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Learning Goals (Planning/Design): When students finish the spring, they should be able to:

  1. Identify problems that are interesting and important
  2. Read a paper and extract useful information from it
  3. Identify and fill gaps in their own knowledge
  4. Formulate general strategies to address problems
  5. interesting research problems for which synthetic biology would be an appropriate approach
  6. Find relevant reports from the primary literature and summarize those reports' salient findings
  7. Plan a synthetic biology approach to address an interesting research problemPropose a specific implementation of a strategy
  8. Design experiments to demonstrate that implementation
  9. Design the DNAs necessary to implement the proposed strategy
  10. Design the cloning strategy necessary to construct those DNAs

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DateGoal/Activity
Feb 5
  • Intro: uh ..... olive oil? If available.
  • What is synbio? How is it different than bioengineering?
  • Semester overview / expectations
    • Instructor / advisor roles
  • Project possibilities
    • Weiss lab biases
    • Student roles / specializations
  • Project list - assignments
  • How to find a paper
  • How to read a paper
  • Homework: find and read (at least) one paper about the "state of the art" on your problem
    Come next week prepared to discuss one specific problem
Feb 12

GOAL: Narrow down to six projects

TPS: Paper reading experience

Learn more about reading papers; science-as-storytelling; group brainstorming

  • White board silent brainstorming
    • Project owner gives title, specific problem
    • Others: other problems, solutions, observations, connections, approaches
  • Review projects together
  • Vote or self-assort to six projects (1-3 people each)
  • TPS: paper-reading experience
  • Papers II
    • TPS: paper-reading experience
    How to present a paper
    • Concept map: parts of a paper ; < – > parts of an experiment
    • Introduction to science-as-storytelling
    • Intro to record keeping.
  • Homework: meet as a group, find and read one paper about your project; come prepared to present it (with slides)ONE EXPERIMENT
Feb 19

GOAL: Narrow down to three projects

  • Intro: ??
  • Each group presents (10 min each)
  • Vote or self-assort to three projects
  • Intro to synbio as a problem-solving strategy
    • Parts, circuits, input / processing / actuation
  • Homework: meet as a subgroup (with advisors, this time); propose two synbio-based approaches; come up with one relevant paper for each.
Feb 26

GOAL: Narrow down to two projects.

  • Intro: ??
  • Each group presents.
  • Vote one project off the island. (Preference voting?)
  • Classwork & homework: swap projects. (Ie, if you were working on Project #1, this week you work on Project #2. The one that was voted off self-assorts.)
    Propose two (different) synbio-based approaches; come up with one relevant paper for each. 
Mar 6

 

Mar 12 
Mar 19

Final project selection.

  • Review and vote.
  • Identify holes in knowledge, ways forward.
Mar 12 
Mar 19 
  • Project presentation, then feedback about
    • working / group project structure (what are the parallel tracks?)
    • risks?
    • positives / benefits?
Mar 26SPRING BREAK
Apr 2 
Apr 9 
Apr 16 
Apr 23 
Apr 30 

May 7

 
May 14 


Bootcamp planning notes:

 - Safety training: get the ball rolling tomorrow.

  • TC bootcamp: smaller groups – does project involve TC at all?
  • Geneious and cloning together: plan the plasmid, build the plasmid, check the insilico RE map, do the RE
  • Make the plasmids built in the colonig bootcamp count – even if the advisors have to dictate the plasmids
  • Plan: thurs evenings split: 1 hr w/ Ron (planning / design / specification), 1 hr on dry skills (Geneious, etc.)
  • Probably 2 more meetings each week: 1 subgroup meeting with an advisor for planning / specification, 1 (wknd afternoon) for wet skills
  • Human practices - talk to other experts.