BioCoRE Control Panel


Control Panel Summary Page The BioCoRE Control Panel is an application 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 be used to send chat messages back and forth among your project members. You can also jump directly to other BioCoRE modules from the Control Panel.


The Control Panel File menu contains options to edit preferences, and logout. The Edit menu contains copy and paste options. If you have text selected you can choose 'Copy' and the text will be copied to the system clipboard. Similarly, 'Paste' will take the contents of the system clipboard and insert it into the message window. Note that these options are only available if you are on a project tab (not the summary tab).

The Project menu contains a list of shortcuts to the various BioCoRE applications. The options in the project menu won't be active unless you have selected a particular project's tab. Once you have done that, each option that you choose is specific to the project you are on, and there are options for:

The scripting menu provides access to the scripting capabilities of the Control Panel. More information on scripting is available.

The Help menu contains documentation and informational links.

Summary Tab

The summary tab gives you an "at a glance" summary of what is going on in your projects. The table lists all of the projects that you are involved in as well as current members logged in (note that there could be users logged in that do not have their Control Panel's open. This could cause a discrepancy between the number listed here and the quantity of names listed in the User List for a project) and the number of unread message board messages that exist in that project.

Clicking on the table headers ("Project", "Users Logged In", "Unread Messages")won't do anything. However, clicking within the table will do something. If you click on:

If you "click-n-drag" the vertical line in between the headers of two columns, such as the vertical line in between the words "Project" and "Users Logged In", you can change the width of each column. These new widths will be retained until you log out of the Control Panel.

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

Project-specific events show up in the project tabs. If a user posts a new message board message, notification of that will show up here. The subject will be given and the text will be "clickable". Clicking on the text will open the message board message in a web browser. When users save new files to the BioFS, notification will show up here and the file will be loaded if you click on the notification text. Chat messages show up here (discussed below) and, for the All User Test Project, notification of users opening and closing Control Panels and logging in and out. When a user first logs into BioCoRE, the Control Panel automatically retrieves recent information from the server so that you know what has been happening recently.


The BioCoRE Control Panel is very useful for instant communication between you and your collaborators. At the bottom of the window there is a "Message" line. Text that you type in this box will be sent to everyone else's Control Panel that is in your project. They will be notified that you have sent a message and they can then read and respond to it.

If you type a URL into your message the URL will automatically become clickable as long as you enter it in the form or

As you are chatting, you can recall previous messages that you have sent by pressing the up and down arrows on your keyboard. The last 50 messages for each project are automatically stored and can be used to quickly resend a message.

All of the text sent via the Control Panel is automatically logged for your convenience. You can go into the Message Board and select "Control Panel Chats' from the dropdown box in the upper left corner and review previous chats. The "search" feature of the Message Board is very handy for this.

Sometimes you might wish to make sure that a person sees a message. It might be of general interest to everyone in the project, but you want to make sure that a particular person is aware of it. You can send a 'directed' message to a user by prefixing your text with the user's name followed by a colon. For instance, if you wish to send the message "Be sure to look at that output" to the user jsmith you would type:

jsmith:Be sure to look at that output
This will cause a special sound to play for them, even if they are on that tab when the message arrives. (This assumes they have "sound" turned on. If they have sound turned off they will not be notified)

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. This will cause a new tab to show up where you can hold a private conversation with that user. Only you and your recipient will be able to see the messages in that private tab. See the private message section for more information.

Polls and Quizzes

From time to time someone in a project that you are enrolled in might have a question that want to ask the project members. BioCoRE provides quizzes and polls to facilitate this. ("quiz" and "poll" will be used interchangeably in the following text) Each poll has a defined starting time. The poll administrator might choose to have the poll start as soon as they configure it, or they can choose a specific starting time. Regardless of the method chosen, once the poll has actually started, each member that is logged in at the time will have their Control Panel display the poll and they will have the opportunity to answer it.

The poll will be displayed in a popup window and will look something like the window shown to the right. The name of the window will be either "BioCoRE Quick Poll" or "BioCoRE Quick Quiz". Basically, a quiz has a correct answer, that the administrator has defined. A poll doesn't have a predefined answer. Immediately below the title is the project to which the poll is associated.

Polls can be either multiple choice or fill in the blank. Depending on the exact configuration of the poll, you might be able to enter a comment to go along with the answer. The poll administrator can choose to give the poll a specific ending time. If this has happened, you will see the End time: for the poll. Alternatively, the poll might be open ended, and you won't actually see the End time: listed. If an ending time is listed, this is the Control Panel's best guess estimate of when the poll will end, based on the time on your computer. The time on the server actually determines when a poll will end, so there might be small discrepancies. The webpage will give the actual ending time, according to the server, under the Polls/Quizzes option.

  • Once you have answered the poll, you can click "Submit" to send the answer to the BioCoRE server. Once you have submitted your answer you won't be able to change it.
  • If you don't wish to answer the poll at this time, but want to do so before it closes, you can chose 'Delay Answer' and you will be eligible to answer the poll at a later time. You will be reasked the poll the next time you start the Control Panel, or you can go to the website and click on Polls/Quizzes and chose the desired poll and then the option to [Answer Now] which will cause the Control Panel to redisplay the poll for it.
  • If you don't wish to answer the poll you can Decline To Answer. Once you have done this you will not be allowed to answer the question later.

    Private Conversations

    On occasion, you might wish to have a conversation with another project member that isn't of interest to the entire project. In this case, you can hold a private conversation with a user. By clicking on a user's name in the user list or by using the /msg command you can initiate a private chat. When you do this the project window splits into tabs. The 'All Chats' tab contain the normal, non private chats for the project (the Titin project in this case). Then, each private conversation has a tab as well. In this case, bob's Control Panel has a private chat with ann. Once you are done with a private chat, you can click on the 'Click Here To Close' note, and the tab will be closed. Note: Once you do that, you won't be able to see the chats in your Control Panel. You can still look at the chat history in the webpage.

    Embedding Links In your Chats

    As noted above, if you type a URL into your message the URL will automatically become clickable as long as you enter it in the form or simply This also works for https://, ftp://, and even file:// (Note that whoever clicks on the link will have to be sharing your filesystem for file:// to work.

    In addition to entering links in the above manner, you might want to customize the text that shows up. For instance you might want to see:

    Check out cnn.
    To do this, you can use the following notation:
    [url text to show]
    So, the above would be entered as:
    Check out [ cnn]
    If you want to enter a URL that contains spaces, you need to encode them as %20.

    Bold, Italics, and Color in Chats

    To include a bold, italic, or colored style within a chat message, you can use the following tags: For example, the messages:
    This is a <b>bold</b> message
    This is an <i>italicized</i> message
    This is a <font color=green>green</font> message
    This is a <font color=#FF0000>red</font> message
    will be displayed as
    This is a bold message
    This is an italicized message
    This is a green message
    This is a red message

    Slash Command Reference

    A set of commands exist that can be used in the chat windows. All of these commands start with a forward slash, and we have tried to make them follow the standard IRC methodology as much as possible.


    There is a fair amount of customization that can be done for the Control Panel. You can set these customization options by selecting "Preferences" under the "File" menu. This will open a webpage to the customization section. (You can also get here by selecting "Utilities" in the left sidebar of any webpage and going to the general Control Panel preferences.

    There are three preferences pages that deal with the Control Panel. These three pages are selectable from the row of links near the top of any preferences page:

    Changing the browser that the Control Panel uses to open links

    If you are on Windows, the Control Panel will use whatever the default browser is that you have set for your system. If you wish to change this, your preferred browser should have an option somewhere to make it the Windows default.

    If you are running using Web Start on a unix system, you need to tell Java Web Start your preferred settings. You need to find the javaws program that was installed when you installed Java Web Start. This will launch the Web Start control panel/console. From the File | Preferences menu you can set the path to the web browser that you choose to use. After doing this, you should be able to restart your Control Panel and be in good shape.

    We have noticed a few strange quirks with Java 1.4.2 Web Start. For some reason, the Web Start control panel/console doesn't seem to want to start. If this is happening to you, you can manually edit the configuration file. It is in ~/.java/.deployment/ and will need to have a line that looks like:


    Note: Here in our group, everyone basically uses Firefox on various Unix platforms. We have the BioCoRE control panel set up to open links in a new tab in our running Firefox window. If you wish to do this, go our script library at and download webnewtab. Tweak the paths as needed, make sure the script is executable, and then point javaws to that webnewtab script as the "browser" to run.

    One user submitted an alternative to webnewtab that you are also free to review if you wish. The core issue is that javaws seems to always embed a new-window option in the command line that it uses to call the browser. This script removes that.

    args=`echo $@ | sed 's/,new-window//'`
    $BROWSE $args &


    For maximum convenience while using BioCoRE, we suggest that you do a little bit of installation.

    This installation is discussed at:

    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.

    Error Messages

    Could not show the document.  
    Do you have web start set up properly?
    (See Help | Documentation)
    This message can appear in a popup window when the Control Panel tries (and fails) to load a browser window to show a webpage. The Control Panel opens a web browser when you click on a cell in the summary table, choose items from the menu, or when you click on a link in the chatting windows.

    This error means that the Control Panel tried to open a browser window, but Java Web Start had problems. This is usually because Web Start has incorrect path information for your browser. Run the Java Web Start configuration program on your computer and look in the Preferences for browser setup and make sure that the values look correct.

    If you have problems running the configuration program and are on unix, you might have better luck editting the 'properties' files directly. Assuming you are running java webstart version 1.4 or higher, edit ~/.java/.deployment/ and look for a line that starts with deployment.javaws.browserPath and verify that it contains a valid browser path.

    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
    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)
    This message can appear in a the java console if the Control Panel has problems talking to the server securely. In the first reason, the problem is probably on your end. In the second, the problem is probably with the BioCoRE server that you are connecting to.


    If you've made it to this point in the manual you know all that you need to know to use the Control Panel effectively. However, this section will give a little more information on what is going on behind the scenes.

    All communication between the BioCoRE server and the Control Panel is encrypted. You will notice a little box that appears during startup that says "Creating Secure Connection". During this time, Java is initializing random numbers and doing other low-level functions that insure that it can create secure connections. The time duration of this box depends on the speed of your computer, but 10 or so seconds is about average.

    If the BioCoRE webserver is not using a properly signed secure server certificate, the Control Panel won't be able to talk securely to the server, and it will fall back to using standard HTTP connections.

    The Control Panel tries to create a socket connection to the server so that the server can notify the Control Panel the instant that events occur. If the Control Panel is not able to create this connection, it will fall back to checking with the webserver on a regular basis via standard HTTP to see if any new events have occurred.