ETH 2006 Half adder

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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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==The Model ==
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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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Overview
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* [http://en.wikipedia.org/wiki/Full_adder half/full adder in wikipedia]
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==TO DO's==
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*'''Parts''' Model the whole System with Sensing, Pop's duplexer and Half adder (Marco and Franz)
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*Make a picture of the whole model with te different parts in it (Alexandra)
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*Finish AND and XOR Gates DNA (Marko and Sven) to order it
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*Read the literature on the XOR and AND Gates, check carefully for strains needed and compatibility of the parts
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*'''OK''' Check wether the strains are available (Robert)
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*'''OK''' Model the IPTG Sensing device (Robert)
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*'''OK'''Ask for the Plasmid with the light sensing device (Olga)
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*Model whether a different strength of input is necessary for the AND and XOR Gates ('''Who?''')
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*Finish modeling the second AND Gate and find a biological way to implement it and write the DNA and order it (Marco and Robert)
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*Prepare a protocol for parts assembly (Olga)
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*Assemble the different parts that can already be assembled (Arthur, Olga and Alexandra)
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*Make a drawing of the DNA to have an overview of which parts will be consecutively on the same DNA piece (Alexandra)
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*Find promoters for the Pops duplexer (2 promoters in total)
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'''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
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== Idea: Pattern recognition ==
== Idea: Pattern recognition ==
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* [[media:Half-adder.pdf|slides]] (pdf, 352KB)
* [[media:Half-adder.pdf|slides]] (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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*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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====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====
*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 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])
*a chemical sensible promoter (chemical to be defined)
*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;0.2M) [[: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;0.7M) [[: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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====== modular scripts======
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* contains a <code>createXXX()</code> script for each module. the created module contains
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** function handles for reaction rates: '''r'''
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** stoichiometric matrix: '''N'''
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** constants (inside of the function handles)
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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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** ''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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''Con's:''
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[[ETH_2006_Half_adder_Old_Stuff|Old models & stuff]]
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* cheap copy of “bio-film” project ([http://partsregistry.org/cgi/htdocs/SBC04/index.cgi iGEM 2004])
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* sensational experiments, have little in common with half adder
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* maybe that a ''big vision'' is lacking
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* general/practical benefit? (counter-argument: is this required?)
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* too simple?

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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