College of Veterinary Medicine

Veterinary Microbiology & Pathology

Program PLASMID


PLasmid Analysis System and Marker IDentification (PLASMID), V0.91, 03 Jun 08

PLASMID is a tool for designing plasmid microarrays by using existing mixed microarray data or using virtual microarray data. PLASMID combines clustering methods, probe ranking methods and stepwise discriminant analysis to aid in the design of optimized, mixed-plasmid microarrays. These microarrays can be used subsequently for classification and comparative genetics of plasmids.

PLASMID is freely available for academic users. This version is for Windows XP and Windows Vista, but future releases will accommodate other operating systems.

Please note that this program requires Java software to be installed on the same computer. If you do not have Java software installed, please go to: http://java.sun.com/javase/downloads/index.jsp, get jre version 1.6 or higher.

 

Installation instructions for Windows XP and Vista:

1. Download plasmid.zip to your computer. Unzip content to some directory. A folder "plasmid" will be created.

2. Along with the unzipped folder you will find two .dll libraries: edu_wsu_plasmid_stats.dll and mingwm10.dll. Copy them where your PATH system variable points to, or add to your PATH system variable the name of the directory where these libraries will reside. Note that these two dll files must be in the same directory. (If your are unsure how to adjust the PATH variable, contact your system administrator).

3. PLASMID is ready to run! The executable file is located in ../plasmid/bin/plasmid.exe. Double click plasmid.exe.

Sample Dataset.

Along with executables files and .dll libraries, plasmid.zip includes also a sample dataset file MixedMicroarray_Cmy2.txt,  which contains a 43 x 576 matrix of mixed-plasmid microarray (MPM) results. The matrix value at (i,j) is the intensity value of the ith plasmid and jth probe. Plasmid and probe names are given in the zeroth column and zeroth row, respectively.

To use the dataset with PLASMID:

1. Choose File -> Load Microarray data->Choose file MixedMicroarray_Cmy2.txt -> Press Open.
2. Choose Microarray -> Follow the Wizard for probe reduction to do probe reduction work until Finish.

To save the results of the calculations:

1. In the left panel click on '+'.
2. Right click on Preduce0 (a popup menu will be shown "Open", "Save", "Delete"). Choose Save.
3. For Windows users: if you choose Save, the results can be best viewed in WordPad.

 

Installation instructions for Mac OS X:

coming soon ...

 

We appreciate your comments, suggestions, and questions. Email us at plasmid@vetmed.wsu.edu.



Last Edited: Aug 24, 2008 3:40 PM
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