Readme.txt
Created: 2005/01/01
Updated: 2005/01/26  (name change from ORIGEN to ORIOGEN)
Updated: 2005/08/16  (add tutorial)
Updated: 2008/08/26  (version 3 changes)
Updated: 2010/04/29  (more version 3 changes)
Updated: 2012/10/01 (version 4.01)


In the following we provide a general description of how to get started with the software. 
The user may find the help buttons in various screens useful.


Step 1 (Download Java Runtime): ORIOGEN requires Java 1.4.2 or newer. Install JAVA Runtime
Environment on your computer. This is a free software that can be obtained
from the internet. At the time of the creation of this Readme.txt the following
urls can be used to access the latest Java Runtime Environment:

For Solaris/Unix:  

	http://developers.sun.com/prodtech/os/index.html


For Mac OS X 10.1 and newer versions:  

	http://www.versiontracker.com/dyn/moreinfo/macosx/21527

or simply use Apple's Software Update to get the latest Java installed.

For Windows 98/2000/XP:  

	http://www.versiontracker.com/dyn/moreinfo/win/10284


Step 2 (Download ORIOGEN): Download the software from:

	http://dir.niehs.nih.gov/dirbb/oriogen/index.cfm

Several files are downloaded in a single zip file. Users should extract these files 
into a folder of their choice on their hard drive. Among these files the only three 
files a user needs to pay attention to are given below.  The remaining files are 
needed for processing the software.

	(a)	Readme.txt (This file)

	(b)	ORIOGEN.jar  (the software)

	(c)	example.txt

	For illustration purposes we have included a data set that was published in 
	Lobenhofer et al. (2002). Cite this publication (see below for reference) if 
	you decide to use this data in any of your publications. The data consists of 
	1900 genes (arranged in rows) measured at 6 time points with 8 observations (n=8) 
	per time point. Thus there are 48 columns of data starting on column 3. The first 
	two columns are gene id and gene descriptor/name. 

		Lobenhofer, E., Bennett, L., Cable, P., Li, L., and Afshari, C., (2002). 
	Regulation of DNA replication fork genes by 17beta estradiol. Molec. Endocrin., 
	16, 1215-1229.


Step 3 (Extract ORIOGEN files): Browsers can act differently when downloading a .zip file. 
Some automatically extract the file, creating the "ORIOGEN" folder. If
your browser did not auto-extract, then locate the "oriogenV3.zip"
document and either double-click it -or- launch your unzip application
and extract it. Examples of free applications for Mac and PC include
Stuffit Expander Standard Version.

(NOTE: ORIOGEN will NOT run correctly if you attempt to run it from within the zipped folder).

Step 3 (Clean up): The "ORIOGEN" folder can be left anywhere in your 
computer, however if you would like to tidy up you can move 
it to your "Programs" directory (PC) or Applications folder (Mac). 

Step 4 (Create shortcut): Create a shortcut or alias of the "ORIOGEN.jar" Java 
application and place that in a convenient location.

Step 5 (Start using ORIOGEN): Double click on the shortcut or alias of "ORIOGEN.jar" 
that you created to start the program. Follow the tutorial below to run an analysis
using the example data.




Tutorial:

T1 (Start ORIOGEN):  Double-click on the ORIOGEN.jar file to start the program. 
This will result in two pop-up windows.  

	(a)	Introduction to ORIOGEN:  This window provides background information 
		about the methodology used in the software and its limitations.  
		Close this window when done.  

	(b)	Inputs:  Click on the Help button at the bottom of the window. A pop-up 
		window called "ORIOGEN Help" will appear – this contains all information 
		regarding the format of the input and output files and other useful 
		information regarding various entries in the input window. Close this 
		window or move it to the side when done. 

T2 (Analysis Type): Select the appropriate analysis type. The two options are the classic
ORIOGEN or multiple pairwise comparisons. See the descriptions in the Help for more information
on these.

T3 (Input File name):  Once sure the input file of interest is in the desired format, 
the user may return to the Input window and either enter the file name (along with 
the path) in this block or click on the Browse button and select the file. For example, 
you can select the "example.txt" file located in the same folder as ORIOGEN.

T4 (Output File name):  Enter the output file name (along with the path) or click on 
the Browse button to provide the path.

T5 (Total number of dose groups or time points):  Enter the number of dose groups or 
time points in the data. For instance there are 6 time points in the breast cancer 
cell line data available in the "example.txt" file.  Hence enter 6 in this case.

T6 (Vector of sample sizes per dose/time point):  Enter the number of  samples at each 
dose/time point with entries separated by a comma.  For example, in the case of 
"example.txt", there are 8 samples at each time point.  Hence enter 8,8,8,8,8,8.

T7 (Number of initial bootstrap samples):  Input the desired number of initial bootstrap 
samples. A recommended value is 2000 initial bootstraps. 

T8 (Number of final bootstrap samples):  Input the desired maximum number of bootstrap 
samples used by the adaptive algorithm. A recommended value is 50000 bootstraps  

T8 (FDR level for performing the actual test):  Enter the desired level of significance. 
For our example, enter 0.1. 

T9 (Bootstrap random seed):  Enter a seed for the random number generator or let the 
computer pick its own.

T10 (Accept inputs):  Click on the OK button at the bottom of the screen. 
This will pop-up a new screen called "Profile Selection".  

T11 (Inputting desired profiles of interest):  Use the radio buttons in the top left panel 
of the "Profile selection" screen to select the profiles of interest.  For example, in the 
case of the "example.txt" data we may consider all possible non-cyclical profiles -- 
decreasing profile, 4 different umbrella profiles, 4 different inverted umbrella profiles 
and 1 increasing profile.  In this case, we would click the "All Non-Cyclic Profiles"
selection and then click on the "Add selected profile(s)" button.

T12 (Start processing): Once all the desired profiles have been selected, click on the 
"Start Processing" button to begin the processing.  
