ETH 2006 Half adder

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Contents

The Model

Overview

TO DO's

  • Parts Model the whole System with Sensing, Pop's duplexer and Half adder (Marco and Franz)
  • OK Make a picture of the whole model with te different parts in it (Alexandra)
  • Finish AND and XOR Gates DNA (Marko and Sven) to order it
  • Read the literature on the XOR and AND Gates, check carefully for strains needed and compatibility of the parts
  • OK Check wether the strains are available (Robert)
  • OK Model the IPTG Sensing device (Robert)
  • Ask for the Plasmid with the light sensing device (Olga)
  • 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)
  • Prepare a protocol for promoter testing (Olga and Alexandra)
  • Promoter and degradation tagged reporter protein testing (Arthur, Olga and Alexandra)

Important: we should order the DNA as soon as possible then if we order it next week we would only have 1.5 weeks for testing our system

Idea: Pattern recognition

→ Illustration of the concepts:

  • slides (pdf, 352KB)
  • handout (pdf, 268KB)
  • An implementation of a half-adder or full-adder: 1-bit adder with carry
    → [http://en.wikipedia.org/wiki/Full_adder half/full adder in wikipedia]

Main Goal:

  • Write something with a chemical on a petri plate (like ETH for example)
  • Let Bacteria grow uniformly on the plate
  • Expose the plate to a picture (black and white) of the same pattern
  • Result:
    • Bacteria gets green when pattern on the plate and picture match (light and chemical)
    • Bacteria does not express fluorescent protein when pattern on the plate and picture match (no light and no chemical)
    • Bacteria gets red when pattern on the plate and picture do not match

From the ingenieur point of view

  • Half Adder
  • = opportunity to build an AND and an XOR Gate

From the biologist point of view

  • AND Gate: presence of chemical induces the production of an inactive protein, which is activated by a second protein (produced when light is present): the first protein is then activating GFP production
  • XOR Gate: I think Marko had a good idea about that (I didn't really got it)
  • a light sensible promoter (there are some, see [http://partsregistry.org/Featured_Parts:Light_Sensor here]). The promotor used is on in the dark, so we can work in the light.
  • a chemical sensible promoter (chemical to be defined)

Modeling

Modeling Overview
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
  • 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

Parts

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.

Old Stuff

Old models & stuff

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