| Title | Description | Category | Tags |
|---|---|---|---|
| Addama |
The Adaptive Data Management Service Architecture provides web applications and services, and defines REST APIs to facilitate rapid application development. |
Web Services | |
| 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 |
| 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 | |
| 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. |
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| 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 | |
| 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 | |
| Gaggle |
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, Intergration, 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: |
Analysis Software | Database |
| 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 |
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