Gepasi 3, Answers to Frequently Asked Questions

INDEX
1.General 
2.Installation / unistallation 
3.User interface 
4.Simulation engine 


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General

1.1 What is Gepasi?

A.  Gepasi is a Microsoft Windows program intended for the simulation of the
    kinetics of systems of chemical and biochemical reactions. The program is
    aimed at the study and teaching of the behaviour of such systems. Gepasi is
    able to simulate the steady-state and time-course behaviour of reactions in
    several compartments of different volumes. The user supplies the program
    with information about the stoichiometric structure of the pathway, 
    kinetics of each reaction, volumes of the compartments and initial 
    concentration of all chemical species. The program then builds the 
    differential equations that govern the behaviour of the system and solves 
    them. Results are produced in a flexible way so that data can be imported
    into spreadsheets or other data processing programs. The data can also be
    plotted in 2D and 3D graphs directly from the program (by using the package
    gnuplot that is distributed with Gepasi). Gepasi has the ability of 
    scanning ranges of values of the system parameters and produce a mapping of
    the behaviour of the system within these ranges. Gepasi characterises the
    steady states that it finds using Metabolic Control Analysis and linear 
    kinetic stability analysis. 


1.2 Why is Gepasi free, when even academic books are sold? 

A.  The comparison is not bad, Gepasi 3 has ove 30000 lines of C and  C++ 
    code and the help file contains over 24000 words, totalling one man year's
    work. An academic book could be sold for more than $100, and equivalent 
    commercial software could trade for much more. However the idea behind 
    Gepasi is that the average biochemist should find it easy to model and 
    simulate. Gepasi is being distributed as free software to help boost the 
    usage of computer simulation in biochemistry. This product is, 
    nevertheless, fully protected by international copyright treaties. Further 
    versions of Gepasi or add-on modules may be distributed as shareware or in
    some other commercial format. 


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Installation / uninstallation

2.1 I cannot install Gepasi. When I try to run the program setup.exe an
    error message is displayed that says an illegal instruction was executed
    and the program closes. What is wrong?

A.  You have the wrong hardware version of the program. You probably have an
    Intel computer and are trying to run the DEC Alpha version (or vice versa).
    Make sure you get the right version for your hardware. If you downloaded
    Gepasi through the Internet or in a CD-ROM the file gep3xxa.zip is for the
    Alpha and the file gep3xxi.zip is for the Intel. If you obtained Gepasi in
    a floppy disk, the label clearly indicates which version it is. 


2.2 I uninstalled Gepasi but at the end a message was printed saying that
    not all components had been removed. What are these components and what can
    I do to remove them?

A.  The uninstall program only removes the files that it installed in the first
    place. This message appears when the directory (folder) where Gepasi was
    located contains other files (or folders). These other files are not 
    removed by the uninstall program and therefore the folder where Gepasi was
    installed could not be deleted. You can use file manager or the windows
    explorer to remove the remaining files and the folder if you are sure you
    do not need them. 


2.3 Can I install Gepasi 3 in Windows 3.1x with Win32s?

A.  No. The reason is that Gepasi is multi-threaded and Win32s does not support
    more than one thread. (By the way the "s" in Win32s stands for "subset".)

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User interface

3.1 I have defined the reactions of a model but later on I found I had mistyped
    one of the reactants. I corrected it but now I have one extra metabolite
    which I do not want. How can I delete it?

A.  To get rid of any metabolites that do not participate in any part of the
    model call the reactions dialog box and press OK. Gepasi then deletes
    metabolites that do not have any involvement in the model (those that are
    not substrates, products or modifiers of any reaction). If the metabolite 
    you mentioned persists in the model after calling the reactions dialog then 
    it is because it participates in reactions (possibly as a modifier). 


3.2 Open a gepasi file, change something (say delete some outputs on the task
    menu), then change your mind and re-open the same file. First, one is not
    asked whether to save the changed file, and second, nothing actually
    changes: the new file is not loaded at all.

A.  This is a well known problem with the Microsoft foundation classes (MFC)
    that Gepasi uses. Basically the MFC framework does not load a file fresh
    from disk if it is the one being edited at that time. To get around this do
    the following: 

            1.do File/New, at this point you are asked if you want to save the 
              changes, reply "no" 
            2.do File/Open and load the file again, you will have the older
              (unmodified) version of the file 


3.3 I read in the help file about a "plot page" but I cannot see such a page in
    Gepasi. How do I access this page? 

A.  You don't see this page because you did not include the "gnuplot" option 
    when installing the program. You have two options: a) uninstall and 
    reinstall (be sure to include gnuplot this time) or b) get a copy of 
    gnuplot, install it on your computer; in Gepasi go to the Options menu,
    Add-on modules and type the full path of wgnuplot.exe in the appropriate
    box. Both these methods will activate the plot page. 


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Simulation engine

4.1 Some models take an excessive long time to execute while others that are of
    similar complexity, run much faster. What is wrong? 

A.  Go to the time course page and make sure that the speed control is set to
    "Faster". On some computers even a slight displacement from the maximum
    might slow the simulations by a significant amount. 


4.2 I want all the data to be output on one single file but the program 
    crashes. What should I do? 

A.  You cannot have time course and steady-state output to a single file. It is
    impossible. If you have set both filenames to be equal the simulation 
    engine crashes. To fix this change the name of one of the files. From 
    version 3.01 onwards Gepasi does not allow the user to specify the same 
    file for both tasks. 

4.3 Is there a way of processing a series of simulations without having to 
    manually load and start each one?
    
    Yes. From version 3.02 onwards there is a command line version of Gepasi
    (the file bgepasi.exe) that can do this. This program is only for
    processing simulations and so you must have to build and save the  *.gps
    files with the normal version of Gepasi. As an example, to run the hmm.gps,
    chemos1.gps and seqfb.gps files in one go, you would type the following
    command in a console (DOS box):
    
       bgepasi hmm.gps chemos1.gps seqfb.gps
    
    In Windows NT it is easy to schedule batches of simulations to run during
    the night by using the AT command:
    
       at 23:50 "bgepasi hmm.gps chemos1.gps seqfb.gps"
       
    (You must have administrative previleges to use the WinNT AT command)
