Difference between revisions of "DNA Melting Report Requirements"

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[[Category:20.309]]
 
[[Category:20.309]]
 
[[Category:DNA Melting Lab]]
 
[[Category:DNA Melting Lab]]
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{{Template:20.309}}
 
  
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===Report outline===
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* Follow the [[20.309:Lab Report Guidelines|lab report general guidelines]].
 +
* Please do '''not''' include your Part 1 report in this final report.
 +
* Provide a thorough and accurate discussion of error sources, measurement uncertainty, and confidence in your results. An outstanding error discussion is an essential element of a top-notch report.
 +
* One member of your group should submit a single PDF file to Stellar in advance of the deadline. The filename should consist of the last names of all group members, CamelCased, in alphabetical order, with a .pdf extension. Example: <code>CrickFranklinWatson.pdf</code>.
 +
* Remember to append your Matlab code at the end of the pdf file.
 +
* Not including the appendix, the report should not exceed 10 pages.
  
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Use the following format for your report:
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==Part 2 report outline==
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# Haiku:
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# Report submittal format
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#* Compose an entertaining, exhilarating, thought-provoking, or melancholy Haiku on the subject of DNA melting.
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#;Size of your lab manual file submitted MUST be less than 20 MB
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# Abstract:
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#;Post only pdf, with code included in the pdf at the end, not separately
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#* In one paragraph containing six or fewer sentences, summarize the investigation you undertook and key results.
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#;Include last name of each group member in the '''filename''' of the pdf you post. I would rather spend time carefully grading your report than renaming your files because every other group named theirs "DNA Report Part 2" or the like.
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# Introduction and Purpose:
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#Results
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#* Provide a succinct introduction to the project, including the purpose of the experiment, relevant background material and/or links to such information.
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#;Samples run:List all of the samples you characterized (length/match/ionic strength)
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#* Summarize the ways in which this part of the lab differs from Part 1.
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#;Data plots:All plots should be complete with title, axis labels, and legend. Plot both your experimental data and the best fit curves from the DNA melting mode. ''Plots in this section should include only data that was created by your group's own hands in the lab.'' Analysis of other people's datasets belongs in a different section (see below).
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#* Keep the length to one or two short paragraphs, no more than 1/3 of a page.
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##Single set of axes with plots of dsDNA concentration versus temperature for ALL raw data from all "known" samples that you ran.
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# Apparatus:
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##Single set of axes with plots of &Delta;dsDNA concentration/&Delta;temperature vs temperature for same.
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#* Document your instrument design.
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##Similar figure, single axes, showing results for unknown sample, possibly including other samples run for comparison.
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#** Describe your apparatus with sufficient detail for another person to replicate your work. Assume the reader is familiar with the concepts of 20.309 and has access to course materials.
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#;Model Parameter Determination: Show comparisons of your data to expected sigmoidal curve from the thermodynamic model and compare each to the "expected" result obtained from DINAmelt or another melting curve simulator.
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#**  Detail your electronic and optical subsystems. Include component values, gain values, cutoff frequencies, lens focal lengths, and relevant distances.
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##These plots should be in the "ideal" format. For each sample type: Fit a model to your melting curve data. Correct the data using the parameters obtained from your fit. Average the corrected curves for all successful runs of that sample type. Finally, compare each of those corrected, averaged curves to the ideal curve for that sample type. (Ideal curves are obtained using your fitted &Delta;S and &Delta;H in the basic thermodynamic model.)
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#** It is not necessary to document construction details, unless you built an instrument that was significantly different than the lab manual suggested.
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##Also include an example or two of plots in the "as-observed" format, showing your model fitted it to the as-observed data, along with a plot of your model using your initial guesses.
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#** Refer to schematics and diagrams in the lab manual instead of copying them into your report. Use reference designators (such as R7, C2) to refer to call out particular components in schematic diagrams.
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#;Unknown determination: Finally, include averaged, corrected data and a modeled response for your unknown sample either on the above dsDNA and &Delta;dsDNA plots, or in separate plots.
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#* Why not include a nice snapshot or two of the instrument? So lovely.
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#;Table of estimated thermodynamic parameters for each sample. Include estimated &Delta;H, &Delta;S, and T<sub>m</sub> values (by multiple methods)
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# Procedure:
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#;Comparative data analysis and plots:Plots of any data you analyzed that came from other groups
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#* Document the procedure used to gather your data.
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#;Data analysis overview:Informative '''Bullet point''' summary of your data analysis methodology. Teach us what you did.
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#** Refer to procedures in the lab manual. Describe any changes you made.
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#;Discussion of results:'''Bullet point''' discussion of results. Compare your results to theoretical models and/or other group's datasets. Be concise, but express yourself clearly.
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#** Report instrument settings for each trial, including control software parameters.
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#'''Sources of error:'''Detailed discussion of error sources. Indicate whether each source causes a systematic or random distortion in the data. (The uncertainty from a random error decreases with additional experimental runs; systematic error does not.) Consider all possible sources of error including all aspects of your instrument, the oligo design, the dye used, the experimental methodology, and the analysis methodology.
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# Data:
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# Instrument documentation
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#* Plot all of your raw data, fluorescence vs. block temperature, on the smallest number of axes that clearly conveys the dataset. Include only data generated by your own group.  
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#;Block diagram and schematics:Include component values, relevant distances, and possibly a photograph or two. It is not necessary to document construction details, but do show your work in determining your component values, distances, etc.
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#** Data from the many sample runs overlaps, which makes presenting so much data on a small number of axes a real challenge.  
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#;Signal to noise results
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#** Devise a combination of line colors, line thicknesses, and marker symbols that produces clear plot. If two sample types have a great deal of overlap, there may be no choice but to plot them on separate axes.
−
#;Design evolution:'''Bullet point''' summary of changes you made to your instrument design to address problems in the lab.
+
#** One approach that works well for some datasets is to plot a subsampled version of each trial using discrete markers. Vary the color and form to differentiate between sample types and individual trials.
 +
#* Report your signal to noise results.
 +
# Analysis:
 +
#* Use bullet points to explain your data analysis methodology.
 +
#* Document the regression model you used to analyze your data
 +
#** See [[DNA Melting: Model function and parameter estimation by nonlinear regression]]
 +
#** Explain the model parameters using bullet points or in a table.
 +
#* Plot <math>V_{f,measured}</math> and <math>V_{f,model}</math> versus <math>T_{block}</math> for a typical run of each samples type. Use the smallest number of axes that clearly conveys the data.
 +
#* For a typical curve, plot residuals versus time, temperature, and fluorescence, ([http://measurebiology.org/wiki/File:Residual_plot_for_DNA_data.png example plot]).
 +
#* Provide a table of the best-fit model parameters and confidence intervals for each experimental run. Also include the estimated melting temperature for each run.
 +
#* For at least one experimental trial, plot <math>\text{DnaFraction}_{inverse-model}</math> versus <math>T_{sample}</math> ([http://measurebiology.org/wiki/File:Inverse_cuvrve.png example plot]). On the same set of axes plot DnaFraction versus <math>T_{sample}</math> using the best-fit values of &Delta;H and &Delta;S. Finally, plot simulated dsDNA fraction vs. temperature using data from DINAmelt or another melting curve simulator.
 +
# Results:
 +
#* Identify your unknown sample (or state that your investigation did not provide a conclusive answer).
 +
#* Quantify the confidence you have in your result.
 +
# Discussion:
 +
#* Discuss the validity of assumptions in the regression model.
 +
#* Discuss any atypical results or data you rejected.
 +
#* Compare your data to results from other groups and/or instructor data.
 +
#* 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.
 +
#* Discuss significant error sources.  
 +
#** Consider the entire system: the oligos, dye, the experimental method, and analysis methodology, and any other relevant factors.
 +
#** Indicate whether each source likely caused a systematic or random distortion in the data.
 +
#** Present error sources, error type and their resultant uncertainty on your data and results in a table, if you like.
 +
#* Discuss additional unimplemented changes that might improve your instrument or analysis.
  
 
==Lab manual sections==
 
==Lab manual sections==
Line 36: Line 63:
 
*[[DNA Melting: Simulating DNA Melting - Basics]]
 
*[[DNA Melting: Simulating DNA Melting - Basics]]
 
*[[DNA Melting Part 1: Measuring Temperature and Fluorescence]]
 
*[[DNA Melting Part 1: Measuring Temperature and Fluorescence]]
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*[[DNA Melting Report Requirements for Part 1]]
 
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*[[DNA Melting: Simulating DNA Melting - Intermediate Topics]]
 
 
*[[DNA Melting Part 2: Lock-in Amplifier and Temperature Control]]
 
*[[DNA Melting Part 2: Lock-in Amplifier and Temperature Control]]
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*[[DNA Melting Report Requirements for Part 2]]
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*[[DNA Melting Report Requirements]]
  
 
{{Template:20.309 bottom}}
 
{{Template:20.309 bottom}}

Latest revision as of 18:50, 16 April 2017


  • Follow the lab report general guidelines.
  • Please do not include your Part 1 report in this final report.
  • Provide a thorough and accurate discussion of error sources, measurement uncertainty, and confidence in your results. An outstanding error discussion is an essential element of a top-notch report.
  • One member of your group should submit a single PDF file to Stellar in advance of the deadline. The filename should consist of the last names of all group members, CamelCased, in alphabetical order, with a .pdf extension. Example: CrickFranklinWatson.pdf.
  • Remember to append your Matlab code at the end of the pdf file.
  • Not including the appendix, the report should not exceed 10 pages.

Part 2 report outline

  1. Haiku:
    • Compose an entertaining, exhilarating, thought-provoking, or melancholy Haiku on the subject of DNA melting.
  2. Abstract:
    • In one paragraph containing six or fewer sentences, summarize the investigation you undertook and key results.
  3. Introduction and Purpose:
    • Provide a succinct introduction to the project, including the purpose of the experiment, relevant background material and/or links to such information.
    • Summarize the ways in which this part of the lab differs from Part 1.
    • Keep the length to one or two short paragraphs, no more than 1/3 of a page.
  4. Apparatus:
    • Document your instrument design.
      • Describe your apparatus with sufficient detail for another person to replicate your work. Assume the reader is familiar with the concepts of 20.309 and has access to course materials.
      • Detail your electronic and optical subsystems. Include component values, gain values, cutoff frequencies, lens focal lengths, and relevant distances.
      • It is not necessary to document construction details, unless you built an instrument that was significantly different than the lab manual suggested.
      • Refer to schematics and diagrams in the lab manual instead of copying them into your report. Use reference designators (such as R7, C2) to refer to call out particular components in schematic diagrams.
    • Why not include a nice snapshot or two of the instrument? So lovely.
  5. Procedure:
    • Document the procedure used to gather your data.
      • Refer to procedures in the lab manual. Describe any changes you made.
      • Report instrument settings for each trial, including control software parameters.
  6. Data:
    • Plot all of your raw data, fluorescence vs. block temperature, on the smallest number of axes that clearly conveys the dataset. Include only data generated by your own group.
      • Data from the many sample runs overlaps, which makes presenting so much data on a small number of axes a real challenge.
      • Devise a combination of line colors, line thicknesses, and marker symbols that produces clear plot. If two sample types have a great deal of overlap, there may be no choice but to plot them on separate axes.
      • One approach that works well for some datasets is to plot a subsampled version of each trial using discrete markers. Vary the color and form to differentiate between sample types and individual trials.
    • Report your signal to noise results.
  7. Analysis:
    • Use bullet points to explain your data analysis methodology.
    • Document the regression model you used to analyze your data
    • Plot $ V_{f,measured} $ and $ V_{f,model} $ versus $ T_{block} $ for a typical run of each samples type. Use the smallest number of axes that clearly conveys the data.
    • For a typical curve, plot residuals versus time, temperature, and fluorescence, (example plot).
    • Provide a table of the best-fit model parameters and confidence intervals for each experimental run. Also include the estimated melting temperature for each run.
    • For at least one experimental trial, plot $ \text{DnaFraction}_{inverse-model} $ versus $ T_{sample} $ (example plot). On the same set of axes plot DnaFraction versus $ T_{sample} $ using the best-fit values of ΔH and ΔS. Finally, plot simulated dsDNA fraction vs. temperature using data from DINAmelt or another melting curve simulator.
  8. Results:
    • Identify your unknown sample (or state that your investigation did not provide a conclusive answer).
    • Quantify the confidence you have in your result.
  9. Discussion:
    • Discuss the validity of assumptions in the regression model.
    • Discuss any atypical results or data you rejected.
    • Compare your data to results from other groups and/or instructor data.
    • 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.
    • Discuss significant error sources.
      • Consider the entire system: the oligos, dye, the experimental method, and analysis methodology, and any other relevant factors.
      • Indicate whether each source likely caused a systematic or random distortion in the data.
      • Present error sources, error type and their resultant uncertainty on your data and results in a table, if you like.
    • Discuss additional unimplemented changes that might improve your instrument or analysis.

Lab manual sections

</div>

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