Frequently Asked Questions
home page

Index

1. General
   1. What is Gepasi?
   2. Why is Gepasi free, when even academic books are sold?
   3. Since Gepasi is no longer updated, what software should I use instead?
2. Installation / unistallation
   1. I cannot install Gepasi...
   2. When I uninstalled Gepasi I was told that not all components had been removed...
   3. Can I install Gepasi 3 in Windows 3.1x with Win32s?
3. User interface
   1. I have one metabolite that is no longer used in my model. How can I delete it?
   2. Reloading the current file does not work!
   3. I read in the help file about a "plot page" but I cannot see it. How do I access this page?
4. Simulation engine
   1. Some models take an excessive long time to execute. What is wrong?
   2. I want all the data to be output on one single file but the program crashes. What should I do?
   3. Is there a way of processing a series of simulations without having to manually load and start each one?

General

1.1 What is Gepasi?

• 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?

• The comparison is not bad, Gepasi 3.0 has just over 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 ideal 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.

1.3 Since Gepasi is no longer updated, what software should I use instead?

• Gepasi has not been updated since 2002. It has no modern features and only runs on Microsoft Windows. If it works for you then continue using it, but you are highly encouraged to switch to the sofware that superseded it: COPASI. COPASI runs on all common operating systems (Windows, Apple OS X, and Linux) and it provides a wider range of modelling and simulation methods than Gepasi. For example, COPASI is capable of running models in the stochastic kinetics approach (a.k.a. "Gillespie algorithm"), and to allow discrete events. COPASI is able to read your Gepasi models, simply open the .gps file with COPASI and your model will be imported. COPASI has a much better support of SBML than Gepasi, being able to read/write SBML levels 1, 2 and 3 (unlike Gepasi which can only read/write level 1.1). Overall you will be much better served with COPASI! Note that Gepasi's developed will not fix any bugs that may be discovered in Gepasi; this software is now unmaintained.

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?

• 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 gep30xa.zip is for the Alpha and the file gep30xi.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?

• 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?

• 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.")

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?

• 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, that is 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.

• 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 hile about a "plot page" but I cannot see such a page in Gepasi. How do I access this page?

• 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.

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?

• 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?

• 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. Version 3.01 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)

Last modified: 26 September, 2016	Copyright © 1996-2016 Pedro Mendes