20.109(F13): System engineering report

Overview

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.

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

Logistics

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 emailed to your lab instructor.

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: Novmber 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 11 pages. The following rough division is recommended:

• Introduction: 2-3 pages
• Methods: 1.5-2 pages
• Results: 2-2.5 pages
• Discussion: 2.5-3.5 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:

below is from S13; revise

Abstract

Please keep the number of words under 250.

• 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 applies to your entire report.

Introduction

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?

Methods

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!

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 a mutation had the effect that it did, consider what follow-up experiments you might try. In addition to drawing conclusions from your own data, you are expected to spend some time considering your classmates’ data. (Include the mutants most relevant to your own results rather than every mutant in the class.)

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, if your sequencing reactions worked, there is no need to present the redundant diagnostic digest that you used to quickly check your construct. The suggested list of figures below should be suitable for most of your write-ups, but you are welcome to make changes with good reason.

• Schematics/diagrams
  • Depiction of your design strategy for mutants
• Figures
  • Sequencing
  • SDS-PAGE
  • Titration curves for WT and mutant protein
• Tables or just text
  • Cell pellet observations – color and relative growth rates
  • Purified protein concentration
  • K_D and/or Hill values for relevant model(s)

Evaluation

The full descriptive rubric for lab reports can be found on the guidelines page. Methods and Results will be graded by Dr. Stachowiak or Dr. Hughes-Alford and the rest of the report will be graded by Professor Jasanoff, weighted about 1/3:2/3.