ETH Zurich 2006

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(→filling in the details: actually, we have a DESIGN PROCESS now! wow!)
(→design process: start to add content)
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=== design process ===
=== design process ===
-
Ideally, this could be documented as a hierarchy of global specification -> structural specification steps (ie after-the-book engineering process). Even if nobody had that in mind probably we can mold wathever actually happened into this pattern.
+
''This could be documented as a hierarchy of global specification -> structural specification steps (ie after-the-book engineering process). Even if nobody had that in mind probably we can mold wathever actually happened into this pattern.''
-
This would mean we get chapters like this:
+
==== system level ====
-
* system level
+
===== system behavorial specification =====
-
** behavorial specification
+
-
** process structure (sensing, half adder, reporters)
+
-
** deployment structure (distribution on the plasmids)
+
-
** assembly procedure
+
-
** test procedure
+
-
** test results
+
-
* device level
+
-
** chemical sensing
+
-
*** present alternatives, show how the existing IPTG sensing device fullfills our specifications made on system level
+
-
*** where we got it and link to theyer documentation
+
-
*** assembly procedure
+
-
*** test procedure
+
-
*** test results
+
-
** light sensing
+
-
*** present alternatives, show how the existing light sensing device fullfills our specifications made on system level
+
-
*** where we got it and link to theyer documentation
+
-
*** assembly procedure
+
-
*** test procedure
+
-
*** test results
+
-
** half adder
+
-
*** separate into one subdevice per output -> subdevice structure
+
-
** reporters
+
-
*** show alternatives
+
-
*** reason for choice
+
-
*** structure on parts level
+
-
* subdevice level
+
-
** XOR gate
+
-
*** present alternatives
+
-
*** modeling
+
-
*** assembly procedure
+
-
*** test procedure
+
-
*** test results
+
-
** AND gate
+
-
*** present alternatives
+
-
*** modeling
+
-
*** assembly procedure
+
-
*** test procedure
+
-
*** test results
+
-
* parts level
+
-
** for every part we use
+
-
** DNA sequence
+
-
** where we got it from
+
 +
# 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
 +
 +
            light  no light
 +
chemical    A        B
 +
no chemical  B        C
 +
 +
The outputs can be reported by fluorescent proteins, the mapping of states to outputs is arbitary, our choice is:
 +
 +
A: green
 +
B: red
 +
C: no fluorescence
 +
 +
Considering the green and the red output as being separate, the logic mapping the input states to the output states is AND for the GFP and XOR for the RFP. Together they amount to a half adder logic.
 +
 +
===== system structure =====
 +
 +
The whole process can be brought into a common input, logic, output form:
 +
 +
[light sensing]-----[      ]--[output A]
 +
                    [ logic ]
 +
[chemical sensing]--[      ]--[output B]
 +
 +
===== system deployment =====
 +
 +
''distribution on the plasmids, strains''
 +
 +
===== system assembly procedure =====
 +
 +
===== system test procedure =====
 +
 +
===== system test results =====
 +
 +
==== device level ====
 +
 +
===== chemical sensing device =====
 +
 +
====== variants ======
 +
 +
show how the existing IPTG sensing device fullfills our specifications made on system level
 +
 +
====== assembly procedure ======
 +
 +
where we got it and link to theyer documentation
 +
 +
====== test procedure ======
 +
 +
====== test results ======
 +
 +
===== light sensing device =====
 +
 +
====== variants ======
 +
 +
show how the existing light sensing device fullfills our specifications made on system level
 +
 +
====== assembly procedure ======
 +
 +
where we got it and link to theyer documentation
 +
 +
====== test procedure ======
 +
 +
====== test results ======
 +
 +
===== logic (half adder) device =====
 +
 +
As stated in the [[#system behavorial specification]] the logic is made up of one AND and one XOR gate:
 +
 +
        [          ]-------[    ]
 +
A >----[ 1:2 copy ]      [ AND ]----> X
 +
        [          ]--, ,--[    ]
 +
                      X
 +
        [          ]--' '--[    ]
 +
B >----[ 1:2 copy ]      [ XOR ]----> Y
 +
        [          ]-------[    ]
 +
 +
===== reporters =====
 +
 +
====== variants ======
 +
 +
====== structure on parts level ======
 +
 +
==== subdevice level ====
 +
 +
===== XOR gate =====
 +
 +
====== variants ======
 +
 +
====== modeling ======
 +
 +
====== assembly procedure ======
 +
 +
====== test procedure ======
 +
 +
====== test results ======
 +
 +
===== AND gate =====
 +
 +
====== variants ======
 +
 +
====== modeling ======
 +
 +
====== assembly procedure ======
 +
 +
====== test procedure ======
 +
 +
====== test results ======
 +
 +
==== parts level ====
 +
 +
for every part we use:
 +
* DNA sequence
 +
* where we got it from
 +
 +
(links to the registry)
 +
 +
''
Maybe this could mostly be a hierarchy of links to the registry because it's preferable to have as much documentation in the registry as possible anyway. This is nice because it emphases our incredibly systematic engineering approach and documents the processes too which could also serve for coordination of the work in progress.
Maybe this could mostly be a hierarchy of links to the registry because it's preferable to have as much documentation in the registry as possible anyway. This is nice because it emphases our incredibly systematic engineering approach and documents the processes too which could also serve for coordination of the work in progress.
 +
''
==== Reserved parts in the registry====
==== Reserved parts in the registry====

Revision as of 16:09, 11 October 2006

ETH Team 2006


standing (L-R): Marco, Alexandra, Arthur, Olga, Dimo, Marko, Robert; in front (L-R):

Franz, Michael



Adding numbers is easy, isn't it? 1234 plus 5678, for example, is 6912. But how do engineers add binary numbers instead of decimal ones? And how, in the end, can this be done by a living cell? We, the members of the ETH Zurich 2006 iGEM team, are currently working on these questions, whereas the last one seems to be not trivial.

What the addition of numbers has to do with pattern recognition, how our model and the mathematical analysis look like, and how the experiments are realized will be explained on these wiki pages. We wish you a pleasant time with our pages. Enjoy it!



Contents

Coordination

TODOs

Modeling

  • Parts Model the whole System with Sensing, Pop's duplexer and Half adder (Marco and Franz)
  • Model whether a different strength of input is necessary for the AND and XOR Gates (Who?)
  • Finish modeling the second AND Gate and find a biological way to implement it and write the DNA and order it (Marco and Robert)

Lab

Responsible: Robert for the preparatory experiments, Olga for the assembly and testing of the gates.

  • Read the literature on the XOR and AND Gates, check carefully for strains needed and compatibility of the parts (Who?)
  • Prepare a protocol for parts assembly (Olga)
  • Assembly of the light sensing device from the parts we received from UCSF Voigt's lab (Arthur)
  • Assembly of the chemical sensing device (Franz, Dimo, Robert, Marco, Marko, Olga)

Documentation

Responsible: Alexandra for the registry, Franz for the presentation, Arthur for the Wiki.

  • enter lab experience report to registry
  • restructure the Wiki, identify lacking information and find people who can provide it (Arthur)
  • Make a picture of the whole model with te different parts in it (Alexandra)
  • Make a drawing of the DNA to have an overview of which parts will be consecutively on the same DNA piece (Alexandra)
  • Find promoters for the Pops duplexer (2 promoters in total) (Michael)

Schedule

Available as Google Calendar: [http://www.google.com/calendar/render?cid=pqi8ni6gnfj5r3o0np0h4smrr4@group.calendar.google.com iGEM 2006 ETH Zurich]

Thu 20.7., 1700: kickoff meeting in CNB E 121
27.7.-3.8. 1st group phase
Define project in more detail within two groups
Thu 27.7., 1700: meeting of entire group to share ideas
Thu 3.8., 1700: decision on final project
15.8. 1700
Tutorial "Modelling of AND gate"
Until 20.8.
Finalize DNA design, order it
September,October
Implement design (registry bio-bricks, ordered DNA)
27.9.
Fix the flight dates and send the proposed flights to Jörg
23.10.
Latest point to start getting our presentation going and to finish the iGEM wiki documentation
30.10.
Project documentation on the Wiki has to be complete
4./5.11.
Jamboree in Boston

Participants and availability


Progress report and documentation

Initial project ideas

The fruits of some brainstorming and research

proposed projects

We split up the whole team into two groups, each proposed a project after these two weeks.

It was decided to further pursue the Half adder project idea.

design process

This could be documented as a hierarchy of global specification -> structural specification steps (ie after-the-book engineering process). Even if nobody had that in mind probably we can mold wathever actually happened into this pattern.

system level

system behavorial specification
  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 
           light   no light
chemical     A         B
no chemical  B         C

The outputs can be reported by fluorescent proteins, the mapping of states to outputs is arbitary, our choice is: 

A: green
B: red
C: no fluorescence

Considering the green and the red output as being separate, the logic mapping the input states to the output states is AND for the GFP and XOR for the RFP. Together they amount to a half adder logic.

system structure

The whole process can be brought into a common input, logic, output form: 

[light sensing]-----[       ]--[output A]
                    [ logic ]
[chemical sensing]--[       ]--[output B]
system deployment

distribution on the plasmids, strains

system assembly procedure
system test procedure
system test results

device level

chemical sensing device
variants

show how the existing IPTG sensing device fullfills our specifications made on system level

assembly procedure

where we got it and link to theyer documentation

test procedure
test results
light sensing device
variants

show how the existing light sensing device fullfills our specifications made on system level

assembly procedure

where we got it and link to theyer documentation

test procedure
test results
logic (half adder) device

As stated in the #system behavorial specification the logic is made up of one AND and one XOR gate: 

       [          ]-------[     ]
A >----[ 1:2 copy ]       [ AND ]----> X
       [          ]--, ,--[     ]
                      X
       [          ]--' '--[     ]
B >----[ 1:2 copy ]       [ XOR ]----> Y
       [          ]-------[     ]
reporters
variants
structure on parts level

subdevice level

XOR gate
variants
modeling
assembly procedure
test procedure
test results
AND gate
variants
modeling
assembly procedure
test procedure
test results

parts level

for every part we use:

  • DNA sequence
  • where we got it from

(links to the registry)

Maybe this could mostly be a hierarchy of links to the registry because it's preferable to have as much documentation in the registry as possible anyway. This is nice because it emphases our incredibly systematic engineering approach and documents the processes too which could also serve for coordination of the work in progress.

Reserved parts in the 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.

modeling

Matlab scripts for ODE simulation

modular scripts
  • contains a createXXX() script for each module. the created module contains
    • function handles for reaction rates: r
    • stoichiometric matrix: N
    • constants (inside of the function handles)
    • state (concentration) changes (the ode dy values) can be computed by: N · r
  • modules can be connected using the createInOutConnector() script. the result is again a module, consisting of the connected basic modules.
  • sim_1_1 and sim_1_2 can be used to simulate modules with 1 input/1 output and 1 input/2 outputs respectively.
  • both basic modules and compound (connected) modules can be simulated
  • simulations contains the first samples, simulating
  • scripts: [http://csb.inf.ethz.ch/igem-2006/matlab_modules.zip matlab_modules.zip] (<0.1M)
old scripts

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

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

Sensoring

  • [http://csb.inf.ethz.ch/igem-2006/matlab_sim_iptg.zip matlab_sim_iptg.zip] (<0.2M) →simulation results

assembly

chemical sensing

2006/10/03
Made LB-Agar plates with antibiotics
2006/10/04
Transformed cells, plated them
2006/10/05
Found plates empty after 18h on the table, put into incubator at 37°C
2006/10/06
picked cultures onto fresh plates

Useful Documents & Links

see here

Retrieved from "http://2006.igem.org/wiki/index.php/ETH_Zurich_2006"
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