Running GenMAPP Builder

These instructions assume that you are running GenMAPP Builder on the Windows XP Machines in the Seaver 120 computer lab.

Download and Extract GenMAPP Builder

• Click on this link to download the latest version of GenMAPP Builder to your desktop.
• Extract the files using the 7-zip utility which has been installed on these machines.
  • Right-click on the file and select the menu item, 7-zip > Extract here.
  • Note that the native Windows unzip utility will not extract these files properly.
  • WinZip will extract them, too, but 7-zip will be faster.

Download and Extract Data Source Files

• Download UniProt XML and GOA files from Integr8
  • Browse to the page for your species. For example, the Vibrio cholerae page.
  • Click the Download link.
  • Click to download the complete proteome set in XML format (save it to your Desktop).
    • These files are updated on a monthly basis. The date of the last update can be found on the current status page. Note the release versions for Integr8, UniProt, and InterPro, and the release date as version control for your group.
  • Right-click on the link to download the GO annotations and select "Save target as" or "Save link as" and save the GOA file.
    • Note: Since the GOA file is a text file, your browser will not automatically download it when you left-click on the link. Instead, it will try to open the file in your browser window. Since it is a large file, this could take a long time if your internet connection is slow.
    • The version information can be found on the GOA page under "GOA News". Record the version information for "GOA Proteome Sets" and the date they were released for version control for your group.
• Download the GO OBO-XML formatted file from the Gene Ontology download page. Click on the link for "obo-xml.gz"
  • This file is uploaded daily, the time will be stated near the upper-right side of the page under "Current ontology statistics" as Pacific Standard Time (PST). Note the version, date, and time listed there as version control for your group.
• Extract the UniProt XML and GO OBO-XML .gz files.
  • Right-click on the file and select the menu item 7-zip > Extract here.

Create New Database in Postgres

• Launch PGAdmin III by going to Start menu > PostgreSQL 8.4 > pgAdmin III
• Double-click on PostgreSQL 8.4 (localhost:5432) on the upper left hand side of the window.
  • This is the equivalent of connecting you to the server.
  • It will prompt you for a password. The password is: Phe1oSer3Tyr4
• Right click on "Databases" and Select "New Database"
• Give the database a name in the "Name" field and click OK. You now need to tell the database what tables to have.
• Click on your new database icon in the treeview on the left.
• Go back to your gmbuilder-2.0b59 folder that you extracted to your Desktop. Open the folder called "sql". Right click the file gmbuilder.sql. Select the menu item "Open with" and choose the Notepad program. Select All and Copy all to the clipboard.
• Back in PGAdmin III, select your database so it is highlighted and then click on the SQL pencil icon.
• You will see information in the upper panel (it is actually the SQL query that created the database). Delete this information. Paste the gmbuilder.sql text into the upper panel.
• Click the run icon which looks like a green arrow.
• You should get a message like "Query returned successfully with no result in 15583 ms." This query now created all the tables in the database (although there is still no data in them).
• Close the query window (you don't need to save the query because you have already run it).
• To double check that all is OK, open the + signs for the database to see the number of tables, it should be 140 (it becomes 141 later, after you complete the Process GO Data step below).

Importing Data into the Postgres Database

• Launch GenMAPP Builder by double-clicking on the gmbuilder.bat file.
• Select File--> Configure Database
  • "Host or address" should be "localhost" (it should default to that).
  • "Port Number" should be "5432" (it should default to that).
  • "Database Name" should be the name of the database you created in pgAdmin III in the previous steps.
  • "Username" is "postgres" (you will need to type this the first time).
  • "Password" is Phe1oSer3Tyr4 (note that this is the same password you typed in pgAdmin III to connect to the database.
• Click on the OK button.
• Select File > Import UniProt XML...
  • Navigate to the UniProt XML file that you extracted previously (it should be on the Desktop) and click the Import button.
  • This should take about 5-7 minutes, record the time it took to import (the computer will report this to you when it is done).
• Select File > Import GO XML...
  • Navigate to the GO OBO-XML file that you extracted previously (it should be on the Desktop). Click the Import button.
  • This should take about 5-7 minutes, record the time it took to import (the computer will report this to you when it is done).
• Click OK to the message asking you to process the GO data. This should also take 5-7 minutes. Record the time it took to process (the computer will report this to you when it is done).
• Select File > Import GOA file...
  • Navigate to the .goa file that you downloaded (it should be on the Desktop) and click on the Import button.
  • This should take less than 1 minute. Record the time ti took to import (the computer will report this to you when it is done).

Exporting a GenMAPP Gene Database (.gdb)

• Select File > Export to GenMAPP...
• Type a name in the Owner field (or else it won't let you export). Dr. Dionisio and I use "LMU Bioinformatics Group" and click Next.
• Create GenMAPP Database: click on the Specify File button and accept the default folder and file name. It will create the file in the export folder of your gmbuilder-2.0b59 folder.
  • Leave the radio button on "Full Database" and click the Next button.
• Select "Move all" for both the upper and lower panels. Click Next.
• A window will ask you to verify the system tables. Clicking Next in this window starts the import process.
  • Record the starting and ending times from the black console window. An export of the Vibrio cholerae Gene Database should take about 50-55 minutes.
    • The progress bar that appears is not really accurate. It goes from 1% to 66% to 67% to 100%. Just be patient.

Complete a Gene Database Testing Report

• Gene Database Testing Report Sample