Difference between revisions of "DNA Melting Report Requirements"

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# Model parameters
 
# Model parameters
 
#* Develop a model for the melting experiment and use nonlinear regression to determine best-fit parameters.  
 
#* Develop a model for the melting experiment and use nonlinear regression to determine best-fit parameters.  
−
#* Explain the model parameters using bullet points.
+
#* Explain the model parameters using bullet points or in a table.
 
#* Include a table of the best-fit model parameters and confidence intervals for each experimental run.
 
#* Include a table of the best-fit model parameters and confidence intervals for each experimental run.
−
#* Use the smallest possible number of plots to show <math>V_{f,measured}</math> and <math>V_{f,model}</math>
+
#* Use the smallest possible number of plots to show <math>V_{f,measured}</math> and <math>V_{f,model}</math> plotted versus <math>\theta_{block}</math>
 
#* Plot one of the following for at least one experimental run:
 
#* Plot one of the following for at least one experimental run:
 
#** residuals versus time, temperature, and fluorescence, (example plot: [http://measure.mit.edu/~20.309/wiki/index.php?title=File:Residual_plot_for_DNA_data.png]) '''or'''  
 
#** residuals versus time, temperature, and fluorescence, (example plot: [http://measure.mit.edu/~20.309/wiki/index.php?title=File:Residual_plot_for_DNA_data.png]) '''or'''  
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#** Confidence is quantitative.
 
#** Confidence is quantitative.
 
# Results and discussion
 
# Results and discussion
−
#* Include a table of estimated thermodynamic parameters, &Delta;H, &Delta;S, and T<sub>m</sub>. Use multiple methods to find T<sub>m</sub>.
+
#* Include a summary table of estimated thermodynamic parameters, &Delta;H, &Delta;S, and T<sub>m</sub>. Use multiple methods to find T<sub>m</sub>.
 
#* Compare your data to results from other groups or instructor data.
 
#* Compare your data to results from other groups or instructor data.
 
#* Discuss significant error sources.  
 
#* Discuss significant error sources.  
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#* Document the electronic and optical systems.
 
#* Document the electronic and optical systems.
 
#** Include component values, gain values, cutoff frequencies, lens focal lengths, and relevant distances.
 
#** Include component values, gain values, cutoff frequencies, lens focal lengths, and relevant distances.
 +
#** Feel free to reference schematics in the lab manual instead of copying them into your report. Use the reference designators (such as R7, C2) to refer to components in the schematics.
 
#** It is not necessary to document construction details.
 
#** It is not necessary to document construction details.
 
#* Why not include a nice snapshot or two of the instrument?
 
#* Why not include a nice snapshot or two of the instrument?
 
#* Include your signal to noise results
 
#* Include your signal to noise results
−
#* Give a bullet point summary of major changes that you made to your instrument design between the end of Part 1 and the end of Part 2 to address problems in the lab.
+
#* Give a bullet point summary of problems you encountered in the lab during part 2 and changes that you made to your instrument and methodology to address those issues.
−
#**What were those problems and how well did each change address it?
+
  
 
==Lab manual sections==
 
==Lab manual sections==

Revision as of 23:36, 18 November 2012

20.309: Biological Instrumentation and Measurement

ImageBar 774.jpg


Format

  • One group member must submit a single PDF file no larger than 20 MB to Stellar before the deadline.
  • The name of the submitted file must consist of the last name of each group member separated by underscores: <LastName1>_<LastName2>_<LastName2>.pdf
  • Include computer code in an appendix at the end of the file. Do not submit code separately.
  • Present data properly. Follow the 20.309:Lab Report Guidelines. Include a descriptive title, axis labels, and legend on all plots.
  • Begin the report with a cover page that lists the full names of group members, your assigned DNA sample number, the type of investigation (length/ionic strength/complementarity), and a haiku about DNA melting curves.


Failure to follow the format guidelines will result in ridiculously large grade penalties

Report outline

  1. Abstract:
    • In one paragraph of less than six sentences, summarize the investigation you undertook and key results.
  2. Raw data
    • Plot all of your raw data, fluorescence vs. block temperature, on the smallest number of axes that clearly convey the dataset. Include only datasets generated by your own group.
    • On similary-grouped sets of axes, plot ΔdsDNA fraction/Δtemperature versus temperature. Filter high-noise outliers in the derivative where appropriate.
  3. Model parameters
    • Develop a model for the melting experiment and use nonlinear regression to determine best-fit parameters.
    • Explain the model parameters using bullet points or in a table.
    • Include a table of the best-fit model parameters and confidence intervals for each experimental run.
    • Use the smallest possible number of plots to show $ V_{f,measured} $ and $ V_{f,model} $ plotted versus $ \theta_{block} $
    • Plot one of the following for at least one experimental run:
      • residuals versus time, temperature, and fluorescence, (example plot: [1]) or
      • use best-fit parameters and the inverse of your model function to transform the fluorescence voltage into dsDNA fraction versus sample temperature (example plot: [2]). Plot $ \text{DnaFraction}_{inverse-model} $ on the same set of axes with DnaFraction model data using the best-fit values of ΔH and ΔS. Also include a simulated dsDNA fraction versus temperature curve obtained from DINAmelt or another melting curve simulator.
    • Comment on strengths and shortcomings of the model.
      • Discuss the validity of underlying assumptions.
      • Discuss the residuals (or transformed data) plot and parameter confidence intervals.
  4. Unknown sample determination:
    • Plot results for your unknown sample, including those from your other samples for comparison.
    • Identify your unknown sample and state your level of confidence in the answer.
      • Confidence is quantitative.
  5. Results and discussion
    • Include a summary table of estimated thermodynamic parameters, ΔH, ΔS, and Tm. Use multiple methods to find Tm.
    • Compare your data to results from other groups or instructor data.
    • Discuss significant error sources.
      • Indicate whether each source likely caused a systematic or random distortion in the data.
      • Consider the entire system: the oligos, dye, the experimental method, and analysis methodology, and any other relevant factors.
      • Present error sources in a table, if you like.
  6. Analysis
    • Use bullet points to explain your data analysis methodology.
  7. Instrument documentation
    • Document the electronic and optical systems.
      • Include component values, gain values, cutoff frequencies, lens focal lengths, and relevant distances.
      • Feel free to reference schematics in the lab manual instead of copying them into your report. Use the reference designators (such as R7, C2) to refer to components in the schematics.
      • It is not necessary to document construction details.
    • Why not include a nice snapshot or two of the instrument?
    • Include your signal to noise results
    • Give a bullet point summary of problems you encountered in the lab during part 2 and changes that you made to your instrument and methodology to address those issues.

Lab manual sections

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