1. Melbourne Uni 2008

2. What is iGEM? International Genetically Engineered Machine competition Started in 2003 within MIT

3. What is iGEM? Now a global competition 54 teams, 750 students, 19 countries

4. What is iGEM Teams of students use principles of synthetic biology to create biological systems

5. What is Synthetic Biology? Builds on genetic engineering technologies Adds a set of guiding principles to aid coordination of activities Standardisation Abstraction

6. Lego BrickBioBrick Standardisation

7. Abstraction

8. 2008 Team Project BioClock

9. A customisable regulatory system One signal switches between multiple states Signa l 1 2 3

10. InputOutputLogic BioClock System State 2 State 3 State 1 t=1 t=2 t=3 123

11. How will it work? Two methods currently being looked at Ideal implementation through a binary counting system Contingency plan using a linear system Both will have the similar components, with different interactions

12. Linear Model Signa l

13. State 1 Mechanism State 2 Mechanism State 3 Mechanism State 1 Mechanism Signa l State 2 Mechanism Signa l Linear Model

14. Signa l State 1 Mechanism State 2 Mechanism State 3 Mechanism State 1 Mechanism Signa l State 2 Mechanism State 1 Mechanism Signa l

15. Linear Model Signa l State 1 Mechanism State 2 Mechanism State 3 Mechanism State 2 Mechanism State 3 Mechanism Signa l State 2 Mechanism

16. Design Small teams researching different parts of system Signaling Riboswitch Positive feedback Modeling

17. Signaling System Signal Sensor

18. Riboswitch RiboLockRiboKey

19. Positive Feedback Feedback loop that upregulates itself

20. Signa l State 1 Mechanism State 2 Mechanism State 3 Mechanism State 1 Mechanism Signa l State 2 Mechanism Signa l Where they fit in Signal SensorRiboswitch Positive Feedback

21. Binary Model

26. Genetic map from circuit

27. Binary Model

28. Time Division Tasking

30. Modeling with two colours

31. Current output of two colour model

32. Goal We want to count as high as possible in binary Example with two colour system:

33. Sensitivity Analysis Code program that will produce sensitivity plot Plot sensitivities against each kinetic parameter to to select best proteins

34. Timeline MarchAprilMayJune JulyAugust Septembe r October Sensitivity testing of model Kinetic testing of components Assemble Systems Test systems Prepare for Jamboree Post results Novembe r 8-9 2008

35. Budget Lab Expenses$10,000 Sequencing3,000 Synthesising3,000 SELEX3,000 Consumables1,000 Jamboree Expenses$22,000 iGEM Registration$1,000 Jamboree Fee$1,000 Accommodation$2,000 Flights$18,000 Total$32,000

36. Questions 2008