Waterloo

From 2007.igem.org

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<center><font size="6">[[Image:UWLogo.jpg]] University of Waterloo iGEM Team </font></center>
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<center> [[Image:UW_iGEMLogoHeader.png | 935px]] </center>
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<br>
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== Our Team ==
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{| style="border-spacing:0px; border-width:thin; border-color:black; border-style:solid"
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The UW iGEM team is a very interdisciplinary group. Our team members span the four faculties of Science, Mathematics, Engineering, and Applied Health Sciences and include the programs of Biology, Health Studies, Computer Science, Bioinformatics, Computer Engineering, Electrical Engineering, Chemical Engineering, and Mathematical Physics at undergraduate and graduate levels. Even our professor advisors are cross-appointed to two other faculties.  Our diverse backgrounds bring together a wide range of skills and ideas to the iGEM project. iGEM is giving us the opportunity to learn.  
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|-
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| style="font-size:x-large; font-weight:bold; border-bottom-width:thin; border-bottom-color:black; border-bottom-style:solid; font-size:x-large; font-weight:bold; padding:5px; background-color:#FBCC30" | Our Team
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|-
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| style="padding:5px" | [[Image:Group photo mimi1.JPG|470px|left|thumb|Undergraduate Members]]  [[Image:UW_Advisors.jpg|407px|center|thumb|Faculty and Graduate Advisors]]
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| style="padding:5px" | The UW iGEM team is a very interdisciplinary group. Our team members span three faculties: Science, Mathematics, and Engineering, and represent a wide range of undergraduate programs: Biology, Biomedical Sciences, Biochemistry, Computer Science, Bioinformatics, Computer Engineering, Electrical Engineering, Chemical Engineering, Systems Design Engineering, and Mathematical Physics.
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== Our Design ==
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Drawing on our diverse backgrounds, we bring a wide range of skills and modes of creative thinking to our iGEM project. The iGEM competition is providing us with an opportunity to become more familiar with the emerging field of synthetic biology in an engaging and fun atmosphere.  In addition to gaining experience in the design, construction, and analysis of genetic circuits, we are also meeting the challenge of bringing together a large, diverse group toward a common goal.
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Our project is a light-controlled 1-bit adder.
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=== The Inputs ===
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We will be using red light as one of the inputs and blue light as the other.  The red light will be detected by the previously used Cph1/EnvZ fusion protein ([http://partsregistry.org/Part:BBa_I15010 BBa_I15010]). 
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The blue light input will be derived from the ''Myxococcus xanthus'' carotenogenesis system, a list of relevant references can be found below.  In the event this input should prove difficult to implement, we will use a chemical input instead.
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{| style="border-spacing:0px; border-width:thin; border-color:black; border-style:solid; width:100%"
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|-
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| colspan="4" style="border-bottom-width:thin; border-bottom-color:black; border-bottom-style:solid; font-size:x-large; font-weight:bold; padding:5px; background-color:#FBCC30" | Our Project
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|-
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| colspan="4" style="padding:5px; font-size:large" | Abstract
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| colspan="2" style="vertical-align:top; border-bottom-width:thin; border-bottom-color:black; border-bottom-style:solid; padding:5px" | The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome.
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'''Blue-light References:'''
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Half adders are used as building blocks for full adders, which perform calculations similar to long addition but in binary. They are also an essential component in a device called the Arithmetic Logic Unit (ALU), a fundamental building block for the central processing unit in a modern computer. ALUs perform simple and complex operations such as bitwise logical operations and mathematical operations.
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# Moraleda-Muñoz A, Pérez J, Fontes M, Murillo FJ, Muñoz-Dorado J. (2005) ''Molecular Microbiology'' '''56''' (5):1159-68
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The constructs for the half adder were built in parallel as well as the testing constructs. A future extension to this project would be to create a full adder. More information on each stage of the project is available below.
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# Browning DF, Whitworth DE, Hodgson DA. (2003) ''Molecular Microbiology'' '''48''' (1):237-251
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# Whitworth DE, Bryan SJ, Berry AE, McGowan SJ, Hodgson DA. (2004) ''Journal of Bacteriology'' '''186''' (23):7836-46
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# Whitworth DE, Hodgson DA. (2001) ''Molecular Microbiology'' '''42''' (3): 809-819
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# López-Rubio JJ, Elías-Arnanz M, Padmanabhan S, Murillo FJ. (2002) ''The Journal of Biological Chemistry'' '''277''' (9):7262-70
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| colspan="2" style="border-bottom-width:thin; border-bottom-color:black; border-bottom-style:solid; padding:5px; vertical-align:middle" | [[Image:Design schematic.jpg|thumb|center|475px|Schematic Design of the Biological Half-Adder]]
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|-
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| style="width:25%; border-right-width:thin; border-right-color:black; border-right-style:solid; font-size:large; text-align:left; padding:5px; background-color:#FBCC30" | [[Project | Project Design]] || style="width:25%; border-right-width:thin; border-right-color:black; border-right-style:solid; font-size:large; text-align:left; padding:5px; background-color:#FBCC30"  | [[Modelling | Mathematical Modelling]] || style="width:25%; border-right-width:thin; border-right-color:black; border-right-style:solid; font-size:large; text-align:left; padding:5px; background-color:#FBCC30" | [[Construction_and_Testing | Construction and Testing]] || style="width:25%; font-size:large; text-align:left; padding:5px; background-color:#FBCC30" | [[Future_Work | Future Work]]
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|-
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| style="vertical-align:top; border-right-width:thin; border-right-color:black; border-right-style:solid; padding:5px" |
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* Binary addition and boolean logic
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* Half-adder vs. full-adder designs
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* Biological half-adder implementation
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| style="vertical-align:top; border-right-width:thin; border-right-color:black; border-right-style:solid; padding:5px" |
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* Modelling the gene regulatory network
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* Simulation results
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| style="vertical-align:top; border-right-width:thin; border-right-color:black; border-right-style:solid; padding:5px" |
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* Strategy for half-adder construction
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* Testing constructs for device
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* Test execution plan
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* Submitted parts
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| style="vertical-align:top; padding:5px" |
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* Explanation of a full adder
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* Gene design for full adder
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* Implementation plan
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|}
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We have chosen to use light as an input for many reasons: it does not require altering the media, it can be turned on and off rapidly, and it has extremely high resolution and accuracy.
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=== The Logic Gates ===
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{| style="border-spacing:0px; border-width:thin; border-color:black; border-style:solid; width:100%; text-align:center"
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|-
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| style="font-size:x-large; font-weight:bold; font-size:x-large; font-weight:bold; padding:5px; background-color:#FBCC30; border-bottom-width:thin; border-bottom-color:black; border-bottom-style:solid; text-align:left" colspan="15" | Acknowledgements
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| colspan="3" | [[Image:Fsf_logo.gif|150px]] || colspan="3" | [[Image:MEF_logo.gif|150px]] || colspan="3" | [[Image:SFF_Logo.gif|150px]] || colspan="3" | [[Image:WEEFLogo.jpg|150px]] || colspan="3" | [[Image:WatSEF_Logo.jpg|150px]]
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| colspan="3" | [http://www.science.uwaterloo.ca/fsf/index.html Faculty of Science Foundation ] || colspan="3" | [http://www.student.math.uwaterloo.ca/~mefcom/ Mathematics Endowment Fund ] || colspan="3" | [http://www.eng.uwaterloo.ca/~sff/ Sir Sanford Fleming Foundation] || colspan="3" | [http://www.weef.uwaterloo.ca/ Waterloo Engineering Endowment Fund] || colspan="3" | [http://www.science.uwaterloo.ca/~watsef/mainpage.html Waterloo Science Endowment Fund]
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|-
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| colspan="15" | &nbsp;
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|-
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| colspan="5" | [[Image:UW_EngFacLogo.PNG |150px]] || colspan="5" | [[Image:UW_SciFacLogo.PNG|150px]] || colspan="5" | [[Image:UW_MathFacLogo.PNG|150px]]
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| colspan="5" | [http://www.engineering.uwaterloo.ca University of Waterloo Faculty of Engineering] || colspan="5" | [http://www.science.uwaterloo.ca University of Waterloo Faculty of Science] || colspan="5" | [http://www.math.uwaterloo.ca University of Waterloo Faculty of Mathematics]
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| colspan="15" | &nbsp;
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|-
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| colspan="5" style="padding:5px" | [[Image:UW_Waterloocrest.PNG | 150px]] || colspan="10" style="text-align:left; padding:5px" | We would like to thank the following people for their support and guidance:
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* Dr. Trevor Charles
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* Dr. Barbara Moffatt
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* Dr. Joshua Neufeld
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In order to have a functional adder, we are designing an AND gate as well as an XOR gate.
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<center>
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== Supporters ==
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  [[Waterloo | Home ]] | [[Project | Project]] | [[Modelling | Mathematical Modelling]] | [[Construction_and_Testing | Construction and Testing]] | [[Future_Work | Future Work]]  
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We would like to thank:
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</center>
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[http://www.science.uwaterloo.ca Faculty of Science] — [http://www.math.uwaterloo.ca Faculty of Math] — [http://www.engineering.uwaterloo.ca Faculty of Engineering]
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[http://www.weef.uwaterloo.ca Waterloo Engineering Endowment Fund] — [http://www.mef.uwaterloo.ca Mathematics Endowment Fund]
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Latest revision as of 04:02, 27 October 2007

UW iGEMLogoHeader.png


Our Team
Undergraduate Members
Faculty and Graduate Advisors
The UW iGEM team is a very interdisciplinary group. Our team members span three faculties: Science, Mathematics, and Engineering, and represent a wide range of undergraduate programs: Biology, Biomedical Sciences, Biochemistry, Computer Science, Bioinformatics, Computer Engineering, Electrical Engineering, Chemical Engineering, Systems Design Engineering, and Mathematical Physics.

Drawing on our diverse backgrounds, we bring a wide range of skills and modes of creative thinking to our iGEM project. The iGEM competition is providing us with an opportunity to become more familiar with the emerging field of synthetic biology in an engaging and fun atmosphere. In addition to gaining experience in the design, construction, and analysis of genetic circuits, we are also meeting the challenge of bringing together a large, diverse group toward a common goal.


Our Project
Abstract
The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome.

Half adders are used as building blocks for full adders, which perform calculations similar to long addition but in binary. They are also an essential component in a device called the Arithmetic Logic Unit (ALU), a fundamental building block for the central processing unit in a modern computer. ALUs perform simple and complex operations such as bitwise logical operations and mathematical operations.

The constructs for the half adder were built in parallel as well as the testing constructs. A future extension to this project would be to create a full adder. More information on each stage of the project is available below.

Schematic Design of the Biological Half-Adder
Project Design Mathematical Modelling Construction and Testing Future Work
  • Binary addition and boolean logic
  • Half-adder vs. full-adder designs
  • Biological half-adder implementation
  • Modelling the gene regulatory network
  • Simulation results
  • Strategy for half-adder construction
  • Testing constructs for device
  • Test execution plan
  • Submitted parts
  • Explanation of a full adder
  • Gene design for full adder
  • Implementation plan


Acknowledgements
Fsf logo.gif MEF logo.gif SFF Logo.gif WEEFLogo.jpg WatSEF Logo.jpg
[http://www.science.uwaterloo.ca/fsf/index.html Faculty of Science Foundation ] [http://www.student.math.uwaterloo.ca/~mefcom/ Mathematics Endowment Fund ] [http://www.eng.uwaterloo.ca/~sff/ Sir Sanford Fleming Foundation] [http://www.weef.uwaterloo.ca/ Waterloo Engineering Endowment Fund] [http://www.science.uwaterloo.ca/~watsef/mainpage.html Waterloo Science Endowment Fund]
 
UW EngFacLogo.PNG UW SciFacLogo.PNG UW MathFacLogo.PNG
[http://www.engineering.uwaterloo.ca University of Waterloo Faculty of Engineering] [http://www.science.uwaterloo.ca University of Waterloo Faculty of Science] [http://www.math.uwaterloo.ca University of Waterloo Faculty of Mathematics]
 
UW Waterloocrest.PNG We would like to thank the following people for their support and guidance:
  • Dr. Trevor Charles
  • Dr. Barbara Moffatt
  • Dr. Joshua Neufeld 


  Home  |  Project |  Mathematical Modelling |  Construction and Testing |  Future Work
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