ETH 2006 Half adder

From 2006.igem.org

Revision as of 11:30, 26 September 2006

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LAB WORK

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) (∼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
  • AND-tRNA → simulation results
  • 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.

Old Stuff

Old models & stuff