Project List

• Excavator 2.0
• Prospect
• Prospect_pipeline
• Cubic
• Jpop
• DomainParser 2
• Excavator 1.0
• RDC Prospect
• Promoco
• P-MAP  P-MAP server
• PRIME

If you have any problems with these programs, please email bug@csbl.bmb.uga.edu

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Open Source Projects

Excavator 2.0

Excavator is a computer software program for gene expression data clustering. It uses a set of unique clustering algorithms developed by the Computational Systems Biology Lab (CSBL) at the University of Georgia. Excavator represents data internally as a minimum spanning tree and outputs results to the user through the use of a micro-array data window, graphs, and a dendrogram viewer.

OS	Version	Complete Archive	Source JAR	Binary JAR	Documentation
Linux	1.0	excavator.tar.gz	excavatorSource.jar	excavatorBinary.jar	excavatorDocs.tar.gz
Windows	1.0	Coming soon
Mac OSX	1.0	Coming soon

People Involved
Dong Xu | Victor Olman | Jizhu Lu | Dustin Beadle | Ying Xu

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Cubic

Online Description

Cubic is a tool developed by the Computational Systems Biology Laboratory at the University of Georgia to be used for protein binding site prediction. Cubic was originally developed by Dr. Victor Olman and then was further developed and optimized (upto 10 times speedup on single-CPU machines) by Dr. Jizhu Lu. Cubic accepts up-stream sequences and a few other parameters as input and generates a set of binding sites and their statistical significance as output.

JCUBIC is a Java-based GUI for CUBIC program which can be used for transcription factor binding site prediction.

• CUBIC_2.0.4 Source Code

• Full CUBIC_2.0.3 Package
• CUBIC_2.0.3 Binaries (Linux)
• CUBIC_2.0.3 Source Code

• Full CUBIC_2.0.2 Package
• CUBIC-2.0.2 Binaries (Linux)
• CUBIC-2.0.2 Source Code

Graphic Interface
• JCubic-1.1.tar.gz

ChangeLog

OLD:

2.0.1
• Full CUBIC_2.0.1 Package
• CUBIC_2.0.1 Binaries (Linux)
• CUBIC_2.0.1 Source Code

2.0
• Full CUBIC_2.0 Package
• CUBIC_2.0 Binaries (Linux)
• CUBIC_2.0 Source Code

Graphic Interface
• JCubic-1.0.tar.gz (as of April 27th, 2005 this fixes a broken post)

Victor Olman, Jizhu Lu, PhuongAn Dam, Zhengchang Su, Ying Xu. CUBIC: Search for Binding Sites. CSB 2004: 666-667

People Involved
Victor Olman | Jizhu Lu | Ying Xu

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Jpop

JPOP (Joint Prediction of Operons) program JPOP is a set of java programs and Mathlab scripts to aid in the prediction of operon structures. JPOP integrates three sources of genomic information to predict operon structures in a sequenced genome:

1) COG (cluster of orthologs) assignments;
2) Phylogenetic profiles of genes;
3) Intergenic distances between gene pairs.

Version 0.1 download

Citation of the program:

Xin Chen, Zhengchang Su, Ying Xu and Tao Jiang. Computational prediction of operons in Synechococcus sp. WH8102. Gemone Informatics 15: 211-222, 2004.

People Involved
Xin Chen | Zhengchang Su | Ying Xu | Tao Jiang