Software

GenePattern:
Contact: Michael Reich, Broad Institute (Dana Farber ICBP)
http://www.broad.mit.edu/genepattern
GenePattern is a software package for the analysis of molecular profiles, e.g., genome-wide microarray expression signatures. It includes a collection of analytic and visualization tools, interfaces for the easy construction of analytic pipelines and integration of new modules without additional programming. Gene Pattern is available for MacOS, Windows, and Linux platforms.

GeneCruiser:
Contact: Michael Reich, Broad Institute (Dana Farber ICBP)
http://www.genecruiser.org
GeneCruiser is an annotation tool that allows users to map genes from genomic databases to Affymetrix probes, find information about Affymetrix probes in genomic databases and find where Affymetrix probes are located in the human genome.

Gene Set Enrichment Analysis (GSEA):
Contact: Michael Reich, Broad Institute (Dana Farber ICBP)
http://www.broad.mit.edu/gsea/
GSEA is a computational method that determines if a given set of genes shows statistically significant differences between two biological states. It is useful for interpreting the results of gene expression studies.

Pathway Logic Assistant (PLA):
Contact: Carolyn Talcott, SRI (LBNL ICBP)
http://pl.csl.sri.com/
PLA implements the Pathway Logic vision. Pathway Logic is an approach to modeling biological entities and processes based on a simple but powerful logic, rewriting logic. It uses rewrite theories to formalize the informal models that biologists commonly use to explain biological processes; currently it is used for signal transduction and metabolic networks in mammalian cells. Pathways leading from different initial conditions can be generated automatically from collections of network elements and networks can be perturbed in silico.

Triple Array Model:
Contact: Tim Huang, OSU (OSU ICBP)
http://www.biostat.iupui.edu/Faculty/LANG%20LI.htm
This is a set of Splus statistical functions that can assess the correlation among gene expression, DNA methylation, and histone acetylation. Empirical Bayesian model is constructed to estimate the posterior probabilities for genes with altered expression, DNA methylation and histone acetylation status measured in a triple-microarray system. Their correlations are modeled and tested by a weighted linear regression.

TFBS Mixture Model:
Contact: Tim Huang, OSU (OSU ICBP)
http://www.biostat.iupui.edu/Faculty/LANG%20LI.htm
This is a set of R functions that can simultaneously perform TFBS pattern recognition, TFBS pattern selection, and target class prediction. The mixture model is composed of a random background TFBS distribution and an ordered pair-wise TFBS distribution. An E-M algorithm is developed to conducted for TFBS pattern selection, and target class prediction. It is successfully used to predict ERĄ direct up/down targets.

Order-Conserve TFBS Model:
Contact: Tim Huang, OSU (OSU ICBP)
Under Construction
This is a set of JAVA scripts that can predict the conserved TFBS between human and mouse based on their relative position. It is a new alignment method on the predicted TFBS between human and mouse¡¦s promoter. It is still under-construction.

Bisulfite Sequence Converter
Contact: Tim Huang, OSU (OSU ICBP)
http://cancer.informatics.indiana.edu/Nephew_lab/bisulfite_sequencing.htm
Bisulfite Sequence Converter is a web-service with an easy-to-use interface which enables primer design for bisulfite modified DNA. Given a DNA sequence of interest, the program returns the unmethylated and methylated sequences for the given sequence. The user can then check their methylation specific PCR or bisulfite sequencing primers with other programs, such as Amplify.

Heritable Clustering Algorithms
Contact: Tim Huang, OSU (OSU ICBP)
http://www.stat.ohio-state.edu/~statgen/SOFTWARE/Pathway/
This is a collection of Matlab codes that can be used to perform clustering analysis of data based on methylation profiles and phenotypic values. In particular, it contains routines that implement an AIC-like criterion for selecting number of clusters, Hybrid Clustering Algorithms, Likelihood-Based Clustering algorithm, and a pathway discover program that links the clusters into a tree progression format.

GDVTK- Genome Data Visualization Toolkit
Contact: Tim Huang, OSU (OSU ICBP)
http://bioinformatics.med.ohio-state.edu/GDVTK
GDVTK consists of a set of data structures and core for developing web-based applications to present genomic annotations in visual form. We employ GDVTK to develop a data management system for the storage and query of promoter CpG islands and the associated methylation and genetic changes, histone modifications and chromatin status in cancer cell lines, neoplastic epithelium, and tumor stroma.

ICBP-OSU/IU IntraWeb
Contact: Tim Huang, OSU (OSU ICBP)
http://epigenetics.med.ohio-state.edu
The IntraWeb provides consultation for the analysis and reporting of microarray data produced by the CICB investigators. We provide methods to address problems inherent to the analysis of large, complex epigenomic data sets. This program also integrates relevant data from CICB projects with other distributed resources, such as GenBank and CaBIG (Cancer Biomedical Informatics Grid), into a centralized data warehouse. The database, which is under development, will be made available to all the investigators through a user-friendly, secure web interface.

CViT
Contact: Tom Deisboeck, Massachusettes General Hospital (MGH ICBP)
https://www.cvit.org/
CViT¡¦s overall goal is to develop a module-based tool-kit for modeling and simulating multiscale cancer growth dynamics following a complex systems approach.

DIG, the Duke Integrated Genomics information system
Contact: Mark DeLong (Duke ICBP)
https://dig.cgt.duke.edu/
DIG provides a rich source of data and tools for exploration of genomic information from experimental, observational and literature sources. DIG includes advanced facilities for PubMed searches on key words and phrases as well as graphical interrogation of results using the GraphExplore software.

Graph Explore
Contact: Quanli Wang (Duke ICBP)
http://graphexplore.cgt.duke.edu/
GraphExplore is a comprehensive and easy-to-use environment for dynamically exploring large graphical structures. GraphExplore is able to dynamically retrieve information about the objects in the network from the Internet. You can either specify a relevant URL for each object or let GraphExplore query a relevant website with key words identifying objects of interest.

BFRM: Software for Sparse Bayesian Factor Analysis & Regression Modeling
Contact: Carlos Carvalho & Mike West (Duke ICBP)
http://icbp.genome.duke.edu/bfrm.html
The framework of sparse latent factor modeling coupled with sparse regression and anova for multivariate data is relevant in many exploratory and predictive problems with very high-dimensional multivariate observations. The statistical methods and computational analysis represented in BFRM is generic and will apply in many areas of application.

Dynetica: A Simulator of Dynamic Networks
Contact: Lingchong You (Duke ICBP)
http://labs.genome.duke.edu/YouLab/software/dynetica/index.php Dynetica provides a graphical construction of kinetic models of various biological systems, defined in terms of components in the system and their interactions. The program automatically generates the ordinary differential equations, time course simulations using either deteriministic algorithms or stochastic algorithms, and sensitivity analysis.

Software under development: Multi-scale tumour invasion simulator:
Contact: Sandy Anderson, Univ. Dundee (Vanderbilt ICBP)
http://www.maths.dundee.ac.uk/~sanderso/academic.html
A GUI driven simulation tool for the prediction of solid tumour growth in different microenvironments based on the Hybrid Mathematical Model of Solid Tumour Invasion (Anderson, 2005).

BioSig:
Contact: Bahram Parvin, LBNL (LBNL ICBP)
http://biosig2.lbl.gov:8443/biosigstruts/ BioSig is an integrated software package for LIM, experimental design, data collection, and managing computed quantitative representation of data. It is being used as a one-time data entry point for expression array, protein array, and imaging assays. It has an integrated visualization module for querying images and their computed quantitative representationas a function of treatment regimes