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Revision as of 14:38, 28 August 2006

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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:

• slides (pdf, 352KB)
• handout (pdf, 268KB)

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])
• 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

Modeling

Matlab scripts for ODE simulation

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
• [http://csb.inf.ethz.ch/igem-2006/matlab_sim_and2.zip matlab_sim_and2.zip] (<0.1M) →simulation results
• [http://csb.inf.ethz.ch/igem-2006/matlab_sim_and3.zip matlab_sim_and3.zip] (<0.1M) →simulation results
• [http://csb.inf.ethz.ch/igem-2006/matlab_sim_and4.zip matlab_sim_and4.zip] (<0.1M) →simulation results

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
• [http://www.tik.ee.ethz.ch/~brockho/igem2006/matlab_sim_xor2.zip matlab_sim_xor2.zip] (<0.1M) →simulation results
• [http://www.tik.ee.ethz.ch/~brockho/igem2006/matlab_sim_xor3.zip matlab_sim_xor3.zip] (<0.1M) →simulation results

Old Stuff

Old models & stuff

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.

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?