- Scientists & Leadership
- ISB Research
- Education & Outreach
|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.
|VERA and SAM||
The need for appropriate statistical methods for coping with error in DNA microarray measurements is widely recognized.
|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.
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.
RF-ACE is an efficient implementation of a robust machine learning algorithm for uncovering multivariate associations from large and diverse data sets.
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.
|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.
The Adaptive Data Management Service Architecture provides web applications and services, and defines REST APIs to facilitate rapid application development.
DoDoMa is a tool that automatically identifies transcription factors with matching DNA binding domains, and returns all associated position weight matrix (PWM).
|mspecLINE||Web Application||Integration, Literature, MS/MS|
|PIPE2 (Protein Information and Property Explorer)||Web Application||GO, Protein list, Visualization|
A web service for enhanced P-value estimation in permutation tests
ProbTF is a web server that enables the analysis of DNA sequences using mouse-specific position weight matrices from the TRANSFAC™ database.
Pubcrawl is an application that combines literature based semantic distances with protein domain interactions to dynamically create network topologies of terms.
|Proteomics Toolkit||Web Application||Java, MS/MS, Proteomics|
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|
PeptideProphet 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 Software||C++, MS/MS, Proteomics, PSM, TPP, Validation|
|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|
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|