ETH 2006 Half adder

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====Main Goal:====
====Main Goal:====
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*Write something with a chemical on a petri plate (like '''ETH''' for example)
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# Write something with a chemical on a petri plate (like '''ETH''' for example)
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*Let Bacteria grow uniformly on the plate
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# Let Bacteria grow uniformly on the plate
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*Expose the plate to a picture (black and white) of the same pattern  
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# Expose the plate to a picture (black and white) of the same pattern  
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*Result:
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# Result:
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**Bacteria gets green when pattern on the plate and picture match (light and chemical)
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#*Bacteria gets green when pattern on the plate and picture match (light and chemical)
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**Bacteria does not express fluorescent protein when pattern on the plate and picture match (no light and no chemical)
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#*Bacteria does not express fluorescent protein when pattern on the plate and picture match (no light and no chemical)
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**Bacteria gets red when pattern on the plate and picture do not match
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#*Bacteria gets red when pattern on the plate and picture do not match
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==Implementation==
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====Implementation from the ingenieur point of view====
====Implementation from the ingenieur point of view====
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*we would need to give a kind of first signal to the system (to don't have light reactions before a certain moment, otherwise we have to work in a dark room...), an activation signal after the bacterias have grown on the plate
*we would need to give a kind of first signal to the system (to don't have light reactions before a certain moment, otherwise we have to work in a dark room...), an activation signal after the bacterias have grown on the plate
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====Chemical Sensing====
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==== Pro's & Con's====
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* Lactate  lacI represses, IPTG induces ([http://partsregistry.org/Part:BBa_R0011 BBa_R0011] or [http://partsregistry.org/Part:BBa_R0010 BBa_R0010] )
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* Tetracycline, TetR inhibitor, Tet inducer by inhibiting TetR (or aTc, it's analog)  ([http://partsregistry.org/Part:BBa_R0040 BBa_R0040])
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* 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] /
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[http://partsregistry.org/Part:BBa_I13637 BBa_I13637] / [http://partsregistry.org/Part:BBa_I13653 BBa_I13653])
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* simple sugar Arabinose ([http://partsregistry.org/Part:BBa_R0080 BBa_R0080])
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* 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.
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====PoPS --> 2x PoPS Converter====
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We will also need a device providing two times the same output signal, according to the input. This is needed to supply the AND and the XOR gate with the input signals, sensed by the system.
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<center>
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[[Image:ETH_2006_popsdoubler1.png|400 px|PoPs doubler idea 1]] [[Image:ETH_2006_popsdoubler2.png|400 px|PoPs doubler idea 2]]
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</center>
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ToDo:
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*Decide if we need this part: On August 16, Jörg said it is possible to link the DNA sequences of the gates, responsible for the inputs, directly to the output of the sensing devices
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*If we decide to use the PoPS doubler device we need to decide which implementation we favor (Idea 1 is, from my point of view, better because the outputs are synchronized --[[User:Dimo|Dimo]] 05:49, 17 August 2006 (EDT))
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*Of course, this part should also be tested in the lab
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==Modeling==
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=====Selected XOR/AND Model Variants=====
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Now in accordance with the Matlab code below:
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* [[media:eth-parts-and-xor.pdf|eth-parts-and-xor.pdf]] (&sim;0.3M) [[:image:eth-parts-and-xor.pdf|file versions]]
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* [[media:eth-parts-and-xor2.ppt|eth-parts-and-xor.ppt]] (&sim;0.4M) [[:image:eth-parts-and-xor.ppt|file versions]]
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Older versions of the XOR gates, but with slides explaining the light sensing device (built by UT Austin 2005 team) can be found within this file: [[media:eth-xor.pdf|eth-xor.pdf]] (483KB)
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=====Matlab scripts for ODE simulation=====
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unzip the file, each zip file contains 2 files: <code>sim_xxx.m</code> and <code>ode_xxx.m</code>.
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: <code>ode_xxx.m</code> : contains the differential equations, i.e. the model
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: <code>sim_xxx.m</code> : sets the parameters, calls the simulator and plots the result (this is the one to run, but the other is also needed).
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* [http://csb.inf.ethz.ch/igem-2006/matlab_sim_and1.zip matlab_sim_and1.zip] (&lt;0.1M) &rarr;[[ETH_Sim_And1|simulation results]]
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* [http://csb.inf.ethz.ch/igem-2006/matlab_sim_and2.zip matlab_sim_and2.zip] (&lt;0.1M) &rarr;[[ETH_Sim_And2|simulation results]]
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* [http://csb.inf.ethz.ch/igem-2006/matlab_sim_and3.zip matlab_sim_and3.zip] (&lt;0.1M) &rarr;[[ETH_Sim_And3|simulation results]]
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* [http://csb.inf.ethz.ch/igem-2006/matlab_sim_and4.zip matlab_sim_and4.zip] (&lt;0.1M) &rarr;[[ETH_Sim_And4|simulation results]]
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* [http://csb.inf.ethz.ch/igem-2006/matlab_sim_xor1.zip matlab_sim_xor1.zip] (&lt;0.1M) &rarr;[[ETH_Sim_Xor1|simulation results]]
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As a result of the meeting on August 17, we will from now on concentrate on the AND versions 2 and 3.
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=====Older Presentation of AND Model Variants including the ODEs and simulation results=====
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The simulation results within the following slides can also be found via the above links.
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* [[media:eth-odes-and-xor.pdf|eth-odes-and-xor.pdf]] (&sim;0.5M) [[:image:eth-odes-and-xor.pdf|file versions]]
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* [[media:eth-odes-and-xor.ppt|eth-odes-and-xor.ppt]] (&sim;1.0M) [[:image:eth-odes-and-xor.ppt|file versions]]
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==Parts==
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We have already reserved parts for the adder and the gates in the registry the description of which are still tentative:
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* Half adder: [http://partsregistry.org/Part:BBa_J34000 BBa_J34000]
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* AND gate: [http://partsregistry.org/Part:BBa_J34100 BBa_J34100]
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* XOR gate: [http://partsregistry.org/Part:BBa_J34200 BBa_J34200]
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== Pro's &amp; Con's==
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''Pro's:''
''Pro's:''
* meaningful from engineering point
* meaningful from engineering point

Latest revision as of 14:42, 26 October 2006

back to → ETH 2006 Main Page → Meat Monitor idea → other project ideas

Contents

Half-adder or Full-adder

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]

Idea: Pattern recognition

→ Illustration of the concepts:

Main Goal:

  1. Write something with a chemical on a petri plate (like ETH for example)
  2. Let Bacteria grow uniformly on the plate
  3. Expose the plate to a picture (black and white) of the same pattern
  4. 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

Implementation from the ingenieur point of view

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

Implementation 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])
  • a chemical sensible promoter (chemical to be defined)
  • we would need to give a kind of first signal to the system (to don't have light reactions before a certain moment, otherwise we have to work in a dark room...), an activation signal after the bacterias have grown on the plate

Pro's & Con's

Pro's:

  • meaningful from engineering point
  • valuable parts for synthetic biology
  • stepwise proceeding applicable (→ intermediate and partial results!)
  • experiments visually attractive
  • probably simple enough

Con's:

  • cheap copy of “bio-film” project ([http://partsregistry.org/cgi/htdocs/SBC04/index.cgi iGEM 2004])
  • sensational experiments, have little in common with half adder
  • maybe that a big vision is lacking
  • general/practical benefit? (counter-argument: is this required?)
  • too simple?
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