Frequently Asked Questions
1. How to run?
There is a war package under path: BioWeb/war. Firstly, unpack it in tomcat deployment administration web page. Secondly modify "db.properties" database configration file in tomcat's webapps directory. Thirdly import db/createDb.sql to create database in DB2 database server.
Fourthly, sorry because DB2's JDBC driver is not GPLed, you need to copy JDBC driver
$(DB2_INSTALL_DIR)/SQLLIB/java/db2jcc4.jar
to Apache tomcat's lib directory:
$(TOMCAT_INSTALL_DIR)/lib
Lastly get tomcat and db2 ready, then input the following url:
http://localhost:8080/BioWeb
Now go to the administration page:
http://localhost:8080/BioWeb/backend
Configure the correct url of GraphServlet and GraphApplet, these two parameters are used to tell client applet(to display enzyme graph) where is service and to tell the browser where is applet client program. Don't care it too much, the easiest way is just replace "localhost:8080" with THE CORRECT DOMAIN ALIKE OR IP ALIKE ADDRESS, so that the visit can favorably access your website.
Okay, your system should be properly installed. The remainnning thing is to upload a database, see F.A.Q #2.
2. How to get database?
We support two different bioinformatic database, BRENDA and enzyme, you can access them through the following urls:
http://expasy.org/enzyme/
http://www.brenda-enzymes.info/
3. Why I can't see a progressbar while uploading a database?
We are currently sorry about this, because the browser can't receive the updating information while "talking to" server. It is more convenient to upload a file reside on remote server. Now I don't have a good idea about resolving it, if you have an idea, you can send me a E-mail and I would like to take your opinions. :-)
4. Why it called EZMWeb while using BioWeb instead?
EZMWeb stand for "Enzyme Web", while because we find it is collide with another project hosted on sf.net, and we don't want to change internal name. Sorry, :-) this is really unexpected~ and forgive our obstinacy.
5. How much time it will cost for a database import?
BRENDA database import is a big operation, while Enzyme database is smaller than BRENDA, BRENDA database import need approximately 17 hours to import, and Enzyme database only need 20 minutes to import. I test these statistics in my notepad, Intel Core2 T5450, 667MHz, Memory: 1GB, Hardisk: 160GB/5400rpm.
