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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__NOTOC__
 
 
* Follow the [[20.309:Lab Report Guidelines|lab report general guidelines]].
 
* 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.
 
* 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>.
 
* 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.
  
 
==Part 2 report outline==
 
==Part 2 report outline==
 +
# Haiku:
 +
#* Compose an entertaining, exhilarating, thought-provoking, or melancholy Haiku on the subject of DNA melting.
 
# Abstract:  
 
# Abstract:  
−
#* In one paragraph of fewer than six sentences, summarize the investigation you undertook and your key results.
+
#* In one paragraph containing six or fewer sentences, summarize the investigation you undertook and key results.
 
# Introduction and Purpose:
 
# 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.
 
#* Provide a succinct introduction to the project, including the purpose of the experiment, relevant background material and/or links to such information.
−
#* Note the ways in which this part of the lab differs from Part 1.
+
#* Summarize the ways in which this part of the lab differs from Part 1.
−
#* Keep the length to one short paragraph, no more than 1/3 of a page.
+
#* Keep the length to one or two short paragraphs, no more than 1/3 of a page.
 
# Apparatus:
 
# Apparatus:
−
#* Document the critical components and operational parameters of your instrument that would be necessary for another person to replicate your work. Focus on the electronic and optical subsystems. Assume the reader is a person familiar with the concepts of 20.309 and has access to all course materials.
+
#* Document your instrument design.
−
#** Include component values, gain values, cutoff frequencies, lens focal lengths, and relevant distances.
+
#** 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.
−
#** 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.
+
#** 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.
+
#** It is not necessary to document construction details, unless you built an instrument that was significantly different than the lab manual suggested.
−
#* Why not include a nice snapshot or two of the instrument?
+
#** 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.
 
# Procedure:
 
# Procedure:
−
#* Document the procedure used to gather your data. As above, include only information beyond that of the lab manual, but provide information necessary to reproduce your results.
+
#* Document the procedure used to gather your data.  
−
#* Describe sample preparations and the sequence of their measurement.
+
#** Refer to procedures in the lab manual. Describe any changes you made.
−
#* Make note of all settings used in the experimental control software.
+
#** Report instrument settings for each trial, including control software parameters.
−
# Data Review:
+
# 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. Hint: Avoid plots that overlap near the melting temperature unless those plots result from the same sample type.
+
#* 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.  
−
#* On a similar number of axes, with perhaps the same grouping of sample types, plot &Delta;dsDNA fraction/&Delta;temperature versus temperature ([[File:Delta_Vf_Delta_theta_versus_theta.png example plot]]). See [[DNA Melting: Model function and parameter estimation by nonlinear regression#ΔF/Δθ versus θ plot|this section]] for details. Your plot should not look [[File:Not_like_this.png like this]].
+
#** Data from the many sample runs overlaps, which makes presenting so much data on a small number of axes a real challenge.  
−
#* Include your signal to noise results.
+
#** 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.
 
# Analysis:
 
# Analysis:
−
#* Develop a model (that accounts for the effects described in [[DNA Melting: Model function and parameter estimation by nonlinear regression]]) for the melting experiment and use nonlinear regression to fit this model to the data and obtain best-fit parameters.
+
#* Use bullet points to explain your data analysis methodology.
−
#* Explain the model parameters using bullet points or in a table.
+
#* Document the regression model you used to analyze your data
−
#* Use bullet points to explain your data analysis methodology. In particular, explain the use of your model toward determination of your primary outcome: a measure of the oligo melting temperature.
+
#** See [[DNA Melting: Model function and parameter estimation by nonlinear regression]]
−
#* To demonstrate that your model visibly fits the measured data, provide two or more representative examples of <math>V_{f,measured}</math> and <math>V_{f,model}</math> plotted versus <math>T_{block}</math>. Include the best fit and the worst fit, not including data that appears to be an atypical result.
+
#** Explain the model parameters using bullet points or in a table.
−
#* For the best and worst fits, plot residuals versus time, temperature, and fluorescence, ([http://measure.mit.edu/~20.309/wiki/index.php?title=File:Residual_plot_for_DNA_data.png example plot]) and comment on the results.
+
#* 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:
 
# Results:
−
#* Provide a table of the best-fit model parameters and confidence intervals for each experimental run.
+
#* Identify your unknown sample (or state that your investigation did not provide a conclusive answer).
−
#** Highlight the estimated thermodynamic parameters, &Delta;H, &Delta;S, and T<sub>m</sub>. Use multiple methods to find T<sub>m</sub>.
+
#* Quantify the confidence you have in your result.
−
#** Discuss the confidence with which the model parameters have been determined. Confidence is quantitative.
+
−
#* For all experimental trials, use the inverse of your model function <math>\text{DnaFraction}_{inverse-model}</math>, the best-fit parameters and the observed fluorescence to '''plot estimated dsDNA fraction versus sample temperature''' ([http://measure.mit.edu/~20.309/wiki/index.php?title=File:Corrected_DNA_data.png example plot]). On the same set of axes '''plot DnaFraction model data using the best-fit values of &Delta;H and &Delta;S'''. Also '''plot a simulated dsDNA fraction vs. temperature curve''' obtained from DINAmelt or another melting curve simulator.
+
−
#** Plot these results on the smallest number of axes possible that clearly conveys your results. Hint: Avoid plots that overlap near the melting temperature unless those plots result from the same sample type.
+
−
#* 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.  To do this, compare the unknown sample to the three knowns with Matlab's anova1 and multcompare functions.
+
−
#*** Confidence is quantitative.
+
 
# Discussion:
 
# Discussion:
−
#* Comment on strengths and shortcomings of the model.
+
#* Discuss the validity of assumptions in the regression model.
−
#** Discuss the validity of underlying assumptions.
+
#* Discuss any atypical results or data you rejected.
−
#** Discuss the residuals (or transformed data) plot and parameter confidence intervals.
+
 
#* Compare your data to results from other groups and/or instructor data.
 
#* 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.
 
#* 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 that remain after your changes.
+
#* Discuss significant error sources.  
−
#** If you cannot connect an error source to an estimated quantitative effect (sign and order of magnitude) on your measured data and/or the results your analysis, then it is probably NOT significant and you should not include it.
+
−
#** 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.
 
#** 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.
 
#** Present error sources, error type and their resultant uncertainty on your data and results in a table, if you like.
−
# Conclusion:
+
#* Discuss additional unimplemented changes that might improve your instrument or analysis.
−
#* Restate the highlights of your report and present final, summary comments on the experiment.
+
−
#* Make note of any surprising results.
+
−
#* Restate your determination of the unknown sample type and the confidence of that determination.
+
−
#* Discuss additional unimplemented changes that might improve your instrument or analysis toward a more confident sample determination.
+
−
#* Comment on any other recommended changes for future iterations of the DNA Melting Lab.
+
  
 
==Lab manual sections==
 
==Lab manual sections==

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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