Metabolic Pathways at MaizeGDB - Installation instructions

PATHWAY TOOLS + MAIZECYC DATABASE INSTALLATION/DOWNLOAD GUIDE FOR MAC

Created: March 28, 2013

Installing Pathway Tools to your computer has the advantage of reaching and visualizing the data quickly.


The instructions here are provided for MaizeCyc on a Mac, but it is straightforward to install CornCyc on a Linux-based system as well.


Installing Pathway Tools

  1. Go to the Pathway Tools site download site: http://biocyc.org/download.shtml.
  2. You will need to obtain a license for download (free for academia)
  3. Download Pathway tools .dmg file from the Pathway Tools FTP site (Tier 1 is sufficient)
  4. Folllow the instructions provided by the Pathway Tools team, but double-clicking the .dmg file to install it on your machine by accepting the default parameters works in most cases.


Downloading the MaizeCyc database

  1. Go to the FTP site: http://ftp.maizegdb.org/MaizeGDB/FTP/metabolic_resources/MaizeCyc_install_files/
  2. Download maizecyc2.0.2.tar.gz to your machine (the version number can be different)
  3. Open the "Finder"
  4. Go to this directory: /Users/taner/ptools-local/pgdbs/user (change "taner" with your username)
  5. Put the maizecyc file in that directory
  6. Create and keep a copy of the tarred maizecyc database somewhere in case you mess up the database when you are playing with Pathway Tools.


Unzipping the MaizeCyc Database

  1. Open a "Terminal" Window. (If you don't know where it is, go to "Applications" folder in the Finder, then "Utilities", and double-click Terminal)
  2. Type "cd /Users/taner/ptools-local/pgdbs/user" and press "return" (change "taner" with your username)
  3. Type "ls" and press "return". You should see maizecyc2.0.2.tar.gz file there.
  4. Type "tar -xvzf maizecyc2.0.2.tar.gz" and press "return". You should now see the maizecyc directory.


Starting Pathway Tools

  1. Open a "Terminal" window
  2. Type "cd /Users/taner/pathway-tools" and press "return" (change "taner" with your username)
  3. Type "./pathway-tools" and press "return".
  4. Wait just a little: you should now see the X-windows open up.
  5. There are some survey questions: you can ignore bunch of them.
  6. You should now see "Pathway Tools".
  7. Press the "Escherichia Coli" in the drop-down menu on the top left corner, choose "Zea mays". That's our database!