[Bio] / SCDemoTools / README Repository:
ViewVC logotype

Annotation of /SCDemoTools/README

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.1 - (view) (download)

1 : efrank 1.1
2 :     This directory (~fig/ModelEditor) contains the ModelEditor for the
3 :     SuperComputing demo.
4 :    
5 :    
6 :     To Run
7 :     ======
8 :     1. cd PyGUI
9 :     2. python main.py (linux)
10 :     pythonw main.py (Mac)
11 :    
12 :     Good Things to Show
13 :     ===================
14 :     1. Go to Catalog. Open Seed. Open http://localhost/FIG/. Navigate down
15 :     and open Buchnera Aphidicoloa SG by selecting it and hitting LOAD in
16 :     bottom right corner.
17 :     2. Do again for E. coli K12
18 :     3. Go to Navigator page.
19 :     4. Show how you can open up the tree (the engineering view of a model or
20 :     reconstruction) and navigate. Selecting any node shows reactions on
21 :     the right.
22 :     5. Right click in the left pane of the Navigator page. Play with the
23 :     commands. For example, add a new Root Node and call it "My Model"
24 :     o Select that.
25 :     o Right click and add a subelement. Call it biochemistry
26 :     o Go to one of the organisms you already loaded. Open it up. Pick
27 :     a node and select it. See that it has reactions.
28 :     o Now right click and "Copy Branch".
29 :     o Go down to MyModel and select Biochemistry. Right click and do Paste.
30 :     6. You can righ click in the reaction listing to cut/paste at reaction level.
31 :    
32 :     ***>7. Go to Buchnera, go to Citrate cycle.
33 :     o Select it
34 :     o Right click and execute "Visualize with Cytoscape"
35 :    
36 :     ***>8. Go to Ecoli. Go to Citrate cycle. Visualize Citrate cycle.
37 :     ***>9. Visually compare the results and point out that you can see
38 :     that parts of citrate cycle are missing in Buchnera (a symbiont)
39 :    
40 :     10. Go to Catalog page. Right click. "New Seed Server" pops up. Click it.
41 :     Enter the name of another server, e.g., "http://somenode.foo.edu/FIG/"
42 :     Show that you can connect to multiple servers.
43 :    
44 :    
45 :     Updating the Code
46 :     =================
47 :    
48 :     1. cd SCDemoTools
49 :     2. ./doUpdates
50 :     3. You need to do that on each node before you use it, if you want the update.
51 :     4. NOTE!!! You do NOT need to update the ModelEditor when Seed is updated.
52 :     They are independent
53 :    
54 :    
55 :     Troubleshooting
56 :     ===============
57 :     1. Nothing shows up when searching:
58 :     o Make sure the "Data source" dropdown is pointing at the Seed server,
59 :     and not at BSS or Wit.
60 :    
61 :     o cd to FaST. Run the command regressSeed to run regression tests on
62 :     the seed server to make sure it is ok, as far as ModelEditor goes.
63 :     The script will check localhost. You can give a host name, e.g.,
64 :     regressSeed http://foo.bar.edu/FIG/
65 :    
66 :    
67 :     Initial Setup
68 :     =============
69 :    
70 :     0. This should all be done for you already.
71 :     1. To bootstrap, put in your environment:
72 :     export CVSROOT=:ext:efrank@biocvs.mcs.anl.gov:/disks/cvs/bio
73 :     export CVS_RSH=ssh
74 :     2. 3 packages should be checked out from CVS:
75 :     cd ~fig/ModelEditor
76 :     cvs co FaST
77 :     cvs co PyGUI
78 :     cvs co SCDemoTools
79 :     3. make two links:
80 :     cd ~fig/ModelEditor
81 :     ln -s SCDemoTools/README
82 :     ln -s SCDemoTools/setup
83 :    
84 :     4. Hook setup into your .bashrc:
85 :     source /home/fig/ModelEditor/setup
86 :    
87 :     5. relogin to get environment set. A snapshot of a usable environment is
88 :     at the bottom of this file as an example.
89 :    
90 :    
91 :    
92 :    
93 :    
94 :     CVSROOT=:ext:efrank@biocvs.mcs.anl.gov:/disks/cvs/bio
95 :     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
96 :     CYTOSCAPE_HOME=/home/fig/ModelEditor/Cytoscape
97 :     CYTOSCAPE_COMMAND=/home/fig/ModelEditor/Cytoscape/cytoscape.sh
98 :     PYTHONPATH=..:/home/fig/FIGdisk/FIG/Packages:/home/fig/FIGdisk/env/linux-mysql/lib/python2.2/site-packages
99 :     CVS_RSH=ssh
100 :     CYTOSCAPE_DISPLAY=localhost:10.0
101 :     DISPLAY=localhost:10.0

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3