View source for Systems biology - model import

[[File:systems_biology_import.png|thumb|'''Figure 1'''. Steps to import a model.]]

To import SBML model, do the following (Figure 1):
<ol>
<li>Find the folder in the BioUML repository where you want to download the model (for example, use the temporary folder in the tree: <i>data/Collaboration/Demo/Data/Temp</i>). Then, right-click on this folder and select <b>"Import"</b>.
<li>In the window that opens, click on the <b>"Computer"</b> button and find the document with the model in the file system of your computer.
<li>Select this document and click on the <b>"Start"</b> button. After that, the model will appear in the BioUML repository and will be opened in a new workspace tab.
</ol>

<h2>Adjusting model layout</h2>

[[File:systems_biology_layout.png|thumb|'''Figure 2'''. Steps to perform the model layout.]]

To change the default layout of the model, use <b>Layout</b> tab in the right bottom panel (Figure 2).

Currently, BioUML contains the folloing layout schemes:
*[[Hierarchical layout]] (default)
*[[Orthogonal layout]]
*[[Force directed layout]]
*[[Cross cost grid layout]]
*[[Grid layout]]

Select the desired scheme and click on the <b>Prepare layout</b> button [[File:Execute_icon.png]]. The newly generated layout will be shown on the right in the same tab. Then, click on the <b>Apply layout</b> button [[File:Add2docpane_icon.png]] to apply this layout to the model diagram in the document pane.

<h2>Basic model editing</h2>

To edit any entity or reaction of the model, click on the corresponding element in the diagram and then click the <b>Edit</b> button [[File:Edit_icon.png]] (Figures 3-4).

<gallery>
File:systems_biology_egiting_entities.png|'''Figure 3'''. Egiting entities.
File:systems_biology_egiting_reactions.png|'''Figure 4'''. Egiting reactions.
File:systems_biology_egiting_parameters.png|'''Figure 5'''. Egiting parameters.
</gallery>