BioCoRE Change Log (Year 2000)

Note: If you are logged into BioCoRE when the codebase is updated you might need to exit and restart your browser to get the newest version of the java applets.

Information about BioCoRE updates is given below:

December 19, 2000

  • Control Panel: Mostly fixed the scrolling in the project windows. It now properly scrolls as the user is viewing chats. However, on some versions of Netscape the applet doesn't automatically scroll to the bottom of the very first project that you look at after logging in (kv).
  • Message Board: Deleted the 'reply to this message' line from the new message preview (mb).
  • Revised the User List (available from the Utility button at the bottom of the main page for each project) so that the logged on users are listed in Bold and centered the Y/N for being logged in (mb).
  • Fixed the html parser so that it recognizes tildes (~) as being valid in an html link (mb).
  • Message Board: Increased the width of the text entry box from 60 to 70 columns (kv).
  • Message Board: Fixed a buglet where a newline was erroneously getting added to the subject of a message (mb).
  • Fixed a bug where the direct URL link wasn't getting set correctly if the user was coming in via https (kv).
  • Revised link and form printing so that the project ID is explicitly specified. This should make it easier to work on multiple projects in multiple windows at one time (kv).

    December 12, 2000

  • Control Panel: Notification (sound and red tabs) is no longer being sent for people who are simply relogging in (kv).
  • Control Panel: Fixed a Heisenbug where the control panel was randomly not able to start because of the ordering of messages that it was getting from the server (kv).
  • Control Panel: Started sorting messages before sending them to the applet instead of making the applet do it. This speeds up the applet initialization (kv).

    December 5, 2000

  • Access to BioCoRE now defaults to a secure SSL connection. Please use this connection so that all transferred data is properly encrypted.
  • Control Panel: Fixed a bug where the project information screen wasn't getting closed if the user logged out (kv).
  • Control Panel: Revised the time format that gets printed for messages within the past 12 hours. It now just displays the time (and not the date). This provides 4 more viewable characters on the first line (kv).
  • Notebook: Fixed a bug that wasn't allowing the user to 'reply' to a message that had quotes in the subject (mb).
  • Fixed a bug where people weren't properly getting removed from the collaboratory 'logged in' list when they were force logged out due to inactivity (kv).
  • Revised the wording on five of the questions on the registration form to hopefully provide a higher reliability score in the next analysis (db).
  • Control Panel: Reduced the amount of time that the control panel waits between checking for updates from the server from 1 second down to 0.5 seconds. This should make the control panel seem more responsive at a very low cost to the user (kv).
  • Reviewed and reworked a change that went out last week that was converting quotes to html when they didn't necessarily need to be (mb).

    November 28, 2000

  • Notebook: Added the ability to delete messages. If you are working in the All User Test Project you can only delete your own messages. If you are working in a different project you can delete your own messages or you can delete other people's messages IF you have the project password. You can't yet delete entire trees of messages, but this capability is forthcoming (sk).
  • Notebook: Added a preview so that you can look at your notebook message and try it out before actually committing it to the Notebook (mb).
  • Revised the registration to require a valid email address (kv).
  • Control Panel: Fixed a bug where the Help menu was staying visible with the 'about' item was chosen (kv).

    November 21, 2000

  • NAMD Config File Generator has been released to public. Please try it out and let us know what you think (get to it from the main page for the project that wish to work on) (hw)!
  • Control Panel: The entire summary table is now clickable. If you click on the name of the project it will take you to the main toolbox page. If you click on the number of users it will take you to the 'user list' html page. If you click on the unread message number you go to the notebook listing (kv).
  • Control Panel: added a help menu item that lets the user: view recent updates to BioCoRE, and pulls up and 'about' box (kv).
  • NAMD Config File Generator (change from beta): "parameter format" removed (hw).
  • NAMD Config File Generator: corrected spelling on reassignIncr (hw).
  • NAMD Config File Generator: The interaction of the 3 parameters reassignFreq, reassignTemp, reassignIncr is as follows (hw):
    • if a reassignFreq is given, then the reassignTemp must also be given.
    • reassignTemp is valid only if reassignFreq has been set.
    • reassignIncr is valid only if reassignFreq has been set.
    • reassignHold is valid only if reassignIncr has been set.
  • Changed the name at the top of the primary html page from Control Center to Toolboxes to reduce confusion between this and the applet (kv).
  • Fixed a bug where add user/delete user wasn't working on projects where some of the users had never logged in (mb).
  • Right-justified the 'help' button that appears at the bottom of each of the html pages (kv).
  • Fixed a bug in the database that was causing the 'silent server restart' to not work correctly. This should work OK now (kv).

    November 14, 2000

  • Added the ability to delete users from a project, assuming that you have the project password (mb).
  • Notebook: The 'Add' icon was still showing up if you chose to 'reply' to another message. (see October 24, 2000). It has been removed (kv).
  • Control Panel: Added a check every 30 minutes to see if there are any new messages waiting on the server.
  • Control Panel: Tested and working nicely on Netscape 6 (for Windows 98,NT; not yet tested on linux). Note: Other applets that we are using (VMD, NAMD-CFG) will NOT work on Netscape 6 because of Java differences. This will obviously change in the future.
  • Revised the server so that it can be restarted without requiring users to log out and then log back in. It should handle it much more gracefully now.

    November 7, 2000

  • Release of a new tool for the TB group members (will be released to everyone after a short trial period) that allows users to easily create and modify NAMD configuration files (hw).
  • Control Panel: applet now knows when it isn't authorized to do things with the server and will tell the user via a popup box. It then gives the user a chance to log in again (kv).
  • Control Panel: sound now works on the Macintosh (rb).
  • Added a 'Please Wait" notice to the white page that you get immediately upon login that gets redirected after 1 second (kv).
  • Added a small login window that fits inside the applet window. Before, BioCoRE would put the large version of the login window into the tiny browser window and it didn't look very good (kv).
  • Control Panel: Fixed a bug where it wasn't accurately telling when a person relogged versus actual logging in (kv).
  • Utilities: Removed the option to change projects. This is something that is meant to be done via the control panel. If you want to open the main window for a particular project this can be done via the project menu in the control panel (kv).

    October 31, 2000

  • Notebook: Set it so that the sender gets a copy of the email that is sent out when a new message is posted (to the non 'all user' project) (kv).
  • Control Panel: Support for the Macintosh under IE/iCab (rb).
  • Utilities: Due to security reasons, removed the link to the User List from the utilities page if the All User project is selected (mb).
  • Control Panel: Fixed bug where wrong person was being attributed with sending a message to the message board (kv).
  • Control Panel: Fixed bug with applets randomly loosing authentication with the server (kv).
  • Set it up so that the user can 'reload' the control panel by selecting an option on the main window. Only works well if the user is already logged in. I need to set it up so that it handles the relogging properly (kv).
  • Registration: Fixed a broken link to the security information (kv).
  • Utilities: Revised the date printing to look more reasonable (mb).

    October 24, 2000

  • Control Panel released (kv).
    • Java Swing applet. You need to have Swing installed.
    • Instant updates of chats
    • Easy project overviews via the summary table
    • Customizeable (and will be a lot more so as I get time to work on it)
    • Many other cool features
  • Added page to utilities menu that tells who is logged in and the last time that they logged in (mb).
  • Changed the name 'Notebook' to 'Message Board' inside the notebook component of the collaboratory. This should fit in better with our concept of the "notebook" being the entire area and what we currently have (the Message Board) just being a small part of it (kv).
  • Set the main page table menu up so that the color is customizeable (mb).
  • Fixed a bug where the option to 'send email about the new message board message' wasn't getting handled right when the user actually tried to click on the link the email to read the message. (It wasn't correctly determining the project (kv).
  • Fixed a bug where one of the server threads could crash if the user logged out, clicked 'Back' in their browser until they got to the project selection screen (right after login in their history) and then tried to submit again. I wasn't checking to make sure that they were logged at that point because I was assuming that they were (*smack*) (kv).
  • Notebook: removed the 'Add' icon from the top of the 'Add a message page'. If you are already there, there isn't a need to have a link to it. This will hopefully make it more clear that one needs to hit 'Save' to actually save the message to BioCoRE (kv).

    October 17, 2000

  • Notebook: Added sorting methods so that you can choose to see contents by date, author, topic (sk).
  • Revised the registration form so that affiliation/title start with blank lines and added a "Non-profit" option to the affiliation (mb).
  • Fixed a bug that was causing one of the server threads to crash if a person attempted to log out when they were already logged out. This bug was introduced last week when I added to code to prevent multiple logins (kv).
  • Revised the color-picker on the preferences page to only print one color table and let you choose which item to revise by choosing the proper radio button (mb).

    October 10, 2000

  • Monitoring Program: Fixed a bug on IE where IE isn't following the commonly accepted way of doing things concerning sockets. By doing this, however, some functionality was lost in the monitoring program. Should the server die, the clients will no longer be informed of this. This doesn't happen very often anyway, so it hopefully won't be an issue (kv).
  • Fixed a bug that was allowing a person to log in multiple times. Now, when you relog it will simply log out your previous session (kv).
  • Revised the registration form to first ask for affiliation and, based on that choice, to ask for a specific title (mb).
  • Revised the preferences page to show a color-picker for the different colors and allow the user to preview the results before sending (mb).
  • Fixed a bug with sending mail that was causing it to throw an (uncaught) exception if it couldn't send the mail, yet there were no invalid email addresses it was trying to send to (kv).
  • Notebook: Improved date presentation in the contents (sk).
  • Notebook: Improved search that no longer includes spaces, etc in the exact search (sk).
  • Notebook: Changed the layout of the header. Moved the 'show contents' dropdown box over to the left side and added a 'close notebook' button to the line. Removed the 'close notebook' line from down below the messages. Hopefully this will help reduce the odds of accidentally hitting the 'close notebook' button when meaning to hit something else (kv).

    October 3, 2000

  • Started printing explicit build number/time information in an html comment at the bottom of each page. This essentially shows the number of times that we have released BioCoRE since October 3, 2000 (kv).
  • Utilities: Changed the number of blank boxes for adding people to a project from 5 to 10 per a request from a user (kv).
  • Notebook: Fixed a html-izing bug where it wasn't working right if the user actually typed in actual html. It was trying to html-ize html. Now it attempts to be intelligent and realize if it is in html and, if so, to not change it. It isn't working perfect yet, but it is closer (kv).
  • Shrunk the footer information (about BioCore, the FAQ, the copyright, etc) down by a line by putting the about BioCoRE and the FAQ link on the same line (kv).

    September 19, 2000

  • Notebook: Fixed a bug where it wasn't recognizing the dash as being a part of a valid URL (kv).

    September 12, 2000

  • Removed the literal URL from the main page along with the definition of FAQ to reduce the size of each html request by about 65 bytes (kv).

    August 29, 2000

  • Fixed a small problem in the user registration where it was allowing a non-entry on a couple of drop down boxes. This now requires the user to actually select one of the options (kv).
  • Changed the 'Need Help?' icon down in the lower right corner to just say 'Help?'. Hopefully this is still obvious, and it takes up a little less screen real estate (kv).

    August 22, 2000

  • Added a brief "blurb" to the invalid username/password message that is seen on login to say that the user can always have a new password sent to them via email (kv).
  • Made it so that the sender doesn't get sent a copy of the 'there is a new message in the notebook' email. This will eventually be an option so that if the user requests it they have have it (kv).

    August 15, 2000

  • Added a checkbox to the license page to verify that people agree to the license before continuing the registration process (kv).
  • Notebook: Added a line break to the page that sends a message because it wasn't displaying properly on Macintoshes (kv).
  • VMD: Added a simple check to try and start VMD from the default Windows VMD install directory. Hopefully this will let it work on more Windows systems (kv).

    August 1, 2000

  • Removed the project creation password so that anyone can now start a project. Any project that has not been accessed for a 6 month period is subject to deletion (kv).

    July 25, 2000

  • Removed virtual formatting from notebook messages. Now, what you see is what you get in the message. Hopefully this will make it easier to create properly formatted messages (kv).
  • Chat: changed the "chunk" size of a chat line from 255 characters to 64k characters. Because of the database, we were chunking very long chat messages at 255 characters. This restriction has been removed and chunking won't start until 64k characters are written in a single chat line. At the same time we also fixed a small bug we found where we were opening too many database connections. (Please don't feel compelled to test this feature just to see if it works. These messages have to be stored) (hw, kv).

    July 18, 2000

  • Removed some 'hight' tags that were erroneously showing up in the login page (kv).
  • Reversed the ordering of the 'new user' and 'evaluation' lines on the login page (kv).
  • Notebook: Added an option (for the non All User project) to send out an email to project members when you post a notebook message (kv).

    July 12, 2000

  • Monitoring Tool: Fixed a bug where the script file being written had a line that was exceeding 255 characters which was causing it to not work correctly (kv).
  • Monitoring Tool: Removed the word 'Release' from the NAMD option (kv).
  • Monitoring Tool: Changed the start job screen to remember previous architecture/queue choices (rb).
  • Monitoring Tool: Changed the update time on the running programs screen from 1 second to 2 (rb).
  • Monitoring Tool: Fixed a bug where the monitoring tool was locking occasionally on job submission. This appeared to the user to be a relatively random thing but it was being caused by a timeout problem with the ssh'ing (kv).
  • Monitoring Tool: Changed the job start/fail messages to be much more descriptive. They now tell the user why a job has failed rather than just that it has failed (kv).

    July 4, 2000

  • Notebook: Fixed a bug where it wasn't recognizing the underscore as being a part of a valid URL (kv).
  • Monitoring Tool: Sending descriptive reason if the job doesn't start (kv).
  • Monitoring Tool: Fixed flickering in running job list (rb).
  • Monitoring Tool: Added a window to view stdout from a running job (rb).
  • Monitoring Tool: Renamed temporary files to include description given (kv).

    June 27, 2000

  • Notebook: When a http: href is inserted into a message it should now be automatically converted into a link for viewing. This should also work for ftp:, etc. When the link is clicked on, a new window will pop up (kv).

    June 20, 2000

  • New interface for when you run VMD. It is now more user-friendly with regards to the security certificate, etc (rb).
  • Notebook: removed the images for next/previous message and just used plain href links that show the subject (kv).
  • Remove the http:// that gets printed at the bottom of each page. It is still encoded in the URL, it just doesn't show in the page (kv).
  • Notebook: Removed an image call from the header to speed things up a little bit and replaced it with a wide HR (kv).
  • Changed the word 'NEW' to 'UNREAD' and made it so that when you compose a new message it automatically is marked as 'READ' for the author. This only affects new messages, so messages written before this system was implemented will still be marked as unread (kv).

    June 13, 2000

  • Added the option for each user to set their own preferences. This is available from the Utility Menu (kv).
  • Added code to let each user set a default project. Once this is done the user doesn't have to choose their project when they log in. They can always change or remove the default project by going to the Utility menu and selecting the link to change a project (kv).
  • Removed the 'Change current project' link from the Utility menu if the user is only enrolled in one project (kv).
  • Notebook: Added personalized checking of which messages haven't yet been read by each user. The very first time that someone logs in after this change it says that all messages are unread (since it doesn't have any knowledge of what you read before it started keeping track) (kv).
  • Notebook: Made it so that when you change the dropdown box up in the corner from regular messages to chat, etc that it automatically goes to the contents of the new selection. This uses javascript (kv).
  • Notebook: Increased the size of the 'add message' box by 10 lines (kv).
  • Notebook: Changed the display of the date/time so that it puts an asterisk between the date and the time instead of using a colon. This should reduce confusion (kv).
  • Notebook: Changed the names of various buttons/links to make them more user friendly (kv).
  • Notebook: Fixed a "feature" where it was printing out a whole bunch of HTML HREF messages that it shouldn't have been. These weren't showing up in the html page, so they weren't causing a problem, exactly. They were just causing unnecessary work on the server and the network pipe between the server and the client (kv).
  • Notebook: Changed it so that the URL for the internal notebook links now just contains the name Notebook instead of the previous version which had the absolute path in it. This cuts down quite a bit on bytes transferred (kv).
  • Notebook: Reduced the number of database transactions significantly to load the contents of the notebook. On our test servers it went down by about 95% (kv).

    June 6, 2000

  • Notebook: Fixed a typo that was popping up when you closed the notebook. It was saying NotebooK (rb).
  • Removed the numbers on the footer section of the pages and added the explicit URL of BioCoRE (kv).
  • Changed instances of the word 'on-line' to 'virtual' during the registration process (db).
  • Removed the word BioCoRE from the title of the login page since it was being printed twice (kv).

    May 31, 2000

  • Notebook: The database was set up to allow subjects up to 40 characters long. This was changed to allow subjects of up to 255 characters (kv).

    May 23, 2000

  • Reduced the size of the control center to eliminate wasted space and generally improved the symmetry of the page (hw).
  • Fixed a bug with sending private messages in Chat. Before, they weren't getting logged correctly to the notebook. That is now fixed (hw).
  • Fixed the problem with the control panel not looking correct in Internet Explorer (hw).
  • Fixed the bug where the last line in a notebook message wasn't getting saved (rb).
  • Added an option on the login page to send out a password if it was forgotten (kv).
  • Changed the way that session information is being saved on the server. Reduced by two the number of database accesses for each web hit. Should make the server capable of handling a much higher load (kv).

    May 18, 2000

  • Moved the computer that biocore was on. Now it is located at biocore.ks.uiuc.edu rather than the previous location on one of our normal machines (rb, kv).
  • Changes the title of the default page to remove the word 'main' (kv).
  • Notebook: added ability to step forwards and backwards within a thread (sk).

    May 9, 2000

  • Changed the names of some of the pages to make them more precise (kv).
  • Improved the wording of the 'welcome to a new project' message that gets emailed out to new project participants (kv).

    May 2, 2000

  • Chat: Increased width of the user's box to make the display work out right if the user has a name that is larger than what we were expecting (hw).

    April 25, 2000

  • Changed URL references from http://www.ks.uiuc.edu/Research/collaboratory to http://www.ks.uiuc.edu/Research/biocore/ to reflect the new, preferred URL for BioCoRE (kv).
  • Added the help button to a number of the pages in the Utility section. These were previously missing. (kv).
  • Fixed a minor bug where the 'current project' name on the title bar wasn't getting changed to the new project name immediately after creating a new project (kv).
  • Added a javascript check in the registration process to make sure that people type in a number when asked (as opposed to something like 'none' or 'zero') (kv).
  • Chat: In the lobby of the chat rooms, the 'NO ACTIVE CHANNEL' option in the dropdown box was deleted. The default switched to 'Create a New Channel', unless there is an ongoing chat. In that situation the ongoing chat is the default. (hw).
  • Chat: In the lobby the user can now hit 'enter' after typing a new channel name and the channel will be created (no matter what is in the dropdown box) (hw).
  • Notebook: word wrapping in now in (sk).
  • Notebook: When you reply to a message the original message has a greater-than symbol (>) at the beginning of each line of the original message (sk).

    April 11, 2000

  • Changed email references to biocore@ks.uiuc.edu instead of collaboratory@ks.uiuc.edu (kv).

    April 4, 2000

  • Added the option to change the current working project via the Utility menu instead of having to logout and back in again (kv).
  • Notebook - Chats appear in tables (sk).
  • Notebook - Drop down box added to let people choose which type of message they want to view. Defaults to just notebook entries but chat entries can be chosen upon request (sk).

    March 28, 2000

  • Fixed a minor bug with information being lost after a user timed out. BioCoRE is set up to automatically log people out after a set amount of time (it is currently 2 hours, but will eventually be user customizable). If a user tries to do something after that time they are forced to type in their password again to retrieve the page they were requesting. In some cases it was forgetting the information that they were requesting. This has now been fixed (kv).
  • Made image references machine-independent so that we can more easily move the code if we need to (kv, sk).
  • Added checking to not allow someone to register twice. We had a few problems with this in the past (kv).
  • Fixed a bug in the code that happened right after creating a new project. BioCoRE wasn't properly switching the project creator over to the new project (kv).
  • Added a direct feedback form link to the bottom of the pages (kv).
  • Notebook - Text window now wraps around (sk).
  • Notebook - Project Name in contents screen has been removed (sk).
  • Notebook - Close button now pops up a screen with the contents on it (sk).
  • Resized basic table to reduce amount of "wasted" green space (hw).
  • Chat - Changed entry method so that users can now choose the names for their channels instead of having to choose from a set list (hw).
  • Chat - Changed the maximum number of people per channel to 100 (hw).

    March 13, 2000

  • Rather significant changes to the way that database connections are made. Should speed things up quite a bit. Changed interface to 'Chat' as requested by users. Made the text entry box multiline and changed the wording on some of the buttons to make them more descriptive.
    The initials given in parenthesis denote the person responsible for the change:
  • mb - Mike Bach
  • db - David Brandon
  • rb - Robert Brunner
  • jd - Jay DeSouza
  • sk - Sameer Kumar
  • kv - Kirby Vandivort
  • hw - Hui Wang