BioCoRE - Biological Collaborative Research Environment

Online Configuration

We are going to call your install directory $BIOCORE_HOME. EVERYWHERE YOU SEE $BIOCORE_HOME REPLACE IT WITH YOUR CHOSEN DIRECTORY.

Start Tomcat (by executing $BIOCORE_HOME/packages/tomcat/current/bin/startup.sh) and we'll get into setting up a few more BioCoRE parameters.

Once you have Tomcat started, point your web browser (modify appropriately for machine and port if necessary) to: 

https://localhost:8443/biocore/nonsecure/admin

Assuming everything has worked properly, you will be asked some questions about setting up a maintenance account.

If it didn't work properly, the connection between BioCoRE and MySQL probably deserves the blame.

You should be able to check the file $BIOCORE_HOME/packages/tomcat/current/conf/catalina.out and, near the end, find a line that looks something like: 

INFO: Server startup in 9151 ms

If you don't have the "Server startup" line, look around in that file for other errors. For instance, if something is wrong with the database parameters that you specified in the biocore.xml file, you will probably see many lines that look something like the following, with a lot of Exception text in between: 

DBCP borrowObject failed: java.sql.SQLException: Server connection failure during transaction.
Attempted reconnect 3 times. Giving up.

In the event that you have database problems, check and double check the username, password, and url values that you specified in the biocore.xml file. If you do have database connection problems, expect a few error emails to the email address specified in the biocore.xml file. Also, the log file location that you specified in your biocore.xml file will probably contain additional information if anything has went wrong.

Assuming everything worked correctly, you should be on a page that is discussing the initial setup and maintenance account creation.

  • You should have received email from the Theoretical and Computational Biophysics Group by this time giving you some important information. Copy that information into the two text boxes given (CollabName, eventServerURL).

  • If you have to specify a proxy to be able to connect to secure websites on the Internet, you need specify the proxy machine name and port for the parameters ProxyHost and ProxyPort.

  • Type in the password that you chose for the event server for eventServerPassword). For the eventServerPassword, you need to type in the password that you gave when you registered to run an event server (on this form). Be careful to not mistype.

  • You have to assign the BioCoRE maintenance user a password. This password will be needed to made maintenance changes to the BioCoRE server later on. (i.e., any time you go to /nonsecure/admin) This is NOT the password that you gave in the step where you registered for an event server. This particular password is one that you are setting RIGHT NOW.

    When you have given this information, submit the form and wait about 30 seconds while BioCoRE initializes. Behind the scenes, your BioCoRE server is busy verifying the event information provided (by contacting our event server here), creating a sample project which your users can use to evaluate BioCoRE, and installing the maintenance user. 

  • If the database ever gets corrupted, you might need to completely
reset it.  To do this, first you need to shut down Tomcat.
Then, you need to run the following from a terminal:


    $DBMS_HOME/mysql/bin/mysql \
--defaults-file=$DBMS_HOME/scripts/my.cnf \
-u root -p 

    

When asked for a password, enter the mysql root password.


    
Then, type in the command:


    DROP DATABASE biocore;

    

Note:  This is a very dangerous command and shouldn't ever be typed once you
get your server up and running.  This should only be used if you have
problems getting the server going in the first place.  This will remove all
of your database entries and render your current BioCoRE server totally
useless.  So, you don't want to type it unless you are having problems 
getting the server working correctly in the beginning.


    
Next, recreate and repopulate your database using the same commands 
as in the MySQL 
installation instructions.  Follow the instructions to recreate 
the database and make the tables for BioCoRE.


    
After doing the above, restart Tomcat.


    
Then, go back to the top of this page and try again.
    • Assuming all goes well, you will be presented with a page where you can login using the maintenance password to set (and later modify) various parameters for your BioCoRE server. So, go ahead and type in the maintenance password and choose to see the Parameters Page.

  • serverBaseSecure, serverBaseNonSecure You need to give the URL 'prefix' that users will use to access BioCoRE. An example value for serverBaseSecure might be: 
    https://your.machine.edu:8443/biocore/
    and for serverBaseNonSecure: 
    http://your.machine.edu:8080/biocore/
    If you are using a port redirector or are behind a strong firewall you will probably need to enter special values for serverBaseSecure and serverBaseNonSecure.
    • Port redirector use case: You might be running a port redirector that redirects ports 80 and 443 to 1080 and 1443, respectively. You would want people to use the normal ports, so you would enter http://your.machine.edu/biocore/ and https://your.machine.edu/biocore/.
    • Firewall/private network use case: Let's say that you have an internal private network (running on 192.168.xxx.xxx) and you have a firewall machine that is accessible at your.machine.edu. BioCoRE is running on a machine on the internal network (let's call it 192.168.1.100) and you have all web requests automatically getting forwarded from the firewall machine to your BioCoRE machine on the internal network. You would want to enter http://your.machine.edu/biocore/ and https://your.machine.edu/biocore/ in these two fields. Note that if you are using a forwarder in this way that you could have problems with listeners (such as the Control Panel). Read the section below on the startingListenerPort for additional information.

  • techSupportEmail needs to be a valid email address of who can be contacted with questions about BioCoRE. There are various locations in BioCoRE where users can contact tech support, and the email address they are given is is specified by this parameter.

  • When a user logs out of BioCoRE they are automatically redirected to another website. That website is specified by the collaboratoryWebPageURL parameter. On our server we have this set to the BioCoRE website URL.

  • The commonName parameter is used to distinguish your BioCoRE server from other BioCoRE servers. This name will show up throughout BioCoRE. We suggest something related to your research group. For instance, on our main server we have a commonName of 'TCB-UIUC' and throughout BioCoRE the term 'TCB-UIUC BioCoRE' shows up for the user to see.

  • Listeners (such as Control Panels) can create persistent connections with the server. If you are running a firewall or other port blocking mechanism, you might need to specify which port or ports you want the server to use when allowing connections. If your listeners seem particularly slow to receive information from the server, a port blocker could be the culprit. We suggest that you leave these fields blank unless you have reason to specify beginning and ending ports. The server does a good job of finding a port normally, and if you start limiting the ports you run the risk of the server not being able to find a port at all. startingListenerPort and endingListenerPort can be used to specify a range of ports that you want the server to use. If you specify the same value for both, the server will only allow connections on a single port. If the server can't obtain a port in the range that you specify (because the ports are already in use, or it doesn't have permission, etc) it will print an error to the logs and not start up. So, you want to give as large a range as possible, and we additionally suggest using a high port range (with numbers above 1023). Typical values for these fields might be: startingListenerPort=25000 and endingListenerPort=25010. With that range, the server would typically always set up a connection port on port 25000. But, if it couldn't obtain 25000 it would attempt to obtain 25001, etc. Again, we recommend that you leave this blank unless you have reason to use it.

  • The GlobusrunPath parameter tells the server where your globusrun binary resides. If you haven't installed Globus (and you probably haven't), just leave this blank.

  • For Job Monitoring, you can restrict certain user names from being available for job accounts. This can be an issue depending on how SSH is set up on the server. If the server's SSH doesn't require a password for some accounts, and Tomcat is running as one of these users, it would be possible for a user to do unintended things as that unix user. By listing that account name here, the server won't allow that name to be used.

  • The bylawURL parameter needs to be full URL that points to the bylaws for your local server. The bylaws are additional rules and regulations that you expect your users to follow and can be set to say whatever you want, within the confines of our license agreement with you. We have included a sample set of bylaws in the distribution that we gave you. If you wish, you can make that into a webpage and set this URL to point to that (be sure to read over it and change the text appropriately). Or, if you wish, you can leave the field blank, and the users will not be prompted to agree to any local server bylaws.

    Because the BioCoRE server creates online communities, we do suggest that you use a set of bylaws.

    You shouldn't ever change the CollabServer or the eventServerURL unless you are told to do so by us. If you need to use a Proxy, you can refer to the previous descriptions on how to use it.

    All changes made on this page require the maintenance password again (for safety), so be sure to type it before submitting.

    Next Step: Final issues.
    Back to the installation page

    Feedback

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