############### NOMAD README #######################

NOMAD, an open source system for storing and querying the results of 
microarray experiments. It is being developed in conjunction between three 
labs at the University of California, San Francisco and Lawrence Berkeley 
National Laboratory.

NOMAD handles microarray data from the time the chip's image has been 
described in a text file up to the execution of complex analyses. The 
system is being continually broadened to encompass other partner software, 
but we have concentrated on its use in conjunction with Axon's GenePix 
and Mike Eisen's AERIE analysis engine.

For installation instructions read the documentation in the doc subdirectory
Please also read the "Important Notes" section below and the RELEASE_NOTES, 
describing important limitations of the current release

To use NOMAD, use your web browser and go to the address
http://your.host.here/NOMAD

You will be presented with a screen prompting you to log in, you will
need to create a user account. Click on the Create User link on the
bottom left of the page and fill in your details as prompted. You will
be taken to a page telling you that the account was created
successfully, click the link to log in. Enter your username and password
into the boxes provided (NB, the pasword and username are
case-sensitive). Once logged in you will find youself on your NOMAD home
page. From this page you can access the different parts of NOMAD and
using the treeview frame on the left, browse your projects, experiments
and arrays.

For more detailed usage instructions please consult either the tutorial
built into NOMAD, or the USAGE document in the docs subdirectory.
(Note:These are incomplete and/or absent in the alpha release)

######################### Important Notes ##############################

1) Full validation of text enter as parameter names is not yet
   performed.
	Certain charcters cause problems when NOMAD tries to use them as
	column names in MySQL. Please avoid starting parameter names
	with a number or including a hyphen ('-') anywhere in the name
  
	If you do use a character that causes problems NOMAD will not
	warn you, or produce an error message, however the data will not
	be written correctly to the database. 

	This issue is expected to be resolved in future releases by 
	performing checks on the names of parameters and warning when a 
	illegal character is used.

2) Number of queries while using navigation tree is limited.
	The current version of NOMAD can only perform qnavigation tree
	queries with up to 30 "Blocks", 30 Experiments and 30 Arrays. 
	This limitation is expected to be resolved in future releases of
	NOMAD. 
	
3) The spots from arrays submiited to a pre-alpha version of NOMAD will not 
	show up in queries.
	This is because we changed the way spots are stored. The next
	release will re-enable access to these spots.

4) Please READ the information about upgrading from pre alph releases if 
	you are doing such an update, there is critical information on
	the website at sourceforge.

5) Aerie must be installed as /usr/local/aerie/aerie to work with NOMAD


In order to obtain the tarball, you must register first for software 
downloads at
http://rana.lbl.gov/EisenSoftwareRegistration.htm

The aerie tarball is available from http://rana.lbl.gov/downloads/aerie/



For more information see <http://ucsf-nomad.sourceforge.net/>



# README v1.01a Last Modified 01/08/2002