- What do I need to have on my computer to run this
model over the web?
- Where can I find a X-server for my machine?
- I am new to X-windows. Can you show me an
step-by-step example of how to use it on MS-Windows platform?
- Can I run the model behind a firewall?
- How do I start the simulation run after I
successfully launch the model from your server?
- How can I view the results?
- Can I change parameter values? Can I save modified
parameter sets?
- Why do I see multiple simulation runs in the
provided parameter sets? How can I change this setting?
1. What do I need to have on my computer to run this
model over the web?
Since XSIM is a
X-Windows based program, you need a X-server running on your local machine.
X-servers are standard on most UNIX/LINUX systems. Windows and Macintosh users
need to install their own X-server. The X-server must be running and set
to accept applications from the NSR server before you can run the models over
the web. For example, UNIX users should type:
xhost +nsr.bioeng.washington.edu
Once you have a running X-server, you can launch XSIM by
clicking on a hyperlink to a model parameter file (by convention, these are
files ending in the suffix .par).
2. Where
can I find a X-server for my machine?
The following vendors
are possible sources of X-servers. Please note the NSR is not associated
with any of the vendors listed here and can not assist with X-server
installation.
PC
Exceed
by Hummingbird (Free evaluation version available)
WinAxe by Labtam Finland Ltd. (Free demo
version available)
Omni X-server by Xlink Technology, Inc.
(Free evaluation version available)
MI/X by MicroImages, Inc. (Free demo
version available)
Mac
OS
X by Macintosh
MI/X by MicroImages, Inc. (Free demo
version available)
3. I am new to X-windows. Can you show me a
step-by-step example of how to use it on MS-Windows platform?
Here is an example of using the free evaluation version of the Omni
X-server with the online demo on our web.
1. Download and
install the Omni X-server.
2. go to "Start" -> "Programs" -> "OmniX V-6.2" and choose "Xconfig". You will see the "X configuration" window popped up. Click on
"Winmode" and choose "Multiple" for Windows mode and check "Track mouse".
This only needs to be done once. Next time you want to use the X-server, you can start with
step 3 directly.
3. go to "Start" -> "Programs" -> "OmniX V-6.2" and choose "PC-X server". You will see a window popped up with title of "Omni X Demo/Root".
4. go to our web site and click on the parameter file names and wait for the model window to show up.
4. Can I run the model
behind a firewall?
Yes, but there are additional requirements. You also need a secure shell client
program (SSH) on your system in
addition to the X-server. Find more about SSH here.
The host you need to connect is "nsr.bioeng.washington.edu",
and the
port is "1234". You also need to provide a parameter file name that
you are interested in exploring.
For example, "circres00_fig2a.par" loads the model with the parameters necessary
to reproduce figure 2a of the paper by Greenstein et al (Circ. Res.
2000).
Note for UNIX users. Please check with your system
administrator to find out if SSH is installed on your machine. If it is
available (usually is), type the following at the UNIX prompt:
ssh nsr.bioeng.washington.edu -p 1234 circres00_fig2a.par
If the default configuration of your ssh client doesn't allow
"X11 forwarding", try the following:
ssh nsr.bioeng.washington.edu -p 1234 -o "ForwardX11
yes" circres00_fig2a.par
Note for MS-Windows users. Please follow the instructions given
below:
1. Download, install and start the X-server on your PC
described in the answer to the 3rd question.
2. Download
FreeSSH and install it on your PC. The download web site and installation
program are in German but don't worry. The program itself is in English. Just
follow the default installation procedure.
3. Launch the program FreeSSH by clicking on the icon and set
the host name, port number and parameter file name (in the "Command"
field"). Here is the screenshot for setting up "circres00_fig2a.par"
as an example.
4. Click "OK" and you are there.
***Only try this if you are behind a firewall and can not launch XSIM by
following the hyperlinks***
5. How do I start the simulation run after I successfully launch the model from your server?
You should see at least two windows on your screen: one specific to the model
you are trying to run, and the XSIM control window. You may need to move
these around if they are layered on top of each other. The XSIM control
window is the same for all XSIM models. You can simply click on "Run"
button in the XSIM control window to start
the simulation. The progress of the simulation is tracked by the
completion bar in the upper right corner of the XSIM control window. Some
models may run so quickly you do not notice the bar change. When the run
is competed, the message "Model run completed successfully will be
displayed in the XSIM control window. Click here
for more information on running models under XSIM.
6. How can I view the results?
Click on "Results" on the XSIM control window and choose "Plot
Area 1" and "Plot Area 2". Find more information on the XSIM
results menu here.
7. Can
I change parameter values? Can I save modified parameter set?
Yes and Yes. You can change parameter values by typing the numbers directly
in the parameter fields in the model windows. To save your own parameter set, click on
"Par-File" in the XSIM control window and choose "Save as
...", then type in a filename. Your parameter set will then be saved in a
directory named after your IP address. If you come in from the same IP address next
time, you will be able to load a previously saved parameter file by selecting
"Load ..." from the "Par-File" menu.
8. Why
do I see multiple simulation runs in the provided parameter sets? How can I change
this setting?
Some parameter sets use one of the XSIM features called "looping"
to do multiple simulation runs with varied parameter values. To see the setting,
click on "Model" in the XSIM control window and choose "Run
Config". You can change the settings such as the number of loops, the
parameter and the set of parameter values you want to examine. Click here
to find more information about "looping".
Contact Zheng Li for
comments and questions.
Copyright © 2000 NSR, University of Washington. All rights reserved.
Revised: November 30, 2000
.