View source for Systems biology - manual model construction

==Building from scratch==
<font size="3">
<h5>Creation of a new diagram</h5>
The model development process is initiated by creation of the model network or {{Type link|diagram}}. A new diagram can be made in the <b>Work Space</b> by two methods: 
<ol>
<li>via <b>Control Panel → New Diagram</b> (<b>Note</b>: please select the correct folder for a new diagram in your project area):

<br><br>[[File:Model_fromscratch_Fig1.png]]<br><br>

<li>via the <b>Tree Area</b> by a single click with the right mouse button on the corresponding folder of the project:

<br><br>[[File:Model_fromscratch_Fig2.png]]<br><br>
</ol>

The platform will ask you to select the {{Type link|diagram}} type and specify the {{Type link|diagram}} name you want to create in the work space. In the following, the creation of a new <b><i>“SBML model in SBGN notation”</i></b> will be described.

<br><br>[[File:Model_fromscratch_Fig3.png]]<br><br>

Upon selecting the type of a diagram and clicking <i>Ok</i> button a new node <b><i>New Diagram</i></b> will appear in the <b>Tree Area</b> and the corresponding tab is opened in the <b>Work Space</b> to start the diagram creation.

<br><br>[[File:Model_fromscratch_Fig3_1_18_03.png]]<br><br>

A pathway diagram opened in the work space has a tool bar as shown below: 
<br><br>[[File:Model_fromscratch_Fig4.png]]<br><br>


<h5>Adding a new element to the diagram</h5>

</font size="3">



==Building from BioModels Repository==
<font size="3">
To analyze developed and published model or use this one as a basis for modification/extension, you can employ [https://www.ebi.ac.uk/biomodels/ BioModels] repository the folder of that is represented under <b><i>Databases</i></b> tab in the <b>Tree Area</b> (marked red below). Select the Biomodels repository by a single click with the left mouse button, then double-click will open the subdirectory (Diagrams→Curated).


[[File:Building_BioModels_Fig1.png|1000px]]

<span style="font-size: 90%"> '''Figure 1.''' BioModelsDB repository in corresponding tab of the <b>Tree Area</b>.</span>


To open model of interests, double-click of the left mouse button the model icon in the  <b>Tree Area</b> or a single-click of the right mouse button on the icon and press  <b><i>Open</i></b> in a pop-up window (marked red below).


[[File:Building_BioModels_Fig2.png|1000px]]

<span style="font-size: 90%"> '''Figure 2.''' Opening previously developed model from BioModelsDB in BioUML.</span>


The model diagram (for instance, [https://ict.biouml.org/bioumlweb/#de=databases/Biomodels/Diagrams/Curated/BIOMD0000000211 BIOMD0000000211, Albert2005_Glycolysis]) will be opened in the <b>Work Space</b>, while the model equations and values of the model parameters/variables will be appeared in the <b><i>Model</i></b> tab (marked red below) of the <b>Operations Field</b> (see [http://wiki.biouml.org/index.php/Systems_biology_-_Get_started Get started]).


[[File:Building_BioModels_Fig3.png|1000px]]

<span style="font-size: 90%"> '''Figure 3.''' The <b><i>Model</i></b> tab contains subtabs with details about model entities, variables, equations etc.</span>


To view, edit or modify (including an extension) the model reaction or substance, see the section [http://wiki.biouml.org/index.php/Systems_biology_-_basic_model_editing Basic model editing] of the tutorial, while to simulate the model, look over the section dedicated to [http://wiki.biouml.org/index.php/Systems_biology_-_model_simulation Model simulation].