Stanford/BIOE44:Lab info

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(New page: {{Template:Stanford/BioE44}} <div style="padding: 5px; width: 656px; border: 2px solid #397D02;"> Lab notebooks are kept to document and organize your experimental plans and data. Every l...)
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Lab notebooks are kept to document and organize your experimental plans and data. Every lab requires each researcher to keep one. Yet no two scientists organize their lab notebooks identically, and there isn’t one “right” way for you to keep yours. There are some common elements that all lab notebooks share and some important habits you should develop in keeping your notebook for this class. All lab notebooks should be...
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==Lab Attendance==
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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.
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===1. Complete===
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==Grading==
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Your notebook is a place to collect descriptions of experimental goals, experimental procedures, all the data you collect, and your interpretations of results. Numerical data and calculations should be written directly into your notebook, not on scraps of paper to be entered later. Data in the form of a photo should be taped into your notebook. Printouts and X-ray films can also be taped into your notebook or if reams of paper and large films are being collected, they can be organized in a separate binder and referenced in your notebook.
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{| border="1" cellpadding="2"
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!width="225"|Assignment
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!width="50"|% of Final Grade
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|-
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|Daily Lab Quizzes || 15%
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|-
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|Daily Lab Notebook || 25%
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|-
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|Research Article Review || 30%
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|-
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|Design Project Report & Presentation || 30%
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|}
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===2. Organized===
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==Research Article Review==
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Some scientists arrange their notebooks by date, others by the question being tested. What works best depends on the research itself and the researcher. Since this class has two experimental modules that are performed sequentially, your notebook will, by default, be organized by both date and project. You will keep a record of every lab meeting, including both the date and the Module/Day in your notebook.
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===3. Up to date===
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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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For this class, that means coming to lab with the date, Module/Day, title, purpose, and description already entered in your notebook. It will occasionally be helpful to have data tables ready or some calculations performed as well. “Up to date” also means leaving lab with your protocol and any amendments you made to it, data, and perhaps some interpretation entered in your notebooks. Your notebook does not need a table of contents, but you should realize that most research notebooks do.
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===4. Permanent===
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<biblio>
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Use pen when you write in your notebooks.
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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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==Some other things you should know about lab notebooks==
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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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*They are the property of the research lab itself. Researchers who join the lab after you have left it will get to know you through the notebooks you have kept there. Ideally, your notebooks will reflect your most organized, clear and thoughtful side.
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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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*They are legal documents. Labs in industry have special rules about lab notebooks since patent disputes and court cases often hinge on lab notebook entries.
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*They are both personal and public. It is considered impolite and an invasion of privacy to read someone else’s notebook without their permission. Most people are happy to show you their notebooks when asked.  
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==Evaluation==
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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 your notebook===
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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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The 20.109 teaching assistants will collect the duplicate copy of your notebook pages and evaluate them as follows:
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  Lab Notebook Evaluation
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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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  Date of experiment &radic;- &radic; &radic;+
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  Module#/Day#         &radic;- &radic; &radic;+
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  Title for experiment &radic;- &radic; &radic;+
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  Brief statement of purpose &radic;- &radic; &radic;+
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  Protocol         &radic;- &radic; &radic;+
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  Tables for data entry &radic;- &radic; &radic;+
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  Calculations entered &radic;- &radic; &radic;+
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  Data labeled         &radic;- &radic; &radic;+
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  Summary/interpretation          &radic;- &radic; &radic;+
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  '''Overall'''     &radic;- &radic; &radic;+
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==Things to remember==
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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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Remember the goal of your notebook is to help you repeat your experiments with the same results. Information you should record includes
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'''SLIDE DESIGN''':
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*Centrifuge settings: temperature, speed, time
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*Incubator settings: temperature, time, and shaking speed if applicable
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*Size and types of tubes used
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*Buffers (and their pH)
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*Media
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*Dilutions and how they were prepared
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*Concentrations
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*Volumes used
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*Washes: number, volumes, temperature, solutions used
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*Antibody: dilutions, lot or tube #s
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*Electrophoresis: Agarose or acrylamide percentages, voltages, times
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*The names of people who helped you with your experiment
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You should also note any changes to the protocol such as
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==Design Projects, Reports & Presentations==
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*unexpected delays (“waterbath wasn’t ready so tubes kept on ice for one hour”),
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[details to be discussed Tuesday 11 May]
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*unanticipated conditions (“roller drum found off in AM”)
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*unusual observations (“a large number of cells seemed to be floating”).
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==Late Work==
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<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>
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==Lab Notebooks==
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*[[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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