May 30, 2007

• Reordered the user list on the webpages so that sorting is by last login (kv).
• Fixed a bug with deleting users who hadn't recently logged into BioCoRE (kv).

October 16, 2006

• Job Management:Added the ability to forget/remove jobs from the BioCoRE interface (rb).
• Job Managment:Reeanbled NCSA Cobalt support (rb).
• Control Panel:Autoconvert things like :) into a small smiley face icon. This is preliminary work for allowing users to drag pictures into the control panel that others can see (kv).

September 15, 2006

• Control Panel:The project who's tab you are currently on is now displayed in the title bar (kv).
• Job Management:Fixed a bug that was showing up on the account deletion page (rb).

September 6, 2006

• Job Management:Job accounts can be deleted via the web page now (rb).
• Control Panel:More old chats are now being sent out when a Control Panel starts up (was 20; now 200) (kv).

August 18, 2006

• Control Panel: You can now choose whether or not you wish to see notification of file changes in the server area ( the .ServerFiles directory of each project). This setting only works if you have chosen to see notification of file changes in the BioFS in the first place. The default setting is to NOT see file changes in the server area (kv).
• Notebook:Fixed a bug that was occuring if you tried to search for the space character (kv).
• Added some code to try and fix a user's problem with having to log in twice (once on the web page, once for the Control Panel) (kv).
• Added some code to hopefully cause Google API keys to immediately take effect upon initial input. I think it might have been waiting for the user to relog. More testing is necessary to see if this actually fixes the problem (kv).

August 10, 2006

• Control Panel, VMD Chat: You can now send multiple private messages at once by doing a /msg userA,userB,userC hello where the user names are split by a comma (and no space) (kv).
• Control Panel, VMD Chat: Emotes (/me grins.) now work via VMD Chat, and they also work within private messages (kv).
• Programming Interface:Fixed a bug where cached user information was being stored when new data needed to be retrieved from the server (kv).
• Control Panel:Choosing the 'preferences' option from the File menu now opens the general utilities page. This will hopefully be more intuitive for the user (kv).
• Added documentation for chatting via VMD (mb).

July 13, 2006

• Programming Interface: Various updates to the TCL API that VMD is using. Added in some caching to speed things up (kv).
• Programming Interface: The TCL API is now capable of sending a file attachment with a notebook message (kv).
• Programming InterfaceFixed a bug with the way that TCL was handling the equals sign in messages (kv).

July 7, 2006

• Programming InterfaceFixed a bug with the way that TCL was handling slashes in messages (kv).

June 27, 2006

• Fixed a bug in the email notifications when a new public project was created. The URL sent out in the email needed to have the name of a parameter changed (kv).
• Programming Interface:Added a way to register a full user to the API. TCL implementation done (kv).
• You can now specify a default public project for a new user to join when they register for an account. If you have a public project within BioCoRE, and you have a link for users to use to join BioCoRE, you can embed the project ID in the URL and the users will automatically be added to the project when they create their account. Before, you would have linked to http://biocore.ks.uiuc.edu/biocore/nonsecure/printUserConsent.do and now you link to http://biocore.ks.uiuc.edu/biocore/nonsecure/printUserConsent.do?pid=42. where 42 is the project id you want (kv).

June 20, 2006

• Numerous new commands for the TCL API. See the TCL API documentation for example usage.
• Fixed a bug with hiding and later unhiding a project (mb).

June 12, 2006

• BioFS:More work on the Private directory bug from last release (kv).
• Programming Interface:Work on the tcl version of the API. Tweaks to the biocoreHelper.tcl file to make it properly detect VMD. The API now defaults to the main BioCoRE server URL. This can be changed by resetting ::biocore::URL after reading biocore.tcl. Newest version of the TCL API uses public/private key encryption for sending passwords to the server. So, passwords are safe even over http. If the user doesn't care about the extreme safety of the remainder of the information sent to the server, this allows API usage over http.

June 5, 2006

• Job Management: Enabled support for PSC Bigben and Lemieux (rb).
• Programming Interface:Added a call to the TCL API that gets a list of projects that a user is eligible to join. See TCL API documentation for example usage.(kv).
• Programming Interface:Added a call to the TCL API that let's a user join a project (kv).
• Fixed a place in the sidebar where ampersands in a project name were causing problems (rb).
• Notebook:Fixed a bug where search results for the control panel chats weren't actually sending the user to the proper spot in the history list (kv).
• BioFS:Fixed a bug that users may or may not have actually seen that was occuring when some webdav clients uploaded a file to a user's private directory (kv).

April 12, 2006

• Control Panel:We had a user behind a firewall, and the socket connection between the Control Panel and the server was causing the CP to be non responsive for 3 minutes while the socket connection timed out. This addition incorporates a timeout mechanism that will fail if the connection can't be made within a few seconds (kv).
• Job Management:NCSA Altix (Cobalt) bug fixes (rb).

April 7, 2006

• Job Management:Added support for NCSA Altix (Cobalt) (rb).
• BioFSFixed a bug where files uploaded from Windows were being named with the entire path (C:\etc etc) instead of just the expected filename (mb).
• Control Panel:Sorting of usernames shown in the user list is now case-insensitive (kv).
• Control Panel:Removed pop up boxes if the Control Panel can't connect to the server for its periodic checks. It now just silently tries again after a delay (kv).

March 21, 2006

• BioFS: Web interface time show is now the last update time. Previously the create time of the file was being shown (kv).
• BioFS (WebDAV): Last release's WebDAV changes had adverse effects on Windows and strange characters, so I had to go back in and do some more work on this to get it working everywhere (kv).
• BioFS: Fixed a problem where some characters (like the plus sign, less than, greater than...) weren't getting properly displayed in the web interface. Also, files with strange characters in the name were not being uploaded properly (kv).
• Chat History: Fixed a bug where chat history searches weren't quite working right (kv).

March 17, 2006

• BioFS (WebDAV): Fixed a situation where the ftp-like command line client program 'cadaver' was not able to access folder with special characters in the name (kv).
• Fixed a problem with searching in old control panel chats where the URL wasn't being properly formed (mb).
• Control Panel:Test code to temporary highlight the color of a tab when an event occurs within that project. This occurs regardless of whether or not the tab is already a given color. The intention is to make it more obvious that there are ongoing conversations in a project. It isn't perfect yet, though. For some cases it doesn't seem to be changing the color as it should. Work is ongoing (kv).

March 15, 2006

• Guest Accounts are now in. When a prospective user comes to BioCoRE, they can fill out an abbreviated form, which asks for limited information and get an account on BioCoRE. The guest user can't create projects, or join private projects (and a few other minor things) but can find out more about BioCoRE without having to fill out a large form. They can upgrade at a later point by filling out the rest of the form (kv).
• Control Panel: BioFS operations no longer include the project name when describing files. Delete includes the entire path (instead of just the file name itself) to reduce potential confusion (kv).
• Notebook: Fixed a bug that was showing up if notification email URLs were selected from projects other than the one you were currently in (mb).

February 15, 2006

• Job Management: Fixed a problem with deleting jobs.

February 9, 2006

• New Theme: tcb You can follow the Utilities link in the left sidebar of the web pages to get to the Themes section (mb).
• Notebook: Fixed a database bug related messages with revisions (kv).

February 8, 2006

• Notebook: Added in a test related to messages with revisions that should prevent a rare error we were seeing (kv).
• Control Panel: Parenthesis are now parsed as being part of a URL (kv).

January 11, 2006

• BioFS:WebDAV fix for requesting partial files. I think that the code was copying one byte less than it should have. This will hopefully help with some MacOS X problems (kv).
• Control Panel: Tweaks to the code for allowing bold, italics, color to be more accepting of upper/lower case and quotes (mb).

December 13, 2005

• BioFS: Fix bug to allow files/folders to be added to subfolders of a user's Private folder (mb).
• Control Panel:Added an experimental internal web browser for the Control Panel. You are far better off using your favorite external web browser (like firefox) because it has the latest web features. But if, for whatever reason, you can't get the external browser to work you can choose to use the internal browser by selecting it under the Help menu (kv).
• Control Panel:Experimental file downloading via the Control Panel. If you go to File | Browse BioFS and choose a file, it will actually be downloaded to your local system (if you are on Unix). It currently places the file in /tmp/file. That's the name of the downloaded file. Clearly, a better interface needs to be built for this to be useful. I've had this capability in for some time and decided to go ahead and release it as is (kv).
• BioFS:When you upload a file via the web page, you should get an upload dialog telling you how the upload is proceeding. For small files and fast connections, you might not even notice it. But, for long uploads on slow connections, it should be very helpful. We've had several cases in the past where I think that users were canceling out of the upload because they thought that things had hung/frozen. Hopefully this will help reduce these occurrences (kv).
• Control Panel:Added support for bold, italics, and color in the Control Panel. Use <b></b> for bold text, <i></i> for italics, and <font color="COLOR"></font> for color, where COLOR can be either a hex color code like #FF000 or a Java color constant like "red" or "blue" (mb).

November 17, 2005

• More revisions to how project parameters are passed to the server. This is all in an effort to make BioCoRE more robust for users who might be doing things in multiple projects "at the same time".

November 4, 2005

• BioFS: Fixed a bug that was causing the download of files larger than two gigabytes to fail (kv).
• Correction of more forms to properly handle relogging when changing projects (see October 27 update for more information).
• Fixed a bug where users could set their notifications in a certain way to get emails when they didn't want them (kv).

October 27, 2005

• Job Management: Added in an option to delete jobs that have been submitted (rb).
• Control Panel: Fixed a bug that was causing multi-line pasted chats to not show up in private conversations (kv).
• Control Panel: Added dialog boxes when you run a script from the menu or (alternately) add a script to your Control Panel startup to tell you that the Control Panel succeeded in your request, and to note that you will still need to perform the alternate operation if you wanted it done (kv).
• Revised the format of the .biocoreSession file that is written by the Control Panel in the user's home directory. This affects users who are using the BioCoRE API. If you are using the API, please download and install the latest version of the API, which supports the new format (kv).
• Fixed a bug that was causing new users to not see the welcome page (kv).
• Started addressing a problem that has been occurring for some time if a user was automatically logged out while filling out a form in BioCoRE. Upon relogging, the user would be put back into their default project and not (necessarily) in the project that they were in when filling out the form. Not all forms are correct yet, but we are addressing the problem as we find it.
• Typically, when a non-logged-in user tries to go to a URL within BioCoRE, they are redirected to the login page and then go to their desired destination. This wasn't working through project invitations, which has been fixed. Sometimes, however, the storage of the user's requested page was working too well, and the user was being redirected to that page instead of where they wanted to go at other times during their usage of BioCoRE. This has been fixed as well (kv).
• Added in additional checks in a few places early in the authorization process to make sure that the user was specifying a project id that they were actually a member of, rather than relying on other code to do it (kv).
• Fixed some problems with people logging in who used mixed case in their login names (kv).

October 11, 2005

• Job Management:More tweaks to the code (rb).
• Added in summary pages for the Documents, Workbench, and Notebook modules that new users can click on to get more information about what the various components provide (kv).
• Pictures for the main menu and the summary pages (mb).
• BioFS:Fixed a bug that was causing file deletion notices to not get sent to the control panel (kv).
• BioFS:Had a case where a user aborted a file upload and the file remained locked. Configured partial file uploads so that they will release the lock on the file. If anyone notices problems with this behavior, please let us know (kv).
• Control Panel:Added text to the About box to tell users if they are not running the current version of the Control Panel (kv).

October 4, 2005

• Job Management:File staging updates so that files are now transmitted to and from the BioFS and the computational machines (rb).
• Job Management:Fixed some bugs that were preventing accurate account monitoring (rb).
• Control Panel:Fixed a bug where system messages weren't getting sent to private chat windows (kv).
• Control Panel:Fixed a bug in the XML parsing that occurred when the XML document contained comments (kv).
• API: Added a proof-of-concept TCL control panel to the distribution. Discussed at the TCL API page (kv).

August 31, 2005

• BioFS: Tweaked /biocore/biofs so that it doesn't include links to projects that don't have an index.html file (kv).
• Control Panel: Scripting - Menu and menu items can now be removed. For example usages see the scripts in the BioCoRE Help project (kv).
• Control Panel: Scripting - Added methods to retrieve a particular project tab based on its name or the project id (kv).
• Fixed a bug in XML parsing that was causing it to incorrectly handle documents with returns in the tag name (kv).
• Control Panel: Minor addition to last week's commit that allowed multi line pasting. It wasn't working for private chats (which you can get by clicking on someone's name in the user list, or doing /msg userName message you want to say (kv).
• Scripting: Revised set of who can delete entries to include author and project administrator (mb).

August 25, 2005

• Control Panel: Pasting into the chat entry field now preserves line breaks (kv).
• Control Panel: Clicking on Project | Documents | BioFS now takes you to the top level folder for the project. Before, it took you to the overall top level folder (kv).
• Control Panel: When typing a URL into the chat field, added the ability to specify the text to show, as well as the URL itself (kv). Before, you could say something like Go to http://www.ks.uiuc.edu/ to check it out, and it would look like:

  Go to http://www.ks.uiuc.edu/ to check it out
  

  Now, you can say Go to [http://www.ks.uiuc.edu/ our site] to check it out and you will see:

  Go to our site to check it out
  

• BioFS: Accessing /biocore/biofs via a web browser was causing a technical fault. This has been fixed and now displays a list of public projects. When you click on a public project, you will be taken to the home page for the public project if one has been set up by the project administrator (kv).

August 22, 2005

• BioFS: Revised 'new directory' code to reload the folder view so that the user can see the newly created folder (kv).
• BioFS: Fixed a bug that was causing an error if a person that isn't logged in tries to go to /biocore/biofs/ in their web browser (kv).
• Notebook: Fixed a bug that was allowing a user to delete other's entries when they shouldn't have been able to (kv).

August 5, 2005

• TCL Api:Fixed a problem with parsing of curly braces when saving notebook entries (mb).
• BioFS:Fixed a bug that was causing problems when uploading to a user's /Private directory (kv).

July 8, 2005

• Control Panel Scripting: Added in the ability to parse XML strings within scripts. For an example use case, refer to the cafemenu.py script in the BioCoRE Help (Public) project. A DOMElement is returned, which has methods such as: getName(), getText(), getAttribute(). (kv).
• Utilities:Fixed a error page that was showing up if a user tried to remove themself from a project that they had already been removed from (kv).
• BioFS:The web interface is more tolerant of filenames with non alphanumeric characters now (mb).

June 16, 2005

• Projects: It is now possible to create a public project without the requirement of creating a corresponding private project (kv).
• Public Projects: You can now create web pages that are visible to the entire world. To do these, we suggest doing the following:
  1. In the BioFS folder for the public project, make a subdirectory where you will store the webpages.
  2. Put the web pages in this directory. The index.html file will be automatically accessed and you should use relative paths for images, etc.
  3. Access it! If you have named your public project MyProj and you called your subdirectory www the URL to access it would be: http://biocore.ks.uiuc.edu/biocore/biofs/MyProj/www/
  4. Permission access is based on the 'other' permissions given in the file permissions for the file. Permissions for files in public projects default to "644" which allows anyone to read them. If you have files in your public project that you don't want to be visible to the entire world you can change the permissions via the web interface.
• BioFS: The web interface is more tolerant of filenames with non alphanumeric characters now (mb).
• BioFS: Fixed some bugs where public project files weren't being made visible to non members (kv).
• Control Panel: A user on Windows XP Pro and Java 1.5 was getting a warning when starting the CP about a missing command. The Control Panel now checks for Windows and skips this code (kv).
• Control Panel: URLs of the form www.ks.uiuc.edu are now recognized as being a URL. Before, http://www.ks.uiuc.edu was required for recognition (kv).
• Public Projects: Added explicit text at the top of the web pages to tell the user that they are in a public project (kv).

May 24, 2005

• BioFS: Reverted some code that was causing file transfers of >2 gigs fail (kv).
• Utilities: Fixed a bug that was causing a user to not be able to unhide projects (kv).

May 2, 2005

• Utilities:Tweaks to "inviting users" and "joining projects" pages (mb).
• BioFS:Webdav now honors the 304 "Use local copy" code, which should speed accesses of previously accessed files (kv).
• Control Panel:Added in checking to make sure that a user can actually see file operations (by checking permissions) before notifying them that something has changed (kv).
• Control Panel:Reworked notification of users joining/leaving projects due to some cases where the Control Panel wasn't being updated properly (kv).

April 20, 2005

• BioFS:Fixed a couple of places in uploading files and creating directories that we not giving the user feedback upon failure (kv).
• Utilities:Made it so that project administrators can't remove themselves from a project via the 'remove users from this project' page (mb).
• Job Management:Reenabled the Small Queue for TCB users (rb).

April 15, 2005

• Projects:Project administrators can now choose a small icon to display for their project web pages. It will show up right above the Summary Page link in the left menu bar (kv).
• Utilities:Users can now set an email watch for new public projects that are created. We highly suggest enabling this email watch (kv).
• Main Menu:Hopefully fixed so that each element occurs on its own line in Safari (rb).
• Utilities:Revised removal from a project so that admins aren't allowed to remove themselves if they are the last remaining admin of a project (mb).

April 5, 2005

• WebDAV/BioFS: Fixed a place on MOVE/COPY where we weren't in compliance with the WebDAV spec in regards to default overwrite behavior (kv).
• Job Management: Fixed a few error conditions that might occur if user's didn't have accounts (rb).

March 21, 2005

• BioFS:Added the ability to "watch" the BioFS for changes to a folder. BioCoRE will automatically send email to your email account on record on a periodic basis when changes occur in the folder you are watching. To access this functionality, go to the BioCoRE web interface and choose BioFS from the left column. Navigate to the folder you wish to watch, and choose the 'Edit Watch' link from the upper right corner of the page (kv).

March 14, 2005

• Notification:Reworked notification to be more robust (mb).

March 7, 2005

• BioFS:Fixed some display bugs that were showing up after an error had occurred (mb).
• Notebook:Text used for message bodies is smaller now (kv).

March 2, 2005

• BioFS: Added success notes after uploading files via the web interface (mb).
• Public Projects: Added links for a user to easily join a project when they are previewing it (mb).

February 25, 2005

• Utilities: Added the ability to "watch" the notebook area (Message Board, Lab book, BioLog, VMD States) and have BioCoRE notify you periodically of additions. To enable this, go to the desired project webpage, choose Utilities from the left menu and select Email Options under Current Project (kv).
• Job Management:Added the ability to "forget" jobs. This doesn't remove the job from whatever queuing system it might be in, but it causes BioCoRE to forget its existence (rb).
• NotebookUpdated the lab book to not use Message Board attributes in a few spots (mb).
• BioFS:Fixed a bug in the webpages that was occurring if the user tried to create a new folder with an already existing name (mb).
• Misc: Fixed a few bugs with joining projects and the "forgot password" section (mb).
• Control Panel: When you join a project the tab is now instantly created, rather than needing to relog (mb).
• WebDAV:Handled a bug in DavFS where MOVEs were appending a slash onto the names of all files. Fixed another bug that was occurring when trying to PUT a file into /blah/file.txt/name.pdf (kv).
• Documentation:Updated the VMD Pub/Sync help page (mb).
• Control Panel:Added a 'documentation' menu item to the scripting menu (kv).

February 15, 2005

• Job Management: Revised more of the methods being used for ssh. Please let us know if you notice any irregularities when submitting jobs (rb).
• Control Panel: Tweak to how user lists are displayed to help with the "disappearing user" problem. In theory, if you have a case where your user list has disappeared, you can move off the tab and back onto it and the list will be recreated (kv).
• Public Projects: Added some notes that make it more evident to the user that they are testing a public project without actually being a member of it (mb).
• Passwords: Fixed a bug that was preventing a user from logging in successfully after they had forgotten their password (kv).
• BioFS: Fixed some bugs that were causing unexpected redirections after visiting certain webpages (mb).
• Utilities: Minor fixes to error checking on the notification pages (mb).

February 10, 2005

• BioFS: Implemented the concept of "sticky bits" and enabled it on directories in the BioFS. Under normal Unix-type file permissions, if the permissions on a directory are such that group members can write to the directory, they can delete and move files in the directory regardless of the permissions on the file itself. This means that user X could set permissions on a file in a directory such that only they can read and write the file. Without the sticky bit set, anyone with write permissions on the directory could then delete the file. However, with the sticky bit set, this can't happen. With the sticky bit set, the only people who can delete and move a file under those conditions are: the project administrator, the owner of the directory, and the owner of the file itself (kv).
• Job Management: Revised more of the methods being used for ssh. Please let us know if you notice any irregularities when submitting jobs (rb).
• VMD Load/Save States: Fixed a bug that was occurring when users who weren't members of a public project tried to load states in the project (mb).
• BioFS: Fixed a bug that was occurring when a user tried to upload a file via WebDAV into a nonexistent directory. Fixed a bug where the DAV server wasn't correctly responding when a DAV client tried to unlock a file that wasn't locked (kv).
• Registration: Fixed some bugs that were occurring when users didn't have javascript enabled and were submitting non-integers into the form where integers were expected (kv).

February 8, 2005

• BioFS: Changed the name of the System folder to .ServerFiles. This will hopefully be more understandable for users, and DAV clients can interpret the folder as being hidden if they wish (kv).
• BioFS: Fixed the bug where the file list wasn't getting updated after adding a file via the webpage (mb).
• VMD Load/Save States:Fixed an errant window that was popping up when loading a state. Added error checking for snapshot saving. Fixed error that was occurring when loading a file from the BioFS (mb).
• Job Management: Partially revised the method being used for ssh. Please let us know if you notice any irregularities when submitting jobs (rb).
• Control Panel: You can now choose, by going to Project | Show, whether or not you wish to see notification of BioFS changes. Notification of hidden files (those that start with dot) isn't seen, regardless of the setting (kv).
• Control Panel: Fixed a bug that was causing sound notification to not work entirely accurately (mb).
• Misc: Hopefully made "relogging" more robust. We had some cases where people weren't being taken to the expected webpage after they had to relog in (kv).

February 3, 2005

• Message Board: Adding new messages now updates the number of unread messages displayed on the summary tab of the Control Panel (kv).
• BioFS/WebDAV:Fixed several bugs. Requesting a filename followed by trailing slashes and text now fails properly. Fixed a bug where the server wasn't responding properly when a Mac client uploaded a new file. Started handling a condition that could occur when the Mac tried to relock a file that it had already locked (kv).

February 2, 2005

• Link Library: Administrators can now edit/delete links by anyone in the project (kv).
• BioFS: Fixed a bug that was occurring when a user copied an entire directory tree from one project to another. Subdirectories weren't getting their project identifier changed properly. Now they are (kv).
• WebDAV: Fixed a bug where, on certain DAV clients for Linux, some subdirectories (those with unusual characters in their names) were showing up twice (kv).

January 31, 2005

• Control Panel Scripting: Revised the menuing system so that it can be modified by scripts. Added a sample script to the BioCoRE Help project that shows how to use this (kv).
• Control Panel: Added a few more debugging statements to the "High" log level to help track down the "missing users" bug. Also fixed a spot on the server that was sending out the user list twice when someone logged in. I don't think this will fix the problem, but it should make Control Panel startup ever so slightly faster (kv).
• Utilities: Fixed a bug where extraneous emails were being sent when a user was promoted to Administrator of a project (mb).
• Misc: Fixed a little (big) bug that was converting quotes ( " ) sent to the database to single ticks ( ' ). Hopefully this hasn't caused too many problems (kv).

January 26, 2005

• Control Panel: The Google license for doing queries from the Control Panel states that multiple users can't share a single key, so this has now been implemented. Before you will be able to do Google queries you will need to get a Google API key. Instructions for doing this are given in the Control Panel help Documentation (kv).
• Utilities: Consolidated the "Change Password", "Miscellaneous", and "Notebook Prefs" page into a single page, which should make things easier to find (kv).
• Revised user invitations to not include certain text unless needed (mb).
• VMD Launcher: Fixed a bug where non standard VMD paths weren't getting properly stored in the browser's cookies. Still not working correctly on all versions of Windows (mb).
• User Information: Fixed a bug where users were visible in the Roles, etc pages even if they hadn't accepted an invitation to join a project (mb).

January 24, 2005

• Notebook: Fixed a bug that was showing up when a user tried to view a notebook message who's parent had been deleted (kv).
• User Information: Fixed a bug that was showing up when a user tried to edit their user information from a public project that they weren't actually a member of at that time (kv).
• BioFS: Fixed a bug that was causing improper error messages when a nonexistent project was specified in the path of a requested file or folder (kv).

January 21, 2005

• Job Management: Added in checks for more error conditions which should help the user experience (rb).
• Project Management: Fixed some bugs with promoting users to be administrators of projects, emails sent to promoted users (kv).
• Link Library: Fixed a blank screen error that was showing up when users tried to edit topics or links (kv).
• Error Handling: Refactored the error handling code so that users shouldn't see blank white screens as much (if ever). This can result in a couple of strange occurrences if something is going wrong on the Summary Page, but, in general, gives a more positive experience (kv).

January 19, 2005

• Notebook: Messages being authored can now be postponed until a later date (mb).
• Summary Page: Revised how older chat messages are retrieved from the database which should greatly speed up the load time of the summary page (kv).
• Control Panel: Help | About now displays the current dimensions of the Control Panel, which can be used to set the default starting size via File | Preferences from the Control Panel, or the Utilities | Control Panel General settings from the web pages (kv).
• Polls/Quizzes: Revised the default setting to not automatically show polls and quizzes in a popup window in the user's Control Panel. This setting can still be turned on via the notification utilities (kv).
• Notebook: Fixed a bug that was showing itself when a message was authored by a now nonexistent user (kv).
• Control Panel: Fixed a bug where the up arrow wasn't consecutively recalling older chat messages properly (kv).
• Notebook: Fixed a bug that was occurring when importing a file into a notebook message (mb).

January 11, 2005

• BioFS: Fixed a bug where the Private directory was inaccessible (mb).
• BioFS: Made it so that all users could view the contents of public project directories (mb).
• Control Panel: Error boxes now pop up if the Control Panel can't communicate with the server properly (kv).
• Control Panel: Reworked the code that handles server restarts and network interruptions to be quite a bit more robust than it was before (kv).

January 7, 2005

• Control Panel: Fixed a bug that was causing users to get automatically logged out after a server restart if they didn't acknowledge the 'New Version of the Control Panel Available' box within 6 minutes (kv).
• VMD Pub/Sync: Fixed a bug that was causing the applet to not load VMD on Windows if the C:\Temp directory didn't exist. Now the applet gets a good temp directory from the system (kv).
• Notebook: A message is now displayed if no visible entries exist (kv).
• Control Panel: Windows that browse the BioFS now have an option to refresh the directory tree. The Control Panel was caching the tree structure, which could become stale over time (kv).
• BioFS: When using the web interface the name of a file can now be changed when copying it (mb).
• TCL API: File upload should work now (mb).
• Scripting: fixed a bug that had been introduced on the 6th that caused recursive loops when using 'send listeners' (kv).

January 6, 2005

• Control Panel: User lists are now sorted alphabetically (kv).
• Control Panel: Added in a simple check for an empty user list before removing the current user list when a new user logs in. This might fix the problem that we are seeing with people getting blank user lists (kv).
• Scripting: Initial documentation on doing scripting. This can be accessed via the Control Panel via Help | Documentation. Then scroll down to the menu section on scripting and the link will be there (kv).
• Scripting: Minor tweaks. If a file can't be found in the BioFS a better error message is now displayed, and the button text on the 'Startup Scripts' window is now more descriptive (kv).

January 4, 2005

• BioFS: Properties windows now pop to the front when requested (mb).
• Notebook: 'Mark All Read' now keeps track of which type of message (Notebook, BioLog, etc) it is for (mb).
• Misc: Added links from the Public Projects page to the summary page for the given project (mb).
• VMD Launch: Fixed a bug where molecules loaded via the Control were getting loaded twice (mb).

December 22, 2004

• User Registration: Fixed a text bug that was occurring if the user didn't check the boxes on the consent form page (kv).
• API: Fixed a bug that was causing notification of notebook additions and deletions via the API to not be sent to the Control Panels (kv).
• Notebook: Revised database calls that should speed up viewing of message lists (kv).
• Summary Page: Fixed a bug that was causing everyone to have the same current task as the user viewing the page (kv).

December 21, 2004

• Summary Page: Fixed a bug where new users were showing up with extremely high inactive times (kv).
• Job Management: Small bug fix for job submissions (rb).
• Scripting: Added a way to automatically execute files at Control Panel startup. You can now specify files from the BioFS that you want to be automatically executed at startup (kv).
• User Registration: Fixed a bug that was causing the registration page to not submit correctly on Internet Explorer (kv).

December 16, 2004

• Control Panel: Revised BioFS notes so that operations on hidden files (filenames starting with a period) don't notify users in the Control Panel (kv).
• Scripting (Late alpha/early beta stage): now has its own menu item. It seems to be mostly stable enough. Note that you might mess up your Control Panel and need to restart it, depending on what you do via the scripting. There is still no documentation other than sample scripts in the BioCoRE Help project (kv).
• Scripting: made it so that you don't have to escape spaces in BioFS path names (kv).
• Scripting: added script listeners for incoming chat, notebook, and link library messages so that you can perform actions when that occurs (kv).

December 14, 2004

• Job Management: Input File uploads for new jobs should work now (rb).
• Control Panel: Fixed a bug where new folders being created in the BioFS weren't properly clickable in the Control Panel window (kv).
• Control Panel: Fixed a bug where URLs with spaces in them weren't getting handled properly by Mac OS X. Spaces and commas are now converted to http safe entities (kv).
• Notebook Import: Fixed a bug where files weren't able to be properly uploaded. There will STILL be a problem if you try to upload a large file as a notebook message. (Anything over about 4,000 characters will probably cause problems) (kv).

December 13, 2004

• Fixed a bug that was causing images for the summary page to be loaded over http all the time. This will hopefully fix a problem that we've noticed on Internet Explorer for windows (kv).
• Control Panel: PDB files can now be specified via the /vmd starting mechanism (mb).
• Notebook: More revisions to the wrap behavior to send the message wrapped as shown on the input screen for adding new messages (mb).

December 10, 2004

• Notebook: Fixed a bug where clicking on 'Go Back' was actually submitting a message (mb).
• Notebook: Revised the wrap behavior to send the message wrapped as shown on the input screen for adding new messages (mb).
• User List: Fixed a bug where invalid dates were causing a blank page (mb).
• VMD Pub/Sync: Wording change when specifying path to VMD (mb).
• Job Management: Summary page/Jobs page revised to show only the jobs for a particular project (rb).

December 9, 2004

• Control Panel: fixed a bug that was causing new users to not show up in the user list (kv).
• Control Panel: Cleaned up the output of the /google command so that it doesn't include all of the <b> and </b>s (kv).
• Control Panel: Fixed a couple of locations where you might have seen exceptions in your java console about not being able to find user 0 (kv).
• Control Panel: BioFS Browser (still in beta) now only allows you to select files (more proof of concept work) (kv).
• Control Panel: Scripting. Still in alpha stage development. Providing you have set your debug level (Help | Debug Level) to LOW or higher, you will now get copies of any scripts that you write saved to your Java Console (kv).

December 7, 2004

• Polls: BioCoRE now supports polls and quizzes. Project administrators (or others, if permission has been given) can pose questions for project members. Polls are set up via the web pages, and, at the appointed starting time, user's Control Panels pop up a box asking the question.
• Control Panel: greatly reduced startup times.
• Control Panel: Private chats are now organized by user, into their own tab.
• Control Panel: Google searches can be performed by saying /google search terms.
• Control Panel: The control panel can perform math by saying /math 3 + 2.
• WebDAV support: largely rewritten; more error cases are now handled.
• The NAMD Configuration File Generator is no longer a java applet. It is now pure HTML and can be viewed by anyone with a reasonably modern web browser.
• BioCoRE web pages are now themed via a preference in the utilities section. There are currently several themes available, and users are invited to submit new themes. Creation instructions are available.
• Project selection is now done via a dropdown box instead of just having a list of links.
• Control Panel:Scripting. This is in alpha stage development and no support is provided for it at this time. No documentation has been written for it yet and is really only included for developer access. Access is under Help | Script Input.
• Control Panel: BioFS Browsing. This is in beta stage development and there are currently no uses for. Under File | Browse BioFS you can view the BioFS. The package that we are using has problems with path names that contain non alphanumeric characters and will cause duplicate entries to show up.

Earlier updates