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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==Format==
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* Follow the [[20.309:Lab Report Guidelines|lab report general guidelines]].
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* One group member must submit a single PDF file no more than 20 MB to Stellar before the deadline.
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* Please do '''not''' include your Part 1 report in this final report.
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* The name of the submitted file must consist of the last name of each group member separated by underscores: <LastName1>_<LastName2>_<LastName2>.pdf
+
* 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.
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* Include computer code in an appendix at the end of the file. Do not submit code separately.
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* 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>.
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* All plots must be presented properly, including a descriptive title, axis labels, and legend.
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* Remember to append your Matlab code at the end of the pdf file.
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* Begin the report with a cover page the lists the full names of all group members, your assigned DNA sample number, the type of investigation (length/ionic strength/complementarity), and a haiku about DNA melting curves.
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* Not including the appendix, the report should not exceed 10 pages.
  
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==Part 2 report outline==
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''Failure to follow the format guidelines will result in ridiculously large grade penalties''
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# Haiku:
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#* Compose an entertaining, exhilarating, thought-provoking, or melancholy Haiku on the subject of DNA melting.
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==Report outline==
+
 
# Abstract:  
 
# Abstract:  
−
#* In one paragraph of less than six sentences, summarize the investigation you undertook and key results.
+
#* In one paragraph containing six or fewer sentences, summarize the investigation you undertook and key results.
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# Raw data
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# Introduction and Purpose:
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#*Plot all of your group's raw data, fluorescence vs. temperature, on the smallest number of axes that clearly convey the dataset. Include only data datasets generated by your own group.
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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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#* On similary-grouped sets of axes, plot &Delta;dsDNA fraction/&Delta;temperature.
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#* Summarize the ways in which this part of the lab differs from Part 1.
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# Model parameters
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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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#* Develop a model for the melting experiment and use nonlinear regression to determine best-fit parameters.  
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# Apparatus:
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#* Explain the model parameters using bullet points.
+
#* Document your instrument design.
−
#* Include a table of model parameters and confidence intervals for each experimental run.
+
#** 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.
−
#* Use the smallest possible number of fluorescence voltage vs. temperature plots to compare the model with best-fit parameters to your data and a simulated result obtained from DINAmelt or another melting curve simulator.
+
#** Detail your electronic and optical subsystems. Include component values, gain values, cutoff frequencies, lens focal lengths, and relevant distances.
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#* Plot one of the following for at least one experimental run:
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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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#** residuals versus time, temperature, and fluorescence, '''or'''
+
#** 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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#** use best-fit parameters to transform the fluorescence voltage into dsDNA fraction versus temperature.
+
#* Why not include a nice snapshot or two of the instrument? So lovely.
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#* Comment on strengths and shortcomings of the model.
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# Procedure:
−
#** Discuss validity of underlying assumptions.
+
#* Document the procedure used to gather your data.  
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#** Discuss the residuals (or transformed data) plot and parameter confidence intervals.
+
#** Refer to procedures in the lab manual. Describe any changes you made.
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# Unknown sample determination:
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#** Report instrument settings for each trial, including control software parameters.
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#* Plot results for unknown sample, including other samples for comparison.
+
# Data:
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#* Identify your unknown sample and state your level of confidence in the answer.
+
#* 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.  
−
#*Use the smallest possible number of plots to compare the unknown sample to the corresponding known sample.
+
#** Data from the many sample runs overlaps, which makes presenting so much data on a small number of axes a real challenge.  
−
# Results and discussion
+
#** 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.
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#* 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>.
+
#** 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.
−
#* Compare your data to results from other groups or instructor data.
+
#* Report your signal to noise results.
−
# Analysis
+
# Analysis:
 
#* Use bullet points to explain your data analysis methodology.
 
#* Use bullet points to explain your data analysis methodology.
−
# Error sources
+
#* Document the regression model you used to analyze your data
−
#* Discuss important error sources.
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#** See [[DNA Melting: Model function and parameter estimation by nonlinear regression]]
−
#* Indicate whether each source causes a systematic or random distortion in the data.  
+
#** Explain the model parameters using bullet points or in a table.
−
#* Consider the entire system: the oligos, dye, the experimental method, and the analysis methodology.
+
#* 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.  
−
#* Present error sources in a table, if you like.
+
#* For a typical curve, plot residuals versus time, temperature, and fluorescence, ([http://measurebiology.org/wiki/File:Residual_plot_for_DNA_data.png example plot]).
−
# Instrument documentation
+
#* 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.
−
#* Document the electronic and optical systems.
+
#* 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.
−
#* Include component values, gain values, cutoff frequencies, lens focal lengths, and relevant distances.
+
# Results:
−
#* It is not necessary to document construction details.
+
#* Identify your unknown sample (or state that your investigation did not provide a conclusive answer).
−
#* Why not include a nice snapshot or two of the instrument?
+
#* Quantify the confidence you have in your result.
−
#* Signal to noise results
+
# Discussion:
−
#* Give a bullet point summary of changes you made to your instrument design to address problems in the lab.
+
#* 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 57: 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]]
 
−
*[[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]]
−
*[[DNA Melting Report Requirements for Part 2]]
+
*[[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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