Omics, Perl |
| SNAPR | A bioinformatics pipeline for efficient and accurate RNA-seq alignment and analysis. | ||
| SpectraST | SpectraST (short for “Spectra Search Tool” and rhymes with “contrast”) is a spectral library building and searching tool designed primarily for shotgun proteomics applications. | Analysis Software | C++, 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 Resource | Database, Proteomics, Public Resource, SRM, Transitions |
| Syntrophy Network Portal | Network and genome exploration database for syntrophic organisms D. vulgaris and M. maripaludis | desulfovibrio, methanococus, network, enigma, EGRIN | Web Service |
| TF Binding site Database - secure | TF Binding site Database | transcription factor, database | Web Service |
| The GESTALT Workbench | Large 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 Software | Analysis, Modeling |
| Trans-Proteomic Pipeline | The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC. | Analysis Software | C++, MS/MS, Proteomics, TPP, Validation |
| Tuberculosis Omics Portal | This 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 |
| VERA and SAM | The need for appropriate statistical methods for coping with error in DNA microarray measurements is widely recognized. | ||
| VisQuick | VisQuick is a Javascript library utilizing the Protovis project to provide configurable, interactive, informative data exploration tools. | Visualization |
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