Difference between revisions of "DNA Melting Report Requirements for Part 1"

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[[Category:20.309]]
 
[[Category:20.309]]
 
[[Category:DNA Melting Lab]]
 
[[Category:DNA Melting Lab]]
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==Report requirements==
 
==Report requirements==
# Report submittal format:
+
* 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>.
#;Size of your lab report file submitted MUST be less than 20 MB.
+
* Include answers to questions embedded in the lab manual (e.g. the questions in the RTD section)
#;Post only pdf, with code included in the pdf at the end, not separately.
+
* The file must be less than 20 MB.
#;Include last name of each group member in the '''filename''' of the pdf you post. We would rather spend time carefully grading your report than renaming your files because every other group named theirs "DNA Report Part 1" or the like.
+
* Include code at the end of the document in an appendix, in the same pdf file, not as as separate upload.
#Report your signal to noise measurement and comment.
+
* Not counting the appendix, your report should be no longer than 10 pages.
#Plot your favorite melting curves.
+
 
#For at least one of those curves (or an average of your best curves), use your code from the simulation to perform a least-squares fit and comment on the results.  
+
==Part 1 report outline==
##What values do you obtain for ΔH and ΔS? Do you trust these values? How would you adjust the model to make a better fit to your data?
+
# Document your circuit design, optical design, and any ways that your instrument differs from the system described in the lab manual.
 +
#* Include values for all of the resistors, capacitors in your circuit.
 +
#* If you have not modified the circuits from their form in the report, you do not need to include the schematic in your report.
 +
#* Draw a block digram of your optical system, including focal lengths of lenses and key distances.
 +
#* Include a picture of your instrument.
 +
# Report your signal to noise measurement.
 +
# Plot at least one melting curve.  
 +
#* The plot should have temperature in &deg;C on the horizontal axis and fraction of double stranded DNA on the vertical axis.
 +
#* On the same set of axes, include a simulated curve generated by DINAMelt, OligoCalc, or another software simulator.
 +
#* Also on the same set of axes, plot the output of the <tt>DnaFraction</tt> function evaluated with best-fit parameters. You may use nlinfit to choose the best-fit parameters or you may choose them manually. (See: [[DNA Melting: Simulating DNA Melting - Basics]])
 +
#* Include a legend.
 +
# Report the estimated melting temperature and the best-fit values of ''&Delta;H&deg;'', ''&Delta;S&deg;''.
 +
# Explain the statistical method you will use to identify your group's unknown sample in part 2 of this lab.
 +
#* State the acceptance/rejection criteria for any hypotheses tests you will use.
 +
#* This page may be a helpful reference: [[Identifying the unknown DNA sample]].
  
 
==Lab manual sections==
 
==Lab manual sections==

Latest revision as of 21:34, 23 March 2017


Report requirements

  • 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.
  • Include answers to questions embedded in the lab manual (e.g. the questions in the RTD section)
  • The file must be less than 20 MB.
  • Include code at the end of the document in an appendix, in the same pdf file, not as as separate upload.
  • Not counting the appendix, your report should be no longer than 10 pages.

Part 1 report outline

  1. Document your circuit design, optical design, and any ways that your instrument differs from the system described in the lab manual.
    • Include values for all of the resistors, capacitors in your circuit.
    • If you have not modified the circuits from their form in the report, you do not need to include the schematic in your report.
    • Draw a block digram of your optical system, including focal lengths of lenses and key distances.
    • Include a picture of your instrument.
  2. Report your signal to noise measurement.
  3. Plot at least one melting curve.
    • The plot should have temperature in °C on the horizontal axis and fraction of double stranded DNA on the vertical axis.
    • On the same set of axes, include a simulated curve generated by DINAMelt, OligoCalc, or another software simulator.
    • Also on the same set of axes, plot the output of the DnaFraction function evaluated with best-fit parameters. You may use nlinfit to choose the best-fit parameters or you may choose them manually. (See: DNA Melting: Simulating DNA Melting - Basics)
    • Include a legend.
  4. Report the estimated melting temperature and the best-fit values of ΔH°, ΔS°.
  5. Explain the statistical method you will use to identify your group's unknown sample in part 2 of this lab.

Lab manual sections

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