CH391L/S14/FinalProjectRubric

Presentation
Your group should prepare a slide presentation covering the same material as the written report. Each person in a group is expected to present for roughly 5 minutes (max 20 min per group) with 10 minutes for questions afterward. Your peers will give you written comments at the end of class that point out areas in your proposal to improve for the written report.

Written Proposal
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?
 * What else do we need to know to understand your project?
 * Experimental Methods
 * What are you making? Describe this on two levels (see below).
 * Circuit/metabolic pathway diagram explaining the overall logic and function (TinkerCell?)
 * Annotated DNA sequences of final constructs showing parts and genes (Genome Compiler)
 * 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?
 * What might the failure of your design mean?
 * 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.
 * If someone fails to contribute this should be brought to the instructor's attention in private WELL in advance of turning in the final report.

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.

Grading
The following rubric describes the expectations for the final group projects, including the "mile markers", the oral presentation, and the final revised report.

Final Project Rubric

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.


 * TinkerCell CAD system
 * Synthetic Biology Open Language



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:
 * Genome Compiler (we will perform a tutorial in class)
 * ApE - A plasmid Editor (shareware)
 * Geneious - commercial (free version does not allow editing)