| Tool |
Outline, installation and resources |
| Athena |
Description: A tool very well suited to those who are new to modelling. Athena is divided into three parts that can be viewed simultaneously. There is a canvas at the top of the screen where SBGN based species may be added. Species can then be connected via reaction arcs to create a network. A list of icons on the left hand side of the GUI list the different species that are available. These include entities to represent genes, promoters, compartments, and nucleic acids. To the right hand side there is a module viewer pane where species names and concentrations may be modified along with the value and names of rate constants. Immediately below the drawing canvas is a simulation pane that is exceptionally straightforward to use. It consists of a start button to initiate the simulator and a reset button. Simulation start and end times can also be conveniently set. Athena did not allow the SBML for the Nijhout model to be imported and it was not apparent why. Instead a simple two species reversible reaction was created and a simulation was run (Figure 6a).
Installation: Full functionality of the tool requires installation of the Systems biology workbench http://sys-bio.org/. Once this is installed Athena may be downloaded and installed from (http://athena.codeplex.com/) and executed with a Windows executable file (SetupAthena.msi).
Resources: A detailed guide to Athena is available at http://arxiv.org/pdf/0902.2598.pdf |
| Cell Designer |
Description: Developed by the Institute for Systems Biology in Japan (http://www.celldesigner.org/index.html) It has an intuitive user interface and in particular has a GUI that is suitable for visualizing existing models and for designing models diagrammatically in a ‘drag and drop’ fashion. The GUI was straightforward to use. There was no difficulty in exporting SBML models from it. It was also very capable of importing SBML models directly from the Bio models website; therefore we imported the model by Nijhout et al. One slight drawback was that the diagram associated with this model looked crowded and a little confusing when viewed using this software (Figure 6b). Cell Designer comes equipped with a simulation and parameter analysis suite. Results could be plotted or written to a file for further analyses using alternative software.
Installation: A Windows executable file (CellDesigner-4.2-windows-installer.exe) was downloaded from (http://systems-biology.org/software/celldesigner/celldesigner-42.html). Desktop icon then was installed and doubled clicked to access the software.
Resources: The cell designer web site contains a list of models specifically built using this software: http://www.celldesigner.org/models.html. Also, a comprehensive online tutorial is available:
http://www.celldesigner.org/help/CDH_QT.html |
| Copasi |
Description: GUI based modelling tool. Capable of stochastic and deterministic modelling. Divided into two components: model building/simulation, model analysis/output. Copasi offers a number of analysis techniques including, sensitivity analysis for exploring changes to the values of species concentrations and for examining changes to rate constants and rate laws. It is also able to detect steady states of models and has an optimization facility where the model can be fitted to time course data. Copasi was found to be a very suitable tool for those that are new to modelling. All tasks were carried out on GUI which is well laid out and intuitive. As a result we used it to both construct our own folate model and for testing the predictive capabilities of the folate model by Nijhout et al.
Installation: straight forward download from the Copasi Web site (http://www.copasi.org/tikiindex.php?page=downloadnoncommercial). This was followed by double clicking on the downloaded Microsoft Windows executable file (Copasi-35-Win32.exe). An icon was then displayed on the desktop of the computer, which was double clicked each time access to the software was needed.
Resources: A comprehensive guide to the functionality of Copasi has been published by the developers and interested readers are referred to it [81]. Users should also access the supporting documentation and video clips on the Copasi web site (http://www.copasi.org/tiki-view_articles.php) |
JDesigner
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Well suited to a nutritionist who is looking for a straightforward introduction to computational modelling.
GUI based tool, which allows models to be constructed on a canvas with nodes used to represent the species and reaction arcs connecting them. Species are selected from a horizontal network bar. The interface is well laid out with all the icons visible and intuitive (e.g. metabolites, proteins, nucleic acids). After creating a simple model, a simulation was run using an additional piece of software known as Jarnac. Rate laws and parameters were entered via dialog boxes, which appeared after clicking on a reaction arc in the diagram. They also allowed rate expressions not included to be defined. One slight disadvantage that was found when using this tool was that diagrams became crowded and a little difficult to understand. Therefore care needs to be taken with species labelling etc. It was very straightforward to import the model by Nijhout et al. to JDesigner. However there did not appear to be a direct way to do this from Bio models. Rather the SBML opened directly with JDesigner. As a result the model was displayed on the canvas (Figure 6d).
Installation: A windows executable file (SBW-2.9.0-win32-installer.exe (66.6 MB)) was downloaded from (http://sbw.kgi.edu/software/jdesigner.htm) JDesigner is installed with other software including Jarnac. One slight issue, it was not apparent immediately that JDesigner had been installed successfully and we had to do a search for the software.
Resources: The JDesigner home page contains a link to a PDF that contains further instructions on how to use JDesigner (http://sbw.kgi.edu/sbwWiki/sysbio/jdesigner). |
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