MONOD version $Version$
The Modeler's Notebook and Datastore
(c) 2003 The Molecular Sciences Institute
http://monod.molsci.org
monod@molsci.org

Monod is a web-based environment supporting collaborative work by
scientists studying complex intracellular signaling pathways.


CHANGE LOG

v1.0b4  (May 23, 2002)

    * Initial beta release

v1.10  (October 25, 2002)

    * Revision control
    * Permissions control
    * Default keywords, permissions, and papers
    * User and group administration
    * Output filtering (by date range and keyword)
    * PubMed search integration (rudimentary; improvements pending)
    * ToolTips
    * Major performance improvements (counterbalanced by the huge
          performance hit caused by revisions and permissions)
    * Much easier installation process
    * Lots of bug fixes

v1.11  (October 31, 2002)

    * Critical bugfixes re. adding notes, files, species states, etc.
    * Improved error emailing

v1.20  (December 10, 2002)

    * Automatic PDF downloading
    * Permissions system now applies to file downloads as well
    	(plugged security hole).

v1.21  (December 12, 2002)

    * Critical bugfixes re. file uploading, downloading, and permissions

v1.30  (February 6, 2003)

    * Postgres 7.3 compatibility
    * Support for multiple nomenclatures
    * Automatic linking to external databases (presently just for
        S. Cerevisiae, but the mechanism is extensible)
    * Vastly improved PDF downloading, including handling of accounts for
        specific journals

v1.32  (February 10, 2003)

    * Bugfix release

v1.33  (April 29, 2003)

    * Reorganized distribution package; merged binary and source distributions
    
v1.41  (July 11, 2003)

    * Rebuilt database layer using XDoclet
    * Database schema prepared for future GUI
    * SBML Level 2 import (using parser by Marc Vass)
    * Basic support for Models and Experiments
    * Numerous minor features and bugfixes

v1.42  (August 11, 2003)

    * Major performance overhaul
    * Refactored permissions & deletion filtering scheme
    * Updated to use Resin-EE 2.1.10 (patched Resin required)

v1.43 (September 11, 2003)

    * Critical bug fixes
    * SBML Level 2 export (beta, using generator by Marc Vass)

v1.44  (October 8, 2003)

    * Initial Monod Desktop prototype release

v1.45 (October 14, 2003)

    * Monod Desktop changes

v1.462 (December 19, 2003)

    * Monod Desktop changes

v1.47  (February 19, 2004)

    * Miscellaneous Monod bug fixes:
    * MND-72: "Search PubMed" for Add Paper functionality failed
    * MND-73: "Use PubMed Info" for Add Paper functionality failed
    * MND-77: Can't get "in process" citations from PubMed

v1.50rc1  (March 15, 2004)

    * Third party component upgrades
      * Caucho resin upgraded to v2.1.12
      * XDoclet upgraded to v1.2
      * log4j upgraded to v.1.2.8
  
    * Miscellaneous Monod bug fixes:
      * MND-5  PaperWidget.addAuthor does not exist
      * MND-6  Papers (sometimes?) show wrong publication year
      * MND-18 FileUpload failure should "rollback"
      * MND-30 PaperWidget.addspecies, .addprocess broken
      * MND-50 Create new user & assign password immediately is broken
      * MND-52 Add Paper manually is broken: requires PMID
      * MND-53 PubMed paper import doesn't use user Defaults (or does it?)
      * MND-55 Check for duplicate papers on import
      * MND-56 Get things to compile with XDoclet 1.2 release version
      * MND-59 Internal eror messages aren't printed correctly when adding a 
               keyword fails
      * MND-65 Coreobjects are mysteriously cloned instead of revised
      * MND-71 NoteWidget.save() returns to old revision, not new revision
      * MND-76 Add species complex doesn't show all available species
      * MND-80 Provide configs to rotate debug logs, which otherwise grow very
               large
      * MND-82 Patching resin-ejb.jar is a hassle
      * MND-85 script for postgres database vaccuming to be bundled for 
               software release
      * MND-86 "search pubmed" fails to show any results
      * MND-88 excp on "search pubmed" result page when tried to link out to 
               pubmed OR to import paper
      * MND-90 Security hole: deep cloning may allow reading forbidden records

v1.51  (April 22, 2004)
    * This release is for Monod Desktop.  Please refer to Monod Desktop 
      changelog.html for details.

v1.52  (May 28, 2004)
    * This release is for Monod Desktop.  Please refer to Monod Desktop 
      changelog.html for details.

v1.523 (June 15, 2004)
    * MND-93 add paper failed due to value longer than varchar(255)
    * This release is for Monod Desktop.  Please refer to Monod Desktop 
      changelog.html for details.

v1.5.2.6  (July 15, 2004)
    * This release is for Monod Desktop.  Please refer to Monod Desktop 
      changelog.html for details.

v1.5.2.6.1  (July 15, 2004)
    * Repackaged netbeans (monodDesktopDashboard-1.5.2.6.1.nbm) to include 
      a missing jar file.

 
Todos (summary)

    * Please see, and contribute to, http://bugs.molsci.org for bug reports

    * Handling of numerical parameters
    * More compact graphic design
    * P2P communication between servers
    * Better treatment of binding sites, complexes, and states
    * GUI
    * Integration with Multivalent Browser for PDF annotation