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• NAMD

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• MDFF

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• VND (Neuronal)

• Other

• Outreach

• Introduction
• Installation
• Menus
• Summary Tab
• Project Tabs
  • Event Notification
  • Chatting
  • User List
• Slash Command Reference
  • msg: Private Messages
  • me: Emotes
  • vmd: Starting VMD
  • help: Help
• Customization
  • Changing the browser the Control Panel uses for links
• Error Messages
• Infrastructure

Introduction

The BioCoRE Control Panel is a small Java program that is designed to keep you, the BioCoRE user, informed of the latest occurrences in your BioCoRE projects and give you an easy way to communicate and to navigate.

The Control Panel will automatically notify you of project events (such as new message board messages, users logging in and out, etc) and can also be used to send chat messages back and forth among your project members. You can also jump directly to other BioCoRE applications from the Control Panel.

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• Close Window - This option will close this Control Panel. It will not log you out of BioCoRE, though. This can be useful in cases where you might be running 2 Control Panels on two different computers and want to close one of them without actually logging out of BioCoRE on the other computer.
• Preferences - This option will open a web page with the current user preferences for the Control Panel displayed. See the customization section for more information.
• Clear Tabs - After you have been away from the Control Panel, you might notice that all of your project tabs have changed colors. This color changing occurs when events happen within those projects, but you might not be concerned about the events for one reason or another. Choosing this option automatically removes the color from all of the tabs. (This option used to be more useful when tab behavior was different than it is today)

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• Logout - This option will close the Control Panel and invalidate your BioCoRE session information. If you have a browser open to a page within BioCoRE, you will be asked to log in again when you click on a link if you have logged out of the Control Panel.

• Project Summary - Opens a webpage to summary page.
• Workbench - Cascading menu option for workbench applications.
  • Job Submission - Opens a webpage for the main job management page.
  • Launch VMD - Opens webpage to the Java applet that can launch VMD on your local computer.
  • -VMD States - Opens a web page that lists the saved VMD states for the current project.
  • NAMD Configuration File Generator - Opens webpage to the Java applet that lets you easily prepare NAMD configuration files.
• Notebook - Cascading menu option for notebook applications.
  • Message Board - Opens webpage to the message board, which contains threaded discussion, saved VMD states, BioLog entries, and archival Control Panel chats.
  • Lab Book - Opens a web page to the Lab Book, which lists users' entries of what they have been working on.
  • Biolog entries - Opens a web page to the Biolog entries page, which lists the outputs of command line commands that users have chosen to save.
  • Website Library - Opens webpage to website link library, which is a project-wide bookmark file.
  • Chat History - Opens a web page to the chat history, which lists all previous chats from the Control Panel.
• Documents - Cascading menu option for document managment.
  • BioFs - Opens webpage into the BioFS shared filesystem.

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• Utilities - Opens webpage to the utilities/preferences screen. Some of the items on this page are project specific, and some aren't.
• Public Projects - Opens a web page listing the public projects that any BioCoRE user can join.
• Show - Let's you choose the type of information that you wish to see in this project's information window.
  • Chats - Chat messages sent from one user to another in the project.
  • User Login - Notifications when a user logs into BioCoRE. Defaults to off. This information only shows up in the All User Test Project.
  • User Control Panel Starts - Notification when other users actually start the Control Panel. This defaults to on, since it provides more useful information. This information shows up in the All User Test Project.
  • User Control Panel Closes - Notification when other users actually close the Control Panel. This defaults to on, since it provides more useful information. This information shows up in the All User Test Project.
  • User Logout - Notifications when a user logs into BioCoRE. Defaults to off. This information shows up in the All User Test Project.
  • Notebook Changes - Notification when users post new messages to the message board.
• Show Timestamp - Normally, each statement in the information window is prefixed with a timestamp. These timestamps have been made as unobtrusive as possible, but if you wish to turn them off, you can do so by selecting this option.
• User Information - Opens webpage to information about each of the users in the project. This option won't work on the All User Test Project due to security concerns.

• BioCoRE FAQ - Opens a web page to the BioCoRE Frequently Asked Questions list.
• Documentation - Opens a webpage to this file.
• Recent Updates - Opens a webpage to the list of recent server updates.
• Debug Level - The Control Panel has built in debugging information that is available if needed. This can normally be left at "Off", but if needed it can be changed. "Low" provides the least additional information where "High" provides maximum debugging information. This value is reset to "Off" each time you start the Control Panel. You will need to have the java console open to see the messages.

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• About - Informational dialog about the Control Panel, including the current software version number.

Also, when an event occurs, the color of the box the project name is in will change color along with the corresponding tab. See Event Notification for more details.

Project Tabs

Each BioCoRE project in which you involved will have a project "tab" in the Control Panel. New users are only involved in one project, the "All User Test Project" (sometimes called the AUTP). As you become familiar with the BioCoRE environment you can create your own projects or you will be asked to join other BioCoRE projects by your collaborators. On each tab is the title of the project. Private projects are shown in black text, while public projects are shown in white text.

Event Notification

jsmith:Be sure to look at that output

User List

The user list, on the right side of the window, lists the project users that currently have a Control Panel open (with the exception of the All User Test Project. Users aren't listed in that project for security reasons). This gives you a quick way to determine exactly who is available for chatting and who isn't and also provides the "private" chat functionality. If you wish to send a private chat to a single user in the project, you can do so by click on their username in the user list. A box will pop up, and you can type your private message. No one in the project except the person you are sending to will see the message. This feature isn't intended to be used on a regular basis. The concept of BioCoRE is that project information should be available to all of the project members, but private chatting is a capability that does come in handy from time to time.

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• /msg: Private Messages

  You can send a private message directly via the message box by using IRC-style syntax, which is:

  /msg recipient text of message
  

  So, something like:

  /msg jdoe hello there
  

  would send the private message "hello there" to user jdoe in the current project. You can only send private messages to users if they are logged in. Note the restrictions mentioned in the User List section concerning private messages.

• /me: Emotes

  You can send "emotes", or actions to the other's Control Panels by using the IRC-style emote syntax, which is:

  /me action text
  

  So, something like:

  /me thinks that we are on the right track.
  

  would print the following to the project's chat window:

  johndoe thinks that we are on the right track.
  

• /vmd: Starting VMD

  You can start VMD with a specified PDB file from the Protein Data Bank with the command:

  /vmd PDBcode
  

  For example:

  /vmd 1TIT
  

  will start VMD and display the molecule Titin.

• /help: Help

  You can retrieve the current list of slash commands by saying:

  /help
  

  If you want detailed help on a command, such as the /msg command, you can say:

  /help /msg
  

• General Preferences:
  • Using Java Web Start: - You can have the Control Panel automatically start using Java Web Start if you wish. (See the installation section for more information). If you wish, you can also set yourself up to not have a Control Panel start by default, but we highly discourage this setting as you lose many nice features.
  • Control Panel Size: - This lets you set the size of the Control Panel window. If you are running the Control Panel as an applet, this is a big concern. As an applet, you can't resize the Control Panel by simply grabbing a corner with the mouse and moving it. That doesn't work, due to browser problems. So, you can set the size, in pixels, of the Control Panel window. If you are using Web Start, you still might want to "tweak" these settings, because this sets the initial size of the BioCoRE window.

    You can also change the font size for the text that shows up in the project tab window.

  • Sound: - The Control Panel will try to notify you when events occur. This notification can occur via the tabs changing colors, and by sound (see Notification, below). If you don't want any sound playing, make sure this is disabled. If you do want sound playing, enable this checkbox. We recommend sound, because it lets BioCoRE be used as intended: You can leave it running down in the corner of your screen and "forget about it". It will notify you when something happens.
  • Message of the day - The Control Panel has a "Message of the day" feature. This feature pops up a box when you first log in giving you a useful tip for using BioCoRE, or giving a list of what has recently changed in BioCoRE. We suggest leaving this option enabled so that you can learn about features that you might not have been aware of, and can be kept informed of important updates to BioCoRE.
  • Tabs - You can choose which "side" of the Control Panel that you want the tabs to appear on. For instance, if you want the tabs running down the left side of the window, you can choose "Left". I normally leave the Control Panel down at the bottom of my desktop, so I have the tabs set to "Bottom". That way, I can have other windows covering up most of the Control Panel, but I can still see the tabs to see if they have changed colors.
• Control Panel color: You can customize each project's window in the Control Panel if you wish to do so. Some people do this so that they can subconsciously tell their project tabs apart ("Green is All User, Yellow is XXX, Purple is YYY, etc"). Changes on this page only affect the project listed, so other project tabs will stay the way they were.

  You can also have BioCoRE automatically change your colors in the webpages for this project to match so that you are "color coordinated".

• Notification: Control Panel notification is a very powerful, yet slightly complex system. Notification normally occurs when an event happens in a project that you are not currently looking at. For instance, if you are looking at the summary tab, and someone says something in the All User Test Project, notification would occur for the All User Test Project. However, if you are looking at the All User Test Project when someone says something there, you will not be notified (** - Note: IF you directly send a message to someone using the username: method that notification will occur even if on the same screen)

  You can choose special notification for most any event in BioCoRE. Notification is defined as: the color of the project tab changing, and a sound playing. So, you could chose a unique color and/or sound for, as examples:

  1. User A sending a chat message in project 1.
  2. User B posting a message board message (in any project).
  3. Anyone logging in or out.
  4. Anyone posting a chat message.
  In case 4, User A's notification (case 1) would apply if User A did something; otherwise case 4) would apply.

  To set these options you choose the situation you want notification for, and select the color and the sound to play. IF you are using Java Web Start, you can choose sound files that you have on our own web site. If you are using the applet, browser permissions won't allow that.

  The list of current notification preferences is given at the bottom of the page and you can delete certain preferences by selecting their checkboxes and submitting the page.

deployment.javaws.browserPath=/path/to/your/browser

http://www.ks.uiuc.edu/Research/biocore/installation.shtml

If you happen to be on a system where you can't follow the instructions above, BioCoRE will attempt to install a temporary version of Swing for you (only works if you have a browser that supports Java, but not Swing). When you first log into BioCoRE you will be asked to download the Swing package (close to 2 megabytes) and this will be used while you are logged into BioCoRE. Each time you log into BioCoRE this will be repeated.

Could not show the document.  
Do you have web start set up properly?
(See Help | Documentation)

Going nonsecure.  Couldn't connect secure.  This can happen for one of
two reasons:
1) If you are not using Java 1.4+, do you have JSSE installed? (The
above error will probably be something about
java.lang.ClassNotFoundException)
2) The BioCoRE server you are connecting to might not have a true
secure certificate installed. (The above error will probably be
something about an untrusted cert chain, couldn't find trusted cert, or
a Failed Connect Test)

The BioCoRE team welcomes any comments, questions, or suggestions that you might have concerning our software! Please email us or fill out our feedback form.