ETH 2006 Half adder
From 2006.igem.org
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Contents |
TO DO's
- Parts Model the whole System with Sensing, Pop's duplexer and Half adder (Marco and Franz)
- 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 (Who?)
- OK Check wether the strains are available (Robert)
- OK Model the IPTG Sensing device (Robert)
- OK 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 parts assembly (Olga)
- Assemble the different parts that can already be assembled (Arthur, Olga and 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)
Important: we should order the DNA as soon as possible then if we order it next week we would only have 2.5 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
→ 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: bacteria two hybrid system
- XOR Gate: TEV and related protease to inactivate two similar transcription factors
- a light sensible promoter (there are some, see here). The promotor used is on in the dark, so we can work in the light.
- a chemical sensible promoter: IPTG
Modeling
Modeling Overview
- 1 Page Overview (pdf) (∼0.2M) all versions
- 1 Page Overview (illustrator) (∼1.3M)
- Modeling Overview (pdf) (∼0.5M) all versions
- Modeling Overview (ppt) (∼0.7M) 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
andsim_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- 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
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: 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.