readme.txt

GESPI 2.0动态系统模拟工具

**************************************************************
* THIS TEXT FILE CONTAINS INFORMATION ABOUT COMPILING GEPASI *
**************************************************************

this is the source code for GEPASI 2.0, release 2.02c

Index

1. COPYLEFT
2. MAKEFILES
3. LIBRARIES
4. COMMENTS
5. ANSI COMPLIANCE
6. HELP TEXT
7. PORTABILITY OF THE SIMULATION ENGINE


1. COPYLEFT

    GEPASI - a simulator of metabolic pathways and other dynamical systems
    Copyright (C) 1989, 1992, 1993  Pedro Mendes
                              University of Wales, Aberystwyth
                              Dyfed, SY23 3DA, United Kingdom
                              email: [e-mail]

    This program is free software; you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation; either version 1, or (at your option)
    any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    (file COPYING) along with this program; if not, write to the Free
    Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.

  All C source code modules contain comments with the copyright notice, and
all *.c files include COPYLEFT.H which has the above copyright notice. In no
circumstances should this be deleted from the source code files. Any new *.c
files added to the project should also comply with this.


2. MAKEFILES

   The following makefiles are available:

     gepasi.mak        Quick C/Win 1.0,  simulation engine, MS-DOS
     gwsim.mak         Quick C/Win 1.0,  Simulation, MS-Windows
     gwtop.mak         Quick C/Win 1.0,  Topology, MS-Windows
     gepasi.hpj        MS Help Compiler, Help, MS-Windows

       these makefiles require that the source code files are in a directory
       with the following path:  c:\source\gepasi . If you want to change this
       you are responsible for the alterations in these make (project) files.

     Makefile.unx   cc, simulation engine, unix

       this makefile compiles the simualtion engine with the standard (?) C 
       compiler, cc. It has only been tested in a DEC 5830 running Ultrix 4.2. 
       Before using it, it should be renamed to 'Makefile'


3. LIBRARIES

  To compile GWSIM (Simulation) and GWTOP (Topology) the MS-Windows 3.0 or 3.1 
libraries must be in the INCLUDE path and you must also have a resource
compiler. The simulation engine does not require any libraries other than the
standard C libraries, including support for double precision floating-point
calculations. 


4. COMMENTS

  The source code contains comments explaining what is being done. New bits 
of code should be well explained inside comments and it would be useful to 
add the date when such changes were made, by whom and an address (email 
should be enough). 

  Each module has at the top a large block of comment lines providing a title 
for the code block and also a list of compilers that have successfully handled 
it. If you managed to compile this code with a different compiler, please add 
it to the list. This should greatly facilitate other users efforts in 
compiling GEPASI. 


5. ANSI COMPLIANCE

   As much as possible, the code is compliant with the ANSI standard. However, 
the code has not been thourogly tested and there are certainly some parts that 
need to be changed to the standard.

   The LSODA package, which was primarily converted from the original FORTRAN 
version with the AT&T f2c program, is notably a non-compliant part. For 
example, there are no function prototypes and the old K&R style of function 
declarations is still used. This is going to be corrected in future versions.


6. HELP TEXT

   The text of the help file can be found in GEPASI.RTF, in Rich Text Format.
This text can be used to build other help files, like man pages, etc. 

7. PORTABILITY OF THE SIMULATION ENGINE

   The floating-point exception handler is not foolproof. It works for the 
environments tested (compiler and OS) but there are no garantees for other 
environments. 

Clearing the screen is a highly non-portable action and therefore the cls()
function (in pmu.c) only clears the screen if compiled under MS-DOS. New 
cls() functions to work with other operating systems are welcome, although
this is by no means a critical need. Functions to read the cursor position 
and to set it (get_cursor() and set_cursor()) are also on the same list. 
Please do not suggest to use the CURSES package, I am trying to keep 
GEPASI's simulation engine independent of libraries as much as possible.


Pedro Mendes
Dept Biological Sciences
University of Wales
Aberystwyth,
Dyfed SY23 3AX
United Kingdom
[e-mail]