Stanford/BIOE44:Lab info

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|Design Project Report & Presentation || 30%
|Design Project Report & Presentation || 30%
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==Research Article Review==
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The class will work in groups of 2 or 3 to read and review the following 5 articles:
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<biblio>
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#Firefly+Plants pmid=17758108
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#MossTransformation pmid=15239842
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#GeneBuildingYeast pmid=19745056
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#RefactoringGenomes pmid=16729053
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#EvolutionaryCapacitor pmid=9845070
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#JurassicPark pmid=17077319
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</biblio>
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#Firefly+Plants: '''Karina, Alex'''
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#Moss Transformation: '''Drew''' <-- demo on Tuesday
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#Gene Building in Yeast: '''Travis, Aaditya, Daniel'''
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#Refactoring A Genome: '''Sunny, Frank'''
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#Evolutionary Capacitance: '''Claire, Sanjay'''
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#Retrovirus Resurrection: '''Scott, Chris'''
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Each team will need to prepare a 15 minute presentation summarizing your reading and critical assessment of each paper.  Your presentation should be 6 slides (not more, not less), following this structure:
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#Cover slide (authors, title of paper, journal)
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#Main finding (explain the single most important discovery or new technology presented in the paper)
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#Primary evidence (how is the main finding supported by the work presented in the paper?)
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#Main weakness (what is the strongest criticism or weakness that can leveled at the work presented in the paper?)
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#Future work (given the work presented in the paper, what are the 3 most important questions to be answered, or tools to be developed, next?)
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#Related reading (list four related research articles that you would like to read next in order to followup on what you've learned from this paper; state your "why" for each paper.
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'''GRADING''': Two-thirds of your grade will be on the content and quality of your six slides (please be concise and clear).  One-third of your grade will be on your presentation.  All readers/presenters should speak during the presentation.
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'''SLIDE DESIGN''': Take a look at the advice [[Media:EvenBetterGMPresentations3.pdf | here]], then use or find your own style!
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'''SCHEDULE''':
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#Firefly+Plants: Class/Lab, 13 May
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#Moss Transformation: Class/Lab, 13 May
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#Gene Building in Yeast: Class/Lab, 13 May
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#Refactoring A Genome: Class/Lab, 13 May
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#Evolutionary Capacitance: Class/Lab, 13 May
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'''SLIDE DESIGN''':
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==Design Projects, Reports & Presentations==
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[details to be discussed Tuesday 11 May]
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==Late Work==
<font color= red><b>Late work for major assignments will be penalized 1/3 of a letter grade for each day late and will not be accepted after a week. Daily quizzes and lab notebooks will not be accepted late.</b></font color>
<font color= red><b>Late work for major assignments will be penalized 1/3 of a letter grade for each day late and will not be accepted after a week. Daily quizzes and lab notebooks will not be accepted late.</b></font color>
==Lab Notebooks==
==Lab Notebooks==
*[[Stanford/BIOE44:Labnotebooks | Suggestions & guidelines for your lab notebook]]
*[[Stanford/BIOE44:Labnotebooks | Suggestions & guidelines for your lab notebook]]

Current revision

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Contents

Lab Attendance

Lab attendance is mandatory and there are no make-up labs. A family crisis or severe illness requiring attention from the infirmary and prohibiting you from all your coursework are acceptable reasons for missing lab and every effort will be made to accommodate you in these exceptional circumstances.

Grading

Assignment % of Final Grade
Daily Lab Quizzes 15%
Daily Lab Notebook 25%
Research Article Review 30%
Design Project Report & Presentation 30%

Research Article Review

The class will work in groups of 2 or 3 to read and review the following 5 articles:

  1. Ow DW, DE Wet JR, Helinski DR, Howell SH, Wood KV, and Deluca M. . pmid:17758108. PubMed HubMed [Firefly+Plants]
  2. Horstmann V, Huether CM, Jost W, Reski R, and Decker EL. . pmid:15239842. PubMed HubMed [MossTransformation]
  3. Gibson DG. . pmid:19745056. PubMed HubMed [GeneBuildingYeast]
  4. Chan LY, Kosuri S, and Endy D. . pmid:16729053. PubMed HubMed [RefactoringGenomes]
  5. Rutherford SL and Lindquist S. . pmid:9845070. PubMed HubMed [EvolutionaryCapacitor]
  6. Dewannieux M, Harper F, Richaud A, Letzelter C, Ribet D, Pierron G, and Heidmann T. . pmid:17077319. PubMed HubMed [JurassicPark]
All Medline abstracts: PubMed HubMed
  1. Firefly+Plants: Karina, Alex
  2. Moss Transformation: Drew <-- demo on Tuesday
  3. Gene Building in Yeast: Travis, Aaditya, Daniel
  4. Refactoring A Genome: Sunny, Frank
  5. Evolutionary Capacitance: Claire, Sanjay
  6. Retrovirus Resurrection: Scott, Chris

Each team will need to prepare a 15 minute presentation summarizing your reading and critical assessment of each paper. Your presentation should be 6 slides (not more, not less), following this structure:

  1. Cover slide (authors, title of paper, journal)
  2. Main finding (explain the single most important discovery or new technology presented in the paper)
  3. Primary evidence (how is the main finding supported by the work presented in the paper?)
  4. Main weakness (what is the strongest criticism or weakness that can leveled at the work presented in the paper?)
  5. Future work (given the work presented in the paper, what are the 3 most important questions to be answered, or tools to be developed, next?)
  6. Related reading (list four related research articles that you would like to read next in order to followup on what you've learned from this paper; state your "why" for each paper.

GRADING: Two-thirds of your grade will be on the content and quality of your six slides (please be concise and clear). One-third of your grade will be on your presentation. All readers/presenters should speak during the presentation.

SLIDE DESIGN: Take a look at the advice here, then use or find your own style!

SCHEDULE:

  1. Firefly+Plants: Class/Lab, 13 May
  2. Moss Transformation: Class/Lab, 13 May
  3. Gene Building in Yeast: Class/Lab, 13 May
  4. Refactoring A Genome: Class/Lab, 13 May
  5. Evolutionary Capacitance: Class/Lab, 13 May

SLIDE DESIGN:

Design Projects, Reports & Presentations

[details to be discussed Tuesday 11 May]

Late Work

Late work for major assignments will be penalized 1/3 of a letter grade for each day late and will not be accepted after a week. Daily quizzes and lab notebooks will not be accepted late.

Lab Notebooks

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