ETH Zurich 2006

From 2006.igem.org

Revision as of 14:21, 6 October 2006

Coordination

TODOs

Modeling

• Parts Model the whole System with Sensing, Pop's duplexer and Half adder (Marco and Franz)
• Model whether a different strength of input is necessary for the AND and XOR Gates (Who?)
• Finish modeling the second AND Gate and find a biological way to implement it and write the DNA and order it (Marco and Robert)

Lab

Responsible: Robert for the preparatory experiments, Olga for the assembly and testing of the gates.

• Read the literature on the XOR and AND Gates, check carefully for strains needed and compatibility of the parts (Who?)
• Prepare a protocol for parts assembly (Olga)
• Assembly of the light sensing device from the parts we received from UCSF Voigt's lab (Arthur)
• Assembly of the chemical sensing device (Franz, Dimo, Robert, Marco, Marko, Olga)

Documentation

Responsible: Alexandra for the registry, Franz for the presentation, Arthur for the Wiki.

• enter lab experience report to registry
• restructure the Wiki, identify lacking information and find people who can provide it (Arthur)
• Make a picture of the whole model with te different parts in it (Alexandra)
• Make a drawing of the DNA to have an overview of which parts will be consecutively on the same DNA piece (Alexandra)
• Find promoters for the Pops duplexer (2 promoters in total) (Michael)

Schedule

Available as Google Calendar: iGEM 2006 ETH Zurich

Thu 20.7., 1700: kickoff meeting in CNB E 121

27.7.-3.8. 1st group phase

Define project in more detail within two groups
Thu 27.7., 1700: meeting of entire group to share ideas
Thu 3.8., 1700: decision on final project

15.8. 1700

Tutorial "Modelling of AND gate"

Until 20.8.

Finalize DNA design, order it

September,October

Implement design (registry bio-bricks, ordered DNA)

27.9.

Fix the flight dates and send the proposed flights to Jörg

23.10.

Latest point to start getting our presentation going and to finish the iGEM wiki documentation

30.10.

Project documentation on the Wiki has to be complete

4./5.11.

Jamboree in Boston

Participants

Marco, Alexandra, Arthur, Olga, Dimo, Marko, Robert,

Franz, Michael

• Michael Friedmann
• Dimo Brockhoff
• Franz Zürcher
• Olga Nikolayeva
• Alexandra Choutko
• Arthur Korn
• Robert Schütz
• Marco Terzer
• Marko Jovanovic

Progress report and documentation

Initial project ideas

The fruits of some brainstorming and research

proposed projects

We split up the whole team into two groups, each proposed a project after these two weeks.

• Meat monitor project (Michael, Dimo, Olga, Arthur, Marko)
• Half adder/pattern recognition project (Franz, Alexandra, Robert, Marco)

It was decided to further pursue the Half adder project idea.

filling in the details

Reserved parts in the registry

We have already reserved parts for the adder and the gates in the registry the description of which are still tentative:

• Half adder: BBa_J34000
• AND gate: BBa_J34100
• XOR gate: BBa_J34200

Chemical Sensing Device

Suggestions for Chemical Sensing Device:

• Lactate lacI represses, IPTG induces (BBa_R0011 or BBa_R0010 )
• Tetracycline, TetR inhibitor, Tet inducer by inhibiting TetR (or aTc, it's analog) (BBa_R0040)
• combination thereof (BBa_I13614 / BBa_13617 / BBa_I13623 / BBa_I13624 / BBa_I13627 / BBa_I13637 / BBa_I13653)
• simple sugar Arabinose (BBa_R0080)
• I see the main difficulty in the spatial separation as the cells are growing in the petri dishes. since the inducers are water-soluble we would have to fix the chemicals onto the petro dish.

modeling

• 1 Page Overview (pdf) (∼1.2M) all versions
• 1 Page Overview (illustrator) (∼1.3M)
• Modeling Overview (pdf) (∼0.5M) all versions
• Modeling Overview (ppt) (∼0.6M) all versions
• IPTG sensing (pdf) (∼0.1M) all versions
• IPTG sensing (ppt) (∼0.2M) all versions

Matlab scripts for ODE simulation

modular scripts

• contains a createXXX() script for each module. the created module contains
  • function handles for reaction rates: r
  • stoichiometric matrix: N
  • constants (inside of the function handles)
  • state (concentration) changes (the ode dy values) can be computed by: N · r
• modules can be connected using the createInOutConnector() script. the result is again a module, consisting of the connected basic modules.
• sim_1_1 and sim_1_2 can be used to simulate modules with 1 input/1 output and 1 input/2 outputs respectively.
• both basic modules and compound (connected) modules can be simulated
• simulations contains the first samples, simulating
  • XOR → simulation results / sensitivity analysis
  • AND-tRNA → simulation results / sensitivity analysis
  • IPTG Sensing →simulation results
  • PoPS Duplexer →simulation results
  • Compound module: IPTG Sensing → PoPS Duplexer →simulation results
• scripts: matlab_modules.zip (<0.1M)

old scripts

unzip the file, each zip file contains 2 files: sim_xxx.m and ode_xxx.m.

ode_xxx.m : contains the differential equations, i.e. the model

sim_xxx.m : sets the parameters, calls the simulator and plots the result (this is the one to run, but the other is also needed).

• matlab_sim_and1.zip (<0.1M) →simulation results → abandoned
• matlab_sim_and2.zip (<0.1M) →simulation results → the pursued version A
• matlab_sim_and3.zip (<0.1M) →simulation results → the pursued version B
• matlab_sim_and4.zip (<0.1M) →simulation results → abandoned

As a result of the meeting on August 17, we will from now on concentrate on the AND versions 2 and 3.

• matlab_sim_xor1.zip (<0.1M) →simulation results → the only pursued version
• matlab_sim_xor2.zip (<0.1M) →simulation results → abandoned
• matlab_sim_xor3.zip (<0.1M) →simulation results → abandoned

Sensoring

• matlab_sim_iptg.zip (<0.2M) →simulation results

assembly

chemical sensing

2006/10/03

Made LB-Agar plates with antibiotics

2006/10/04

Transformed cells, plated them

2006/10/05

Found plates empty after 18h on the table, put into incubator at 37°C

2006/10/06

picked cultures onto fresh plates

Useful Documents & Links

see here