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20.109(S17): Laboratory Fundamentals of Biological Engineering


Schedule Spring 2017        Announcements        Assignments        Homework        Communication
       1. High-throughput ligand screening        2. Gene expression engineering        3. Biomaterials engineering              

BE Communication Lab resources

Throughout the semester you will participate in workshops provided by the manager and instructor from the BE Communication Lab, Dr. Diana Chien, that will help you prepare your major communication assignments. The resources provided at these workshops will be posted here!

Workshop materials

Figures and Captions Slides
Abstracts and Titles (and Writing Tips)
Journal Club and Oral Presentations
Research Article structure and writing process
Research Proposals

To schedule an appointment with a BE Communication Fellow:

For assistance finding research articles, managing citations, etc:

Laboratory notebook guidelines

The purpose of keeping a laboratory notebook in 20.109 is two-fold:

  1. To develop good archiving practices for the future.
  2. To maintain a one-stop resource to remember what you did each day and record the outcome(s).

You will use an online laboratory notebook to document your work in 20.109. Benchling is a free program that allows users to record experimental procedures and results, prepare spreadsheets for calculations, and attach images. An additional feature of Benchling is that it provides tools for analyzing DNA sequence information. Lastly, your Benchling notebooks can be shared with the teaching faculty, which facilitates easier grading.

Though no two scientists organize their lab notebooks identically, and there is not one right way for you to keep yours, there are some common elements that all laboratory notebooks share and some important habits you should develop in keeping your notebook for this class.

Your notebook is a place to archive descriptions of experimental goals, experimental procedures, all the data you collect, and your interpretations of results. Numerical data and calculations should be included and data in the form of photographs, printouts, etc, should be attached directly to your Benchling notebook.

Though it is not necessary to paste the entire protocol into your notebook, the goal of your notebook is to help you repeat your experiments with the same results. You should clearly cite each wiki protocol as you go (ModX-DayY-PartZ), and also include any useful methods details that are either not specified on the wiki or that you deviate from, including:

  • dilutions and how they were prepared
  • final concentrations (if only stocks are listed)
  • protocol changes:
    • unexpected delays (e.g. the waterbath was not ready so tubes were kept on ice for one hour)
    • unanticipated conditions (e.g. the roller drum was not turned on until ~12 h into incubation)
  • unusual observations (e.g. a large number of cells seemed to be floating).

You will generate a notebook entry for every day that you are in the laboratory. To ensure that the information is easy to find, it is important to include the date and module#/day# on every entry.

For this class, that means coming to lab with the date, Module/Day, title, and statement of purpose already entered in your notebook. It will occasionally be helpful to have data tables ready or some calculations performed as well. Up-to-date also means that you complete the entry shortly after every class, including information concerning your results, data interpretation, and a summary statement.

This is a tricky element to preserve when we enter the digital world. There is a legal reason for noting changes from original pages -- if you have a great idea, you need to permanently record the date for patent applications! While it would be fantastic to file patents covering your data in 20.109, it is not likely to happen. However, you should change font color or make notes to show where you have updated text/figures/calculations.

Grading criteria for laboratory notebook

The teaching faculty will examine your notebook entries for a specific day once per module. The specific notebook entry will be collected on the last day of the module. You will not know in advance which day will be evaluated and should maintain all of your entries according the guidelines provided in this section.

Your laboratory notebook entries will be evaluated using the following rubric:

 Laboratory notebook entry component:          Score:
                                               Complete    Partial     Incomplete
 Date of experiment (include Module#/Day#)        1          0.5           0
 Title for experiment                             1          0.5           0
 Statement on the purpose of the experiment       1          0.5           0
 List of protocols                                1          0.5           0
 Notes on protocol changes and observations       1          0.5           0
 Tables for data entry                            1          0.5           0
 Calculations entered and completed               1          0.5           0
 Data labeled                                     1          0.5           0
 Summary and interpretation of data               1          0.5           0
 Information is clear                             1          0.5           0

Oral communication guidelines

Hour-long seminars, 10-minute conference talks, discussion-driven group meetings, and journal clubs are all ways scientists share data orally. While the content, length and purpose of each talk vary, they share certain common elements, including organization, clarity, and proper attribution for the work.

In 20.109 you will be exposed to several methods of oral communication. The individual journal club oral presentation you give in this class will be a 10-minute talk during which you will present an introduction to the topic, relevant data, and a summary. Afterward, you will have the opportunity to answer questions from your classmates and instructors. Realistically, only two or three ideas can be effectively conveyed in such a short time, and even that will require careful planning and practice. The partner research proposal presentation you give in this class will be a 12-minute talk during which you will present an introduction to your field, research plan, and the significance of your project. As with the journal club presentation, you will answer questions from your classmates and instructors.

Format considerations

The timing provided here is for a 10-minute presentation. For longer presentations, the slide count and proposed times may be increased proportionally.

Section Minutes Number of slides DO DON'T
Introduction ~2 2-3
  • Introduce the key concepts that the audience will need to follow your presentation.
  • Briefly state the overall scope and significance of the study -- what is the central question and why is it interesting?
  • Try to summarize background material with a model slide rather than lines of text. If text is needed, bring in the details as you speak using PowerPoint animation.
  • Don't assume you are addressing an expert audience.
  • Don't give more information than is absolutely needed to understand the rest of your talk.
  • Don't put too much information on each slide.
Data ~7 4-6
  • Present the data in a logical sequence, letting each slide build upon the previous ones.
  • Include a title for each slide. The title should be the conclusion and should be unique to the information on the slide.
  • Make every element of your slide visible to the entire room. This means 20-point font or greater.
  • Interpret each slide thoroughly and carefully.
  • Point out strengths and weaknesses of the data along the way.
  • Don't read your talk. Similarly, do not read lists from slides.
  • Don't put much information on each slide. Each slide should make only one point.
  • Never say, "I know you can't read this, but...". Everything on each slide should be legible.
  • Don't be afraid to remind the audience how the data fits into the overall question
Summary ~1 1
  • Review each of your main messages.
  • Clearly state what the study contributed to the field.
  • Don't repeat experimental details.
Question & Answer ? 0
  • Answer the question being asked. If you are unclear about the question, ask for clarification.
  • Respect every question and questioner.
  • Don't take too long with one question. If the discussion is involved, suggest meeting after the talk to discuss it more.

You can find good examples of short talks at MIT World and TED.

Helpful hints

  • A 10-minute talk is NOT a 30-minute talk given while racing through slides and speaking very quickly.
  • Consider ways to transition from one slide to the next to ensure the information is tied together.
  • Practice your presentation in front of people rather than in a room by yourself and practice several times!
  • Familiarize yourself with using a laser pointer and/or slide changer if you will use one during the actual presentation.
  • If you do choose to use a pointer, use it to direct attention to specific elements on the screen, rather than constantly gesturing in the general vicinity of your slide; otherwise, the audience will not know what's important. When you later make your own slides and figures, the apparent need for a pointer may actually mean you need to make a clearer slide.

Written communication guidelines

Formal research articles and less formal lab reports are the principal ways in which scientific data are conveyed to the rest of the scientific community and archived for future examination. In 20.109 you will be exposed to several methods of written communication. As discussed above, you are required to maintain a laboratory notebook. In addition, your assignments will include a short one-page write-up concerning a single experiment, a multiple page report that focuses on data interpretation, and a more formal research article that is similar to a journal publication.

Though each scientific journal has its own formatting idiosyncrasies, the most common elements of a scientific article, in order, are:

  • Title
  • List of authors
  • Abstract
  • Introduction
  • Materials and methods
  • Results, including figures and tables
  • Discussion
  • References


The title should be short (no more than about 10 words), interesting, and it should describe what you discovered in your research. Avoid very broad titles (e.g., 'DNA recombination'), and try to specify your own unique result within the limited space, while still maintaining readability of your title.

List of authors

Indicate that you are the primary author of the report by underlining your name. Others who substantially contributed to your work, such as your lab partner, should also be listed.


The abstract serves as a condensed version (~250 words) of your research article, from background (both context and motivation) to key results to implications for the future. By convention, it should be single-spaced and not include citations.

The importance of a good abstract cannot be overstated, since computers generally index only the words in a paper's title and abstract, and these may be the only parts that many people read. The abstract may also be the way a journal's editor decides whether to send your paper out for peer review or reject it as uninteresting or not relevant.


The introduction provides a framework for the story you are about to tell, and thus serves two main purposes. For one, you must provide sufficient background information for a reader to understand the forthcoming results. Just as importantly, you must motivate the audience to keep reading! How? Reveal the significance of the work through connections to both prior scientific accomplishments and interesting future applications.

Most introductions are "funnel"-shaped in terms of content:

  • Opening paragraph(s): most general, "big picture" paragraph(s). Here you should introduce the reader to the broader context of your experiment and motivate why your research is important. The best introductions tell a coherent story rather than present a dense but unconnected list of facts.
  • Middle of introduction: "zooming in" somewhat. Once the reader has a frame for thinking about your research, you can present background information in more depth and motivation with more specificity.
  • Wrapping up: most specific, a description of your particular investigation. Here you should make your overall methodology clear without getting into minute detail. In many journals, the introduction concludes with a brief preview of key findings and their implications (2-3 sentences total).

Materials and methods

The Methods section should allow an independent investigator to repeat your experiments. Use subsection headings to allow readers to quickly identify experiments of interest to them (e.g., "Protein conjugation to hydrogels" or "Cell culture and fluorescent labeling"). When commercially available kits were used, it is sufficient to cite the name of the kit and say that it was used according to the manufacturer's protocol. The key to a good methods section is developing your judgment for what information is essential and what is extraneous.

Note that the methods section should be written in the past tense, since your experiments are complete at the time you are writing your paper. This section should also be written in complete sentences and paragraphs, not in bullet point form.


The purpose of the Results section is to present your data in a relatively unbiased way, but with some guiding framework. Begin with a short description of the goal and strategy of your overall experiment, and then delve into specific subsections that describe each piece of the work.

Titled subsections help support your high-level narrative and make dense papers easier to read. Effective subsections are organized by functional content, not by order in which the experiments were completed. For example, two successive titles might be "Conjugating lymphoid tissue-associated adhesion proteins to hydrogels" and "T cell migration in protein-coated hydrogels." Less helpful titles for the same content would be "Hydrogel-protein reaction" and "Microscopy and velocity analysis."

To write the Results section, use the figures and tables as a guide. One approach is to start by outlining the points of what you found by going slowly through each part of the figures. Then take the points and group them into paragraphs, and finally order the points within each paragraph. Present the data as fully as possible, including stuff that does not quite make sense at first glance. Ultimately, each subsection should begin with an overview sentence that motivates and introduces the present experiment and end with a sentence stating the primary conclusion reached from that experiment. Subsection headings and figure caption titles can also emphasize the conclusion. The overview and/or concluding sentences should also provide a transition to the previous/next piece of data when possible. Within a subsection, be sure to stick to one topic per paragraph; subsections will generally require a few paragraphs each.

Note that verbs in the results section are in the past tense and passive form. Only established scientific knowledge is written about in the present tense: "the world is round" is an example. You cannot presume that your own data are part of the body of established scientific knowledge. Thus, when you describe your own results, use the past tense: "a band of 1.3 kb was seen," for example. There are exceptions to this general rule, such as "Table 3 shows the sizes of the DNA fragments in our preparation" or "In a 1991 paper, Ebright and coworkers used PCR to mutagenize DNA," which are both acceptable statements.


The purpose of the Discussion section is to interpret and contextualize your data. You should begin by reiterating the purpose of your research and your major findings. Then you might do any or all of the following: connect your findings to other research (published or that of your peers); describe any ambiguities and sources of error in the data, and suggest future experiments to resolve uncertainties; explain where you expect your work may lead, and suggest specific experiments for extending your findings; describe any conceptual or technical limitations of the research. Finally, you should explain the significance of your findings to basic science research and/or to engineering applications. As with previous sections, the discussion should have a clear organization and narrative flow, whether or not you use subsections.


References are generally used in the Introduction and Discussion sections to support any claims that are not common knowledge. Include only those references that pertain to the question at hand. Journals vary considerably in their preferred format for the reference list. For this class, you should list the references alphabetically by the first author's last name. Include all the authors, the title, the name of the journal in which it was published, the year of publication, the volume number, and page numbers. Please carefully follow the punctuation and format requirements.

A typical reference should look like:

Pavletich NP, Pabo CO. Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 Å. Science 1991; 252:809-817.

In the body of your report, this article would be cited as follows:

"The crystal structure of the Zif268-DNA complex has been solved (Pavletich 1991)."

If two or more articles can be cited for this finding, then they are listed alphabetically, separated by a comma.

See also the MIT libraries information on citing sources, here.

Evaluation considerations

The following tables describe the features of research papers that are excellent, good, or need substantial improvement. Your own manuscripts will be evaluated with these features in mind.

Section Goal Evaluation
Excellent Good Needs improvement
Title To give content information to reader
  • Engaging
  • Appropriate
  • Not enough content information or too much
Abstract To concisely summarize the experimental question, general methods, major findings, and implications of the experiments in relation to what is known or expected.
  • Key information is presented completely and in a clear, concise way
  • All information is correct
  • Organization is logical
  • Captures any reader's interest
  • Sufficient information is presented in proper format
  • Would benefit from some reorganization
  • Understandable with some prior knowledge of experiment
  • Some key information is omitted or tangential information is included
  • Some information is misrepresented
  • Some implications are omitted
  • Incorrect format is used
Introduction To identify central experimental questions, and appropriate background information. To present a plausible hypothesis and a means of testing it.
  • Relevant background information is presented in balanced, engaging way
  • Your experimental goals and predictions are clear and seem a logical extension of existing knowledge
  • Writing is easy to read
  • All background information is correctly referenced
  • Relevant background information is presented but could benefit from reorganization
  • Your experiment is well described and a plausible hypothesis is given
  • With some effort, reader can connect your experiments to background information
  • Writing is understandable
  • Background information is correctly referenced
  • Background information is too general, too specific, missing and/or misrepresented
  • Experimental question is incorrectly or not identified
  • No plausible hypothesis is given
  • Writing style is not clear, correct or concise
  • References are not given or properly formatted
Materials & methods To describe procedures correctly, clearly, and succinctly.
  • Sufficient for another researcher to repeat your experiment
  • Procedures could be pieced together with some effort
  • Procedures incorrectly or unclearly described or omitted
Results To present your data using text AND figures/tables.
  • Text tells story of your major findings in logical and engaging way
  • Figures and tables are formatted for maximum clarity and ease of interpretation
  • All figures and tables have numbers, titles and legends that are easy for the reader to follow
  • Text presents data but could benefit from reorganization or editing to make story easier for reader
  • Text includes interpretation of results that is better suited for discussion section
  • Figures and tables are formatted to be clear and interpretable
  • All figures and tables have numbers, titles and legends
  • Text omits key findings, inaccurately describes data, or includes irrelevant information
  • Text difficult to read due to style or mechanics of writing
  • Text difficult to read due to logic or organization
  • Figures and tables missing information, improperly formatted or poorly designed
  • Figures and tables have inadequate or missing titles or legends
Discussion To evaluate meaning and importance of major findings
  • Appropriate conclusions drawn from findings
  • Connections made between experimental findings
  • Connections made between findings and background information
  • Future directions considered
  • Writing is compelling
  • Appropriate conclusions drawn from findings
  • Experimental limitations considered
  • Writing is clear
  • Conclusions omitted, incorrectly drawn or not related to hypothesis.
  • Relationship between experimental findings and background information is missing or incorrectly drawn
  • Writing style and mechanics make argument difficult to follow
References To give credit to foundational work (on which your own study is based)
  • Complete list of reliable sources, including peer-reviewed journal article(s)
  • Properly formatted in body of report and in reference section
  • Adequate list of reliable sources
  • With minor exceptions, properly formatted in body of report and in reference section
  • List is incomplete or includes sources not cited in body of report
  • List includes inappropriate sources
  • List not properly formatted
  • References not properly cited in body of report

Writing style and mechanics Evaluation
Excellent Needs improvement
  • Appropriate for audience
  • Consistent passive or active voice
  • Too simple or too advanced
  • Irregular use of passive and active voice
Word choice
  • Concise
  • Precise
  • Vocabulary (scientific and otherwise) used correctly
  • Avoids contractions and informal wording
  • Verbose
  • Ambiguous, vague, or incorrect
  • Scientific or other vocabulary misused
  • Informal/colloquial tone
  • Sentences and paragraphs well-structured
  • Clear topic for each paragraph and clear transitions between topics
  • Punctuation correct or only minor errors
  • Grammar correct or only minor errors
  • Spelling correct
  • Sentences repetitive or awkward
  • Ideas haphazardly arranged, logic connecting them not clear, paragraphs not focused on one topic each
  • Periods, commas, colons and semicolons misused
  • Significant number of run-on sentences, sentence fragments, misplaced modifiers, subject/verb disagreements
  • Significant number of spelling errors
Scientific format
  • Past tense for describing new findings
  • Present tense used for accepted scientific knowledge and figure legends
  • All sections included and properly formatted
  • Misleading verb tenses
  • Some sections missing
  • Abstract not single-spaced
  • Figures missing legends
  • References not properly formatted

  • You can find parts of this text in an on-line collection of instructional materials used in the Purdue University Writing Lab (http://owl.english.purdue.edu). Other parts are inspired by "How to Write and Publish a Scientific Paper" from Oryx Press by Robert A. Day (ask to borrow a copy from the teaching faculty) or are based on the research and teaching experiences of the teaching faculty.
  • You may also wish to read the article Writing Readable Prose, published in 2006 by the EMBO journal. The authors make a strong case for the role that writing (good or bad) can play in your career development, and the article also explains some elements of clear writing.

Helpful hints

Crafting a cohesive story

  • Your data (Results and Figures) are the heart of your paper. Begin by assembling and understanding these sections as clearly as possible. Then you can write the framing material (introduction and discussion), while compiling relevant references. The final revision is best written once you have all your results. You should generally write the abstract last, once you have a big picture understanding of every element of your investigation. As for the methods section, it can help to write it in short pieces day-by-day, while the procedures are fresh in your mind.
  • The first draft is a record of your ideas; the second draft is a crafted presentation of them. Draft as much of your report as possible early on, so you have the opportunity to revise it before submission. Even better, outline the content and high-level organization of your paper before you even begin drafting.

Representing the data

  • Some readers begin by scanning the figures, so these and their captions should provide a self-explanatory overview of your data. Decide what the data show, then create figures that highlight the most important points of your paper.
  • Tables are used to present text or repetitive numerical data. Graphs or illustrations, collectively called figures, are used to present numerical trends or comparisons, raw data (like a picture of a gel), or a model that explains your work.
  • All tables and figures must have numbers, titles, and captions. Include legends only if they are useful in clarifying the data.
  • When you prepare your figures and tables, keep in mind that it is significantly more expensive for journals to publish figures and tables than text, so try to present the data in a way that is worthy of such added expense. The table below is an example of an ineffective table, where the information could be presented clearly and concisely in one sentence, such as: "In ten experiments carried out at 24°C, ion flow was detected only in the presence of cortical cells."
 Temperature		Repeats		Cortical cells		Ion flow
 24°C			5		+			+
 24°C			5		-			-
  • What should you do when two independent pieces of data suggest two very different conclusions about your overall experiment? The one thing you should not do is state that both conclusions are correct, in different parts of the paper, and hope that the reader will ignore the discrepancy! As a scientist, you must take a holistic view of your analyses. Is there any way to reconcile the two results? Is one method more trustworthy, or is there another indication to favor one conclusion over the other? If you have no way of determining which result is correct with your present data, can you propose future experiments to distinguish more conclusively?

Organizing the details

  • Captions to the figures and tables explain the elements that appear in the illustration. Interpretations about the data are NOT included in the captions. As you write your first draft, you might state the point of the figure or table in a short simple sentence. In later drafts, make sure each element of the figure or table is explained. Your figure captions should be written in the present tense, since you are explaining elements that still exist at the time that you are writing the paper.
  • The readability of your paper can be substantially improved by its organization. Well-chosen subsection titles provide the reader with a distillation of the high-level points you want to emphasize. Be sure to summarize major points - if you do this right, you will feel like you are repeating yourself too much! Each major section of the report should be more or less stand-alone, that is, understandable without having to read the rest of your paper. Be sure to work from big to small to big (from broad points to details and back) throughout your paper. Finally, limit paragraphs to one topic, splitting up longer linked ideas as needed.
  • One difficult task for budding scientific writers is determining what goes in a Results vs. a Discussion section. Even at the professional level, different scientific journals may have different expectations for how much interpretation is appropriate in the Results. A good rule of thumb in most contexts is to draw technical conclusions in the Results, but save scientific conclusions for the Discussion. An alternative framework that should yield similar writing choices is to focus on relatively certain conclusions in the Results, and save more speculative (but still supported!) conclusions for the Discussion.
    • Example of a technical conclusion: "Sequence alignment revealed that both mutants exhibited mutations in at least one of the expected sites and thus were consistent with the possible nucleotide changes that could occur with the library used."
    • Example of a scientific conclusion: "A previously reported model proposes that the OmpR-P phosphatase reaction occurs by hydrolysis rather than direct phosphotransfer from H557 (Hsing 1997). Our mutant is consistent with a change to the structure of EnvZ that facilitates this hydrolysis reaction, thus increasing phosphatase activity while concurrently reducing kinase activity."