MAExplorer Newsletter #1, March 6, 2001
=======================================

We are starting a mailing list to periodically notify interested
parties of major changes and enhancements to the MicroArray Explorer
(MAExplorer).

Since you have expressed an interest in MAExplorer in the past, you
were included in this initial mailing. If you do not wish to receive
further mailings, let us know and we will remove you from future
mailings. The same information will be made available on the Web site,
so if you are interested in following developments in MAExplorer but
don't want the mail you could get the information there.

WEB SITE: http://www.lecb.ncifcrf.gov/MAExplorer
CONTACT:  mae@ncifcrf.gov
PHONE:    301-846-5535 (Peter Lemkin)
          301-846-5539 (Greg Thornwall)
FAX:      301-846-5598


Some of the recent enhancements in the current Version 0.89.08
============================================================== 

1. The user can define and manipulate named sets of genes and named
  lists of hybridization conditions. Operations include: saving genes
  from the Edited Gene List(EGL), genes passing the data Filter, set
  operations including OR, AND, and set difference. You may then
  assign a named gene set to the EGL or "Filter Gene Set", or a named
  condition list to the HP-X, HP-Y or HP-E lists.

2. There is now a graphical "chooser" to select hybridizations for
  HP-X, HP-Y or HP-E condition lists.

3. When running as a stand-alone application, doing a "SaveAs file DB"
  (in the File menu) saves the state of your data-mining session
  so that you may easily restart it from where you left off. The
  state currently includes: named gene and condition sets, filter state,
  pseudo-array display and various other preferences and threshold values. 

4. MAExplorer is available for use with the NCI/CIT mAdb database used
  with ATC arrays (http://nciarray.nci.nih.gov/).  This is described in a
  downloadable PDF file
   http://www.lecb.ncifcrf.gov/MAExplorer/PDF/Using-mAdb-with-MAExplorer.pdf

5. Because MAExplorer can be used with both clones and oligos, we have
  renamed the basic entity "Gene" instead of Clone. The major release
  was changed from Version 0.88.xxx (Clone) to 0.89.xxx (Gene).

6. There is a PDF document showing a number of examples of MAExplorer 
  capabilities
   http://www.lecb.ncifcrf.gov/MAExplorer/PDF/Examples-MAE-session.pdf

7. The Nucleic Acid Research Paper is available on the Web site
   http://www.lecb.ncifcrf.gov/MAExplorer/PDF/lemkin-NAR-2000-Vol28-pp4452.pdf

8. The Reference Manual has been redesigned so it is easier to use. This
  includes dividing it into separately chapters which makes using it on-line
  much faster. Other major improvements include additional material in
  Section 3 on Data Mining, clarifying setting up MAExplorer with other
  arrays in Appendix C. The index has also been improved so it is easier
  to use when printed. The entire manual and dual-resolution figures may
  be downloaded as a Zip file.
   http://www.lecb.ncifcrf.gov/MAExplorer/hmaeHelp.html


Future ehancements under development
====================================

 * A data conversion tool to import a variety of hybridized array data
   types and automatically generate all files for running MAExplorer.

 * New clustering methods

 * Extensible analysis methods

 * Improved graphics

 * Improved documentation and training

 * etc.

Please contact us with your comments, suggestions and problems at
mae@ncifcrf.gov