ETH Zurich 2006

From 2006.igem.org

Contents 1 Coordination 1.1 TODOs 1.1.1 Modeling 1.1.2 Lab 1.1.3 Documentation 1.2 Schedule 1.3 Participants 2 Progress report and documentation 2.1 Initial project ideas 2.2 proposed projects 2.3 filling in the details 2.3.1 Reserved Parts in Registry 2.3.2 Chemical Sensing Device 2.4 modeling 2.4.1 Matlab scripts for ODE simulation 2.4.1.1 modular scripts 2.4.1.2 old scripts 2.5 implementation 3 Useful Documents & Links

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: [http://www.google.com/calendar/render?cid=pqi8ni6gnfj5r3o0np0h4smrr4@group.calendar.google.com 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 Registry

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

• Half adder: [http://partsregistry.org/Part:BBa_J34000 BBa_J34000]
• AND gate: [http://partsregistry.org/Part:BBa_J34100 BBa_J34100]
• XOR gate: [http://partsregistry.org/Part:BBa_J34200 BBa_J34200]

Chemical Sensing Device

Suggestions for Chemical Sensing Device:

• Lactate lacI represses, IPTG induces ([http://partsregistry.org/Part:BBa_R0011 BBa_R0011] or [http://partsregistry.org/Part:BBa_R0010 BBa_R0010] )
• Tetracycline, TetR inhibitor, Tet inducer by inhibiting TetR (or aTc, it's analog) ([http://partsregistry.org/Part:BBa_R0040 BBa_R0040])
• combination thereof ([http://partsregistry.org/Part:BBa_I13614 BBa_I13614] / [http://partsregistry.org/Part:BBa_I13617 BBa_13617] / [http://partsregistry.org/Part:BBa_I13623 BBa_I13623] / [http://partsregistry.org/Part:BBa_I13624 BBa_I13624] / [http://partsregistry.org/Part:BBa_I13627 BBa_I13627] / [http://partsregistry.org/Part:BBa_I13637 BBa_I13637] / [http://partsregistry.org/Part:BBa_I13653 BBa_I13653])
• simple sugar Arabinose ([http://partsregistry.org/Part:BBa_R0080 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
• [http://csb.inf.ethz.ch/igem-2006/whole.ai.zip 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: [http://csb.inf.ethz.ch/igem-2006/matlab_modules.zip 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).

• [http://csb.inf.ethz.ch/igem-2006/matlab_sim_and1.zip matlab_sim_and1.zip] (<0.1M) →simulation results → abandoned
• [http://csb.inf.ethz.ch/igem-2006/matlab_sim_and2.zip matlab_sim_and2.zip] (<0.1M) →simulation results → the pursued version A
• [http://csb.inf.ethz.ch/igem-2006/matlab_sim_and3.zip matlab_sim_and3.zip] (<0.1M) →simulation results → the pursued version B
• [http://csb.inf.ethz.ch/igem-2006/matlab_sim_and4.zip 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.

• [http://csb.inf.ethz.ch/igem-2006/matlab_sim_xor1.zip matlab_sim_xor1.zip] (<0.1M) →simulation results → the only pursued version
• [http://www.tik.ee.ethz.ch/~brockho/igem2006/matlab_sim_xor2.zip matlab_sim_xor2.zip] (<0.1M) →simulation results → abandoned
• [http://www.tik.ee.ethz.ch/~brockho/igem2006/matlab_sim_xor3.zip matlab_sim_xor3.zip] (<0.1M) →simulation results → abandoned

Sensoring

• [http://csb.inf.ethz.ch/igem-2006/matlab_sim_iptg.zip matlab_sim_iptg.zip] (<0.2M) →simulation results

implementation

Useful Documents & Links

see here