Cytoscape

Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. A lot of Apps are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web.  As of March 2014, there are three versions of Cytoscape: Cytoscape 2.x, Cytoscape 3.x, and cytoscape.js. Cytoscape 3.x and cytoscape.js are stable, production versions under active development. Cytoscape 2.x is a legacy product in end-of-life support.

Network Based Stratification (NBS)

NBS is a method for stratification (clustering) of patients in a cancer cohort based on genome scale somatic mutations measurements and a gene interaction network.

Vespucci

Vespucci is a novel algorithm for de novo transcript identification from GRO-sequencing data, along with a system that determines transcript regions, stores them in a relational database and associates them with known reference annotations. As such, it provides a robust system for defining, storing and analyzing diverse classes of primary RNA transcripts that are of increasing biological interest.

HOMER

HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.

spotFinding Suite

spotFinding Suite is a package that uses a machine learning approach to identify single transcripts marked by fluorescence in wide-‐field epifluorescence images. This is particularly useful for single molecule fluorescence in situ hybridization, which is an increasingly commonly used technique.

Integrated Merging of Orthogonal Databases (IMOD)

IMOD is software designed to analyze genome-wide datasets, such as rate analysis, genetic interactions, and drug sensitivity, to identify novel genes that share similar genotypes.

NF-κB Web Model

Computational model to describe NF-κB activation events in response to TNFα or measured IKK activities.

PY-sub

Characterizing the Relationship Between Steady State and Response Using Analytical Expressions for the Steady States of Mass Action Models

Flow-Max

Quantitative deconvolution of CFSE cell population time course data with confidence.

SB2 MatLab

MatLab Simulators from Systems Biology: Simulation of Dynamic Network States (Daniel Hyduke, in Bernhard Palsson’s Lab). “Circles” and “lines” feature extraction method employed in MatLab, as developed in collaboration with Cell Dynamics Core.