Difference between revisions of "DNA Melting Report Requirements"
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==Part 2 report outline== | ==Part 2 report outline== | ||
# Abstract: | # Abstract: | ||
| − | #* In one paragraph of less than six sentences, summarize the investigation you undertook and key results. | + | #* In one paragraph of less than six sentences, summarize the investigation you undertook and your key results. |
| − | # | + | # Introduction and Purpose: |
| − | #* Provide a succinct introduction to the project including the purpose of the experiment | + | #* 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. | #* Note 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 short paragraph, 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 to replicate your work. Focus on the electronic and optical subsystems. | + | #* 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 that person has taken 309 and has access to all course materials (wiki, Stellar, lectures, problem sets, etc). |
#** 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. | #** 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. | ||
| Line 23: | Line 23: | ||
# 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. As above, include only information beyond that of the lab manual, but provide information necessary to reproduce your results. | ||
| − | # Data: | + | #* Describe sample preparations and the sequence of their measurement. |
| − | #*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. | + | #* Make note of all settings used in the experimental control software. |
| + | # Data Review: | ||
| + | #*'''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. | ||
#* On a similar number of axes, with perhaps the same grouping of sample types, plot ΔdsDNA fraction/Δtemperature versus temperature ([http://measure.mit.edu/~20.309/wiki/index.php?title=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 [http://measure.mit.edu/~20.309/wiki/index.php?title=File:Not_like_this.png like this]. | #* On a similar number of axes, with perhaps the same grouping of sample types, plot ΔdsDNA fraction/Δtemperature versus temperature ([http://measure.mit.edu/~20.309/wiki/index.php?title=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 [http://measure.mit.edu/~20.309/wiki/index.php?title=File:Not_like_this.png like this]. | ||
#* ... something about raw signal and band-passed PSDs screen-captured from GUIs ... | #* ... something about raw signal and band-passed PSDs screen-captured from GUIs ... | ||
#* Include your signal to noise results. | #* Include your signal to noise results. | ||
| − | #* Briefly discuss observations and initial conclusions drawn from all data. | + | #* Briefly discuss observations and initial conclusions drawn from all data presented here. |
# Analysis: | # Analysis: | ||
| − | #* Develop a model for the melting experiment and use nonlinear regression to | + | #* Develop a model for the melting experiment and use nonlinear regression to fit this model to the data and obtain best-fit parameters. |
#* Explain the model parameters using bullet points or in a table. | #* Explain the model parameters using bullet points or in a table. | ||
#* 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. | #* 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. | ||
| − | #* To demonstrate that your model visibly fits the measured data, provide | + | #* 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. |
| − | #* For the | + | #* 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. |
# Results: | # Results: | ||
#* Provide a table of the best-fit model parameters and confidence intervals for each experimental run. | #* Provide a table of the best-fit model parameters and confidence intervals for each experimental run. | ||
#** Highlight the estimated thermodynamic parameters, ΔH, ΔS, and T<sub>m</sub>. Use multiple methods to find T<sub>m</sub>. | #** Highlight the estimated thermodynamic parameters, ΔH, ΔS, and T<sub>m</sub>. Use multiple methods to find T<sub>m</sub>. | ||
#** Discuss the confidence with which the model parameters have been determined. Confidence is quantitative. | #** 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 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 ΔH and ΔS. Also | + | #* 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 ΔH and ΔS'''. 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: | #* Unknown sample determination: | ||
#** Plot results for your unknown sample, including those from your other samples for comparison. | #** Plot results for your unknown sample, including those from your other samples for comparison. | ||
| Line 49: | Line 51: | ||
#** Discuss the validity of underlying assumptions. | #** Discuss the validity of underlying assumptions. | ||
#** Discuss the residuals (or transformed data) plot and parameter confidence intervals. | #** Discuss the residuals (or transformed data) plot and parameter confidence intervals. | ||
| − | #* Compare your data to results from other groups or instructor data. | + | #* Compare your data to results from other groups and/or instructor data. |
| − | #* Discuss significant error sources. | + | #* 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. | ||
| + | #** 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. | #** 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. | ||
| − | + | #** Present error sources, error type and their resultant uncertainty on your data and results in a table, if you like. | |
| − | #** Present error sources in a table, if you like. | + | |
# Conclusion: | # Conclusion: | ||
| − | #* Restate the highlights of | + | #* Restate the highlights of your report and present final, summary comments on the experiment. |
#* Make note of any surprising results. | #* Make note of any surprising results. | ||
#* Restate your determination of the unknown sample type and the confidence of that determination. | #* Restate your determination of the unknown sample type and the confidence of that determination. | ||
| − | #* Discuss changes that | + | #* 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. | |
| − | #* Comment on any other recommended changes for future DNA Melting Lab | + | |
==Lab manual sections== | ==Lab manual sections== | ||
Revision as of 17:25, 17 January 2014
- Follow the lab report general guidelines.
- Provide a thorough and accurate discussion of error sources and measurement uncertainty. 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.
Part 2 report outline
- Abstract:
- In one paragraph of less than six sentences, summarize the investigation you undertook and your key results.
- 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.
- Note 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.
- 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 that person has taken 309 and has access to all course materials (wiki, Stellar, lectures, problem sets, etc).
- 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?
- 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 that person has taken 309 and has access to all course materials (wiki, Stellar, lectures, problem sets, etc).
- 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.
- Describe sample preparations and the sequence of their measurement.
- Make note of all settings used in the experimental control software.
- Data Review:
- 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.
- On a similar number of axes, with perhaps the same grouping of sample types, plot ΔdsDNA fraction/Δtemperature versus temperature (example plot). See this section for details. Your plot should not look like this.
- ... something about raw signal and band-passed PSDs screen-captured from GUIs ...
- Include your signal to noise results.
- Briefly discuss observations and initial conclusions drawn from all data presented here.
- Analysis:
- Develop a model for the melting experiment and use nonlinear regression to fit this model to the data and obtain best-fit parameters.
- Explain the model parameters using bullet points or in a table.
- 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.
- To demonstrate that your model visibly fits the measured data, provide two or more representative examples of $ V_{f,measured} $ and $ V_{f,model} $ plotted versus $ T_{block} $. Include the best fit and the worst fit, not including data that appears to be an atypical result.
- For the best and worst fits, plot residuals versus time, temperature, and fluorescence, (example plot) and comment on the results.
- Results:
- Provide a table of the best-fit model parameters and confidence intervals for each experimental run.
- Highlight the estimated thermodynamic parameters, ΔH, ΔS, and Tm. Use multiple methods to find Tm.
- 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 $ \text{DnaFraction}_{inverse-model} $, the best-fit parameters and the observed fluorescence to plot estimated dsDNA fraction versus sample temperature (example plot). On the same set of axes plot DnaFraction model data using the best-fit values of ΔH and ΔS. 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.
- Confidence is quantitative.
- Provide a table of the best-fit model parameters and confidence intervals for each experimental run.
- Discussion:
- 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.
- 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 that remain after your changes.
- 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.
- Present error sources, error type and their resultant uncertainty on your data and results in a table, if you like.
- Comment on strengths and shortcomings of the model.
- Conclusion:
- 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.
