ETH 2006 Half adder

From 2006.igem.org

(Difference between revisions)
Jump to: navigation, search
(→PoPS --> 2x PoPS Converter)
m (→Idea: Pattern recognition)
 
(55 intermediate revisions not shown)
Line 13: Line 13:
====Main Goal:====
====Main Goal:====
-
*Write something with a chemical on a petri plate (like '''ETH''' for example)
+
# Write something with a chemical on a petri plate (like '''ETH''' for example)
-
*Let Bacteria grow uniformly on the plate
+
# Let Bacteria grow uniformly on the plate
-
*Expose the plate to a picture (black and white) of the same pattern  
+
# Expose the plate to a picture (black and white) of the same pattern  
-
*Result:
+
# Result:
-
**Bacteria gets green when pattern on the plate and picture match (light and chemical)
+
#*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 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
+
#*Bacteria gets red when pattern on the plate and picture do not match
-
 
+
-
==Implementation==
+
====Implementation from the ingenieur point of view====
====Implementation from the ingenieur point of view====
Line 34: Line 32:
*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
-
====Chemical Sensing====
+
==== Pro's & Con's====
-
* 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.
+
-
 
+
-
 
+
-
 
+
-
==Modeling==
+
-
=====Matlab scripts for ODE simulation=====
+
-
unzip the file, each zip file contains 2 files: <code>sim_xxx.m</code> and <code>ode_xxx.m</code>.
+
-
: <code>ode_xxx.m</code> : contains the differential equations, i.e. the model
+
-
: <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).
+
-
* [http://csb.inf.ethz.ch/igem-2006/matlab_sim_and1.zip matlab_sim_and1.zip] (&lt;0.1M) &rarr;[[ETH_Sim_And1|simulation results]]
+
-
* [http://csb.inf.ethz.ch/igem-2006/matlab_sim_and2.zip matlab_sim_and2.zip] (&lt;0.1M) &rarr;[[ETH_Sim_And2|simulation results]]
+
-
* [http://csb.inf.ethz.ch/igem-2006/matlab_sim_and3.zip matlab_sim_and3.zip] (&lt;0.1M) &rarr;[[ETH_Sim_And3|simulation results]]
+
-
* [http://csb.inf.ethz.ch/igem-2006/matlab_sim_and4.zip matlab_sim_and4.zip] (&lt;0.1M) &rarr;[[ETH_Sim_And4|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] (&lt;0.1M) &rarr;[[ETH_Sim_Xor1|simulation results]]
+
-
* [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]]
+
-
* [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]]
+
-
 
+
-
 
+
-
 
+
-
==Old Stuff==
+
-
[[ETH_2006_Half_adder_Old_Stuff|Old models & 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 &amp; Con's==
+
''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?
Retrieved from "http://2006.igem.org/wiki/index.php/ETH_2006_Half_adder"
Personal tools
Past/present/future years