20.109(F13): System engineering report

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20.109(F13): Laboratory Fundamentals of Biological Engineering

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The culminating assignment for Module 2 will be a research article in which you describe your systems 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. While your Module 1 assignments contained many of the same elements that you'll include here, the research article should be a cohesive document that presents your data and interpretation in the context of a larger story. 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.


Method of Submission

Please submit your completed report on Stellar, with filename Firstinitial_Lastname_LabSection_Mod2.doc (for example, R_Reif_TR_Mod2.doc). Late assignments should be submitted on Stellar as well.

You will complete this assignment individually. Please review the 20.109 statement on collaboration and integrity as you proceed.

First Draft Submission: Submission: November 11th

The first draft of your research article is due by 5 pm on November 11th (Monday) for everyone.

Revised Article Submission: November 27th

Your first draft, with feedback from the technical faculty, will be returned approximately one week after submission. You will then have the opportunity to revise your report for up to a one letter grade improvement. The final draft is due on Wednesday, November 27th, by 5 pm. Please highlight any substantial revisions to your text, for example, by using a different colored font or a track changes function. Also include a short, one paragraph summary of how your changes improve the document

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

Not counting figures, report length should not exceed 12 pages. The following rough division is recommended:

Please take the following guidelines with a grain of salt. Because we are teaching a brand-new module, we necessarily can only estimate the requisite section lengths. You will not be penalized for going modestly over a section limit if you are being thorough yet concise (e.g., 0.5 - 1 page on the methods). Conversely, you might technically stay within a section limit yet use more space than your content warrants, which would lower your evaluation (e.g., note that discussion maximum is based on a thorough class-wide discussion and/or deep mechanistic insights).

  • Introduction: 2-3 pages
  • Methods: 1.5-2 pages
  • Results: 2-3 pages
  • Discussion: 3-4 pages

Concise writing is appreciated and rewarded! In other words, longer is not always better.

Content Guidelines

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


Please keep the number of words under 250.

  • The abstract should be on a separate, first, page and does not contribute to the page length requirement.
  • Do not include references in the abstract.
  • Try drafting this section after you’ve written the rest of the report.
  • If you’re truly stuck, start by modifying one crystallizing sentence from each of the sections of your report.
  • Please do not plagiarize (accidentally or other) the class wiki. This comment applies to your entire report.


This section will set the tone for the remainder of your paper. There are two broad topics that we are covering in Module 2: cancer systems biology and high-throughput experimental techniques. You may choose to frame your study in either of these fields or a mix of both. Remembering the funnel structure of the introduction, consider addressing the following:

  • What is the context of the study that you are presenting? Can you convince your reader that your specific study relates to broader questions or a bigger picture that this research might help clarify? In other words, why is this research interesting?
  • Is there a context for biological engineering that is not too far fetched? You may wish to think about how you can connect some of your discussion to topics you bring up in your introduction.
  • For module 2, you may wish to focus on broad drug resistance implications in cancer or other diseases, systems biology approaches to overcome drug resistance, large scale (high-throughput) experimental approaches for quantifying drug resistance, another aspect of mathematical modeling or high throughput experimentation, or some combination of these topics that you think will intrigue your reader. Keep in mind, you have little space to motivate your work and you need to catch the reader’s attention.
  • Are there some unanswered questions a step below the big picture that this type of work could help answer? What sort of result would be a clear step forward in understanding how drug resistance might be overcome in the clinic? Are human studies relevant to this work? Studies in other organisms (cell lines, mice, etc)?
  • As you bring the reader closer to your specific study, can you clearly describe what aspects drug resistance you have examined, and how you have applied various experimental techniques to understand the output of your experiment/analysis?
  • What were your expectations at the outset of the experiment? (Be sure you’ve clearly explained your hypothesis.) Would your introduction benefit from a brief summary of your (and the class’s as a whole) results? Do these contrast with your expectations?


The methods section will be somewhat more abbreviated than the Module 1 assignment for two reasons:

  • You can assume a niche audience who is somewhat familiar with each procedure. Use the published scientific literature as a guide, and do not omit too many details (as some of the top journals that are really pressed for space do).
  • There are not as many methods!


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, if your sequencing reactions did not work, there is no need to include a figure containing those negative results. Above all, aim to tell a story using the experiments that were completed. The list below contains suggestions for figures that might be informative to your reader. Please expand or subtract as you see fit, keeping in mind that a complete story is told through your hypotheses and your experimental data.


  • Depiction of your experimental design
  • Schematic of signaling pathway(s) of interest


  • Figure 1: Experimental design
    • Modeling output -- perhaps extend what was done on M1D1 to address your specific question even more thoroughly
    • Schematic/diagram/structure of inhibitor(s) used in the study
  • Figure 2: EGFR mutation analysis
    • Include both negative and positive controls
    • Results from your cells of interest
    • For a nice example of how to display this type of data see this paper.
  • Figure 3: EGFR pathway activation
    • Phospho-tyrosine WB results: blots and quantification
  • Figure 4 - ?: Cell viability screen
    • Schematic of plate design
    • Results of your experiment
    • Results across class using your inhibitor (statistics!)
    • Comparison across inhibitors (statistics!)
    • Possibly revisit your signaling cascade schematic/cartoon to graphically illustrate the effects of inhibition


This section should realize all the good practices described in the Module 1 assignment in regards to concisely stating conclusions about your research, 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 a drug had the effect that it did, consider what follow-up experiments you might try. Also, make sure to do a bit of literature digging to determine if your results have any precedent or if your experiments are contrary to what has been reported. Modest speculation as to why that it the case is highly encouraged. The best scientific writers are creative in their discussion sections -- convincing their readers that whatever the results, the study was interesting and contributes to forward movement of the field.

In addition to drawing conclusions from your own data, you are expected to spend some time considering your classmates’ data. Here, you do not need to include ALL the data from the class. Only the data that contributes to the story that you want to tell.


Note: these instructions are specific for your Module 2 research paper.

All works cited should be numbered sequentially and the number should appear in parentheses following the sentence. For example:

Standing behind penguins at the zoo is not advisable (1).

The reference is then included at the end of the document in the References section (that does not count towards your page limit).

1. V. B. Meyer-Rochow and Jozef Gal. Pressures produced when penguins pooh-calculations on avian defaecation. Polar Biol (2003) 27: 56-58.


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