December 5, 2001

  • Job Management: You can now create an Interactive account. For interactive accounts you specify a machine name and login and BioCoRE will use standard SSH to connect to that machine and run a command that you give it. This can be used to run jobs on machines that BioCoRE doesn't officially support yet (rb).
  • Message Board: Fixed a bug that was causing people to get error messages when someone else set a limit on the number of days of old messages to view (kv).
  • Message Board: Fixed a bug that was causing cancel on the "edit an entry" page to throw an error message (hw).
  • Message Board: Fixed a bug where the deleted status wasn't being checked when display next and previous links to messages (rb).
  • Launch VMD: Greatly improved the reliability of VMD startup via BioCoRE by finding and fixing a few timing problems (mb).
  • Utilities: You can now delete yourself from a project if you really don't want to be in it any longer. This doesn't (yet) apply to the All User Test Project (hw).
  • Fixed a bug that was causing some users to get error messages upon login (kv).
  • Message Board: Revised navigation so that it should handle the user using the browser's 'forward', 'back', and 'reload' buttons more cleanly (hw).
  • Utilities: Users can now set the autologout timeout for themselves. Previously, this was defaulting to around 11 hours. You can now set it for whatever you want (hw).
  • Fixed a number of places in BioCoRE that weren't explicitly checking to make sure that the user types in a number before trying to use the value. We should catch this better now (hw).
  • Message Board: The original message author is now also displayed on editted message board entries (hw).

    November 14, 2001

  • Job Management now supports Globus! If you have an account on any of the Alliance machines, you can now use Globus to submit your jobs (sk, rb)
  • BioFS: If a user tries to upload a file with the same name as file that already exists in that directory an error message is now printed (kv).

    November 12, 2001

  • Users changing their email address are now sent email to both the old and the new email address (hw).
  • Message Board: We had a bug in the preview code that was not allowing quotes to be used properly. This has been fixed (hw).
  • File Upload: Fixed a small bug that was causing people to not be able to upload a file if conditions on the server were just right (hw).
  • BioFS: Fixed a bug in the file copy code that was preventing users from being able to copy a file from one directory to another (kv).
  • Fixed a bug that users were seeing sporadically when trying to accept an invitation to a project (hw).

    October 31, 2001

  • Job Management: Queue information is now available for the PSC T3E and TCS (rb).
  • Job Management: Queue files that previous went into the user's home directory now appear in the work directory (rb).
  • Message Board: Some browsers were having problems going to back to 'edit' after 'previewing' a message. (They were loosing the text) This has been fixed (hw).
  • Control Panel: Notification of other user's relogging is no longer occuring (kv).
  • Users can now log into BioCoRE from multiple machines at the same time. One caveat, however, is that the Control Panel follows the user. You can't have multiple control panels at the same time (kv).
  • Users are no longer automatically added to new projects when the project admin 'add's them. They are now invited, and have the opportunity to accept/reject the invitation the next time that they log in (hw).
  • Job Management: Limited the number of jobs showing up in the 'Create a job based on a previous job' dropbox to 10 (mb).
  • When a user first logs into BioCoRE and is taken to the change password screen, they are now presented with a 'welcome to BioCoRE' screen after that (kv).

    October 17, 2001

  • Job Submission: Added a 'select all' button to the checkboxes for choosing jobs to delete/forget (mb).
  • Preferences: Fixed a bug where the control panel colors were not getting set correctly in certain situations (mb).
  • Registration: Fixed a bug where users were capable of entering non-numbers in number fields if they had javascript turned off. We now check this on the server side (kv).
  • Message Board: Revised the 'preview' code so that it should loose message text anymore on some browsers (hw).

    October 11, 2001

  • Message Board: Control Panel chats now show up 10 at a time instead of showing all of them at once (hw).
  • Job Submission: More work on navigation (rb, hw).
  • Message Board: Revised the header (the part with the 'show', the 'add' button, and the 'search' box) to be smaller so it doesn't take up as much screen space (kv).
  • Job Submission: Made a way for users to delete/forget multiple jobs at once by checking the jobs that should be deleted and then choosing a button to 'delete checked jobs' (mb).
  • Message Board: 'Sort by Date' is now oldest first, newest last instead of newest first, oldest last (kv).
  • Message Board: Fixed a bug where subjects were not getting turned into proper html (< and > were being passed through without being converted to &lt; and &gt; (kv).

    October 4, 2001

  • Job Management: You can now create a new job based upon a previous job. This can be used to speed up submissions of new jobs (mb).
  • Job Management: Queue information can now be retrieved from within BioCoRE (hw).
  • Job Management: BioCoRE gets much more powerful as users create projects and organize their jobs, communications, etc. according to project. For this reason, job submissions to the All User Test Project have been limited. Users may submit 5 more jobs to the All User Test Project, and then they need to start submitting jobs to different projects that are based on the topic that they are working on (mb).
  • Job Management: Textual changes to clean up the GUI presentation (rb, hw, mb).
  • Summary Page: should load faster now due to database performance tweaks (kv).
  • Summary Page: users can now choose to summarize particular pieces of the summary page rather than showing the full view (mb, kv).
  • Message Board: cleaned up the html parsing code more to work better with displaying URLs, etc (mb).
  • Job Management: On the details of a job, the 'View the Files of BioFS' link now actually takes you to the BioFS where the files are (mb).

    September 14, 2001

  • There is now a link to create a new project from the top green bar (kv).
  • Job Management: More information is now being given when choosing an account to use for a job (hw).
  • BioCoRE now works (mostly) on PDAs and Lynx. No support for java applets on these platforms/browsers yet (kv).

    September 13, 2001

  • Job Submission: Information from jobs prior to today are being stored in the BioFS in the System/OldJobs directory. Information from new jobs will be store in the System/Jobs directory (rb).
  • Job Submission: Queue status can now be retrieved (except for PSC) from with BioCoRE by going to the Account Details screen (hw).
  • Web Links to BioCoRE pages should now have a more discernable color (blue instead of black) (mb).
  • Summary Page: removed additional "Go To" links for each section and, instead, made the name of the section clickable (mb).
  • Job Submission: Links now exist in job details and account details to link to the associated account and joblist, respectively (hw).
  • Summary Page: reduced load time by quite a bit by rewriting code that gets recent additions from BioFS (mb).

    September 7, 2001

  • Job Submission: More items are now links to other parts of the job submission area. For instance, job details now have a link to the account information, etc (hw).
  • Job Submission: Jobs in lists are now color coded based upon their status (finished, running, etc) (hw).
  • BioCoRE is now caching some information about user names, etc rather than requesting it from disk, which should cause a slight speed increase in loading some pages (kv).
  • BioFS: For PDB files (which can be viewed with JMV) and link to the JMV release notes has been added to the properties window in the BioFS (mb).
  • Control Panel: Implemented some code that should decrease (by a factor of 10 or so) the number of http requests that the Control Panel has to do during initialization. This should speed that up quite a bit (kv).
  • Job Submission: When a user creates a new account this new account is tested so that the user knows whether or not they mistyped anything (rb).

    August 28, 2001

  • Project Summary Page: Added job status for each project (mb).
  • Project Summary Page: The user can choose which summary items they wish to see (recent file changes, users logged in, etc) (mb).

    August 22, 2001

  • Project Summary Page: Added recent link library additions, recent BioFS file additions (mb).
  • A brief message was added to the menu area at the top of the html pages to hopefully make it clear that the menu bar is actually a menu bar (kv).

    August 15, 2001

  • Project Summary Page: Added current task that project members are working on (only visible for projects other than the All User Test Project (mb).
  • Project Summary Page: Added an option to make this the default project when a user logs in (mb).
  • Control Panel: Deleted an Information menu item from the Projects menu that was duplicating information available in the User Information screen (mb).
  • Message Board: Fixed a display bug where the header and footer lines were showing up after a person had logged out (hw).
  • Message Board: Added an option for the user to only view the last XX days of messages, rather than having to look at all of them (hw).
  • BioFS: Fixed a bug where a user wasn't being allowed to move a directory that they owned to a different project (kv).
  • Job Submission: Added the "training" queue at PSC (rb).
  • Message Board: It is now possible to view messages that have been deleted from the message board (hw).

    July 25, 2001

  • BioFS: Text files are now editable. Complete revision control is not yet in, but this lets you edit html, tex, etc files (kv).
  • Job Submission: Job list now includes the project name that the job is associated with (rb).
  • Job Submission: Job output is now being saved to the BioFS and can be viewed by other members of your project. A "System" directory has been created in each project that contains files that BioCoRE itself is using. A summary file is located in the Jobs directory under System that can be used to figure out what jobs are available (rb).
  • BioFS: A permission system similar the unix file permission system is now in place (kv).
  • NAMD Configuration File Generator: Files can now be loaded from the BioFS (hw).
  • Notebook: "No messages to display" is now being printed if there aren't yet any messages (kv).
  • Fixed a bug in the html displaying in the notebook to accept ampersands as being part of a valid URL in a message (mb).
  • Fixed a bug that was showing up in the notebook and the BioFS if a user tried to upload a file without actually giving a file now. Now BioCoRE responds gracefully (hw, kv).
  • The main menu now takes you to the top level BioFS directory for a given project when you click on 'Documents|BioFS'. Before, it was taking a user to their own top-level directory (kv).
  • When starting VMD from the notebook, it now automatically starts instead of requiring the user to click more times (mb).

    July 17, 2001

  • BioFS: Changed the MIME type of unknown files from */* to text/plain (kv).
  • Control Panel: Moved the 'Open Main' menu option (under 'Project') to the top of the menu and renamed it 'Project Summary' (kv).
  • BioFS: The properties window for a file now gives the BioCoRE file id (kv).

    July 10, 2001

  • Fixed some typos in the preference pages (mb).
  • Revised the location of the links that were in the dark bars at the top and bottoms of the screen (kv).
  • BioFS: Files now open in a new window. This can be a bit confusing if your browser doesn't understand how to process a particular type of file. In this instance you will get a new, blank browser window and a file dialog will show up in front of that. You will need to close the blank window when you have downloaded the file (kv).

    July 3, 2001

  • Job Submission: The browser's back button now works like it should (rb).
  • Job Submission: The page for running jobs now defaults to no auto-refresh, but this can be modified by clicking on the link at the bottom of the page which will activate an automatic 30 second refresh (rb).
  • Job Submission: GUI monitoring of NAMD jobs is now available (rb).
  • Job Submission: BioCoRE now properly detects when a job has been killed by the queue and sets the status appropriately (rb).
  • Control Panel: If you click on the number of unread messages in the summary tab on the control panel you will now be taken to the section of the notebook table of contents with the first unread message, rather than the top of the table of contents (hw).
  • BioFS: Files can now be copied from one directory to another (kv).

    June 20, 2001

  • Job Submission: Revised layout slightly; added an account description box (rb).
  • BioCoRE should now fully work with Internet Explorer. Applets that required security certificates (the NAMD Config File Generator and the VMD Launcher have been modified to work with the Internet Explorer security model (hw).
  • We are working on rewriting the way that VMD is launched from within BioCoRE. A side-effect of this is that Publish/Sync is currently offline. We'll let you know when it is restored.
  • BioFS: fixed a bug that was preventing directories from being given a certain name if a directory with that name already existed anywhere in the filesystem (kv).

    June 6, 2001

  • Fixed a bug that was causing the login screen to not show up correctly if the control panel was logged out due to inactivity (kv).
  • BioFS: Size is now displayed in the directory listing (kv).
  • Fixed a null pointer bug that was causing problems for new users registering for accounts (kv).
  • Users can now choose to see notification of their own notebook messages in their control panel (mb).
  • Fixed a null pointer bug that was causing the notification preferences page to not show up correctly for some users (mb).
  • Fixed a bug that was causing each user's inactivity timer to get reset when their control panel received a message from the server. Now users have to actually interact with the server to get their inactivity timer reset (kv).

    May 31, 2001

  • Revised the width of the project menu entries so that more can fit on a screen (hw).
  • Summary Page: Users now have inactive time listed next to their names (kv).
  • Job Submission: Listings (of jobs and accounts) are now sorted which should give more consistent views to the user (rb).
  • The footer of each page now includes the current time on the user's machine. This lets a page "date" itself (kv).

    May 30, 2001

  • There are now menus at the top of each web page that can be clicked on to take you to the various parts of BioCoRE (hw).
  • When you first login to BioCoRE you are now taken to the summary page. The summary page tells you who is logged in, recent notebook messages, etc (kv).
  • Job Submission: Various asthetic changes to make the display more useful to the users (rb).
  • VMD Launcher: We now try to find VMD and, if we can't, we ask the user where it is at (mb).

    May 23, 2001

  • BioFS: Files and directories can now be moved to other directories (kv).

    May 22, 2001

  • BioFS: In the primary view the `complete path line' given at the top of the page is now clickable, which takes the user straight to the directory level that they click on (kv).
  • BioFS: The type (extension) of the file is now printed in a different column on the view page. Also, the time printing has been shortened to just the date. Specific times can be obtained from the Properties window (kv).
  • BioFS: Fixed a bug where the project directory wasn't getting automatically created when a project was added (kv).
  • BioFS: Files can now be renamed (kv).

    May 15, 2001

  • Put in the initial version of the BioFS filesystem. It allows collaborators to share files among project members but still is lacking quite a few of the features that we have grown to expect from a standard filesystem (kv).
  • Revised the basic BioCoRE look so that it isn't nearly as green (kv, hw).
  • Revised the main toolbox page to present information to the user in a more clear manner (rb).
  • Job Submission: Added support for the PSC TCS machine as well as the deferred and batch queues for the T3E (rb).
  • Notebook: Fixed a problem where BioCoRE was not behaving properly when a user canceled an edit session (hw).
  • Notebook: Fixed a bug that had crept in that was causing html in a notebook message to not be displayed properly (hw).

    May 8, 2001

  • Control Panel: Revised the Swing startup procedure so that when a user comes in that doesn't have Swing installed we first ask them if they want to download a temporary copy that they can use so that they do not have to actually install Swing. This means that they have a 1.8 meg download each time that they don't have swing.jar in cache, but it lets them use the Control Panel without installing Swing (kv).
  • User Information: Users can now change their email address from the utilities screen (mb).

    May 1, 2001

  • Message Board: Previous entries can now be editted (hw).
  • Message Board: When you are creating a new message you now have the option to upload a text file for the message text (hw).
  • Control Panel: Added new menu options under 'Project' for directly jumping to the various tools in the Workbench and Notebook toolboxes. This means that you can go to Job Submission, or the Website Library (or any other tool that we have) by selecting the option from the Control Panel without having to go through the Main toolbox page (kv).
  • Projects: Title and description can now be changed (mb).

    April 24, 2001

  • Job Submission: You can now choose the name of the file where standard out from your job goes. If you don't want to, a default name will be chosen for you (sk).
  • VMD: Added a link to the `Launch VMD' page that takes you to the saved VMD states for that project (kv).
  • Job Submission: Revised the max length allowed for input directories and filenames from 80 up to a much larger number (rb).
  • Job Submission: Lots of behind-the-scenes bug fixes that should make job submission more reliable (rb).
  • VMD Publish/Sync: Added proper detection of Windows systems and fixed it so that all states that are published are sent via https (jd).

    April 20, 2001

  • Job Submission: Added support for a new cluster at the Theoretical Biophysics group (rb).
  • Job Submission: Removed the text box for entering the number of desired processors on queues where you don't need to choose the number of processors (such as Scyld linux queues) (rb).
  • Control Panel: Revised the startup code so that it is, hopefully, more reliable (kv).

    April 17, 2001

  • Control Panel: Fixed a bug where the number of users logged in for a newly added project was showing up as zero (mb).
  • Control Panel: Set default color and sound for Control Panel applets. This had gotten deleted at some point (mb).
  • Control Panel: Fixed a bug where the number of unread messages shown in the summary tab was including deleted messages that a user hadn't read (kv).
  • Preferences: Fixed a bug that was causing a page error if the notifications page was requested and a user had not yet set any notifications (mb).
  • Job Submission: Additional error checking for form entries so that more incorrect submissions are being caught (rb).
  • Job Submission: Set the path to look for ssh in to take care of those situations where the user doesn't have ssh in their path (rb).
  • Control Panel: Fixed a bug that was showing up periodically on startup that prevented the control panel from initializing correctly. Hopefully it will always start up the way it should now (kv).
  • User List: Fixed a bug where the last login date wasn't being set on a user-by-user basis for those users that are logged in (mb).

    April 10, 2001

  • Job Submission: You can now use BioCoRE's job submission tool to submit any job to the PSC T3E, NCSA's Origin 2000, or the TB group's machines (assuming you have an account on the machine). We provide additional support for NAMD simuations but any job can now be submitted and monitored (stdout monitoring) via BioCoRE's web interface (rb).
  • Job Submission: Various text changes to make it more intuitive (rb).
  • Job Submission: Fixed a bug that was causing an error if a user clicked on the 'Job' button without having created any accounts (rb).
  • Control Panel: The control panel now attempts to detect whether or not the server is behind a firewall and whether or not it is behind a proxy. If either of these cases happen, the control panel uses a different method to get its chats, etc. This isn't a final solution, but one that will hopefully help (kv).
  • Message Board: Changed 'Group by' to 'Sort by' and made 'Show' bold so that it matches other elements of the page (kv).
  • User Information: Changed the way that the time was being displayed so that it matches the rest of BioCoRE (mb).
  • Revised the welcome message that gets emailed to new users to include the name of the local BioCoRE server (kv).

    April 3, 2001

  • Control Panel: When changing a notification sound you can now `test' the sound before actually submitting the change. This lets you make sure that you have entered the sound correctly (mb).
  • Control Panel: The 'About' menu option (under 'Help') now prints out your username (kv).
  • Revised the authorization scheme to allow people to deep-link into a particular BioCoRE page easier (kv).
  • Website Library: Started auto-wrapping the text in the text box (hw).

    March 27, 2001

  • Website Library: Added subtopics. Each topic can now have subtopics which can be used to further group websites together (hw).
  • VMD Publish/sync: Fixed a bug where it wasn't sync'ing properly for projects other than the All User Test Project (jd).
  • Fixed a bug in the registration process where people couldn't set their title if the affiliation was changed (mb).
  • Removed control panel notification of forced logouts (kv).
  • Website Library: Fixed a bug where new links were not always getting added if the user chose to send notification to other (hw).
  • Website Library: Topics are now being sorted by date. Links inside a topic are sorted by popularity (hw).
  • VMD Publish: Removed the button for 'Synchronize' that shows up inside VMD since we don't have that functionality yet (jd).

    March 20, 2001

  • Job Submission: Added support for the NCSA Origin 2000. Job submission and monitoring now allows users with the appropriate supercomputer accounts to submit NAMD runs to the Theoretical Biophysics group machines, and the PSC T3E as well as the NCSA Origin 2000. (rb)
  • New Feature! When you launch VMD through BioCoRE you will be presented with an additional window that allows you to publish a molecular state to BioCoRE and later retrieve it from the Message Board. In the Message Board you can select `Saved VMD Sessions' from the dropdown box and choose a published state that you wish to view. We have many interesting additions to this planned, but, if you use VMD, please give it a try! (jd)
  • Job Submission: Fixed a bug where relative paths were not working correctly. Because of csh/sh differences, using the tilde to represent your home directory won't work. If you are in a position to need it, you will need to specify the absolute path (rb).
  • Job Submission: Improved the performance of the job start/end monitoring, so that it reuses a single ssh connection. (rb)
  • Job Submission: Fixed several bugs in the job output collection and improved its performance. There are still some conditions where it may fail to retrieve the entire output file, which I will be working on fixing. (rb)
  • Revised the page that shows user information so that you can easily switch from project to project while on that page. Also explicitly added printing of project name and description to that page (mb).
  • Message Board: New users (and others!) now have a "Mark All Read" link that they can use to quickly catch up to the current state of the messages (sk).
  • Control Panel: Fixed a bug where new users to a project were getting shown login/logout messages for people not in their project (mb).
  • Control Panel: For notification you can now choose to not change the tab color and/or to not play a sound for a particular event (mb).
  • Website Library: Removed a blank line that was showing up after links which a user themselves had added to the index (kv).
  • More work on changing the names from BioCoRE to noting the local server (hw).

    March 13, 2001

  • BioCoRE now incorporates a new computational job submission tool. This tool will allow you to manage accounts on your computational resources and run and keep track of your jobs. It currently supports NAMD simulation runs on our local (UIUC TB group) machines, and the PSC T3E. To take advantage of this tool, you must also have an account on one of those machines. We plan to support more supercomputers and applications soon, so keep checking in for updates (rb).
  • We have started changing the name that appears for BioCoRE from simply being BioCoRE to actually noting the local server that it is running on. This will result in you, the user, seeing something like 'TB-UIUC BioCoRE' instead of simply 'BioCoRE'. This lets us (and you) easily differentiate between different BioCoRE servers. (hw).
  • Fixed a bug where ' (apostrophes) were turning into \' when notification of a new message board message was being sent to email/control panel windows (kv).
  • Revised some code in the user registration and the color choosers that was causing the page to reload, which was causing some problems under Netscape 6 (mb).
  • Fixed a small grammatical error in the page that was showing up welcoming you to BioCoRE each time that you logged in (kv).

    March 10, 2001

  • We now have an official certificate to use for signing our java applets so this should make it quite a bit easier to access applets like the VMD Launcher and the NAMD Config File Generator. You will still have to give the applet's permission to access files on your system, etc., but you will no longer have to go through the multi-step process of accepting our test certificate (kv).
  • New Feature! You can now store biographical information that can be viewed by other individuals in your projects. In addition, for each project you can now store your role, your schedule, and your current tasks. Others in that project can then easily view what everyone is working on, etc. This information is accessible from the user list page. This page can be accessed for a project in a number of different ways. From the Control Panel: Selecting the number of users logged into a particular project on the summary tab or, if you are on the chat window for a particular project you can select the `Project' menu and choose `User Information'. If you are working in the toolbox area for a project you can go to the Utilities menu and select `User List' also. (mb)
  • Website Link Library: You can now edit links that you have added. In addition, you can choose whether or not to send a note to other's Control Panels when you add/edit a new link (hw).
  • Main: Changed the link 'launch VMD' to 'Launch VMD' (kv).

    March 6, 2001

  • New Feature! BioCoRE now provides a website library for your project. If you look in the Notebook area of the toolboxes page you will see a link for Website Library. This essentially acts like a project-wide bookmark file. If you have any weblinks that you feel would be useful to other project members please add them! Each link is placed inside a particular topic (you first need to create a topic for the links and then you or anyone else can add links to that topic) If you were the person that added something, you can delete it also. (Edit functionality will be coming next week) Please try it out and let us know what you think! (hw).
  • Subject-based Chat: Fixed a bug that was causing the page to not load properly. (This happened as a result of changing some "unrelated" database code on the backend) (hw).

    February 27, 2001

  • Control Panel: Extensive revisions to notifications. You can now fully customize both the tab notification color as well as the sound that is played when an event happens. You can choose to have certain sounds/tab colors when a particular person does a particular action in a particular project, or any combination of this (mb).
  • Preferences: Added a notice to not resize the window. If you do, netscape crashes for some reason (mb).
  • Revised the text slightly that is shown when a user first logs in. It now provides a link to our tour for those that don't have Swing so that they can see what the Control Panel looks like (kv).
  • Control Panel: If you have the information window (from the Project menu) open and change projects, the information window changes to match the new project now (mb).
  • Utilities: The user list is now sorted so that the people logged in show up first (mb).
  • Projects: Fixed a bug where members weren't getting sent email when they were added to a project. (kv).

    February 20, 2001

  • NAMD Config File Generator: "PMEInterpOrder", "PMETolerance" and "cellOrigin" were previously generating an error if not given. Since they have default values this restriction has been removed. Fixed a bug that was causing view text/save to take a long time to show up. Removed "targetTemp" as being an option. Fixed a typo in "langevinDamping". Removed the requirement for "langevinCol" or "langevinFile" when langevinDamping is set (hw).

    February 13, 2001

  • Control Panel: Fixed a bug that was causing duplicate messages to show up if you closed the control panel window (without logging out) and then 'reloaded' the control panel (kv).
  • Revised the autologout check so that it now checks every 5 minutes to see of anyone has been inactive for too long. Before it was checking when a person actually did logout, which was causing a whole bunch of 'logout due to inactivity' messages to show up at once in the Control Panel (kv).

    February 6, 2001

  • Control Panel: When you start a new project or are added to a project, the new project automatically shows up on your control panel (mb).
  • Message Board: Revised the 'Add New Message' page so that it will not submit if you do not have any text in the 'message text' box. We had a user that was hitting <Return> on the 'Subject' line and this was causing his browser to submit the page without letting him enter message text. This shouldn't happen now (kv).
  • Control Panel: Fixed a bug where an 'old' control panel would give error messages approximately 30 minutes after starting a new control panel. Now the old CP dies like it should (kv).
  • Fixed a bug where people were not able to link straight into a biocore notebook entry via email. Now you should be able to follow the link from the email that you get and go straight to a notebook entry (kv).
  • Message Board: Fixed a bug where the notebook was crashing if a page was 'submitted' without filling in some of the boxes (kv).
  • Control Panel Preferences: Added a brief note telling Internet Explorer users that they needed to relog into BioCoRE to activate changes in the size of the Control Panel (kv).

    February 2, 2001

  • Control Panel: You can now set the size of the Control Panel window. This is done via the preferences menu option (under 'File'). Internet Explorer seems to have some minor problems with it, though. It doesn't really like resizing the window without you logging out and back in (kv).
  • Control Panel: You can now set the size of the font that is used to display the messages that show up in the 'chat' window for each project. This is done via the preferences menu option (under 'File'). (kv)
  • Control Panel: Added a brief note to the preferences html that notes that sound under linux doesn't work (due to some java under netscape under linux bug) (kv).
  • Slightly revised the text that gets sent to new users so that it tells them that they need to have Java Swing installed to use the Control Panel (kv).

    January 30, 2001

  • Fixed a typo (a space needed to be inserted between an email address and the word "and") in the email that was being sent to people that requested a forgotten password (kv).
  • Fixed a bug where the preferences were being set incorrectly if a particular combination of 'global preference set', 'project-specific preference set' was being used (mb).
  • Removed an extraneous ampersand from the URL that was being generated to load the welcome page (kv).

    January 23, 2001

  • Control Panel: Users can now change colors for their project chat windows. This is done on a project-by-project basis and users can change background colors, font colors, etc. Just select 'Preferences' from the file menu of the Control Panel when you have a project tab selected (mb).
  • Message Board: Fixed a bug where the contents of the preview window were showing up twice (kv).
  • Control Panel: When a user logs in we are now sending out notification of any Message Board messages that have shown up recently (mb).
  • The "sample" boxes on the preferences pages now start out with the currently chosen color in their background so that users can see their current choices (mb).
  • Slightly revised the text that gets sent to new users so that it describes how to use the Control Panel to chat with other users (kv).
  • Slightly changed the text on the 'forgot your password?' page so that it tells people to be careful about typing in their usernames, as they won't be told that they were incorrect, for security reasons (kv).
  • Changed the name of the VMD launcher on the main toolbox window from 'VMD' to 'launch VMD' (kv).
  • We have mostly removed the requirement that user's must allow cookies to use the collaboratory. Session information is now being encoded into the URL and form entries. However, this is presenting some difficulties with those people that deep-link into BioCoRE so we have, for the time being, left the cookie on. (NOTE: This has always been a temporary cookie that only existed while you were logged into BioCoRE) (kv).
  • Chat Rooms (not Control Panel): Fixed a bug that was occuring when a user chose a subject with a tick mark in it. Also fixed a small typo that was in a 'help' screen (refresh was spelled incorrectly) (kv).
  • Fixed a tiny little typo in the 'remove user from project' code that showed up if there were problems with the email addresses (mb).

    January 16, 2001

  • Message Board: Fixed a bug where searches were not working correctly if there were tick marks in the search string (kv).
  • Message Board: Fixed a bug where the URL wasn't getting printed properly when email was sent out as a result of a new message on the message board. It was printing httpss instead of https (kv).
  • Histories of the Control Panel chats can now be viewed via the Message Board. It isn't very nice yet (doesn't support searching, sorting, or filtering; the All User Test Project chat is currently about 106k) but it allows the basic capabilities. To view the history, open the Message Board for a project (either select the table box showing the number of unread messages in the summary table of the control panel, or go to a project chat window on the control panel, select 'Open Main' from the project menu and then select Message Board from the html window that opens) and select 'Control Panel Chats' from the dropdown box in the upper left corner (kv).
  • Control Panel: Continued revisions to the preferences: Preferences are now updated on the control panel right after hitting 'submit' (see January 9 updates. You no longer have to reload the Control Panel). Current preferences are now auto selected on the preferences html page that you see. So, if you want to know your current preferences you can go to that page and see them. After hitting 'submit' the preferences page now closes instead of going to the Utility menu. You might need to reset your preferences once to get this actually working the way it should be (mb).
  • Control Panel: Revised so that it checks to see if it is the same version as what is available on the BioCoRE server and, if not, pops up a window telling you that you need to close and restart your browser to get the new version (kv).
  • Control Panel: Removed the tool tip for 'Enter Text' which was showing up over the chat text entry (kv).

    January 9, 2001

  • Control Panel: Fixed a bug where reloaded Control Panels weren't getting put in the same window as the original Control Panel (kv).
  • Revised the main BioCoRE webpage so that users can now log into BioCoRE directly from that page without having to bounce to another page first (kv).
  • Control Panel: We are starting to have the Control Panel save your preferences. Currently only sound and tab placement can be saved, but this will be expanded in the future. To set your preferences, select the 'Preferences' option under the file menu in the Control Panel. Once you have set the preferences you will need to reload the control panel for your options to take effect (mb).
  • Fixed a bug where the wrong number of unread messages were showing up in the Control Panel if a project had deleted messages (sk).
  • Notebook: Fixed a bug where 'sort by author' was not working correctly (sk).
  • Set up the Control Panel so that it tests to see if the user has Swing before actually displaying the applet (kv).
  • Notebook: Added an option to download a message to a file on the user's harddrive. When viewing a message there is a link for 'Download Text'. When clicked, the browser will present the user with a file save box and they can choose where to save the message. Note1: The From:, To:, and Subject: are automatically placed at the top of the file when it is saved. Note2: Depending on the operating system and how the message was originally saved in the notebook there might be Control-M's at the end of the lines in the saved file (kv).
  • Revised the text slightly that is shown when a user first logs in (kv).