ETH Zurich 2006

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=== modeling ===
=== modeling ===
 +
 +
==== Overview====
 +
* [[media:ETH_Modeling_1Page_Overview.pdf|1 Page Overview (pdf)]] (∼1.2M) [[:Image:ETH_Modeling_1Page_Overview.pdf|all versions]]
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* [http://csb.inf.ethz.ch/igem-2006/whole.ai.zip 1 Page Overview (illustrator)] (∼1.3M)
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* [[media:ETH_Modeling_Overview.pdf|Modeling Overview (pdf)]] (∼0.5M) [[:image:ETH_Modeling_Overview.pdf|all versions]]
 +
* [[media:ETH_Modeling_Overview.ppt|Modeling Overview (ppt)]] (∼0.6M) [[:image:ETH_Modeling_Overview.ppt|all versions]]
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* [[media:IPTG_sensing.pdf|IPTG sensing (pdf)]] (∼0.1M) [[:image:IPTG_sensing.pdf|all versions]]
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* [[media:IPTG_sensing.ppt|IPTG sensing (ppt)]] (∼0.2M) [[:image:IPTG_sensing.ppt|all versions]]
 +
 +
====Matlab scripts for ODE simulation====
 +
===== modular scripts=====
 +
* contains a <code>createXXX()</code> 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''' &middot; '''r'''
 +
* modules can be ''connected'' using the <code>createInOutConnector()</code> script. the result is again a module, consisting of the connected basic modules.
 +
* <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.
 +
* both ''basic modules'' and ''compound (connected) modules'' can be simulated
 +
* <code>simulations</code> contains the first samples, simulating
 +
** ''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]]
 +
** ''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]]
 +
* scripts: [http://csb.inf.ethz.ch/igem-2006/matlab_modules.zip matlab_modules.zip] (&lt;0.1M)
 +
 +
===== old scripts =====
 +
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]] &rarr; ''abandoned''
 +
* [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'''
 +
* [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'''
 +
* [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''
 +
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]] &rarr; the only pursued version
 +
* [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''
 +
* [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''
 +
Sensoring
 +
* [http://csb.inf.ethz.ch/igem-2006/matlab_sim_iptg.zip matlab_sim_iptg.zip] (&lt;0.2M) &rarr;[[IPTG_1|simulation results]]
=== implementation ===
=== implementation ===

Revision as of 14:15, 6 October 2006

ETH Zurich

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

ETH Team 2006


Marco, Alexandra, Arthur, Olga, Dimo, Marko, Robert,


Franz, Michael


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.

filling in the details

modeling

Overview

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

implementation

Useful Documents & Links

see here

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