Team:Calgary/Second Life/SBI2

Overview
Updates

Tutorial On Using SL
What We've Learned

Synthetic Biology Interactive

• Overview
• Synthetic Kingdom
• Biobrick Simulator
• Virtual Lab

Notebook & Parts

The Biobrick Simulator is a tool for representing biological molecules and their interactions. Visitors will encounter Biobrick parts (including promoters, translational units, terminators, and operator sites), devices built from these basic parts, RNA polymerase molecules, activator and repressor proteins, and more.




Each of the above biomolecules is represented by an object in Second Life, and interactions between these molecules are programmed into the objects and simulated in world.



The Biobrick Simulator itself lives in a Second Life object commonly called a Heads Up Display (HUD). Your avatar can acquire this virtual object while in Synthetic Biology Interactive, and then use it to display the simulator HUD on your screen:



Each icon is a clickable button to navigate the HUD's screens. Above is the main menu, and below is a selection of levels in game:





The bulk of the Biobrick Simulator's content is contained in a series of 'levels'. Levels do not come with specific goals or objectives, instead each tries to present a new concept in molecular biology or synthetic biology using a simulation of the relevant molecules.

Among the concepts presented:

• Biobricks: The definition of a Biobrick part, and how a device is composed of parts
• Negative autoregulation, what a self regulating gene is, and why this type of control is useful
• Positive autoregulation and cellular memory, how a self activating gene is like a permanent on switch
• 'Logical gates'how we can integrate multiple signals in the cell using cellular components built to mimic electrical and gates, not gates, or gates
• Stable cellular switches to keep track of state, that can be set externally by administering inducers
• The repressilator, and the usefulness of biological oscillators

The simulator's final and most important feature is a tool for designing virtual Biobrick devices, the Biobricker.



Parts can be composed in any order from a small library built into the Biobricker, the resulting devices can then be built by the Biobricker in world. The top row of buttons gives access to menus of promoters, translational units, and other parts.



Parts are added one by one to the device under construction, displayed between the two rows. Each part behaves independently of the others, so it is possible to build devices that work and devices that do nothing productive.



The bottom row of buttons give control over the device under construction, for deleting individual parts, starting over, building the designed device and accessing the help file.

All of the devices from the levels can be built with the Biobricker, and countless other systems can be designed too. It is up to the user to experiment, and determine whether the devices they build do what they actually intend!

For any questions please contact Patrick King at pfking@ucalgary.ca