Views

Assembly View

Assembly View offers an easy-using graphical interface for working with MoDeL, which is a rule-based modeling software for Synthetic Biology. If you haven’t read anything about MoDeL, it is recommended that you read the introduction to it first.
Assembly View is composed of 4 parts: the Main Toolbar, the Biological Components Browser, the Workspace and the Property Panel that is shared throughout Lachesis.

Biological Components Browser

The biological components are the basic units that are used to construct models. On the left are the compartment and plasmid units and on the right is the part searching widget.
MoDeL doesn’t use predefined sites for the sake of flexibility, but in order to provide an easy-using user interface, we allow user to store “default site” for every part. We defined “default site” property for every built-in examples so that new users can play with them before they have enough experience to design models on their own.

Workspace

The workspace itself represents the “root” compartment (usually named “flask”). Since MoDeL only allow compartment nesting of depth two, actually the compartments inserted into the workspace can’t be nested.
You can insert components into the workspace by the method introduced in the Inserting Components section.

Property Panel

The property panel is used throughout Lachesis. It offers a tree view of the current model component (or the entire model) so the properties of it can be viewed conveniently.

Main Toolbar

The main toolbar contains button for editing global model features, e.g. parameters and events, and the rightmost button is used to solve the model (by calling MoDeL) to produce a .sbml file. Just try clicking every of them, they are quite self-explaining.

Inserting Component

To insert compartment, just drag it to the workspace and drop it and it will become a child compartment of the root compartment (represented by the workspace itself).
To insert plasmid, drag and drop it to its desired parent compartment.
Inserting parts is a little more complicated: find the part in the searching widget, then drag and drop it to the workspace. If you drop a part on a plasmid, it would be treated as a sequence of DNA on that plasmid. However, if you drop it on an compartment (or the workspace), it would be treated as a species (protein or molecule) in that compartment.

Editing Component

To edit a component, just double-click it and edit its properties in the pop-up window. Since MoDeL doesn’t allow numbers directly present in the main body part of model definition, all numerical properties (Initial Concentration here) should be set to an redefined parameter. For example, if you want to set Initial Concentration here to 0.3, just create a parameter, e.g. init_concen, set its value to 0.3 and select init_concen here.

NOTE: The ids of everything in a model are in the same namespace and no one can be the same as another, i.e. you can’t give a parameter an id that is the same with a compartment.

Solving the Model

To solve the model, just click the button on the main toolbar. If you are using it for the first time, Lachesis will ask you to locate the main Perl script file of MoDeL (MoDeL.pl). The guide to installation of MoDeL can be found here.
Lachesis will then call MoDeL and you just need to wait until it’s done. The resulting .sbml file will be shown in a new Lachesis main window.

Behavior view

The line editors above are used to determine several global parameters.After it’s done,the time course table below is formed.Then fill it to specify the exact behavior using values.Each of them means the concentration of a certain substance at a certain time.You can also specify each node of substance by changing its name and color (the color will represent the node in the next view).Then switch the tab and you’ll see something like this.

Also you can generate values of the concentrations by drawing rough curves like this

Remember each time you finished a curve,press the button “generate value” and that means the curve take effect.

Switch the tab back and you’ll get something like this

That’s the simple functions of behavior view.

Network view

After you open a SBML file,you can use network view to visualize the network defined by it.

Example below:

The green container represents compartment,the red node represents substance and the blue is reaction.

Use Ctrl + mouse wheel to zoom.

You can double click an item and modify its properties.Also the property widget on the right side is helpful to monitor item properties.

You can also add an item by dragging the buttons above to the scence or remove an item by pressing delete key.

The last 2 buttons are used to edit the lines,the straight arrow means the substance is a reactant or product of the reaction and the other means the substace is a modifier of the reaction.

To add a line ,first click the button,then click on the source node,then click on the destination node.Remember the two nodes are of different type.As for modification,the source must be a substance and the destination must be a reaction.

Each change you make will cause a corresponding modification to the model.

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