ETH 2006 Half adder

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(modular scripts)
(reverted to state of July 31 when we decided for the half adder based on this information. The documentation of our further work was moved to the progress report on the front page.)
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back to → [[ETH Zurich 2006|ETH 2006 Main Page]] → [[ETH 2006 Meat Monitor|Meat Monitor idea]] → [[ETH 2006 Ideas|other project ideas]]
back to → [[ETH Zurich 2006|ETH 2006 Main Page]] → [[ETH 2006 Meat Monitor|Meat Monitor idea]] → [[ETH 2006 Ideas|other project ideas]]
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==[[LAB WORK]]==
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= Half-adder or Full-adder =
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An implementation of a half-adder or full-adder: 1-bit adder with carry
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* [http://en.wikipedia.org/wiki/Full_adder half/full adder in wikipedia]
== Idea: Pattern recognition ==
== Idea: Pattern recognition ==
''→ Illustration of the concepts: ''  
''→ Illustration of the concepts: ''  
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* [[media:Half-adder.pdf|slides]] (pdf, 352KB)
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* [[media:Half-adder.pdf|sliles]] (pdf, 352KB)
* [[media:Half-adder-handout.pdf|handout]] (pdf, 268KB)
* [[media:Half-adder-handout.pdf|handout]] (pdf, 268KB)
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* An implementation of a half-adder or full-adder: 1-bit adder with carry <br/> &rarr; [http://en.wikipedia.org/wiki/Full_adder half/full adder in wikipedia]
 
====Main Goal:====
====Main Goal:====
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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
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====From the ingenieur point of view====
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====Implementation from the ingenieur point of view====
*Half Adder
*Half Adder
* = opportunity to build an AND and an XOR Gate
* = opportunity to build an AND and an XOR Gate
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====From the biologist point of view====
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====Implementation from the biologist point of view====
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*AND Gate: bacteria two hybrid system
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*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
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*XOR Gate: TEV and related protease to inactivate two similar transcription factors
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*XOR Gate: I think Marko had a good idea about that (I didn't really got it)
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*a light sensible promoter (there are some, see [http://partsregistry.org/Featured_Parts:Light_Sensor here]). The promotor used is on in the dark, so we can work in the light.
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*a light sensible promoter (there are some, see [http://partsregistry.org/Featured_Parts:Light_Sensor here])
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*a chemical sensible promoter: IPTG
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*a chemical sensible promoter (chemical to be defined)
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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
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==Modeling==
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==== Pro's &amp; Con's====
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=====Modeling Overview=====
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''Pro's:''
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* [[media:ETH_Modeling_1Page_Overview.pdf|1 Page Overview (pdf)]] (&sim;1.2M) [[:Image:ETH_Modeling_1Page_Overview.pdf|all versions]]
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* meaningful from engineering point
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* [http://csb.inf.ethz.ch/igem-2006/whole.ai.zip 1 Page Overview (illustrator)] (&sim;1.3M)
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* valuable parts for synthetic biology
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* [[media:ETH_Modeling_Overview.pdf|Modeling Overview (pdf)]] (&sim;0.5M) [[:image:ETH_Modeling_Overview.pdf|all versions]]
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* stepwise proceeding applicable (&rarr; intermediate and partial results!)
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* [[media:ETH_Modeling_Overview.ppt|Modeling Overview (ppt)]] (&sim;0.6M) [[:image:ETH_Modeling_Overview.ppt|all versions]]
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* experiments visually attractive
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* [[media:IPTG_sensing.pdf|IPTG sensing (pdf)]] (&sim;0.1M) [[:image:IPTG_sensing.pdf|all versions]]
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* probably simple enough
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* [[media:IPTG_sensing.ppt|IPTG sensing (ppt)]] (&sim;0.2M) [[:image:IPTG_sensing.ppt|all versions]]
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=====Matlab scripts for ODE simulation=====
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''Con's:''
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====== modular scripts======
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* cheap copy of “bio-film” project ([http://partsregistry.org/cgi/htdocs/SBC04/index.cgi iGEM 2004])
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* contains a <code>createXXX()</code> script for each module. the created module contains
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* sensational experiments, have little in common with half adder
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** function handles for reaction rates: '''r'''
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* maybe that a ''big vision'' is lacking
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** stoichiometric matrix: '''N'''
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* general/practical benefit? (counter-argument: is this required?)
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** constants (inside of the function handles)
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* too simple?
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** state (concentration) changes (the ode dy values) can be computed by: '''N''' &middot; '''r'''
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* modules can be ''connected'' using the <code>createInOutConnector()</code> script. the result is again a module, consisting of the connected basic modules.
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* <code>sim_1_1</code> and <code>sim_1_2</code> can be used to simulate modules with 1 input/1 output and 1 input/2 outputs respectively.
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* both ''basic modules'' and ''compound (connected) modules'' can be simulated
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* <code>simulations</code> contains the first samples, simulating
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** ''XOR'' &rarr; [[ETH_Sim_Mod_Xor|simulation results]] / [[ETH_Sens_Xor|sensitivity analysis]]
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** ''AND-tRNA'' &rarr; [[ETH_Sim_Mod_AND_tRNA|simulation results]] / [[ETH_Sens_And|sensitivity analysis]]
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** ''IPTG Sensing'' &rarr;[[ETH_Sim_Mod_IPTG|simulation results]]
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** ''PoPS Duplexer'' &rarr;[[ETH_Sim_Mod_Dupl|simulation results]]
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** ''Compound module'': IPTG Sensing &rarr; PoPS Duplexer &rarr;[[ETH_Sim_Mod_IPTG_Dupl|simulation results]]
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* scripts: [http://csb.inf.ethz.ch/igem-2006/matlab_modules.zip matlab_modules.zip] (&lt;0.1M)
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====== old scripts ======
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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]] &rarr; ''abandoned''
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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]] &rarr; the pursued version '''A'''
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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]] &rarr; the pursued version '''B'''
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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]] &rarr; ''abandoned''
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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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* [http://csb.inf.ethz.ch/igem-2006/matlab_sim_xor1.zip matlab_sim_xor1.zip] (&lt;0.1M) &rarr;[[ETH_Sim_Xor1|simulation results]] &rarr; the only pursued version
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* [http://www.tik.ee.ethz.ch/~brockho/igem2006/matlab_sim_xor2.zip matlab_sim_xor2.zip] (&lt;0.1M) &rarr;[[ETH_Sim_Xor2|simulation results]] &rarr; ''abandoned''
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* [http://www.tik.ee.ethz.ch/~brockho/igem2006/matlab_sim_xor3.zip matlab_sim_xor3.zip] (&lt;0.1M) &rarr;[[ETH_Sim_Xor3|simulation results]] &rarr; ''abandoned''
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Sensoring
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* [http://csb.inf.ethz.ch/igem-2006/matlab_sim_iptg.zip matlab_sim_iptg.zip] (&lt;0.2M) &rarr;[[IPTG_1|simulation results]]
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==Parts==
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==== Reserved Parts in Registry====
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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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====Chemical Sensing Device====
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Suggestions for Chemical Sensing Device:
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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] / [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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==Old Stuff==
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[[ETH_2006_Half_adder_Old_Stuff|Old models & stuff]]
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Revision as of 14:44, 6 October 2006

back to → ETH 2006 Main PageMeat Monitor ideaother 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

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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