Computer Software for Math 430 and Math 635
Analytical and Computational Neuroscience








For assignments and projects, we will be using the program XPP-AUT, a differential equation solving package developed by G. Bard Ermentrout.  XPP is installed on all AFS machines and can be run directly from an AFS machine or can be run remotely.  To run XPP-AUT directly on an AFS machine, simply enter ``xpp file.ode'' at the prompt where file.ode is an ascii file containing your differential equations (see assignment handouts or Online Tutorial).  When running, XPP creates a number of different windows that rely on a Xwindows manager.  This requires that specific steps are taken when running it remotely, especially from a MS-Windows PC (see instructions below).

There is also a MS-Windows version of XPP called WinPP that you can download here along with its documentation.  There are some differences between WinPP and XPP but all assignments can be completed equally well using either program.

Resources for XPP:

Instructions for running XPP remotely from an AFS machine:
 
  1. 1. If running from a LINUX or UNIX machine, enter ``xhost +'' in the window you plan to run XPP.  Skip to #3.
  2. 2. If running from an MS-Windows PC, you must have the software Xwindows Terminal Emulator for Windows 9x and NT (download it here).  The PCs in the PC Lab should have this program.  Start the emulator running.
  3. 3. Login to an AFS machine.  Check the load on the machine by entering ``w''.  If the load on the machine is heavy (load average numbers > 3), then running XPP will be slow.  Logout of that AFS machine and login to another AFS machine with a lighter load.  Below is an example output from the command ``w'' on a machine with a low load:
fischer-41 vbooth>: w
11:42am  up  6:01,  4 users,  load average: 0.04, 0.06, 0.07
User     tty           login@  idle   JCPU   PCPU  what
yp2      console      11:32am    10      2      1  dtwm
pt       pts/6        10:46am    53      2         -csh
pt       pts/7        10:35am    42                -csh
vbooth   pts/4        11:42am                      w
fischer-42 vbooth>:
  1. 4. Enter ``who''.  Find your login name in the output list.  In parentheses after your login id is the identifier of your local machine.  Enter ``setenv DISPLAY xxx:0'' where xxx is your local machine identifier followed by ``:'' (colon) and then ``0'' (zero).  Below is an example output from the command ``who'':
fischer-42 vbooth>: who
yp2        console      Sep  6 11:32 (:0)
pt         pts/6        Sep  6 10:46 (ptnt.njit.edu)
pt         pts/7        Sep  6 10:35 (ptnt.njit.edu)
vbooth     pts/4        Sep  6 11:42 (spike.njit.edu)
fischer-43 vbooth>:
  1. 5. You are now ready to run XPP by entering ``xpp file.ode'' where file.ode is an ascii file containing your differential equations (see Online Tutorial or assignment handouts).  Note: this may not work if you are accessing the AFS machine via a local internet provider.