Miami University
Miami University

LICENSE

GPL v3 Logo All of the software downloads, including but not limited to binary packages, source codes, documentation, manuals, and tutorials, are made available under the GNU General Public License, Version 3 (GPLv3). An abbreviated version of the license is presented below. A complete version of GPLv3 along with Frequently Asked Questions (FAQ) are available off GNU website at: http://www.gnu.org/licenses/gpl.html.

PEACE is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

PEACE is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. A complete version of GPLv3 along with Frequently Asked Questions (FAQ) are available off GNU website at: http://www.gnu.org/licenses/gpl.html.

Miami University makes no representations or warranties about the suitability of the software, either express or implied, including but not limited to the implied warranties of merchantability, fitness for a particular purpose, or non-infringement. Miami University shall not be liable for any damages suffered by licensee as a result of using, result of using, modifying or distributing this software or its derivatives.

By using or copying this Software, you the Licensee, agrees to abide by the intellectual property laws, and all other applicable laws of the U.S., and the terms of GNU General Public License (version 3).

SOFTWARE DOWNLOADS

This section provides downloads of the software and documentation associated with PEACE. The primary software package is the comprehensive Java Archive (JAR) file: peace.jar. You may download other packages and documentation depending on your needs. User documentation and video tutorials are available in the documentation page.

File Size Description
peace.jar 2.3 MB The main, comprehensive PEACE GUI (0.96) executable Java Archive (JAR) that encapsulates all the associated files to run PEACE & EAST on a Linux/Windows/OS-X/Windows machine. You must have Java 6.0 (JRE/JDK 1.6) installed on the machine. You may download JRE/JDK from: http://java.com/en/download/index.jsp.
peace.tar.gz 637 KB Just the core parallel clustering engine and EAST assembler (text mode versions) source code in a compressed (gzipped) tar ball. The tar ball contains all the files (including project files used by Eclipse and Microsoft Visual Studio 2008) needed to build the binaries.
peace_src.tar.gz 2.8 MB The complete GPL'd PEACE source code in a compressed (gzipped) tar ball. The tar ball contains PEACE clustering engine, EAST assembler, and the PEACE-GUI source code along with all the files (including project files used by Eclipse and Microsoft Visual Studio 2008) to build the binaries.
manual.pdf 2.1 MB The user guide and manual that provides a detailed description of using PEACE. The manual covers both the GUI and text versions of PEACE.

 

DATA SET DOWNLOADS

A sample data sets of cDNA sequences is provided below for testing and working with PEACE. You may download individual files from the table below. Optionally you may download all the files as a single compressed (gzipped) tar ball via the following link: Download full test dataset.

The data sets a subset of cDNA sequences collected from chlamydomonos. The chlamy.fa file in the tar ball is actually the entire chlamydomonos data set. The others files are subsets that have been created by randomly picking genes, and then taking the ESTs associated with those genes. The number refers to the percentage of the ESTs that were used. For example, chlamy_10pct.fa has 10% of the ESTs (randomly selected) from the original file (chlamy.fa).

File Size Description
chlamy_10pct.fa 9.7 MB The chlamy data set with 10% of the cDNA sequences (randomly selected) from the complete chlamy.fa data file.
chlamy_25pct.fa 26 MB The chlamy data set with 25% of the cDNA sequences (randomly selected) from the complete chlamy.fa data file.
chlamy_50pct.fa 56 MB The chlamy data set with 50% of the cDNA sequences (randomly selected) from the complete chlamy.fa data file.
chlamy_75pct.fa 80 MB The chlamy data set with 75% of the cDNA sequences (randomly selected) from the complete chlamy.fa data file.
chlamy.fa 108 MB The complete chlamy data set of the cDNA sequences.

 

REFERENCES TO OTHER DATA SETS

We use various other data sets (that can be freely downloaded) in our research. These data sets are provided and maintained by other researchers. Below are links to some of the data sets that we have used in our experiments. Please refer to the documentation supplied in the originating web site for details about these data sets

Source Files with Links
WCD A076941.fa, A686904.fa, pub_cot.fasta
EasyCluster Human Cured Data Set, Ricinus communis,
Meta Sim Synthetic Data Set Generated via Meta Sim