20.109(S11): System engineering report

Overview
The culminating assignment for Module 2 will be a research article in which you describe your system engineering investigation. The term research article (as opposed to laboratory report) is meant to indicate your growing maturity as scientific writers, and our growing expectations of you. Your Module 2 paper should approach the quality of the primary scientific literature (excepting its lack of experiment repetition), especially with respect to explaining rather than merely documenting your observations. For more information about research articles vs. laboratory reports see here.

Be sure to review the 20.109 statement on collaboration and integrity as you proceed.

Method of Submission
Please email your completed report to 20109 DOT submit AT gmail DOT com, with filename Firstinitial_Lastname_LabSection_Mod2.doc (for example, S_Hockfield_TR_Mod2.doc).

First Draft Submission: April 12th/13th
The first draft of your research article is due by 11 am on April 12th (Tuesday) or April 13th (Wednesday), according to which day you have lab.

Revised Article Submission: April 28th/29th
Your first draft, with feedback from both the writing and the technical faculty, will be returned on April 21st (Thursday) or 22nd (Friday). You will then have the opportunity to revise your report for up to a one letter grade improvement. The final draft is due on April 28th (Thurday) or 29th (Friday), according to which day you have lab. Please highlight any substantial revisions to your text, for example, by using a different coloured font.

Formatting Expectations

 * Your main document (excluding figures) should be/have
 * .doc (preferred) or .pdf
 * 12-pt font
 * with 1-inch margins
 * double-spaced (excepting the abstract)
 * Figures can be made in a separate drawing program (such as powerpoint), and should be submitted as .pdf

Guidelines on Length
We are running this module for the first time, so we encourage you to use your judgement about report length. Our best guesses for each section are:


 * Introduction: ~3 pages
 * Methods: ~2-3 pages
 * Results: ~3-4 pages
 * Discussion: ~3-4 pages

These lengths will depend on several factors, such as (1) how much information about the systems you roll out in the introduction versus the results, (2) how much you say about the modeling in the results versus the discussion, and (3) how much you say about another design in the results versus the discussion. Not counting figures, report length should not exceed 15 pages. Concise writing is appreciated and rewarded!

Content Guidelines
Begin by reading the general guidelines for scientific writing. A few notes specific to Module 2 are below:

Discussion and Citations
This section should realize all the good practices described in the Module 1 assignment, but do so at a more advanced level. You will be expected to cite the broader scientific literature more thoroughly than before, both to set up your investigative question in the introduction and to inform your analysis in the discussion. You should also propose specific future experiments and otherwise show that you deeply understand the meaning and significance of your results; for example, if you have a hypothesis about why your modification didn't work, consider what follow-up experiments you might try to prove it. In addition to drawing conclusions from your own data, you are expected to spend some time considering one other data set (ideally one that is closely related to or otherwise sheds light on your own). You should not write about all of the designs, as this approach will make your paper too unfocused.

Suggested Figures
In most research endeavours, you will collect more data than you ultimately publish. In the spirit of writing a research article, in this assignment you should present only essential data. For example, there is no need to present the gel you ran to purify the digested backbone. The suggested list of figures below should be suitable for most of your write-ups (but not in the listed order!), but you are welcome to make changes with good reason.


 * Schematics/diagrams
 * Depiction of your design strategy for DNA modification
 * Figures
 * IPTG:lacZ transfer function (real data)
 * B-gal output of original and your newly designed model system
 * Original edge detector plate image
 * Solid culture images for original and newly designed model system
 * Sequence analysis
 * Modeling figures/narrative
 * Transfer function (Fig 6) for 'broken' system --> why broken?
 * Transfer function (Fig 6) for 'fixed' system --> how fixed?
 * All other (14) figures for 'fixed' system
 * explain the path/logic from lab data (theoretically) to transfer functions to spatial simulations to edge detection by light
 * turns out Figures 3 and 4 are redundant with Figures 1 and 2, and can be omitted

Evaluation
The full descriptive rubric for lab reports can be found on the guidelines page.