BioCoRE Control Panel
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
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
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).
- Browse BioFS - Browse the BioFS filesystem. You can't really
do anything with this option other than look at the structure of the
- 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.
- 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.
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
- Project Summary - Opens a webpage to the summary page for
- Documents - Cascading menu option for document management.
- BioFS - Opens webpage into the BioFS shared filesystem.
- Workbench - Cascading menu option for workbench applications.
- Job Submission - Opens a webpage for the main job
- 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
module that lets you easily prepare NAMD configuration
- 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.
- Polls/Quizzes - Opens a web page to the list of polls and
quizzes for this project.
- 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
- 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 notification only 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.
- Manual Script Input - For simple scripts, or for testing,
you can enter scripts manually. This option will open a text window
where you can type in the script that you wish for the Control Panel
- Execute Script From BioFS - If you have saved the script in
a file in the BioFS, you can choose this option execute the script.
A file browser window will be displayed where you can choose the file
you wish to execute.
- Startup Scripts - The Control Panel can store a list of
files that you wish to execute every time that you start up. If you
have certain actions that you wish to always be available, etc., you
list the scripts here and they will always be there for you upon
The Help menu contains documentation and informational links.
- 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
- 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. All debugging output
is sent to the Java console.
- Browser Choice - The Control Panel can open web links that users
post in their chat messages. The best way to do this is to use the external
web browser that you normally use (Firefox, Mozilla, etc). This is the
default setting of 'External'. However, Java includes a way to parse html
files, and if you choose 'Internal', this parsing method will be used for
the remainder of your Control Panel session. This internal method isn't
capable of showing most of today's webpages accurately. However, if the
external browser won't work for some reason it is a useful way to see
something for a web link.
- About - Informational dialog about the Control Panel, including
the current software version number. Other information that is
provided includes the user's login name, as well as the current
dimensions of the Control Panel window. This can be helpful for
saving a new dimension that you want to use at Control Panel
startup. Once you have the Control Panel at the dimensions you
wish for future sessions, you can go to About and get the new
dimensions and the go to File | Preferences and set the new
dimensions for the Control Panel.
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.
- A project name - The Control Panel tab will switch to that project.
- A number of users - A web page will be opened to the user
information page for the project row that you clicked on. Note
that, for security reasons, the user list for the All User Test
Project can't be listed. So, if you click on the number for that
project you will get a rejection screen.
- A number of unread messages - A web page will be opened to
the message board area in the BioCoRE notebook. The message
index will be showing and the first unread message should be
visible (Non-Control-Panel-Note: If you have limited the number
of days of old messages to view for that project, the first
unread message might not be visible. If this occurs you can
change the limit on the number of days of old messages that you
wish to view).
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.
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
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
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
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)
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
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
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
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
www.domain.com. This also works for
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 [http://www.cnn.com cnn]
If you want to enter a URL that contains spaces, you need to encode them as
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:
- For bold, enclose the text in <b>...</b>
- For italics, enclose the text in <i>...</i>
- For color, enclose the text in <font color=COLOR>...</font>, where COLOR is either a hexadecimal color code such as #FFFFFF, or one of several simple colors that Java understands, like "green" or "blue".
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.
You can retrieve the current list of slash commands by saying:
If you want detailed help on a command, such as the /msg command,
you can say:
/google: Google Queries
Query Google for a set of search terms:
Will print the top entries in Google for "biocore".
/google -spell hipopotamus
which will give the proper spelling of "hippopotamus".
Setting up the Control Panel
Before you can legally do Google queries from within the Control Panel,
obtain a Google API license. This is a one time operation that will
allow you to perform up to 1,000 google queries per day directly from
your BioCoRE Control Panel.
You need to go to http://www.google.com/apis/ and perform step #2, where you Create
a Google Account. (If you already have a Google account you can simply
sign in) This will allow you to obtain an API license key, which will
look something like:
Next, you need to go to the BioCoRE Utilities page and click on
Personal Preferences, into which you can copy the key.
/math: mathematical expression solver
If your BioCoRE server has an additional package installed, you can
have the control panel evaluate mathematical expressions by prefixing
the expression with "math ". For instance, in the chat window you could
/math 3 + 2
and, if the server has the additional math package installed, it will
If the server doesn't have the additional package you will be told.
The math package includes the ability to use parenthesis, sin(),
asin(), sinh(), ln(), log(), angle(), abs(), rand(), mod(), sqrt(),
sum(). For more information you can browse the JEP website.
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.
/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. Once you send a private
message to a user, a new tab will open where you can hold a conversation
with the user. See the private message section
for more information. If you use the /msg method of sending a private
message you can send a message to multiple people at once.
/msg recipient1,recip2,recip3 text of message
will send the text of the message to the three users listed. When
typing the list, separate the users names with a comma AND NO SPACE.
/vmd: Starting VMD
You can start VMD with a specified PDB file from the Protein Data Bank with the command:
will start VMD and display the molecule Titin.
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
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:
- General Preferences:
- 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".
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 an event (such as someone saying something) occurs
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:
In case 4, User A's notification (case 1) would apply if User A did something; otherwise case 4) would apply.
- User A sending a chat message in project 1.
- User B posting a message board message (in any project).
- Anyone logging in or out.
- Anyone posting a chat message.
To set these options you choose the situation you want notification
for, and select the color and the URL of the sound to play.
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.
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/deployment.properties 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
http://www.ks.uiuc.edu/Development/MDTools/scripts/ 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.
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
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/deployment.properties 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
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.