Recent update information is always available from the Control Panel by going to "Help | Recent Updates".
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).
May 12, 2003

Control Panel:VMD sessions can now be started from the Control Panel. VMD will be launched and a PDB file will be loaded from the RCSB. Usage is: /vmd <PDBID> where PDBID is the ID from pdb.org (mb).
WebDAV:Fixed a bug that was allowing writes to the main directory (sk).
Notebook:You can now choose which area of the Notebook that you wish to search, rather than automatically searching everything (mb).
Fixed a bug where some users couldn't be added as administrators (mb).



April 11, 2003


Control Panel:Tabs no longer change to have an asterisk to
denote activity.  Rather, the summary table cell background for a particular
project changes if there is activity.  This works cleaner on various
platforms (rb).
VMD Saved States:Fixed a problem with "local files getting
uploaded" that was occuring on Windows (mb).
WebDAV:Fixed some bugs that was causing the Linux mount.dav
to not be able to write correctly, and fixed a timezone bug (sk).
Control Panel:There is now an Edit menu that has Copy and
Paste options.  Mac OS X Java wasn't able to Cut and Paste without this.
It does work for other platforms as well (rb).



March 24, 2003


VMD Saved States:If the user attempts to save a state this is
using a local file they are now prompted to upload the file to the BioFS.
Future views of the state will then use the file from the BioFS (mb).
Control Panel:Tabs that are denoting "activity" (by changing
colors) now also have an asterisk appear in front of their name.  This
was required because of the way that the new version of Java on the
Macintosh handles tabs (rb).
Control Panel:The state of tabs (whether turned on or off) is
now saved across Control Panel startups (rb).
WebDAV:Files saved via WebDAV now send notification to the
Control Panel (sk).
Fixed an SQL bug that was causing problems with creation of public
projects (mb).
Control Panel:Fixed a bug that was causing the initial window
to not get redrawn (rb).
Preferences:Fixed a long-standing bug that would cause
Netscape 4.x to crash if the window was resized while on a "color
chooser" page (dd).
Changed references from BioCoRE User Agreement to BioCoRE User
License (kv).




February 26, 2003


Control Panel:Beta Feature:  Tabs can be turned on or off
now via a checkbox on the summary page.  If a new message comes in on a
hidden tab, it will cause itself to appear (rb).
Fixed some typos in email that is sent to new project members (mb).
Fixed a bug that was causing project deletions to not work properly
(mb).
VMD Saved States:Fixed a bug that was causing users to not be
properly warned if they tried to save a state with a local file (mb).
Revised the number of entries that show up in the Control Panel
chat history web pages from 20 to 50 (mb).




February 12, 2003


Cleaned up the text in some of the email messages that are being
sent to users when they join projects, change email addresses (mb, kv).
Control Panel: Added menu items that point to the list of public
projects and the FAQ (mb).
Public Projects: Made it so that the administrator can change
viewable areas in both the public and private side (mb). 
Hidden Projects: Fixed various issues with the Control Panel
display so that it is accurate (mb).



January 31, 2003


Job Management: Fixed a problem that was causing new
account creations to fail (rb).
Bug fixes for Hide/Show, and public projects (mb).
NAMD Configuration File Generator: Fixed a bug as a result
of yesterday's release that was keeping it from loading (kv).




January 30, 2003


Projects: Users can now create public areas for projects
that they are working on.  Project administrators can choose which
areas of the project (chats, notebook messages, etc) they wish to
be public and then any BioCoRE member can look at the specific 
public pieces (mb).
Projects: Project administrators now have the ability
to delete projects once they are no longer active (mb).
Projects: Users can now choose to hide projects that they
are involved in.  The user is still a member of the project; it
just doesn't show up as a tab on their Control Panel nor as a quick
link at the top of the web pages (mb).
Notebook: Users now have an option of whether or not they
want to see the "Next Message", "Previous Message", "Next Unread
Message", and "Previous Unread Message" links when they are viewing
the text of a message.  By turning these links off it can speed up
message access considerably by saving extra database queries.  This
option is set via the Utilities menu (kv).
Utilities: Revised the Utilities page slightly by giving
some explanatory text to some of the items listed (kv).
Fixed a bug that was causing newly promoted Administrators of
a project to not have Adminstrator rights until they relog (mb).
Added a check in the user setting for the auto logout timeout
so that a non positive number can't be specified (mb).




January 21, 2003


Job Management: Added support for the NCSA linux cluster
machines, Platinum and Titan (rb).
WebDAV:Updates to make it implement file locking and to work 
more cleanly on Apple Macintoshes (sk).
Revised instances of Theoretical Biophysics to Theoretical and 
Computational Biophysics to reflect the new name of the group (kv).
Control Panel:Fixed a bug that was causing people with
certain special characters in their username/password to not be able to
log in via the Control Panel's login popup dialog (kv).



December 9, 2002



Server source code is now available.  Server code in binary form
has been available for some time, but we now have server source code
available.
VMD Load/Save state:Fixed a bug where the script wasn't
propery changing the saved state script text when loading a molecule
from a saved state on Windows (mb).
Added an explicit warning to pages of the All User Test Project
telling users that data posted to that project is visible by all (rb).
Job Management:Slightly revised the wording of the account
creation pages to incorporate Globus information more prominently (rb).
Notebook:Made the titles of the various notebook areas more 
prominent to help avoid confusion (kv).
Control Panel:Users now receive notification of their
own link library additions (mb).



November 18, 2002


Fixed a bug where multiple project designations were getting put
on requests when a user first logged in.  This was causing some people
to get Internal Server Errors (kv).
Notebook:Fixed a bug that was causing people to not see
notification of new notebook entries in the Control Panel unless they
had a flag set to see their own (mb).
VMD Load/Save state:Fixed a bug that was causing some filetypes
to not load properly on Windows (mb).
WebDAV:More bug fixes for beta release.  Very preliminary
documentation now exists at:
http://biocore.ks.uiuc.edu/biocore/html/webdavinstall.html (sk).
Job Management:Fixed a bug that was causing BioCoRE to not
totally forget jobs if they were deleted using the checkboxes on the
main job page (rb).
BioLog: The BioLog entries in the notebook now have a link
to the biolog html help page (kv).



November 11, 2002


WebDAV:Bug fixes.  Should be more stable under Mac OS X
now.  Fixed a bug that was causing a user to show up as logging in
twice when they used WebDAV.  Documentation is forthcoming (sk).



November 5, 2002


New Feature!:A WebDAV module is now in beta testing
for access to the BioCoRE filesystem.  To access this on, point your
WebDAV client to:
https://machine.biocore.is.running.on.edu/biocore/webdav
(sk).
VMD Saved States:DCD and PSF files can now be saved and
loaded from saved states.  The DCD and PSF files exist in the BioFS
just as with PDB files (mb).
VMD Saved States:The TK windows that are being added to
VMD to handle saving and loading states from BioCoRE can now be
expanded without looking bad (mb).
Control Panel:User's own chats are now slightly lighter than
others to help identify them (mb).
Administrators of a project can now designate other members as
admins via a link on the Utilities page (mb).
Notebook:The page for adding a new entry now has a 'Cancel'
button (mb).
Create Project:Fixed a small bug that was causing the first 
check box to be slightly larger than the rest, and also changed the
colors to use the user defined colors instead of always using green
 (mb).
Lab Book:Fixed a bug that, in specific cases, was causing
clicking on 'Add New Entry' to take you to the page to add a new
'Message Board' message instead of a Lab Book entry (mb).
Notebook:Removed 'chat' entries from search results.  This
'chat' is an old chat system that BioCoRE used.  Control Panel chats
are still searchable (mb).
Job Management:Removed a message that stated that BioCoRE
doesn't upload files, since it now has that capability (rb).
VMD Saved States:Fixed a web page presentation bug that was
causing two lists of saved states to show (mb).
Fixed some grammatical typos in the mail messages that were getting
sent when a user deleted themselves from a project (mb).
Notebook:Fixed a problem with entering less than and greater
than symbols in  notebook messages (mb).
Revised the email that gets sent to users requesting a new password
so that the URL link that it includes for BioCoRE takes them to the
'change password' page (kv).



October 4, 2002


Notebook:Removed the 'Add a New Entry' button at the top of the
page on the pages where you are typing and previewing a new message (kv).
Notebook:Fixed a bug that was causing new entries to appear to
not be submitted properly (kv).
Lab book:Added the ability to edit and delete lab book entries.
These editted and deleted entries are tracked for revision control (kv).
Notebook:Added the ability to undelete messages IF you are the
owner or the project administrator (kv).



October 2, 2002


VMD Launcher: Revised to work with the newest betas of VMD (mb).
Lab Book: Fixed a few minor appearance bugs that hadn't been
caught for the last release (kv, mb).
Fixed a bug that was causing the 'Back' button on the Mac IE browser to
not function properly in all cases (rb).
Control Panel: Fixed a bug that was causing the chat history
'Previous' and 'Next' buttons to not work correctly (kv, mb).



September 26, 2002


New Lab Book:  BioCoRE now contains a lab book module that can
be used by project members.  The lab book operates similarly to how
the message board operates except that there is no option to edit or
delete entries (kv).
Notebook:  The notebook area is now listed in a more explicit
fashion in the left menu bar.  Rather than having a single link to the
message board, there are now links to the message board, saved VMD
states, BioLog entries, etc.  This should make it easier for users to
find the different notebook sections within BioCoRE (kv).
Preferences:  Fixed a bug that was causing color choices to not
show up in Mozilla (mb).
Clicking on a different project name in the project list now takes you
to the same general area in the new project as you were in on the old
project (mb).
BioFS:  Fixed an HTML bug that was causing the file selection window
to not display properly (rb).



September 16, 2002


Job Management:Files can now be downloaded from the remote
system to the BioFS when a job has completed (rb).
Control Panel:The 'Project' menu has changed slightly.  The
BioFS is now in the 'Documents' submenu (kv).
Control Panel:Added {, }, and + as being valid characters in URL that the
Control Panel and Message Board recognize (kv).
Control Panel:Fixed a bug where notification wasn't always getting
sent to the right project in the Control Panel when a new file was added
to the BioFS (kv).
Control Panel:When the BioCoRE session file is written,
(during Control Panel startup) a message is now printed to the java
console.  



August 19, 2002


BioFS: Users can now sort displays by the different columns (mb).
Summary Page: Made text consistent with respect to number of
recent entries (kv).
Control Panel:Added the pound sign as being part of a valid URL
(mb).
VMD Launcher:Fixed some problems that were showing up when launching
VMD on non-netscape browsers related to Unix/MacOSX (rb).



July 15, 2002


Control Panel:/me allows you to send text to
the other users without being an actual chat message, ala the IRC-style
action (kv).
Control Panel:Private chats are now being stored and can be
retrieved later by the sender and receiver (kv).
Job Management:The PSC Lemieux "debug" queue is now supported
(rb).
JMV:The JMV window now has a "close window" link (mb).



July 3, 2002


BioFS:JMV 1.0 is now part of BioCoRE.  With 1.0, users can
save JMV states to the BioFS and other users can use JMV to view the
states.  JPEG images can also be saved (mb).
Control Panel:/help now provides brief
information on the various "slash" commands that exist in the chat
window (kv).



June 25, 2002


BioFS:JMV 0.8 is now being used for viewing PDB files (mb).
Control Panel:You can now send private messages to users by
typing in the command: /msg recipient text into the text
window, instead of needing to click on their name in the user list (kv).
Control Panel:When starting the Control Panel, personalized 
messages won't sound audibly if you have already seen them now (kv).
Job Management: Added in a check to handle users killing a
job and then not getting any text output (rb).



June 12, 2002


Control Panel:Bug fixes for the "multiple control panels" (kv).
Control Panel:The divider bar between the chat area and the
user list for projects is now a little bit wider.  This makes it easier
to click on the arrow in the bar if you need to (kv).
BioFS:Fixed a bug that was preventing the "Change Permission"
window from showing up for a file (mb).
Notebook:Fixed a GUI inconsistency that was causing the Current
Page number to show up below the left side bar after doing a search on chats
(hw).
Message Board:Fixed a bug that occurred when editting a message
and only changing the subject (hw).
VMD:Fixed a bug where the 'vmd' directory wasn't getting 
created for new projects (mb).
VMD:Fixed a bug that was causing molecule images to not show
up in the "saved states" view (mb).



June 11, 2002


Job Management:For new SSH based jobs, BioCoRE now attempts
to get an estimate of the number of CPU hours used by a job and
displays this in the job details (rb).
Control Panel: While the Control Panel is starting up it now
displays "Initializing..." on the summary tab instead of "-1" which it
used to do (kv).
Control Panel: Preliminary: You can now have multiple 
Control Panels open at the same time, so you can have one going on your
desktop as well as your laptop.  A new menu item has been added to the
File menu that simply closes the Control Panel but does not
log you out of BioCoRE (kv).
Control Panel: The Web Start version now has a window title
of BioCoRE Control Panel instead of ControlPanel, which it was
previously (kv).
Summary Page:Fixed a bug where recent files added to the
BioFS were not clickable (mb).
Job Management/Globus:Revised the error message that gets
printed if the user's grid proxy is invalid to hopefully make it more
clear what is happening (sk).
BioFS:Fixed a file locking bug where users were getting
warned that files were locked when they, in fact, were not (sk).
Utilities:For deleting users from a project, you are now
presented with a user list with checkboxes instead of a dropdown box
for selecting users (mb).



May 28, 2002


Message Board:Various optimizations to handle large numbers
of messages.  Database query time has been reduced by a factor of 3 or
4 for many queries (kv).
Link Library:Addition of links now generates a line in the
Control Panel chat that can be clicked on to go to a site (mb).
Summary Page:New folder creations now show up in the "recent
files" list (mb).
Job Management:Account creation is now more descriptive if
it fails.  It more thoroughly attempts to explain what went wrong (rb).
BioFS:Added code to prevent moving a folder into itself or
one of its subdirectories (mb).
Job Management:"Start" and "End" files used by job
submission are now being stored in $HOME/.biocore/jobs rather than the
work directory (rb).
Fixed a bug where colors were sometimes getting improperly forwarded
from a project with explicit colors to a project that didn't have colors
set (mb).



May 14, 2002


The javascript menus that were being printed at the tops of the web
pages are no longer being used.  There is now a left sidebar that
includes links to the different pieces of BioCoRE.  Projects can be
changed via the project links at the top of every page.  In addition,
many minor changes have been made to the HTML for BioCoRE (kv, mb, hw,
rb).
Message Board: You can now upload text files when editting 
messages (hw).
Job Management: Added the ability to easily select all the
jobs in the list on the "All Jobs" page (mb).
Control Panel: Revised documentation to include an "error"
section that lists common errors (kv).
BioFS: File sizes now print with commas in them to seperate
millions from thousands from ones (kv).
Preferences: When you select a notification setting, the
settings for that particular notification are now initialized to
their previous setting instead of just using a default (mb).
Summary Page: Recent BioFS files no longer includes some 
files that were getting put in 'System' (mb).
Message Board: Fixed a bug where text that user typed wasn't
getting properly copied when uploading a text file (hw).
VMD Publish: Fixed a problem with saving multiple states
with the same name when saving thumbnails (mb).
Control Panel: Pressing the 'down arrow' when typing text
will now clear the current text (kv).
Fixed a bug where users were seeing duplicate project links 
immediately after creating a new project (mb).
Control Panel: Dates older than 6 days are now printed using
the Month Day Hour:Minute format.  Previously this was 7 days (kv).
Control Panel: Fixed a bug that had been introduced that
caused text in the chat windows to not be selectable.  Now, if using
Web Start, this text is selectable and can be copied to other
applications on your desktop (kv).



April 26, 2002


VMD Publish: Images are now uploaded with the session,
so users can view what a saved state will look like before loading
VMD to retrieve it (mb).
Control Panel: Changing the slider location on one projects
window now changes it for all the project windows (kv).
Summary Page: Recent BioFS files now show the size in bytes
of the file (mb).
Fixed a bug that was showing up related to Java Web Start if the
user had cookies explicitly turned off (hw).
Added a link to the places where Web Start is mentioned that points
to the Web Start helper html page (mb).
BioFS: Removed an extraneous > that was showing up in
file names (mb).



April 18, 2002


Job Management: BioCoRE now will upload job related files
from the BioFS to the supercomputer site.  You can store your job files
in the BioFS, and tell BioCoRE to upload them to the supercomputer for
execution.  You no longer have to copy the files over manually before
submitting via BioCoRE (rb).
Control Panel: A manual now exists.  It is available under the
Help menu from the Control Panel itself or via the BioCoRE website (kv).
Control Panel: You can now use the up and down arrows when
chatting to recall previous chats you have sent in that session (kv).
Control Panel: You can now send someone a "directed" message
in your projects.  Start your message with their username: and a special
sound will play on their Control Panel to let them know that something
important has arrived (kv).
Control Panel: Revised socket code, which makes the Control
Panel more robust in cases where users change networks (relatively
common with laptops) (kv).



April 10, 2002


BioFS: Any file can now be viewed as "text" by selecting
the option in the Properties window (kv).
BioFS: Added in a check to make sure that users were typing
in file names when then wanted to upload a new file to the BioFS (kv).
Control Panel: Revised Web Start's login window so that
pressing <ENTER> moves you to the next field (or submits the
form, depending on where you are (kv).
Control Panel: Fixed a bug when users were getting
autologged out and the Control Panel was terminating the monitoring for
new messages after relogging (kv).



April 4, 2002


Job Management: Added support for the Pittsburgh
Supercomputer Center's TCS: Lemieux (rb).



April 3, 2002


New Project: On the page where users decide to accept an
invitation for a new project, there is now an option to make the new
project the default project for a user (hw).
Revised sections of BioCoRE where the project administrator was
being asked for their project password.  Now, the admin flag is set for
users, and those users can automatically perform the project functions
(jd).
Message Board: Users can now choose whether or not they wish
to receive email about new messages in a particular project.  Before,
the messages were automatically sent out if the author of the new
message wished.  Now the recipient can choose to override the author's
wish and deny the email (kv).
Job Management: Made the list of queues at NCSA more
complete (rb).
Revised the look of the main Utility page.  Hopefully this will
make options easier to find (kv).
Job Management: Fixed a bug that was causing files to not be
properly deposited to the BioFS if the user specified a path in the
name of their output file (rb).
Summary Page: If the Control Panel chats have web addresses
in them, they are now automatically made into clickable links (kv).
Control Panel: Fixed a bug where new project members were
showing up twice in the user list for that project (kv).
Started emphasizing the Web Start version of the Control Panel more
in a few different areas.
Control Panel: Reworked the code that handles when users
have been automatically logged out so that it is more consistent with
what you would expect (kv).
Control Panel: text in the user list for each project now
states that you can send private messages by clicking on a users name
(kv).
Link Library: Fixed a bug where 'null' was sometimes getting
displayed for descriptions if the user hadn't entered a value (hw).
Preferences: Fixed a bug where colors were getting set
incorrectly when new projects were added (mb).
Revised the text of the email that gets sent out when a user
deletes themself from a project so that it is grammatically correct
(hw).
Summary Page: Job Management files no longer show up in the
list of recently changed BioFS files (mb).



March 26, 2002


Control Panel: Fixed a bug with the "blinking" code that was
causing an exception message to show up in the java console sometimes
(kv).
Summary Page: Revised the wording of the note about
accessing the Control Panel (mb).
Control Panel: Users logging in will now only change the all
user test project tab (kv).
Control Panel: On Windows, changed the icon from the Java
coffee cup to a script B (kv).
Preferences: Revised how notifications are chosen by the
user to hopefully make the page more clear.  These settings can also
determine whether or not certain messages should even appear in the
Control Panel (mb).
Control Panel: Information about the BioFS (new files, etc)
now gets sent when a user logs in (mb).
Message Board: VMD  saved states can now be editted (hw).
Revised the format of dates in some of the BioFS.  Still a work in
progress to revise all BioCoRE dates so they pass through the same
formatting rules (kv).
Control Panel: Sound is no longer automatically played upon
startup (mb).
Summary Page: Fixed error in text of page title so that it
now says that it is a summary page (mb).
BioFS: File upload now works with cookies disabled (kv).




March 18, 2002


Message Board: Fixed a bug where BioCoRE wasn't loading
indexes or messages if there were too many messages in that project
(kv).
JMV: Fixed a bug where JMV was failing improperly if Java 3d
was not installed (mb).
Control Panel: If a project tab has more than one
notification color that it is trying to tell the user about, it will
cycle through the colors instead of only displaying the most recent one
(kv).
Control Panel: Mac OS X handles some of the initial java
calls differently when starting the Control Panel, and special cases
have been included to handle this (rb).



March 10, 2002


Job Management: Fixed a bug that had caused some buttons to
disappear (mb).
Summary Page: Options are now set from the Utilities menu for
different choices that the user might have concerning this page (mb).



March 6, 2002


VMD Launcher: No longer says 'click start to launch VMD'
when launched from a saved state.  Unused gray bar at bottom of applet
is now gone (mb).
BioCoRE is doing a better job now of remembering your current page
when you change projects via the menu (hw).
Summary Page: Users can now choose to see recent biolog
entries (mb).
Control Panel: BioFS changes are now sent to the Control
Panel.  Users can click on a BioFS filename in the Control Panel and it
will be loaded (mb).
Job Management: Made the job startup code a little more
tolerant of bad network connections by extending the length of time
that it waits before failing (rb).
VMD Launcher: The "pub/sync" window now has a project
dropdown that can be used to switch between projects (mb).
Control Panel: A sound will no longer be played when the
Control Panel starts if no new messages have arrived (mb).



February 27, 2002


VMD Launcher: Reworked the windows launching code to make it
more robust (mb).



February 26, 2002


Control Panel: Users can now send private chat messages to
other users in their project by clicking on the desired user's name in
the logged in users list in each project tab.  These messages can only
be viewed by the sender and the recipient and are not archived within
BioCoRE (kv).
Control Panel: Fixed a bug with Netscape, Web Start, and
URLs that have commas in them.  Webstart doesn't properly pass the URL
to Netscape, and so I coded around it (kv).
Control Panel: With future releases, the Control Panel
should autodetect new version available on the server and give the user
a message that they need to log in again to get the new version (kv).




February 22, 2002


A new user agreement and bylaws are in place that supercede the old
versions and continued use of BioCoRE assumes agreement with these new
documents.
Control Panel: The Control Panel now lists logged in users for
their projects (except for the All User Test Project, which is
restricted for security reasons).  The chat window is divided and the
user list is on the right and the chats appear on the left (kv).
Fixed a bug that was causing logins to not work if the user
has disabled cookies in their browser (hw).
Summary Page: All of the main areas on can now be removed if
they are not important for the user.  Removed areas can be re-enabled
via the 'Utilitities | Misc preferences' link.  In addition, the Job
information can now be minimized as well (mb).
Notebook: Current sort order is now more clear in the index.  The
current sort is given in bold (hw).
The green bars at the top and bottom of each page are now thinner
so that they don't take up as much space (kv).




February 15, 2002


BioFS: Directories can now be deleted IF empty (kv).
VMD Launcher: Fixed a bug that was causing the menus to
not work right on the VMD Launcher html page (hw).
BioFS: If the user clicked 'cancel' on the 'create new
folder' popup box, a directory with a name of 'null' was getting created.
This is no longer happening (kv).
Control Panel: Slightly revised the SSL URL checking so that
it worked more cleanly under the newly released Java 1.4 (kv).
Notebook: Message edits were getting sent to the Control Panel
with the wrong ID, which was causing the wrong message to show up when
clicked.  This has been corrected (hw).
VMD Launcher: Fixed a loophole where session IDs were being
saved in states from VMD, which opened a small security hole.  This has
been closed (mb).
Control Panel: It is no longer possible to drag the message entry
box out of the Control Panel.  This was causing some problems with the
size of the box after dragging (kv).



February 12, 2002


Job Management: Fixed a problem where temporary files were
not getting removed properly as the job was being monitored (rb).
Job Management: Fixed a problem at PSC where the node and
processor numbers had gotten reversed in the script that was being generated
(rb).
Menus: Revised the version of the menuing scripts we are using
which gives quite a bit better compatibility with some of the newer browsers
(hw).
Control Panel: Revised the browser launching method for those
using webstart.  We now use Web Start's browser preference.  This preference
can be set by launching the Web Start control center and looking under
preferences.  This preference seems to only be available on Unix.  Other
platforms set the value using a different mechanism (kv).
Control Panel: Secure URLs (those starting with https:// ) are
now clickable in the project tabs (kv).
Control Panel: Added a "Message of the Day" box that can pop
up when users log into BioCoRE.  This is currently defaulting to off but
can be switched on via the Utilities menu.  Once this has more testing it
will default to being on (kv).
Control Panel: Fixed a bug that had broken being able to click
on the number of unread messages in the summary table (kv).
Control Panel/Notebook: the percent sign, the comma, and
the semicolon are now being parsed as being a valid character in a URL (kv).
VMD Launcher: Revised states that are getting saved to more 
accurately be able to reload molecules when the state is viewed (mb).
VMD Launcher: Now says that 'VMD' has been started instead of
'the application' (mb).
The note about using the menus to navigate around in BioCoRE has been
removed (kv).



February 5, 2002

VMD Launcher: VMD can now be launched from Mac OS X if the
user has manually started XFree86 before trying to launch (rb).
Control Panel/Notebook: the pipe character ( | ) is now being parsed
as being a valid character in a URL (kv).
Fixed a bug where users were not being automatically logged out due
to inactivity (kv).
VMD Launching: Slightly rewrote the code for publishing so that it
detects users on Windows more accurately (mb).



February 1, 2002

Control Panel: Appropriate items (Message board notifications and 
http:// URLs) that show up in project windows are now clickable.  A new
browser window will open to the destination given (kv).
Link Library: Fixed a bug where the create date was getting changed
each time that a user clicked on a link (hw).
VMD: More work on getting VMD to launch correctly on earlier versions
of Windows (mb).
Control Panel: The .biocoreSession file (discussed on 
Jan 23) now has its permissions set to '600' on Unix (kv).
Notebook: The notebook was having some "stickiness" problems when
viewing non-message board entries where it would revert the dropbox
back to showing the 'message board entries' as being the current selection
even if it wasn't.  This has been fixed (hw).
Control Panel: Visual representation of the message board entries
has been modified to make them more compact (kv).
Notebook: Fixed a bug with file upload where the user's subject was
getting lost (hw).
Notebook: Revised the max message size from 64k up to 16 megs so that
Biolog entries can be handled properly (kv).
Changed the header of the biolog section of the notebook from 
"Saved VMD sessions" to "Biolog" (mb).
Control Panel: Fixed a bug where users were getting notification of
member additions to projects that they were not members of (hw).



January 29, 2002

Control Panel: A new menu item is available under 'File' which will
automatically clear the notification color on all of your tabs.  Purely
a shortcut (kv).
VMD: Fixed a bug that was causing the Launcher to not properly load
on Windows 95 (mb).
Job Management: Revised file monitoring to use a reduced number of
connections to the remote supercomputer which should make things faster
as well as being nicer to the remote machine (rb).
Message Board: Revised some parsing methods that get called when saving
messages to make them much more efficient, which is particularly noticeable
when saving large messages (kv).
Notebook: Made it so that, when viewing non Message Board entries,
the dropdown stays on your current selection rather than switching back
to 'Message Board' (hw).
Notebook: Removed 'edit' and 'reply' links in the saved VMD session
entries (hw).
BioFS: Revised the file locking so that a user's locks are removed
when they log out of BioCoRE (sk).




January 23, 2002

Message Board:  "Search" now searches Control Panel chats also.  This
makes it easy to find when you were chatting about a particular topic (hw).
Message Board:  Changed buttons from "Previous" and "Next" to "Previous
Page" and "Next Page" when browsing old Control Panel chats to make it more
clear what the button is doing (hw).
BioFS: Administrators of a project can now modify all files in that
project, regardless of the owner (kv).
Utilities: Changed references from "Users Logged In" to "Project
Members" since the lists shown display project members that might not
currently be logged in (kv).
BioCoRE now correctly recognizes "Links" browser requests and treats
them the same as requests from "Lynx" browsers (kv).
Job Management: Fixed a problem that was occuring with users that
had Expired Jobs (rb).
VMD: State saves no longer delete currently existing molecules.  This
allows users to stack states upon top of each other (mb).
BioFS/JMV:  When using JMV to view representations of molecule files
stored in the BioFS, the "Load" button no longer appears on the GUI (mb).
Message Board/Control Panel:  When users save VMD states or BioLog
sessions, that is now sent to other user's Control Panels as being a
VMD state or BioLog session.  Before it appeared to be a regular Message
Board message (mb).
Revamped the Unauthorized user checking so that Control Panels should
work more cleanly when they logout or are automatically logged out due
to time (kv).
Control Panel: When starting the Control Panel via Web Start, a file
is now written in the user's home directory called 
.biocoreSession.  This file contains the following lines:
# BioCoRE API Session Information
#Tue Jan 22 16:17:55 CST 2002
URL=http\://biocore.ks.uiuc.edu/biocore/servlet/
Session=1039796164

and can be parsed and passed to the BioCoRE API to automatically set up
needed information for the API to communicate with BioCoRE (kv).
BioFS: File locking is now in.  Currently this really only affects 
text edits.  If one person in a project chooses to edit a text file (via
the Properties menu for that file) others will not be allowed to modify
that file.  Locks do automatically expire after 24 hours.  This information
is subject to tweaking over the next few weeks (sk).




January 15, 2002

VMD Launching: Fixed a bug that was causing problems with saving
states (mb).
Message Board: Fixed a bug when searching for something with spaces
in it.  It now handles spaces properly (hw).
Control Panel:  You can now log into BioCoRE by launching WebStart on
your computer with a command line parameter of:
http://biocore.ks.uiuc.edu/biocore/servlet/NewMain/applet=app&webstart=yes.



January 11, 2002

Job Management: Added specific Linux cluster queues for the 
Theoretical and Computational Biophysics machines (rb).
BioFS: Main project directories now get renamed when users rename
a project (mb).
Control Panel: Loading webstart now closes the applet control panel
if you have one running (kv).
Control Panel: Rewrote the user/password request form so that it
is prettier (rb).
Control Panel: Project member's Control panels are now notified
when a member chooses to join a project (hw).
Utilities: Revised the menu that gets printed so that preferences
is more noticeable (kv).
Preferences: Fixed a bug that was showing up if the user didn't 
have a web cookie (kv).
Message Board: Users are now reminded that they might have messages
that they are not seeing due to a time limit that they have imposed (hw).



January 4, 2002


Core: New servlet engine running behind the scenes.  This could 
adversely affect things for the next few days or weeks.
Control Panel: An application version is available that can be
started via WebStart (kv).
Message Board: Deletion notices are now sent to logged in user's
Control Panels (hw).
VMD Pub/Sync: Fixed problems that was causing it to not work
correctly on Windows (mb).
Message Board: Users must now preview messages before they can
actually be submitted (mb).
The user list for a project now denotes project administrators (mb).