User guide

Warning: this section is still under construction.

Quick start

SBML plugin is part of standard distributive of BioUML workbench and allows customer to use models in SBML format.

To start work you can create new SBML module or import existing module with SBML models.

SBML Model Repository module contains models that are published at http://www.sbw-sbml.org/ModelsWebPages/ModelRepository.htm. The module can be downloaded from the site and imported into BioUML workbench as usual. 

SBML diagram type is very similar with BioUML standard pathway simulation diagram type and uses the same graphic notation.

Similar with standard pathway simulation diagram type you can use MATLAB plug-in for model simulations. The plugin will generate MATLAB files and starts MATLAB engine for model simulation and results visualization (see plugin user guide for more details).

SBML module type

Special module type is used to store SBML models. Unlike other BioUML modules SBML module type has not 'Data' section. These is due to that all information about species and reactions is defined inside SBML model files.

To create new SBML module select File > New module from main menu, standard 'New Module' dialog will be shown. Specify your module name, select 'SBML module' as module type and click Ok button.

Creating new SBML module.

You can import or export SBML module as usual by selecting select File > Import module or File > Export module correspondingly. See module concept and module functions for further details.
 

SBML diagram type

Special diagram type is used to show SBML models as diagrams. This diagram type is very similar with BioUML standard pathway simulation diagram.

SBML model do not provides information about diagram layout so when you are opening imported SBML model some very simple layout algorithm is used for initial species and reactions layout. Below is example of SBML diagram with simple initial layout.

... example of diagram ...

SBML diagram uses two node types that can be used on the diagram:

• specie - the term species refers to entities that take part in reactions. Further you can specify specie type: chemical substance, gene, RNA or protein. We use the same graphic notation to show specie type as in BioUML standard pathway diagram.
• reaction - chemical reaction.

Only one edge type is used to connect specie and reactions to which it is involved. Again we use the same graphic notation as BioUML standard pathway diagram. Green edges correspond to reactant or reaction product. While other edges correspond to reaction modifiers while edge color specifies the modifier role:

• pink - catalyst
• blue - inhibitor
• red - switch on the reaction
• black - switch off the reaction

How to import some SBML model
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How to export  diagram in SBML format
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How to create new diagram
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How to save diagram
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Diagram editing

You can edit SBML diagram as usual pathway simulation diagram.

While editing of usual pathway simulation diagram is not described yet here will be some explanation.

How to create new compartment
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How to create new specie
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How to create new reaction
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How to edit reaction rate
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Model simulation with MATLAB

SBML diagram type can be used for model simulation using MATLAB plug-in. The plugin will generate MATLAB files and starts MATLAB engine for model simulation and results visualization (see plugin user guide for more details).

While MATLAB plugin is not described yet here will be some explanation.

How to start the simulation
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How to change variable initial value
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How to change parameter value
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How I can see the generated files
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Error processing
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