ETH 2006 Half adder
From 2006.igem.org
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**Bacteria gets red when pattern on the plate and picture do not match | **Bacteria gets red when pattern on the plate and picture do not match | ||
| - | == | + | ====From the ingenieur point of view==== |
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*Half Adder | *Half Adder | ||
* = opportunity to build an AND and an XOR Gate | * = 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 | *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) | *XOR Gate: I think Marko had a good idea about that (I didn't really got it) | ||
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*a chemical sensible promoter (chemical to be defined) | *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 | *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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==Modeling== | ==Modeling== | ||
Revision as of 14:35, 28 August 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:
- 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
Parts
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]
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?
