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
