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
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Go to the Pathway Tools site download site:
http://biocyc.org/download.shtml.
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You will need to obtain a license for download (free for academia)
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Download Pathway tools .dmg file from the Pathway Tools FTP site
(Tier 1 is sufficient)
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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
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Go to the FTP site:
https://download.maizegdb.org/MetabolicResources/MaizeCyc_install_files/
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Download maizecyc2.0.2.tar.gz to your machine (the version number can
be different)
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Open the "Finder"
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Go to this directory: /Users/taner/ptools-local/pgdbs/user (change
"taner" with your username)
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Put the maizecyc file in that directory
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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
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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)
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Type "cd /Users/taner/ptools-local/pgdbs/user" and press "return"
(change "taner" with your username)
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Type "ls" and press "return". You should see maizecyc2.0.2.tar.gz file
there.
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Type "tar -xvzf maizecyc2.0.2.tar.gz" and press "return". You should
now see the maizecyc directory.
Starting Pathway Tools
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Open a "Terminal" window
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Type "cd /Users/taner/pathway-tools" and press "return" (change
"taner" with your username)
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Type "./pathway-tools" and press "return".
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Wait just a little: you should now see the X-windows open up.
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There are some survey questions: you can ignore bunch of them.
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You should now see "Pathway Tools".
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Press the "Escherichia Coli" in the drop-down menu on the top left
corner, choose "Zea mays". That's our database!