View of /SCDemoTools/README

This directory (~fig/ModelEditor) contains the ModelEditor for the
SuperComputing demo.


To Run
======
1. cd PyGUI
2. python main.py    (linux)
   pythonw main.py   (Mac)

Good Things to Show
===================
1. Go to Catalog. Open Seed.  Open http://localhost/FIG/.  Navigate down
   and open Buchnera Aphidicoloa SG by selecting it and hitting LOAD in
   bottom right corner.
2. Do again for E. coli K12
3. Go to Navigator page.
4. Show how you can open up the tree (the engineering view of a model or
   reconstruction) and navigate.  Selecting any node shows reactions on
   the right.
5. Right click in the left pane of the Navigator page.  Play with the
   commands.  For example, add a new Root Node and call it "My Model"
      o Select that.  
      o Right click and add a subelement.  Call it biochemistry
      o Go to one of the organisms you already loaded. Open it up.  Pick
        a node and select it.  See that it has reactions.
      o Now right click and "Copy Branch".
      o Go down to MyModel and select Biochemistry.  Right click and do Paste.
6. You can righ click in the reaction listing to cut/paste at reaction level.

***>7. Go to Buchnera, go to Citrate cycle.
	o Select it
        o Right click and execute "Visualize with Cytoscape"
	
***>8. Go to Ecoli. Go to Citrate cycle.  Visualize Citrate cycle.
***>9. Visually compare the results and point out that you can see
       that parts of citrate cycle are missing in Buchnera (a symbiont)

10. Go to Catalog page.  Right click.  "New Seed Server" pops up.  Click it.
    Enter the name of another server, e.g., "http://somenode.foo.edu/FIG/"
    Show that you can connect to multiple servers.


Updating the Code
=================

1. cd SCDemoTools
2. ./doUpdates
3. You need to do that on each node before you use it, if you want the update.
4. NOTE!!!  You do NOT need to update the ModelEditor when Seed is updated.
   They are independent


Troubleshooting
===============
1. Nothing shows up when searching:
   o Make sure the "Data source" dropdown is pointing at the Seed server,
     and not at BSS or Wit.

   o cd to FaST.  Run the command regressSeed to run regression tests on
     the seed server to make sure it is ok, as far as ModelEditor goes.
     The script will check localhost.  You can give a host name, e.g.,
     regressSeed http://foo.bar.edu/FIG/


Initial Setup
=============

0. This should all be done for you already.
1. To bootstrap, put in your environment:
	export CVSROOT=:ext:efrank@biocvs.mcs.anl.gov:/disks/cvs/bio
	export CVS_RSH=ssh
2. 3 packages should be checked out from CVS:
	cd ~fig/ModelEditor
	cvs co FaST
	cvs co PyGUI
	cvs co SCDemoTools
3. make two links:
	cd ~fig/ModelEditor
	ln -s SCDemoTools/README
	ln -s SCDemoTools/setup

4. Hook setup into your .bashrc:
	source /home/fig/ModelEditor/setup

5. relogin to get environment set.  A snapshot of a usable environment is
   at the bottom of this file as an example.





CVSROOT=:ext:efrank@biocvs.mcs.anl.gov:/disks/cvs/bio
PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/X11R6/bin:/home/fig/FIGdisk/FIG/bin:/home/fig/FIGdisk/bin:/home/fig/FIGdisk/env/linux-mysql/bin:/home/fig/bin
CYTOSCAPE_HOME=/home/fig/ModelEditor/Cytoscape
CYTOSCAPE_COMMAND=/home/fig/ModelEditor/Cytoscape/cytoscape.sh
PYTHONPATH=..:/home/fig/FIGdisk/FIG/Packages:/home/fig/FIGdisk/env/linux-mysql/lib/python2.2/site-packages
CVS_RSH=ssh
CYTOSCAPE_DISPLAY=localhost:10.0
DISPLAY=localhost:10.0