C-ImmSim consists of more than 10000 lines of C code. Thanks to a dynamic memory allocation, to the compressed output mechanism and to other tricks, we can work with a potential number of olecules (cell-receptors, peptides and epitopes) of the order of 2 to the power of 24. The high degree of complexity of the model make it suitable to simulate different immunological phenomena, e.g., the hypermutation of antibodies, the germinal center reaction (GCR), immunization, Thymus selection, viral infections etc.
 
C-ImmSim version 6.3 is available under a LICENSE AGREEMENT that needs to be signed. Instructions on how to obtain the code are found HERE.
 
C-ImmSim can be compiled on any Unix-like machine (Linux, MacOS, etc.) that has auto-configure capabilities. It can be compiled also under Windows by using Makefile.win included in the package.
 
A description of the parameters used by the simulator is available at the parameter page
 
A tool to write the input parameter file is also available (this does not require the LICENSE AGREEMENT):
 
    * Linux binary, kernel 2.6.10-1.771_FC2, libgcc-3.3.3-7 ImmSimIn6.3.linux
    * MacOSX binary, Tiger ImmSimIn6.3.macos
    * Windows Win32 binary ImmSimIn6.3.win32.exe
 
If you want to look at some animations (and you have a fast connection) look here
 
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         C-ImmSim
         Simulation of the Immune System
         Copyright (C) Filippo Castiglione (1995,2008)
________________________________________________________________________________________________
 
 
 
Filippo Castiglione, f [dot] castiglione [at] iac [dot] cnr [dot] it, is the main author.
 
Massimo Bernaschi, m.bernaschi [at] iac [dot] cnr [dot] it, did the optimization and
supervised the implementation of the parallel code.
 
Few of other people sent bug reports, and helpful feedback.  
 
C-ImmSim is the C porting of IMMSIM, the IMMUNE SYSTEM SIMULATOR
originally developed by P.E. Seiden and F. Celada.  (1991)
 
F. Castiglione developed the first version (1995) and afterwards with M. Bernaschi developed a parallel version. The parallel version is not freely available.
 
C-ImmSim has now evolved to take into account other features not included in the original work of P.E. Seiden and F. Celada.
 
In particular, since the first version, the model has been enriched to simulate HIV infection and cancer immunotherapy (more details can be found in the documents contained in the distribution package). Customized versions of C-ImmSim have been developed to simulate hypersensitivity reactions and Epstein-Barr virus infections. These versions are not freely available.
 
This distribution cotains the following files:
  1. total 240
  2. -rw-r--r--    1 filippo  filippo         0 Feb  2 14:44 NEWS
  3. -rw-r--r--    1 filippo  filippo      7831 Feb  2 14:44 INSTALL
  4. -rw-r--r--    1 filippo  filippo     17992 Feb  2 14:44 COPYING
  5. -rw-r--r--    1 filippo  filippo      2335 Feb  3 18:20 configure.in
  6. -rw-r--r--    1 filippo  filippo      1117 Feb  4 09:22 AUTHORS
  7. -rw-r--r--    1 filippo  filippo      6076 Feb  4 10:01 ChangeLog
  8. -rw-r--r--    1 filippo  filippo      3728 Feb  4 10:15 README
  9. -rw-r--r--    1 filippo  filippo        60 Feb  4 10:26 Makefile.am
  10. -rw-r--r--    1 filippo  filippo         0 Feb  4 10:26 stamp-h.in
  11. -rwxr-xr-x    1 filippo  filippo       722 Feb  4 10:26 mkinstalldirs
  12. -rwxr-xr-x    1 filippo  filippo      6472 Feb  4 10:26 missing
  13. -rwxr-xr-x    1 filippo  filippo      5598 Feb  4 10:26 install-sh
  14. -rwxr-xr-x    1 filippo  filippo     60453 Feb  4 10:26 configure
  15. -rwxr-xr-x    1 filippo  filippo     27594 Feb  4 10:26 config.sub
  16. -rw-r--r--    1 filippo  filippo       519 Feb  4 10:26 config.h.in
  17. -rwxr-xr-x    1 filippo  filippo     39311 Feb  4 10:26 config.guess
  18. -rw-r--r--    1 filippo  filippo      4578 Feb  4 10:26 aclocal.m4
  19. drwxr-xr-x    2 filippo  filippo      4096 Feb  4 10:26 src
  20. -rw-r--r--    1 filippo  filippo     10966 Feb  4 10:26 Makefile.in
  21. drwxr-xr-x    2 filippo  filippo      4096 Feb  4 10:26 doc
  22. drwxr-xr-x    2 filippo  filippo      4096 Feb  4 10:26 data
 
 
* The INSTALL file contains a generic description on how to install the code.
 
* The file ChangeLog reports the history of the code updates.
 
* The directory ./src contains the source code and the Makefile.am to generate the Makefile.
 
The directory ./src contains the following
  1. total 45328
  2. 60 -rw-r--r--    1 filippo  filippo     56977 May 14 13:14 behave.c
  3. 28 -rw-r--r--    1 filippo  filippo     27987 May 13 18:05 define.h
  4. 8  -rw-r--r--    1 filippo  filippo      4820 Apr 14 09:07 extern.h
  5. 16 -rw-r--r--    1 filippo  filippo     14645 May 11 11:13 extract.c
  6. 12 -rw-r--r--    1 filippo  filippo     11501 May 11 11:13 global.c
  7. 72 -rw-r--r--    1 filippo  filippo     67276 May 14 09:29 inout.c
  8. 28 -rw-r--r--    1 filippo  filippo     25076 May 14 10:38 interact.c
  9. 8  -rw-r--r--    1 filippo  filippo      6217 May 11 11:13 main.c
  10. 32 -rw-r--r--    1 filippo  filippo     32532 May 13 10:07 Makefile
  11. 4  -rw-r--r--    1 filippo  filippo      1144 Apr  8 17:26 Makefile.am
  12. 40 -rw-r--r--    1 filippo  filippo     39544 Apr 20 10:49 Makefile.in
  13. 12 -rw-r--r--    1 filippo  filippo      9293 May 11 11:13 move.c
  14. 4  -rw-r--r--    1 filippo  filippo      3416 May 11 11:13 ran.c
  15. 20 -rw-r--r--    1 filippo  filippo     18656 May 11 11:13 service.c
  16. 56 -rw-r--r--    1 filippo  filippo     51083 May 14 13:17 various.c
 
* The directory ./data contains input parameter files to be used as templates.
 
* The directory ./docs contains some documents including the License Agreement and an a PDF on * the model and how to run the code.
 
* The files *.in are needed to configure and create the configure script and the Makefile of the * whole stuff. You should not change it. For any configuration option you should change
* src/Makefile instead.
 
 
To install, simply type
  1. ./configure
  2. make
  3. make test
 
To compile under MS Windows use the Makefile.win (i.e., make -f Makefile.win). We have tested this and works. However, further support will not be provided to compile C-ImmSim on Windows platforms.
 
For any question write to f.castiglione [at] iac [at] cnr [at] it
Comments are welcome.
C-ImmSim
This page is written and maintained by Filippo Castiglione (Istituto Applicazioni del Calcolo - CNR, Rome, Italy)
C-ImmSim (version 6 release 3)