CH391L/S12/FinalProjectRubric

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(Representing Synthetic Biology Parts, CIrcuits, and Constructs)
Current revision (13:29, 9 April 2012) (view source)
(Describing your project's DNA sequences)
 
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== Final Project ==
== Final Project ==
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* '''Background and Motivation'''
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Please divide your final project into these areas:
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** Describe the big picture technological, scientific, or societal impact of your project.
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* '''Abstract''' (1 paragraph, 250 words max)
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** Overall summary of your project.
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* '''Motivation''' (1-3 paragraphs)
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** Describe the big picture technological, scientific, or societal impact of your project.  
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* '''Background''' (4-6 paragraphs)
** State of the art: What has been done to tackle this problem before?
** State of the art: What has been done to tackle this problem before?
** Where did the biological parts you are using come from?
** Where did the biological parts you are using come from?
** How have these parts been used before in synthetic biology?
** How have these parts been used before in synthetic biology?
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* '''Methods'''
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* '''Experimental Methods'''  
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** Exactly how will you get the required genes, strains, and plasmids?
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** What are you making? Describe this on two levels (see below).
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** What DNA sequences will you construct? How will you construct them? Be specific down to the level of creating a flowchart describing the oligonucleotide sequences, PCR reactions, cloning reactions, etc., you would use.
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**# Circuit/metabolic pathway diagram explaining the overall logic and function
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** How will you test your constructs? What are the expected results?
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**# Annotated DNA sequences of final constructs showing parts and genes
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** How can you troubleshoot failed experiments? Are there alternative approaches to the same final goal?
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** What are your sources for parts, genes, strains, and plasmids? Be specific. (Plasmid X from AddGene, part Y from the iGEM registry, etc.)
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** How would you construct your DNA sequences in lab?
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*** Imagine a flowchart of PCR reactions, cloning reactions, etc., you would use.
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*** Be specific, but there is no need to actually design primer sequences.
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* '''Computational Methods'''
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** If applicable, describe how you could simulate your system or use computational approaches to better understand your system and improve the chances of your project's success.
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* '''Expected Results'''
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** How will you test your constructs?  
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** What are the expected results? What is a measure of success?
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* '''Troubleshooting''' (2-3 paragraphs)
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** What would you do if your design did not work?  
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** How can you troubleshoot failed experiments or constructs that do not fully function?  
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** Are there alternative approaches to the same final goal?
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* '''Author contributions''' (1 paragraph)
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** Describe what each project member contributed to the final written document.
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** What figures they created, what sections they wrote, what ideas they came up with.
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** You should all contribute to editing the final document.
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The entire document should aim for 10-15 pages double spaced with 1" margins. Longer or shorter is fine if all of the objectives are met.
Your group will be given an opportunity to respond to comments and revise the written part of the project after the final presentation.
Your group will be given an opportunity to respond to comments and revise the written part of the project after the final presentation.
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For your project, you are required to create two representations of your synthetic biology constructs.  
For your project, you are required to create two representations of your synthetic biology constructs.  
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First, you need a high-level flowchart/circuit diagram. I recommend using TinkerCell to create this image. Label standardized parts from the iGEM registry with their numbers. Indicate the sources of non-registry DNA sequences.
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First, you need a high-level circuit/metabolic pathway diagram. I recommend using TinkerCell to create this image. Label standardized parts from the iGEM registry with their numbers. Indicate the sources of non-registry DNA sequences.
* [http://www.tinkercell.com/ TinkerCell CAD system]
* [http://www.tinkercell.com/ TinkerCell CAD system]

Current revision

Final Project

Please divide your final project into these areas:

  • Abstract (1 paragraph, 250 words max)
    • Overall summary of your project.
  • Motivation (1-3 paragraphs)
    • Describe the big picture technological, scientific, or societal impact of your project.
  • Background (4-6 paragraphs)
    • State of the art: What has been done to tackle this problem before?
    • Where did the biological parts you are using come from?
    • How have these parts been used before in synthetic biology?
  • Experimental Methods
    • What are you making? Describe this on two levels (see below).
      1. Circuit/metabolic pathway diagram explaining the overall logic and function
      2. Annotated DNA sequences of final constructs showing parts and genes
    • What are your sources for parts, genes, strains, and plasmids? Be specific. (Plasmid X from AddGene, part Y from the iGEM registry, etc.)
    • How would you construct your DNA sequences in lab?
      • Imagine a flowchart of PCR reactions, cloning reactions, etc., you would use.
      • Be specific, but there is no need to actually design primer sequences.
  • Computational Methods
    • If applicable, describe how you could simulate your system or use computational approaches to better understand your system and improve the chances of your project's success.
  • Expected Results
    • How will you test your constructs?
    • What are the expected results? What is a measure of success?
  • Troubleshooting (2-3 paragraphs)
    • What would you do if your design did not work?
    • How can you troubleshoot failed experiments or constructs that do not fully function?
    • Are there alternative approaches to the same final goal?
  • Author contributions (1 paragraph)
    • Describe what each project member contributed to the final written document.
    • What figures they created, what sections they wrote, what ideas they came up with.
    • You should all contribute to editing the final document.

The entire document should aim for 10-15 pages double spaced with 1" margins. Longer or shorter is fine if all of the objectives are met.

Your group will be given an opportunity to respond to comments and revise the written part of the project after the final presentation.

Group effort (200 pts)

Individual effort (100 pts)

Total (300 pts)

Describing your project's DNA sequences

For your project, you are required to create two representations of your synthetic biology constructs.

First, you need a high-level circuit/metabolic pathway diagram. I recommend using TinkerCell to create this image. Label standardized parts from the iGEM registry with their numbers. Indicate the sources of non-registry DNA sequences.

Example of a circuit drawn using TinkerCell
Example of a circuit drawn using TinkerCell

Second, you need a file showing the full DNA sequence of the construct. For creating the sequence file, I recommend using one of these software programs:

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