C-ImmSim (version 6 release 3)

C-ImmSim (version 6 release 3)

A document describing the major features of the model can be downloaded here: cimmsim-description-examples.pdf.

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 (1995,2009)
________________________________________________________________________________________________

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:
total 240
-rw-r--r-- 1 filippo filippo 0 Feb 2 14:44 NEWS
-rw-r--r-- 1 filippo filippo 7831 Feb 2 14:44 INSTALL
-rw-r--r-- 1 filippo filippo 17992 Feb 2 14:44 COPYING
-rw-r--r-- 1 filippo filippo 2335 Feb 3 18:20 configure.in
-rw-r--r-- 1 filippo filippo 1117 Feb 4 09:22 AUTHORS
-rw-r--r-- 1 filippo filippo 6076 Feb 4 10:01 ChangeLog
-rw-r--r-- 1 filippo filippo 3728 Feb 4 10:15 README
-rw-r--r-- 1 filippo filippo 60 Feb 4 10:26 Makefile.am
-rw-r--r-- 1 filippo filippo 0 Feb 4 10:26 stamp-h.in
-rwxr-xr-x 1 filippo filippo 722 Feb 4 10:26 mkinstalldirs
-rwxr-xr-x 1 filippo filippo 6472 Feb 4 10:26 missing
-rwxr-xr-x 1 filippo filippo 5598 Feb 4 10:26 install-sh
-rwxr-xr-x 1 filippo filippo 60453 Feb 4 10:26 configure
-rwxr-xr-x 1 filippo filippo 27594 Feb 4 10:26 config.sub
-rw-r--r-- 1 filippo filippo 519 Feb 4 10:26 config.h.in
-rwxr-xr-x 1 filippo filippo 39311 Feb 4 10:26 config.guess
-rw-r--r-- 1 filippo filippo 4578 Feb 4 10:26 aclocal.m4
drwxr-xr-x 2 filippo filippo 4096 Feb 4 10:26 src
-rw-r--r-- 1 filippo filippo 10966 Feb 4 10:26 Makefile.in
drwxr-xr-x 2 filippo filippo 4096 Feb 4 10:26 doc
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
total 45328
60 -rw-r--r-- 1 filippo filippo 56977 May 14 13:14 behave.c
28 -rw-r--r-- 1 filippo filippo 27987 May 13 18:05 define.h
8 -rw-r--r-- 1 filippo filippo 4820 Apr 14 09:07 extern.h
16 -rw-r--r-- 1 filippo filippo 14645 May 11 11:13 extract.c
12 -rw-r--r-- 1 filippo filippo 11501 May 11 11:13 global.c
72 -rw-r--r-- 1 filippo filippo 67276 May 14 09:29 inout.c
28 -rw-r--r-- 1 filippo filippo 25076 May 14 10:38 interact.c
8 -rw-r--r-- 1 filippo filippo 6217 May 11 11:13 main.c
32 -rw-r--r-- 1 filippo filippo 32532 May 13 10:07 Makefile
4 -rw-r--r-- 1 filippo filippo 1144 Apr 8 17:26 Makefile.am
40 -rw-r--r-- 1 filippo filippo 39544 Apr 20 10:49 Makefile.in
12 -rw-r--r-- 1 filippo filippo 9293 May 11 11:13 move.c
4 -rw-r--r-- 1 filippo filippo 3416 May 11 11:13 ran.c
20 -rw-r--r-- 1 filippo filippo 18656 May 11 11:13 service.c
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
./configure
make
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.

This page is written and maintained by Filippo Castiglione (Istituto Applicazioni del Calcolo - CNR, Rome, Italy)