"
Team:USTC-Software/aview
From 2011.igem.org
USTC-Software
Contents:
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.
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.
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.
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.
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.
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.
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.
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.
