(Category) BioCoRE Collaboratory FAQ
The BioCoRE Collaboratory FAQ addresses common questions that people have concerning our collaboratory and its uses.
Subcategories:
(Category) Introduction
(Category) Installation
(Category) Registration And Login
(Category) Using the Collaboratory

Answers in this category:
(Answer) Who made BioCoRE?
(Answer) Why do you CapItaLIze BioCoRE the way you do?
(Answer) Won't BioCoRE be too bandwidth/computationally expensive?
(Answer) When can I expect my changes that I asked for to show up in BioCoRE?
(Answer) What about privacy?

(Category) (Category) BioCoRE Collaboratory FAQ :
Introduction
Basic information about the collaboratory
Subcategories:

Answers in this category:
(Answer) Where can I find out more about BioCoRE?

(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Introduction :
Where can I find out more about BioCoRE?
The main BioCoRE website is at:
http://www.ks.uiuc.edu/Research/biocore/
(Category) (Category) BioCoRE Collaboratory FAQ :
Installation
Dealing with getting the collaboratory software installed.
Subcategories:

Answers in this category:
(Answer) How Do I install the BioCoRE program?

(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Installation :
How Do I install the BioCoRE program?
BioCoRE is designed so that users can access most features via their web browser. For browser compatibility, refer to:
http://www.ks.uiuc.edu/Research/biocore/compatibility.shtml
For some pieces of BioCoRE, however, we use Java.
To be able to fully use the BioCoRE control panel you should install Java Web Start. Instructions on doing this are located at:
http://www.ks.uiuc.edu/Research/biocore/javawebstart.shtml
(Category) (Category) BioCoRE Collaboratory FAQ :
Registration And Login
The registration process
Subcategories:

Answers in this category:
(Answer) How do I change my password?
(Answer) How do I login to BioCoRE
(Answer) How do I register for BioCoRE?

(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Registration And Login :
How do I change my password?
If you know your password:

Log in and go to the 'Utilities' menu by clicking on the 'Utilities' link in the bottom left corner of the web page.

Then, select the "Personal Preferences" setting in the first large box.

In the middle of the resulting screen you can enter your old password and your new desired password and then click 'Update' at the bottom of the page.

If you don't know your password:

Go to the login screen and click on the 'Forget your password?' option. You can then type in your username and BioCoRE will send a new password to the email account that you have on record with BioCoRE.

(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Registration And Login :
How do I login to BioCoRE
There are several differents ways to "login" to BioCoRE.
  • The most obvious way is to login via the website. This can be accomplished by going to /http://www.ks.uiuc.edu/Research/biocore/ and logging in via the login boxes on the left side. If you don't have an account, you will need to create one before you can login. You can create a new account by clicking on the "New Account" link right underneath the login boxes.
  • Assuming you have an account (see above bullet if you don't) you can login to BioCoRE by directly opening the BioCoRE Control Panel. To do this, you have to configure Java Web Start to launch the Control Panel. Instructions to help with this are at http://www.ks.uiuc.edu/Research/biocore/javawebstart.shtml#biocore under the heading "Setting up BioCoRE to launch the Control Panel without a browser".
  • When you view the BioCoRE filesystem (the BioFS) via WebDAV, you are technically "logging in" to BioCoRE. Instructions on how to do this are at: http://biocore.ks.uiuc.edu/biocore/docs/webdav.html.

(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Registration And Login :
How do I register for BioCoRE?
The BioCoRE collaboratory requires users to register before gaining access. An overview page has been created with details about registering. To actually register for an account, you can click on the "New Account" link under the login boxes on the left side of the BioCoRE webpage.
(Category) (Category) BioCoRE Collaboratory FAQ :
Using the Collaboratory
Questions about using the collaboratory
Subcategories:
(Category) Running VMD Publish and Sync
(Category) Notebook
(Category) Job Monitoring Program
(Category) Control Panel
(Category) Website Library
(Category) Public Projects
(Category) BioFS Shared Filesystem

Answers in this category:
(Answer) I'm in one of the tools. How do I get back to the summary page?
(Answer) How do I create a new project?
(Answer) How do I change the colors?
(Answer) How do I join a project?
(Answer) How do I remove myself from a project?
(Answer) How can I see a list of all the members of a project?

(Category) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory :
Running VMD Publish and Sync
Details on getting VMD to work.
Subcategories:

Answers in this category:
(Answer) I just found out about BioCoRE, VMD, and the Theoretical Biophysics website. Why doesn't VMD start?
(Answer) Is there a way I can get away without having to grant permission EVERY TIME I want to run VMD?
(Answer) How do I know that the security certificate was imported correctly?
(Answer) Apparently Netscape doesn't think I have the security certificate, but I went through the process. What went wrong?
(Answer) VMD WAS working fine through the collaboratory, and then it quit. What happened?
(Answer) How do I publish a session?
(Answer) How do I retrieve a previously saved session?
(Answer) How do I load a pdb file from the BioFs?
(Answer) When I try to load a session from the Message Board using Internet Explorer, it doesn't work.
(Answer) If someone else publishes a session while I am using VMD, how can I view it?
(Answer) How do I get the "VMD Sessions" window to appear if I'm running Windows 95/98?

(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Running VMD Publish and Sync :
I just found out about BioCoRE, VMD, and the Theoretical Biophysics website. Why doesn't VMD start?
If you are new to our site, there is a good chance that you haven't yet downloaded and installed VMD. This is necessary before you can actually run VMD via your web browser. Go to http://www.ks.uiuc.edu/Research/vmd and download vmd, and then you will have much better luck.
If you DO have VMD on your system and you still aren't having any luck, check out the other questions in this area and one of them will probably help you out.
(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Running VMD Publish and Sync :
Is there a way I can get away without having to grant permission EVERY TIME I want to run VMD?
Note: You do NOT have to reimport the certificate every time that you want to run VMD. You should only have to do that once.
But, your web browser will continually pop up the box asking you each time whether or not you want to grant permission to actually start the program on the hard disk (which happens to be VMD in this case).
You can get around this by clicking the button in that box that says: Remember My Decision. Then, it will remember that you said yes and you won't have to answer the question every single time.
(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Running VMD Publish and Sync :
How do I know that the security certificate was imported correctly?
The process of importing the security certificate to run VMD is probably the most tricky part to getting everything working correctly.
To see if you have certificate, go to the page for running VMD, and tell it to import the certificate. If you already have it, a little box will pop up telling you that you already have the certificate. If Netscape doesn't think you have the certificate, it will once again lead you through the import process.
(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Running VMD Publish and Sync :
Apparently Netscape doesn't think I have the security certificate, but I went through the process. What went wrong?
There are a number of things that might have happened:
1) If you JUST imported the certificate, you will need to reload the page to get VMD to actually run. Do this with a shift-reload.
2) When you click your way through the boxes, you MUST choose the option to trust software programmers from the BioCoRE site. If you do not choose this option it won't work.
3) When you started Netscape, if you got the warning that "Netscape has detected a lock file which may indicate that another user is running Netscape, etc..." this same warning box also mentions that "You may continue to use Netscape, but you will be unable to user the disk cache, global history, or YOUR PERSONAL CERTIFICATES. The security certificate that you get from us is considered one of your personal certificates, so it won't be in effect for this 'warned' netscape.
(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Running VMD Publish and Sync :
VMD WAS working fine through the collaboratory, and then it quit. What happened?
1) When you started Netscape, if you got the warning that "Netscape has detected a lock file which may indicate that another user is running Netscape, etc..." this same warning box also mentions that "You may continue to use Netscape, but you will be unable to user the disk cache, global history, or YOUR PERSONAL CERTIFICATES. The security certificate that you get from us is considered one of your personal certificates, so it won't be in effect for this 'warned' netscape.
2) If you (or anyone with access to the files) have been "messing with" the netscape files, you could have just possibly messed something up in Netscape. Under unix, these files would be located in ~/.netscape and in Windows they are hidden better, but still accessible.
3) Something might have happened to VMD. Try going to a command prompt and typing 'vmd' and see if VMD starts. If not, you have a problem external to the collaboratory.
(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Running VMD Publish and Sync :
How do I publish a session?
When you start VMD from BioCoRE, and you have loaded a molecule in a specific representation, etc, you can then save that state to BioCoRE so other group members can view it.
Once you have the molecule in the representation and orientation that you wish to save, fill in a name and description in the appropriate boxes in the Saved State Window, and click on the "Save state" button. Yur sesson will be saved to BioCoRE.
(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Running VMD Publish and Sync :
How do I retrieve a previously saved session?
If you've started VMD from BioCoRE, select a session from the "Saves sessions" box within the "VMD Sessions" window. A description of this session will appear in the "Description" box. To load it, click on the "Load session from BioCoRE"
In BioCoRE, you can go to the VMD states page in the Message Board by selecting the "List of saved VMD states" link on the VMD page, or selecting "Saved VMD sessions" from the "Show" box in the Message Board. This will give you a list of the saved sessions for this project. Clicking on one of them gives you the script used for saving this session, and you can also see the description given. Click on "START VMD SESSION" link at the top of the page, and VMD will start with that state.
NOTE: Starting a VMD session from the Message Board will not work when using Internet Explorer. We are working on this problem.
(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Running VMD Publish and Sync :
How do I load a pdb file from the BioFs?
To load a pdb file from the BioFs, (BioCoRE's file system), click on the "Load file from BioFs" button in the "VMD Sessions" window. This will bring up a list of all the pdb files in the BioFs for that project. Select the one you wish to load and click "Load".
NOTE: It is important that you save sessions that use files from the BioFs or the RCSB so that all members have access to the files when they wish to load the sessions. If you publish a state that uses a local file, others may not be able to view it.
(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Running VMD Publish and Sync :
When I try to load a session from the Message Board using Internet Explorer, it doesn't work.
Yes, this is a known bug and we are working on it. We apologize for the inconvenience.
(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Running VMD Publish and Sync :
If someone else publishes a session while I am using VMD, how can I view it?
Currently, VMD does not automatically update other users' "VMD Sessions" windows when one publishes a session. To update your window, click on the "Refresh session list" button. This will add any sessions that have been published since you started VMD.
(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Running VMD Publish and Sync :
How do I get the "VMD Sessions" window to appear if I'm running Windows 95/98?
First, running on a version of Windows that old isn't officially supported. We suggest that you upgrade.
1.) If the folder C:\Temp does not exist on your computer, please create the folder.
2.) Start VMD from BioCoRE. This will not start VMD with "VMD Sessions" window, but it will write a file called "tmp.bat" to the C:\Temp folder.
3.) Double-click on C:\Temp\tmp.bat. This will run the file and it should start VMD with the "VMD Sessions" window, allowing you to load and save sessions.
(Category) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory :
Notebook
Using the Notebook
Subcategories:

Answers in this category:

(Category) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory :
Job Monitoring Program
Details on using the Job Monitoring Program
Subcategories:

Answers in this category:
(Answer) I'm getting an error about 'Symantec Java! Cannot find class TB/collab/ui/MainPanel'. Help!

(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Job Monitoring Program :
I'm getting an error about 'Symantec Java! Cannot find class TB/collab/ui/MainPanel'. Help!
Are you running on a Macintosh?
If so... the version of Netscape that ships on the Macintosh has a Symantec bytecode compiler that supposedly supports version 1.1.5 of Java. However, it doesn't ship with the same class files as version 1.1.5 of java that comes with Netscape on Unix and Windows. So, you are missing a class file.
We have also noticed that Netscape for the PC version 4.08 (and presumably versions earlier than that) ship with the Symantec bytecode compiler. They act a little bit different than the newer versions do, but they seem to work ok.
We are working on a solution to this general problem. Check back with us often.
(Category) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory :
Control Panel
Help for using the java-based Control Panel applet.
Subcategories:

Answers in this category:
(Answer) Why are the times wrong in the chat windows?
(Answer) I'm using Web Start on Unix, but it insists on using Netscape instead of the browser that I like for opening web pages. How can I change this?
(Answer) What's all this about Web Start versions versus applet versions of the Control Panel?
(Answer) Why am I getting errors about file locks in my java console?
(Answer) How do I display the Java Console for the Control Panel Web Start application?
(Answer) When I try to run the Java Web Start program I get the splash screen for a few seconds and then it disappears

(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Control Panel :
Why are the times wrong in the chat windows?
Is the time correct on your machine? If so, do you have your machine set up for the proper timezone? This is the most common cause of this problem. Set the timezone correctly (which will probably cause you to need to change the time on your computer's clock so that it is correct) and the control should start displaying the proper time.
(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Control Panel :
I'm using Web Start on Unix, but it insists on using Netscape instead of the browser that I like for opening web pages. How can I change this?
What you need to do is tell Web Start that your favorite browser is "something other than its default", which is Netscape.

You need to run your Web Start manager program. This will be in whatever directory you've installed webstart. The name of it is 'javaws'. You might look in 

/usr/local/javaws/javaws
This will load the Web Start 'manager'. Click on File | Preferences and navigate around a bit and you'll see an entry for the Browser Setup path. Change the 'netscape' to whatever executable you use for your browser and you should be set once you restart the control panel.

Another interesting bug with Web Start occurs when you have a web browser (let's call it X) open, and you have a different browser specified via the manager instructions given above. Web Start will actually attempt to load URLs in BOTH browsers. So, let's say that you have Mozilla open, and you have Netscape specified with the manager. If you click on a URL in the Control Panel, the URL will be opened in Mozilla, and Netscape will be started as well to display the URL. To fix this problem, be sure to set the browser in the manager to the same browser that you normally use.

Note: If you are on Windows, Web Start automatically uses your "default" browser and doesn't have the option to set the browser.

(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Control Panel :
What's all this about Web Start versions versus applet versions of the Control Panel?
There are two distinct and different ways to run the Control Panel, and here is a brief amount of background on the two ways...
The first way is as an applet in your web browser. Historically, this was the only way to run it. To run the Control Panel in a web browser you need a web browser that supported java, and has java swing "installed". The control panel is then tied to the browser. If you shut down your browser, the control panel goes away as well.
Netscape 4.x and Internet Explorer** include a customized version of java that was based off of Java 1.1 and do NOT include java swing. For these browsers, the user needs to download java swing (as is described at http://www.ks.uiuc.edu/Research/biocore/swing_setup.shtml) and install it into their browser.
** Internet Explorer has traditionally included their own version of Java. With recent court decisions I think they might have quit including java altogether.
Newer versions of netscape (6+), Mozilla, and a host of other new browsers do not include java as part of the core package. Rather, they are designed to easily integrate with the java package that is available from sun.com. This is generally considered a good thing, because the browser programmers don't have to write java, and the user can update java to Sun's newest version. Java 1.2 and above automatically include java Swing. So, if you are running on one of these newer browsers, you are almost definitely using sun.com's java, and it already has java swing installed. (this is a simplification of things. You might have a different java than sun's, such as IBMs, or blackdown's, etc. But, as long as the version is 1.2 or greater, you already have Swing)
To further muck with things, on Windows you can install the sun java plugin into internet explorer and it can even be made to override the built in IE java.


The second (and preferred) way to run the Control Panel is via java web start (as described at http://www.ks.uiuc.edu/Research/biocore/javawebstart.shtml). If you run the CP via web start you do NOT need java in your web browser. All you really need is a web browser that is capable of running external programs via the 'mime types' file. In fact, lynx, the popular text based browser, can start the control panel via web start. So, you don't need swing or anything in the browser itself. However, you do need to have webstart installed along with the appropriate entries into the mime types file. Our BioCoRE server sends a file of type 'jnlp' down to your browser and your browser (through the mime types) knows that it needs to run the javaws executable on that file, and then a completely seperate process is running for the control panel. You can then shut down your browser and the control panel keeps on running. Since the Control Panel isn't running as part of the browser, it can complicate things a bit, though. In particular, you might see difficulties with Web Start talking to your web browser. When you click on a URL in the control panel, or when you pick certain menu options, the Control Panel attempts to start a browser and show a certain URL. Java Web Start is designed to provide the functionality of "opening a URL in your preferred browser". It has built in functions that you can call that automatically open a URL using the browser that you have configured the Web Start program to use.
Traditionally, you can run 'javaws' and it has a preferences menu where you can set your preferred browser, your versions of java that you have, etc.

(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Control Panel :
Why am I getting errors about file locks in my java console?
If you are seeing something like: 

> Jan 20, 2004 3:50:18 PM java.util.prefs.FileSystemPreferences syncWorld
> WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException:
Couldn't get file lock.
repeated in your java console, this is due to a bug in some versions of Java 1.4. It is because Java Swing is trying to save preferences in a directory that it doesn't have write permissions to. It isn't anything that BioCoRE is doing. It is purely Java and can be ignored. Also, you can check to make sure that you are using the latest version of Java for the Control Panel. They might have fixed it in a newer version that what you are currently running.
(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Control Panel :
How do I display the Java Console for the Control Panel Web Start application?
Viewing the Java Console

From time to time, it might be useful to view the Java standard out text console. The BioCoRE Control Panel can send debugging information there as can other Web Start programs that you might want to run. In its default configuration, you won't ever see the Java console. To enable it, you need to go into the Java Web Start application manager (On Windows you probably have an application called 'Java Web Start' in your Start menu, and on unix it is probably an application called 'javaws' that might or might not be in your path). On Mac OS X, the console is automatically enabled, and console messages can be found in ~/Library/Logs/Java Console.log, and can be viewed using the Console application in Applications/Utilities.

In the application manager, you can go to File | Preferences and navigate to the Advanced tab where you can enable the Java console. You have the option of having it pop open every time you that you run an application (Show Java Console), or you can have it automatically log the output to a file (Log Output). Personally, I would recommend just having it log the output to a file. That way you don't have an extra window everytime you run an application, but you can still look at the output if you wish to do so. Just choose a log file name that is somewhere that you can remember it. The BioCoRE Control Panel shouldn't ever put too much text there, but some programs can, so you might want to check the size of the log file on occasion.

(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Control Panel :
When I try to run the Java Web Start program I get the splash screen for a few seconds and then it disappears
If your Java preferences files get corrupted, you might find yourself in a position where you can't run the Java Web Start program (I'm not talking about the Control Panel. I'm talking about the program where you can set Java Web Start preferences, such as whether or not to display the java console).

If you find yourself in this position, you have a couple of options:

  1. You can delete your entire Java preferences directory, thereby getting rid of the corrupted file. On windows, this is typically a folder called .javaws and is in your Documents and Settings folder. On unix, this is typically in ~/.java. This can, of course, have undesirable side effects.
  2. You can start manually editting the preferences file itself. On windows this is a file called javaws in a .javaws folder in your Documents and Settings folder. On unix this is ~/.java/.deployment/deployment.properties.

    The file is a text file with name/value pairs. Useful pieces: 

    deployment.javaws.logFileName=/tmp/webstart.txt
deployment.javaws.logToFile=true

deployment.javaws.browserPath=/usr/local/bin/firefox

javaws.cfg.cache.dir=C\:\\Documents and Settings\\yourUserName\\javaws_cache
    The first set (about log files) tells webstart to log the java console output to a file.

    The second set (about the browser path) tells webstart which browser to use. This will probably only be necessary on unix.

    The third command, about the cache directory, is sometimes necessary on Windows and can occur if a user is running on a machine where they don't have permission to write files everywhere.

Once you have changed any of the settings for Web Start, you will need to restart the control panel for them to take effect.
(Category) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory :
Website Library
Website Library is a web based application in BioCoRE. it essentially acts like a project-wide bookmark file. In every project. you can set the category title and description as many as you want by click on Add Main Topic button.For each topic, added the weblinks that you feel would be useful to other project members, you can add them by click AddLink link.Each link is placed inside the particular topic (you first need to create a topic for the links and then anyone else can add links to that topic).A topic or a link can deleted or edited by the owner.
How can I delete the link, subtopic or main topic?
1. Edit or Delete your link:
If only you are the owner, you will see the mark [edit/delete] after the link, click on it you can edit or delete your link.
2. Delete your subtopic or main topic:
If only you are the onwer and the subtopic or topic is empty (there is no subtopic or link in this subtopic or main topic), you will see the mark[edit/delete] after the topic or subtopic description. Click on the "delete", the topic or subtopic will be deleted.

Subcategories:

Answers in this category:

(Category) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory :
Public Projects
Projects publicly available to all users
Subcategories:

Answers in this category:
(Answer) What is the difference between public projects and regular (private) projects?
(Answer) How do I create a public project?
(Answer) Can I make a currently private project public?
(Answer) How do I join a public project?
(Answer) How do I delete myself a public project?
(Answer) I joined a public project, but it is not showing up in my Control Panel, or items are missing from the left sidebar!
(Answer) When I make a public area for an already existing private project, how does the existing project change?
(Answer) If I have a public area in a project, and make it private, then make it public again, what happens to the data? Is the original data restored, or does it come back blank?
(Answer) If I create a public project, then delete it, and then create another public project based on the same private project, is it a new project, or does it retain data from the first deleted public project?
(Answer) How do I differentiate between the public and private areas in a project?

(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Public Projects :
What is the difference between public projects and regular (private) projects?
Public projects are available to anyone in BioCoRE. Users can choose to join public projects themselves, whereas they must be specifically invited to private projects in order to view them. Users do not even have to be members of a project in order to view the data in it. The "Public Projects" link gives a list of available public projects, and from there a user can click on a project title to view the webpage. The user must join the project to add it to his or her Control Panel, though.
(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Public Projects :
How do I create a public project?
To create a public project, click on the "Create Project" link in the left sidebar. In the form presented, select checkbox next to "Do you wish to create public areas for this project?". Then select which areas you wish to be publicly available. You may choose Message Board entries, Control Panel chats, VMD saved states, Lab book entries, Biolog entries, and the Website library. The public project will only appear in the Control Panel if Control Panel chats are public.

After filling out the rest of the form, and clicking "Submit", two projects will be created. One will be the regular, private project, and the other will be the public project. The name of the public project will be the same as that of the private project, with the word "(Public)" appended to the end.

The name of the public project, along with which areas are publicly accessable, can be changed by an administrator from the "Change Project Information/Public Areas" link in the Utilities menu.

(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Public Projects :
Can I make a currently private project public?
Yes. An administrator for the project can create a public project for the private project from the "Change Project Information/Public Areas" link in the Utilities menu. The form looks the same as the "Create Project" form, with the same project informational questions and public area choices. Fill out the form and click "Submit", and the new public project will be created.
(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Public Projects :
How do I join a public project?
Click on the "Public Projects" link in the left sidebar. This will display a table of available public projects. Select the project or projects you wish to join, and click the "Join selected project(s)" button. Then you will be added as a member to the project.
(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Public Projects :
How do I delete myself a public project?
You may delete yourself from a public project in the same manner as deleting yourself from a regular private project. In the Utilities menu, select the "Delete yourself from the current project" link, and submit the confirmation form on the following page. You will then no longer be a member of that project, but you may join again at any time.
(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Public Projects :
I joined a public project, but it is not showing up in my Control Panel, or items are missing from the left sidebar!
Project administrators can choose which areas are publicly accessible. These areas include: Message Board entries, Control Panel chats, VMD saved states, Lab book entries, Biolog entries, and the Website library. If any of these items are not publicly available, they will not be shown in the left sidebar. If "Control Panel chats" are not public, then the tab will not be shown in the Control Panel
(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Public Projects :
When I make a public area for an already existing private project, how does the existing project change?
The existing project does not change. A new project is created with the public project name, and the two are linked together. You can view public project messages from the private project, but not the other way around. From the private project, you also have the option of sending a copy of a Message Board entry to the corresponding public project. If you delete the public project, the public project is unchanged.
(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Public Projects :
If I have a public area in a project, and make it private, then make it public again, what happens to the data? Is the original data restored, or does it come back blank?
If a public area is hidden, then shown again, the original data is kept. For example, if you have a public project with Message Board entries designated public, you may then add public Message Board entries. If you then take away public access to the Message Board, access to those messages is taken away, and no new entries may be added. If you then decide to make them public again, all the old messages are available again, and access to create entries is granted again.

(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Public Projects :
If I create a public project, then delete it, and then create another public project based on the same private project, is it a new project, or does it retain data from the first deleted public project?
If a public project is deleted, then a new public project is created from the original private project, the new public project is entirely new, and retains no data from the original public project.
(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Public Projects :
How do I differentiate between the public and private areas in a project?
The public areas for a project will be in a new project. Tje default name for the new public project is the same as the private project with the word "(Public)" appended to the end, although you have the option of changing the title for this project. In the Control Panel, public projects appear in white text to distinguish them from private project areas.
(Category) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory :
BioFS Shared Filesystem
Shared Filesystem questions
Subcategories:

Answers in this category:
(Answer) How can I sync (synchronize) my BioFS folders with my local computer?
(Answer) How do I configure BioCoRE to automatically send me email when a folder changes?

(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) BioFS Shared Filesystem :
How can I sync (synchronize) my BioFS folders with my local computer?
I have a question regarding BioFS:  is there any way to be able to synchronize 
the content of a folder tree on BioFS with another computer (e.g., by using 
rsync or cvs or something similar). For example, when you store several 
subfolders in a main folder on BioFS with several large and many smaller files, 
it would be great if you could run a sync program to update your working 
directory instead of doing it manually (that is quite time consuming).
This probably isn't the only way to accomplish this, but a likely way would be to use WebDAV and a local backup/sync utility.

WebDAV instructions for the BioFS are available to start accessing the BioFS via WebDAV. If you aren't doing this yet, it has many advantages above and beyond syncronization. Once you have verified that you have WebDAV access working properly from your system, you can start using it for accessing the BioFS.

Next, you will need to find a synchronization utility on your computer. On Windows, this might be a Briefcase program or possibly even a backup utility. On Linux or Unix it might be rsync. You should be able to configure the utility to syncronize the BioFS folder with another folder (a local one) on your system. For help with specific cases, please ask.

(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) BioFS Shared Filesystem :
How do I configure BioCoRE to automatically send me email when a folder changes?
BioCoRE has the ability to automatically send you email when files are added to folders in the BioFS.

This is something that is particularly useful for Dropbox situations where a project team has set up a Dropbox folder where others can deposit files of interest. When someone else leaves you a new file(s) you will automatically be sent email a short time later.

This is a feature that you have to enable, though. It doesn't happen automatically.

To enable it, do the following (hopefully) simple steps:

  1. Log into BioCoRE and pull up a BioCoRE webpage.
  2. Go to the project that you are interested in monitoring: In the upper right corner of the screen, select the project from the dropdown box.
  3. Select the BioFS Shared Filesystem link from the left menu column.
  4. Navigate to the folder that you are wanting to monitor.
  5. Once inside the folder, right above the filelist, you should see some text that looks like: 
    ( Current Email Watch: Not Set [ edit watch ] )
    Click the edit watch link.
  6. Select the timeframe within which you wish to be notified of change to this folder. For dropbox folders, I would recommend 15 minutes. For other folders you might want to have longer times.

    What this means:

    Every 15 minutes (on the hour, :15 after the hour, :30, and :45) BioCoRE will check and see if files have been added or updated in the previous 15 minutes. If so, you will get an email telling you about it. If you have a particularly active folder, you might want to choose a longer timeframe, so that you don't get an email every 15 minutes telling you that something has changed. Most people don't have that active a folder at this time, though.

(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory :
I'm in one of the tools. How do I get back to the summary page?
There is a link called 'Summary Page' in the left sidebar near the top of the page. That link will take you back the summary page.
(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory :
How do I create a new project?
The easiest way is to click on the 'Create A New Project' link which is located right next to the 'Project Summary' link in the green bar at the top of the page.

Alternately, you can go to the Utility screen (by clicking on the Utility link in the lower left corner of the screen. ) and select the option to create a new project.

Once you have created the new project, you are the only individual that is actually registered for the project. You can add other people by choosing the option to do that from the utility screen. A few notes about adding other people to a project:

  • They must already be registered with BioCoRE
  • You need to know their login name for BioCoRE. BioCoRE is designed with security in mind, and there isn't any way that you can simply bring up a list of everyone that has registered with BioCoRE. You need to know the actual login names of the individuals that you wish to add to your project.
    • (Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory :
    How do I change the colors?
    Go to the Utilities menu (by selecting the "Utilities" link in the lower left corner of any web page once you are logged into BioCoRE) From that page, select the "Theme" link in the "Current Project" box. This will take you to a list of available color schemes for BioCoRE projects.
    You can then choose to change colors in the Control Panel or for the current project. You can change the colors on a project-by-project basis or you can choose to have colors affect all of your projects. Project-by-project is useful so that you can use color to quickly distinguish among different projects, but the "global" option is nice so that you only have to set your colors once and it automatically affects all of your projects.
    (Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory :
    How do I join a project?
    If you want to join a public project, refer to the FAQ section on public projects.
    For private projects, you have to be invited to a project to actually join it. The administrator of the project will invite you to a project, and you will receive an email telling you that you have been invited to the project.
    To accept the invitation, you must login to BioCoRE via a web browser. If you are already logged in, a link with the text "Review Project Invitations" will appear in the sidebar when you reload a BioCoRE page. Click on the link, and you can choose to join the project.
    (Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory :
    How do I remove myself from a project?
    There are several options for removing yourself from a project.

  • If you want to permanently remove yourself from a project that you have joined, you can go to the Utilities screen and remove yourself from the project. If you do this, you are no longer in the project and would have to be reinvited to join the project again.
  • If you simply don't want to see anything related to the project, but want to stay in the project, go to the Utilities screen and select the Hide option. This will let you turn projects off but you will remain a member.
  • If you just don't want a project tab in your Control Panel, you can click the checkbox next to the project name on the summary tab and it will cause the project tab to disappear. If anything happens in the project (a new chat, etc) the project tab will reappear so that you can see it.

    This information doesn't necessarily apply to the All User Test Project or to Public Projects. Rules for those projects are slightly different.

    • (Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory :
    How can I see a list of all the members of a project?
    For security reasons, you are not allowed to see the membership of the All User Test Project. For other projects, though, you can see the membership list.

    Once you have logged in and chosen your selected project (upper right corner of the screen, white dropdown underneath the words "Current Project") you can view the members of the project by clicking on the 'User List' link on the left side of the screen near the top.

    This gives the "normal user" view of the user list.

    If you are a project administrator, though you can also view everyone that has been invited to the project but not yet accepted the invitation. To do this, make sure that the current project is the desired one (if you are an administrator of the project the project name will be followed by [ADMIN]), and click on the Utilities link on the left hand columm of the screen. The resulting page will have a Current Project box with Administrator Options. Clicking on the 'Invite users to the current project' link will show a list of current project members and, if you scroll down, the list of users who have been invited but haven't yet accepted the invitation.

    (Answer) (Category) BioCoRE Collaboratory FAQ :
    Who made BioCoRE?
    BioCoRE is being developed by the Theoretical and Computational Biophysics group at the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign. The funding for the project is coming from the National Institutes of Health (NIH).

    The Principal Investigator on the project is Klaus Schulten. The Co-PIs are: Gila Budescu, and Laxmikant V. Kale.

    The current BioCoRE team consists of:

  • Michael Bach (mbach@ks.uiuc.edu)
  • David Brandon (brandon@ks.uiuc.edu)
  • Robert Brunner (brunner@ks.uiuc.edu)
  • Sameer Kumar (sameer@ks.uiuc.edu)
  • Kirby Vandivort (kvandivo@ks.uiuc.edu)
    • (Answer) (Category) BioCoRE Collaboratory FAQ :
    Why do you CapItaLIze BioCoRE the way you do?
    BioCoRE is short for Biological Collaborative Research Environment.
    (Answer) (Category) BioCoRE Collaboratory FAQ :
    Won't BioCoRE be too bandwidth/computationally expensive?
    This is our response to that question, brought up on the Computational Chemistry Mailing List:
    On Wed, Mar 15, 2000 at 10:43:34PM -0800, Eugene Leitl wrote:
    > So, how many truckloads of DEC (Compaq) Alphas have been shipped to > UIUC recently? ;)
    Well, we could always use a few more...
    BioCoRE development is still in the early stages. We have several tools working now, and we have many more ideas which we plan to implement. Thanks for the comments. At this stage, comments and ideas are especially useful. <p> > Seriously, for system sizes and user numbers beyond the trivial we're > talking serious amounts of tightly coupled iron here (you do mention > "Interactive MD" in "Description"). Also, (with the possible exception > of server-side Java), Java VM implementations are known to be so buggy > and slow to be unusable in practice.
    The goal of BioCoRE is to provide integrated tools necessary for researchers in structural biology. Many of those tools, (eg. collaboration notebooks, tools for writing documents/papers) are not particularly bandwidth-intensive, yet would simplify the work of researchers.
    Some tools such as Interactive MD, do require fairly low-latency connections to remote computers (roughly 10Mb/s ethernet speeds, not more exotic LAN technologies). In the next few years, we expect such connectivity to be available to an increasing percentage of our users. In fact, it's the high bandwidth promise of the NGI (Next Generation Internet) which will be available to scientists in many academic research institutions, that has been one of the driving forces behind BioCoRE.
    At the same time, we are thinking about a number of solutions which would allow more interaction between researchers, without requiring great bandwidth. Here's one example: consider researchers working at several sites. Several meet on a BioCoRE chat channel, or in some kind of video conference, to discuss some work. They run VMD and bring up views of their molecules. When one person wants to discuss a particular view to discuss with the others, he triggers a "Publish" function, which connects to the others' VMD sessions and replicates the view. Such a function will not require nearly the bandwidth of IMD, while still facilitating the kind of cooperation which currently requires a face-to-face meeting.
    Currently, we are only planning to use Java for various kinds of network interaction and interface layers, not the hard-core computational components of the collaboratory. So we believe that the performance problems with Java will be secondary. If performance turns out to be a problem, we have no aversion to more traditional languages.
    > I haven't missed the frequent occurance of "distributed" in your > overview article, but does it really work in practice? (I know > VMD/NAMD does, but your approach seems to be different, both because > of use of nonlocal networking with necessarily poor latency and > throughput, and trivial portability at the price of very poor > performance due to Java).
    Well, this is ongoing work, but we are fairly confident that our distributed approach will work. Part of the research will be to discover what works now, and what will work with the infrastructure a few years down the road. We don't plan on re-creating functionality unless it is absolutely necessary. Our approach is to connect up existing component (such as VMD and NAMD) whenever possible. We think that Java will be a good tool for such connections.

    (Answer) (Category) BioCoRE Collaboratory FAQ :
    When can I expect my changes that I asked for to show up in BioCoRE?
    The BioCoRE team tries to be as responsive as possible to user requests.

    If we have told you that something has been changed and you check and it doesn't seem to be fixed, be aware that we only release code updates periodically (usually every week or two). So, your changes will probably be rolled into that release.

    Information about recent BioCoRE releases can be obtained here.

    (Answer) (Category) BioCoRE Collaboratory FAQ :
    What about privacy?
    We are quite committed to privacy concerns and feel just as strongly about SPAM as you do. In the consent form (which you can view at http://www.ks.uiuc.edu/Research/biocore/consent_form.shtml) there is a paragraph that says that we will use information about BioCoRE users EXCLUSIVELY to evaluate BioCoRE and its impact on doing science, in order to make BioCoRE a better tool for you. This is the only thing that we use information about BioCoRE users for.
    This document is: http://www.ks.uiuc.edu/Research/biocore/fom.cgi?file=1
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