December 15, 2003

• Notebook: Fixed an unintended feature of the new email option that was causing all projects to be affected rather than just the one that the user was on (kv).
• Fixed a bug that could cause a user to not be able to log in via the web if they had set a project as default and then 'hid' the project (mb).
• VMD Launch: fixed a bug with launching VMD on Mac OS X (rb).

December 15, 2003

• Notebook: When choosing to send email about a new notebook message, the entire notebook message is now sent rather than a link to the message. Note that email is an inherently insecure medium, so we suggest using the secure web pages to view any notebook messages that might contain sensitive material (kv).

December 10, 2003

• Notebook: Added option to always have BioCoRE send email when a new message is posted (kv).
• WebDAV: Fixed a bug where users could move project directories (sk).
• Notebook: Tweaked search to make it work again for private projects as well as for speed (rb).
• VMD Launch: New beta version (mb).

November 17, 2003

• VMD Launch: Updated to work with VMD 1.8.2 on Mac OS X (rb).
• Control Panel: Fixed a bug that was causing users to not appear in the User List immediately after starting a control panel (kv).

November 14, 2003

• VMD Launch: New beta version. You can now load files into other files. This allows you to load PDB files into PSF files, etc. There is a checkbox in the "Load From BioFS" window that lets you load the selected file into the the top molecule in VMD (mb).
• VMD Launch: Color highlighting should be more accurate now. If a view or a person's name is highlighted, it indicates that they have views published that you haven't seen (mb).
• VMD Launch: Upon closing the BioCoRE VMD window it now prints a message to the VMD console describing how to reopen (mb).
• Control Panel: The Control Panel now receives notification of when other users open and close their own Control Panels. The Control Panel no longer provides notification of when users log in and out, by default. This setting can be adjusted by choosing a project and and then going to Project | Show (kv).
• Notebook: Fixed a search problem where permissions weren't fully correct on public projects (mb).

November 3, 2003

• VMD Launch: New beta version. New menuing system that matches other menus that VMD uses. This fixes the menu problems in some versions of OS X. Fixed bug when Save Siew is clicked rapidly. Added dialog boxes instead of sending questions to the VMD console. Fixed bug where multiple molecules were getting loaded if you clicked Load View rapidly (mb).

October 29, 2003

• VMD Launch: New beta version. Please try it out and let us know how well it works for you. The emphasis for this release is ease of collaborative sessions using the tool (mb).

October 27, 2003

• Revised the consent form to reflect a new validity date, and added a note that users should print a copy for their records.
• Added help text explaining the 'hidden' status for projects (mb).
• VMD Launch: Fixed a bug that would cause VMD to freeze after loading too many states (mb).

September 25, 2003

• BioFS/WebDAV:Fixed problems with 'du' on Linux, and Date/Time issues on some platforms (sk).
• Fixed some lingering issues with making public projects have file system access (mb).
• VMD Launch: Now happens automatically upon going to VMD launch page. You no longer have to click on the 'start vmd' button (mb).
• Job Management:Very experimental support for NCSA Teragrid machine (rb).
• Added the backslash as being a valid URL character for the control panel and the web pages (kv).

September 19, 2003

• VMD Saved States: Now works on Mac OS X with recent versions of VMD (rb).
• Public Projects:File system access is now available for public projects (mb).
• VMD Saved States: List is now sorted in reverse chronological order, with the newest states at the top (mb).
• Public Projects:Fixed a bug where you could access sections of the public project that the adminstrator had not originally set up. (mb).
• VMD Saved States: Fixed a bug where molecules from the RCSB were not getting properly loaded (mb).
• VMD Saved States:The screenshot JPEG is now saved in the BioFS without the full path name (mb).
• Control Panel:Added a brief note to the applet window saying that you must have java installed correctly for it to work. Newer browsers aren't gracefully failing when java is not available and hopefully this will make it more clear to users what their problem might be (kv).

September 9, 2003

• BioFS:Fixed a bug where BioCoRE wasn't detecting the proper type of filenames with uppercase extensions (kv).
• VMD Launch:Fixed a place where a temporary file wasn't getting deleted, and fixed a bug that was causing local files to not be properly saved (mb).
• Control Panel:Fixed a bug where the summary page table entries weren't getting cleared when the user chose 'File | Clear Tabs' (rb).
• Control Panel:Changed the window title to reflect that messages were waiting. This is probably window manager dependent on Unix (kv).
• Made the forward slash (/) character illegal in project names as well as BioFS file/directory names (sk).
• Fixed a bug that was causing Opera 5 to not upload files correctly (kv).

August 19, 2003

• WebDAV: Fixed some problems with WebDAV on windows as well as Linux (sk).
• Control Panel:Added '@' as a valid URL character (kv).
• VMD Launch:Fixed a bug where file URLs were not getting saved properly (mb).
• Fixed a bug in deleting notification preferences (mb).

July 11, 2003

• Control Panel: Fixed a bug where old private messages didn't have the 'private' flag attached to them (kv).
• BioFS: The 'rename' prompt now starts out with the current name of the file for user convenience (kv).
• WebDAV: Fixed some problems with WebDAV on windows as well as when creating files with the tick mark in them (sk, mb).
• WebDAV: Changed the URL to reference the WebDAV version of the BioFS from http://biocore.ks.uiuc.edu/biocore/webdav to http://biocore.ks.uiuc.edu/biocore/biofs so that it is more user friendly (kv).

June 27, 2003

• Control Panel: Fixed a bug where sound wasn't getting activated for users (mb).

June 23, 2003

• Control Panel: For users that leave their Control Panels open overnight: The Control Panel now recalculates time formats shown in chats each night shortly after midnight (kv).
• Notebook: Added a note to end of email messages that users might send each other explicitly telling them how to get out of receiving email messages (kv).
• Notebook: Revised message format so that all users are not listed in the to: list for a message. Also fixed a bug where invited users that had not yet actually accepted an invitation were getting email (kv).
• WebDAV: Updated and enhanced documentation, available at http://biocore.ks.uiuc.edu/biocore/docs/webdav.html (sk).
• API Updates: Various updates to the TCL version of the API. Documentation available at http://www.ks.uiuc.edu/Research/biocore/dev/tcl/ (kv).
• Fixed a bug that was causing users to not be able to log in if they set their autologout times extremely high (mb).
• Job Management: Disabled the special summer school queue at NCSA (rb).

June 16, 2003

• Control Panel: Fixed a bug that was causing no space to show up between a user's name and an action when emoting on older versions of Java (such as the one used by Netscape on certain platforms) (kv).
• Notebook: Pages now stay on the same subcategory when switching projects (mb).
• Control Panel: ftp:// URLs are now parsed as being valid URLs that can be clicked on it a chat (kv).
• Job Management: Revised auto-generated job names for PBS queues so that they are no more than 15 characters, no white space, and start with a letter (rb).
• Control Panel: Added a menu option in the 'Help' menu to set a debug level for the Control Panel. Turning this on will cause debug messages to show up in the Java Console (kv).

June 4, 2003

• Control Panel: Users in the user list for each project are now sorted by user name (kv).
• Control Panel: Fixed a bug that was causing double copies of old messages to appear if: 1) the server had restarted and 2) the user had shutdown an old control panel and started a new one without logging out (kv).

June 2, 2003

• Control Panel: Fixed a bug that was causing the Control Panel to close when project invitations were accepted (kv).
• Job Management: Fixed a bug that was causing job completion to not be correctly determined in certain cases (rb).

June 1, 2003

• Control Panel: More revisions to the start up routines that will hopefully speed up the startup (kv).
• Notebook: Removed some debugging prints that had slipped through. Added cancel buttons on the file upload pages. (mb).
• Notebook Search: Chat searching now shows the login name (mb).

May 30, 2003

• VMD Launcher:Temporarily commented out launching states directly from the web. There is a technical issue that is causing this to not work, but it is still possible to load states from VMD itself. Launch VMD, and then load the state from the special VMD BioCoRE window that opens (mb).
• Job Management:Tweaks to the NCSA IA32 cluster code to make it work better with NAMD and the summer school (rb).
• Control Panel:Revisions to the start up routines that will hopefully speed up the startup (kv).

May 27, 2003

• Job Management:Significant performance improvements; particularly when under high load (rb).
• Job Management:Various user interface tweaks (rb,kv).
• Job Management:Fixed a bug that occurred if a user selected "Done" when choosing files without actually having any files chosen (kv).
• Various user interface tweaks to the 'Add Users to Project' page (mb).
• Control Panel:When started via Web Start, the Control Panel no longer starts in the extreme upper left corner of the screen. It is now indented some (kv).
• Control Panel:Performance improvements at startup. May or may not be noticeable depending upon connection speeds (kv).
• Control Panel:Revised the timeout time on the applet from 30 minutes to 5 minutes so that it will detect new servers more expediently (kv).
• VMD Launcher:User Interface tweaks to make it more self-explanatory (mb).
• Control Panel: Added a line at the top of each chat window that links to previous chats (kv).

May 22, 2003

• VMD Saved States:Fixed a bug that was causing states to not load properly (mb).
• Fixed a bug where users were not getting the 'Accept Project Invitation' link if they logged in directly via Web Start (kv).
• Revised user lists so that they print out in alphabetical order (mb).
• Job Management:Further tweaked the 'add files to job' and 'retrieve files from job' pages so that they are more consistent (kv).

May 21, 2003

• Made it so that users can join projects without having to relog into BioCoRE. If you have been invited to a project, an 'Accept Project Invitation' link shows up in the left sidebar of the BioCoRE web interface that you can click on (kv).
• Job Management: Tweaked the look of the 'add files to job' page so that it is more consistent (kv).
• Various tweaks to make the interface run faster when under load (kv).

May 19, 2003

• Job Management:When selecting files for inclusion from the BioFS, you can now select multiple files from the same directory at once (kv).
• Job Management:Added support for account name selection for the NCSA Linux machines (rb).
• Control Panel:Fixed a bug where the wrong name was showing up when joining a project if the Control Panel was already open when the project was joined (mb).
• VMD Saved States:Various bug fixes to make it work with the newest versions of VMD (mb).

Earlier updates