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Overview

Decision Forest (DF) is a novel pattern recognition method, which can be used to analyze DNA microarray, SELDI-TOF MS and SAR data.

Decision Forest Installation

Step 1. Download forest.zip file to your PC.
Step 2. Unzip forest.zip to any directory.
Step 3. Double click on run.bat in the above directory to launch Decision Forest.

System Setup Check list:

1. Java Running Environment(JRE) or JDK 1.4.0 or later is installed on your PC. JRE and JDK may be downloaded here .
2. java.exe is on your Path environment variable. Your system administrator may help you on this issue.

You may take following steps to check on java.exe:

• Open a Command Prompt window
• Type: java

If you see something like:

Usage: java [-options] class [args...]
(to execute a class)

or java [-options] -jar jarfile [args...]
(to execute a jar file)

You are ready to use Decision Forest. Otherwise, please seek help from your system administrator.

Help Manual

The QuickStart manual is available for downloading.

Articles

1. Hong H, Tong W, Xie Q, Fang H, Perkins R.  An in silico ensemble method for lead discovery: decision forest. SAR QSAR Environ Res. 2005 Aug;16(4):339-47.  Abstract
    
2. Xie Q, Ratnasinghe LD, Hong H, Perkins R, Tang ZZ, Hu N, Taylor PR, Tong W.,  Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method. BMC Bioinformatics. 2005 Jul 15;6 Suppl 2:S4. Abstract
    
3. Tong W, Hong H, Fang H, Xie Q, Perkins R. Decision Forest: Combining the Predictions of Multiple Independent Decision Tree Models. J. Chem. Info. Comp. Sci. 43(2):525 – 531, 2003 Abstract
    
4. Tong W, Xie Q, Hong H, Fang H, Shi L, Perkins R, Assessment of prediction confidence and domain extrapolation of two structure-activity relationship models for predicting estrogen receptor binding activity.  Environ Health Perspect. 2004 Aug;112(12):1249-54. Abstract
    
5. Tong W, Xie Q, Hong H, Fang H, Shi L, Perkins R, Petricoin E. Using decision forest to classify prostate cancer samples on the basis of SELDI-TOF MS data: assessing chance correlation and prediction confidence. Environ Health Perspect. 2004 Nov;112(16):1622-7. Abstract
    
6. Hong H, Tong W, Perkins R, Fang H, Xie Q, Shi L. Multiclass Decision Forest--a novel pattern recognition method for multiclass classification in microarray data analysis. DNA Cell Biol. 2004 Oct;23(10):685-94. Abstract

Contact Information

Please address any questions and suggestions to Dr. Weida Tong at +1-870-543-7142 (voice) or weida.tong@fda.hhs.gov.

For any technical problem and reporting bugs, please send e-mail to NCTRArrayTrackSupport@NCTR.FDA.GOV

For more information, please visit the NCTR/FDA's Center for Toxicoinformatics.