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

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==Report requirements==
 
==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: <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>.
 +
* 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.
 
* The file must be less than 20 MB.
* Include code at the end of the document in an appendix.
+
* 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==
 
==Part 1 report outline==
 
# Document your circuit design, optical design, and any ways that your instrument differs from the system described in the lab manual.
 
# 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.  
 
# 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.
 
#* 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.
 
#* 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.
+
#* 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.
 
#* Include a legend.
 
# Report the estimated melting temperature and the best-fit values of ''&Delta;H&deg;'', ''&Delta;S&deg;''.
 
# Report the estimated melting temperature and the best-fit values of ''&Delta;H&deg;'', ''&Delta;S&deg;''.
# Report your signal to noise measurement.
 
 
# Explain the statistical method you will use to identify your group's unknown sample in part 2 of this lab.
 
# 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.
 
#* 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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