Difference between revisions of "DNA Melting Report Requirements"
From Course Wiki
| Line 14: | Line 14: | ||
==Report outline== | ==Report outline== | ||
| − | #Abstract: | + | # Abstract: |
| − | + | #* In one paragraph of less than six sentences, summarize the investigation you undertook and key results. | |
| − | # | + | # Raw data |
| − | + | #*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. | |
| − | + | #* On similary-grouped sets of axes, plot ΔdsDNA fraction/Δtemperature. | |
| − | # | + | # Model parameters |
| − | + | #* Develop a model for the melting experiment and use nonlinear regression to determine best-fit parameters. | |
| − | + | #* Use the smallest possible number of plots to compare the model with best-fit parameters to your data and a simulated result obtained from DINAmelt or another melting curve simulator. | |
| − | # | + | #* Include a table of estimated thermodynamic parameters, ΔH, ΔS, and T<sub>m</sub>. Use multiple methods to find T<sub>m</sub>. |
| − | + | # Unknown sample determination: | |
| − | + | #* Plot results for unknown sample, including other samples for comparison. | |
| − | + | #* Identify your unknown sample and state your level of confidence in the answer. | |
| − | # | + | #*Use the smallest possible number of plots to compare the unknown sample to the corresponding known sample. |
| − | + | # Comparative data analysis | |
| − | #Analysis | + | #* Compare your data to results from other groups or instructor data. |
| − | + | # Analysis | |
| − | # | + | #* Use bullet points to explain your data analysis methodology. |
| − | # | + | #Discussion |
| + | #*Compare your results to theoretical models and/or other group's datasets. | ||
| + | #* Sources of error | ||
| + | #** Provide a detailed discussion of important error sources. Indicate whether each source causes a systematic or random distortion in the data. | ||
| + | #** Consider the entire system, including all aspects of your instrument, the oligo design, the dye used, the experimental methodology, and the analysis methodology. | ||
# Instrument documentation | # Instrument documentation | ||
#;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. | #;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. | ||
Revision as of 01:34, 16 November 2012
Format
- One group member must submit a single PDF file no more 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.
- All plots must be presented properly, including a descriptive title, axis labels, and legend.
- 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.
Failure to follow the format guidelines will result in ridiculously large grade penalties
Report outline
- Abstract:
- In one paragraph of less than six sentences, summarize the investigation you undertook and key results.
- Raw data
- 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.
- On similary-grouped sets of axes, plot ΔdsDNA fraction/Δtemperature.
- Model parameters
- Develop a model for the melting experiment and use nonlinear regression to determine best-fit parameters.
- Use the smallest possible number of plots to compare the model with best-fit parameters to your data and a simulated result obtained from DINAmelt or another melting curve simulator.
- Include a table of estimated thermodynamic parameters, ΔH, ΔS, and Tm. Use multiple methods to find Tm.
- Unknown sample determination:
- Plot results for unknown sample, including other samples for comparison.
- Identify your unknown sample and state your level of confidence in the answer.
- Use the smallest possible number of plots to compare the unknown sample to the corresponding known sample.
- Comparative data analysis
- Compare your data to results from other groups or instructor data.
- Analysis
- Use bullet points to explain your data analysis methodology.
- Discussion
- Compare your results to theoretical models and/or other group's datasets.
- Sources of error
- Provide a detailed discussion of important error sources. Indicate whether each source causes a systematic or random distortion in the data.
- Consider the entire system, including all aspects of your instrument, the oligo design, the dye used, the experimental methodology, and the analysis methodology.
- Instrument documentation
- 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.
- Signal to noise results
- Design evolution
- Give a bullet point summary of changes you made to your instrument design to address problems in the lab.
Lab manual sections
- Lab Manual:Measuring DNA Melting Curves
- DNA Melting: Simulating DNA Melting - Basics
- DNA Melting Part 1: Measuring Temperature and Fluorescence
- 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 Report Requirements for Part 2
