Tiedoston sisältö

SOMA2 Modelling Environment CHANGES
-----------------------------------

Version 1.4 Aluminium (31 Jan 2012)

  New features and improvements   
    * Grid computing is now supported in SOMA2 with a middleware software
    * "User Info" page updated to contain a tabbed panel and supports several
      new features related grid computing eg. X509 certificate set up and proxy
      certificate renewals for running projects
    * SOMA2 application access control scheme adapted for grid computing 
    * Grid computing related proxy certificates are automatically generated
      upon project submission
    * SOMA2 program execution scheme adjusted to make use of suitable grid
      middleware for submitting and monitoring jobs in grids 
    * All links pointing to external pages are opened in a new browser window
    * "File Manager" is changed from a file grid to a tree grid
    * Support for JMol and JChemPaint structure viewer and sketcher applets added
    * "File Details" page displays interactive table instead of plain HTML
    * All UI buttons now show hover and active effects for more intuitive use
    * Improved and more consistent styling and navigation
    * "Workflow Configuration" shows application configuration in tab panel
    * "Workflow Configuration" hides irrelevant information in "Standard View"
    * "Workflow Configuration" displays erratic groups in configured order instead
      of alphabetical order

  Bug fixes:
    * Empty textfields in molecule modification page no longer lead to empty 
      command file
    * Error checking in workflow configuration won't break in some situations 
      related to files

  Other Changes:
    * Deprecated code related to MDL Isis/Base queries is removed
    * SOMA2 is made to support ExtJS versions 4.0.x
    * SOMA2 is updated to support ChemAxon Marvin version 5.5 and later
    * SOMA2 is updated to support latests versions of XML::Twig
    * "Project Overview" / "Results" views' bottom navigation is removed
    * "Result Details" view shows results in a grid table
    * Updated help and user manual
    * Some unnecessary log entries are no more generated

----

Version 1.3 Magnesium (3 Sep 2009)

  New features and improvements
    * XML program descriptions now include possibility to define validation
      rules for string data types by using regular expressions
    * "User Info" page now shows more specific explanation and reasons for
      "Not Available" programs and services
    * Navigation menu now highlights user's current view in SOMA2 user interface
    * "Project Overview" data table now shows duration of each program run
    * Toolboxes with controls added to "Project List" and "New Project" views
    * "Project List" view now contains possibility to delete several projects
    * Interactive status data updates added to "Project List" view, "Project
      Overview" page and "Molecule Files" table (no manual page refresh needed)
    * In case of failed initial program step, user is now able to easily save
      original input molecules back
    * "File Manager" view now contains a tree menu instead of plain table
    * "Results" view data table now remembers user's sort settings
    * "Results" view table now contains more easy and intuitive way of setting
      visible and hidden data columns and sorting the data columns
    * Improved handling of special data types (images, trajectories, data files,
      etc.) for transfering internal data between separate projects
    * Improved filtering tools in "Results" view
    * Improved visual style for all buttons and navigation menu
    * Improved and more consistent style throughout SOMA2 user interface

  Bugfixes:
    * Fixed a bug causing user set program configuration to disappear in some
      situations
    * Fixed a minor bug in "demo" mode internal cleanup routines
    * Fixed a bug that prevented deletion of projects with faulty status files

  Other Changes:
    * SOMA2 Software license changed from GPLv2 to GPLv3
    * SOMA2 now also supports Opera browser as well as other modern browsers
    * Replaced all dependencies to ActiveWidgets and Overlib JavaScript
      libraries with new interfaces to Ext JS JavaScript library
    * SOMA2 now makes use of Open Babel 2.2.3
    * Updated user manual and documentation to match new version
    * Mechanism for asynchronous requests (AJAX) added
    * All html content is now produced as XHTML 1.0 to add browser interoperability
    * Renamed several program modules for consistency reasons
    * Improvements in somake build tool
    * "Company logo" can now be defined in installation settings to ease
      local SOMA2 customisation

----

Version 1.2 Sodium (1 Jun 2009)

  New features and improvements:
    * Two new program description capsules added (obenergy, obgen) 
    * Example capsule for batch jobs added (identity_batch)
    * Four new model workflows included, making use of new capsules
    * Improved layout for "Project List" table
    * "Add Molecules" views now contain "Add Hydrogens" and "Clean Structure"
      checkboxes for corresponding automatic actions upon upload/sketching,
      based on functionality of Open Babel
    * New "Update Statuses" button in "File Upload Page" for more intuitive
      molecule file preparation status updates
    * "Molecule Files" list table presented now with an interactive table
    * Parameter validation on program configuration pages is now interactive,
      makes "Check Config" button useless
    * Improved layouts for "Submit Project" and "User Info" pages
      (all action buttons moved into toolbox)
    * Several new output format possibities when saving result molecules
    * UNIX group based authorisation is now supported in XML descriptions
    * XML descriptions now support labels for computing hosts (friendly names)
    * E-mail sending feature now supports display of used e-mail address
    * Improved layout of "Result Details" page to handle large number of
      siblings and children for a molecule
    * Improved and unified rendering styles on all views of the SOMA2 UI
    * Improved help texts in SOMA2 UI
    * Improved selection modes, color schemes and structure in all interactive tables
    * Added dynamic column width setting in result tables to clarify contents
    * Improved authorisation components beneath the SOMA2 UI
    * Improved scientific application execution scheme
    * Several improvements and refactoring in the code thoughout the codebase

  Bugfixes:
    * Fixed bug that caused random software errors when loading navigation menu
    * Fixed bug that caused empty "Advanced" level parameters not to reset when
      switching to "Stardard" level in program configuration
    * Fixed bug when resolving user's home directory
    * Fixed bug that caused software error when workflow included removed or
      renamed program capsule
    * Fixed bug in "Filter Tools" where wrong molecule name id was used
    * Fixed bug in "To Default Values", which caused program configuration
      form not to reset after initial page load
    * Fixed bug that caused navigation to disappear when saving a template, if
      user supplied faulty name for the template 
    * Fixed bug that caused user to be able to save a template with empty name
    * Fixed bug in viewing "Execution Status" data, did not work when single or
      double quotes were included in the data

  Other changes:
    * Full support for Firefox 3.x browsers added
    * Workarounds for several rendering problems with Internet Explorer added
    * SOMA2 now makes use of Open Babel 2.2.1
    * Support for Marvin 5.x added
    * Removed all dependencies to XML::Simple Perl library
    * SOMA2 can now be installed in "debug" mode to help in UI development
    * Requirement for passwordless SSH connection to "localhost" removed
    * More strict rules and safety checks for accessing underlying file system 
    * Removed non-intuitive use of boldface links in navigation of SOMA2 UI
    * Updated user manual and documentation for new version
    * Several adjustable parameters added to installation configuration file to
      allow more versatile customisation of SOMA2 installation

----

Version 1.1 Neon (18 June 2007)

  New features and improvements:
    * SOMA2 now has its own file manager program for browsing the file system
    * Experimental "demo" mode to run SOMA2 without authentication or suEXEC
    * Several improvements in input file preparation procedure
    * Several improvements in workflow integrity checks and project submission
    * Improved routines for stopping a running project
    * New CSS style for html tables in SOMA2 user interface

  Bugfixes:
    * Several minor fixes in the SOMA2 user interface

  Other changes:
    * CML-Merger ported from Java to Perl, also adding improvements to the code