BE Communication Lab resources

Throughout the semester you will participate in workshops provided by the Instructors from the BE Communication Lab that will help you prepare your major communication assignments. The resources provided at these workshops will be posted here!

Workshop materials

[Figures and captions]
[Abstracts]
[Oral presentations]
[Manuscript architecture]
[Grant proposals]

To schedule an appointment with a BE Communication Lab Fellow:

• BE Communication Lab

For assistance finding research articles, managing citations, etc.:

• Howard Silver, the MIT Library's biological engineering expert

Laboratory notebook guidelines

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

1. To develop good lab practices for the future.
2. To have a one-stop place to remember what you did each day and what the result was.

Since the F13 semester, we've successfully moved to digital record keeping by using Evernote to keep and share electronic lab notebooks for 20.109. Evernote is a free-ware that is installed on all lab computers. You can download Evernote to your Mac or PC and access your lab notebook in the cloud while outside of the lab. This will allow you to prepare for lab by adding the relevant protocol and prepping Excel sheets (or other data crunching software) for your calculations, etc. Furthermore, your results (gel images, ppt files, graphs, etc) can be attached to each page, making data accessible for easier report preparation.

Finally, Evernote notebooks can be 'shared' with your TAs and teaching instructors to facilitate easier grading. We hope these small changes will make a big impact, keeping even more of the 20.109 process transparent for everyone and allowing easy and instant data sharing.

No two scientists organize their lab notebooks identically, and there isn���t one ���right��� way for you to keep yours. There are some common elements that all lab notebooks share and some important habits you should develop in keeping your notebook for this class. All lab notebooks should be...

1. Complete
Your notebook is a place to collect descriptions of experimental goals, experimental procedures, all the data you collect, and your interpretations of results. Numerical data and calculations should be entered directly into your notebook, ideally not on scraps of paper to be entered later. Data in the form of photographs, printouts, etc., can be attached directly to your Evernote notebook.

2. Organized
Some scientists arrange their notebooks by date, others by the question being tested. What works best depends on the research itself and the researcher. Since this class has three experimental modules that are performed sequentially, your notebook will, by default, be organized by both date and project. You will keep a record of every lab meeting, including both the date and the Module/Day in your notebook.

We suggest keeping one Evernote notebook for each 20.109 Module. You may then share that notebook with the TA for that module and keep your records easily separable.

3. Up to date
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 leaving lab with wiki protocols clearly cited, paraphrased, or copied/pasted in, any amendments you made to said protocols clearly noted, data entered, and perhaps some initial interpretation written up. Your notebook does not need a table of contents, but you should realize that most research notebooks do.

4. Permanent
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, getting into the habit of changing font color or making a *note to show where you have updated text/figures/calculations will be useful for the future.

Some other things you should know about lab notebooks:

• They are the property of the research lab itself. Researchers who join the lab after you have left it will get to know you through the notebooks you have kept there. Ideally, your notebooks will reflect your most organized, clear and thoughtful side.
• They are legal documents. Labs in industry have special rules about lab notebooks since patent disputes and court cases often hinge on lab notebook entries.
• They are both personal and public. It is considered impolite and an invasion of privacy to read someone else���s notebook without their permission. Most people are happy to show you their notebooks when asked.
• As you read these details, you may have asked yourself how an electronic notebook satisfies the 'old school' way of keeping lab records. This is a great question -- and one that we will learn the answer to together during the semester as we try out this new system!

Grading your 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 evaluation and should maintain all of your entries according the guideline 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
 
 OVERALL  /10  			                        

Things to remember:

Remember that the goal of your notebook is to help you repeat your experiments with the same results. You should copy, paraphrase, or 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 hr into incubation)
• Unusual observations (a large number of cells seemed to be floating)

Oral communication guidelines

Scientific data are communicated in many ways. Data can be shared informally through email with a collaborator or in lab group meetings. Data can also be formally communicated as publications in peer-reviewed journals or as presentations at international meetings. Successful scientific careers require both written and oral presentations, and scientific reputations are based on BOTH. It is important to know that every presentation, no matter how informal, can impact your reputation. That's one reason you can find such detailed and numerous guidelines for giving scientific job talks.

Hour-long seminars, ten-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 varies, they share certain common elements, including organization, clarity, and proper attribution for the work.

The individual oral presentations you give in this class will be ten-minute journal club talks. 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 so short a time, and even that will require that you carefully plan what you will say and then practice saying it. You are expected to rehearse and ultimately deliver your talk with a timer running, and to adjust your presentation as needed to stay within the allotted time. Fairness to your classmates demands that you respect the ten-minute time limit.

In addition to the advice below, you should also consult with the BE Communication Lab.

A few tips

• A 10��� talk is NOT a 30��� talk given very fast.
• It will help if you memorize the first few sentences of your talk. After that, sticking too closely to a script can sound artificial, plus you might get really thrown off and stuck if you forget your exact phrasing. A little flexibility is better for both you and the audience.
• Think of ways to transition from one slide to the next: ���The authors then identified the isolated protein using mass spectrometry.���
• Generally speaking, you should figure out how to work the lights, slide projector, curtains, etc. before you begin. In this class, we'll worry about those aspects for you; however, you should get comfortable with the timer, laser pointer (see below), and your software.
• Laser pointers or sticks can be used to direct attention to images on the screen. Be sure to always use a pointer with a specific purpose in mind, rather than constantly gesturing in the general vicinity of your slide; otherwise, the audience will not know what's important. Don���t aim your laser pointer at anyone since it can damage a person���s eyes.
• Keep the lights as bright as possible. If you must turn the lights off for some image to be properly seen, then remember to turn the lights back on. People can and do fall asleep during dark seminars.

How to deal with nerves

• Consider it excitement and turn it into enthusiasm
• Remember that even the most experienced speakers get nervous right before a talk
• Speak in a louder voice
• Speak with variety in your vocal tone (not a monotone)
• Do practice your talk, which will help eliminate crutch words such as ���so,��� ���um,��� and ���like���

Format

You can find examples of short talks here and here

Written communication guidelines

Formal research articles and less formal lab reports are the principal ways scientific data is conveyed to the rest of the scientific community and preserved for future examination. Each scientific journal has its own idiosyncrasies regarding format particulars, but the most common elements of a scientific article, in order of presentation, are:

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

The requirements for each section are outlined below. If you want more information, 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 Robert A. Day���s book, ���How to Write and Publish a Scientific Paper��� from Oryx Press, a copy of which can be borrowed from the teaching faculty. Still other content is based on the research and teaching experiences of former 20.109 instructors Natalie Kuldell and Agi Stachowiak.

Title

The title should be short (about 10 words), interesting, and it should describe what you found. 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.

Abstract

The abstract serves as a condensed version (not >250 words) of your report, from background (both context and motivation) to key results (and how they were found) 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 the words in a paper���s title and abstract, and thus these may be the only parts that many people read. AT MIT we are very lucky to have access to almost any journal we could want, but not everyone is in this position. 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 and not generally relevant.

Introduction

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.

You are welcome to use your own creativity and judgement as to what a good introduction should look like; however, note that 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 any of your experiments. Use sub-section 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 judgement 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 already 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.

Results

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 sub-sections that describe each piece of the work.

Titled sub-sections help support your high-level narrative and make dense papers easier to read. Effective sub-sections are organized by functional content, not by what you did each day in lab. 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 you might take is to start by outlining, in point form, what you found, 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 sub-section 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. (Sub-section headings and figure caption titles can also emphasize said conclusion.) The overview and/or concluding sentences should also provide a transition to the previous/next piece of data when possible. Within a sub-section, be sure to stick to one topic per paragraph; sub-sections will generally require a few paragraphs each.

Note that verbs in the results section are usually in the past tense. Only established scientific knowledge is written about in the present tense: ���the world is round,��� for 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.

Discussion

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 sub-sections.

References

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 paper���s title, the name of the journal in which it was published, its 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 A. 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.

Figures and tables

Some readers begin by scanning the figures, so these and their associated legends 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 repetitive data that is numerical. Graphs or illustrations, collectively called figures, are used to present numerical trends, raw data (like a picture of a gel), or a model that explains your work.

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.

 Temperature		Repeats		Cortical cells		Ion flow
 24��C		        5		+             		+
 24��C		        5		-             		-

The information in Table 1 could be presented in one sentence, such as: ���In ten experiments carried out at 24��C, ion flow was detected only in the presence of cortical cells.��� This is a clearer and more concise way to present the information. In addition, all tables and figures must have numbers, titles, and legends (also called captions).

Figure and table legends
Legends to the figures and tables explain the elements that appear in the illustration. Conclusions about the data are usually NOT included in the legends (the choice is somewhat journal-dependent). As you write your first draft, you might state in a short simple sentence what the point of the figure or table is. In later drafts, make sure each element of the figure or table is explained. Your figure legends should be written in the present tense since you are explaining elements that still exist at the time that you are writing the paper.

Recommended order of assembly for a scientific paper

Your data (results and figures) is the heart of your paper. Begin by assembling and understanding it as clearly as possible. Then you can write the framing material ��� introduction and discussion, while compiling a few relevant references. (Actually, you will write a draft of the introduction about halfway through the module, once you have begun to develop some understanding of the field. 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, you might write it in short pieces day-by-day, while the procedures are fresh in your mind.

Additional scientific writing tips

In our experience, concentrating on the following topics tends to repay student effort.

You may also wish to read the article published in 2006 by the EMBO journal called Writing Readable Prose. It makes a strong case for the role that writing (good or bad) can play in your career development, and also makes explicit some elements of clear writing.

Finally, you'll learn a lot by working with the BE Communication Lab fellows!

Structure and repetition

The readability of your paper can be substantially improved by its organization. Well chosen sub-section titles provide the reader with a distillation of the high-level points you want to make. Take the opportunity early and often 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 read the rest of your paper. Be sure and work from big to small to big (from broad points to details and back) throughout your paper. Finally, limit paragraphs to one topic apiece, splitting up longer linked ideas as needed.

Results vs. discussion

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 somewhat 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."

Holistic view of data

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 than the other or is there otherwise an 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 conclusively decide?

Concision

Eliminate unnecessary words and phrases. Writing concisely takes more effort than writing inefficiently. It also results in more readable text that expresses your ideas more powerfully.

Precision and detail

Being concise is not an invitation to be vague. Be sure to support your claims with specific examples, and to follow through on your ideas with sufficient detail.

Writing is revision

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. Students who plan ahead in this way tend to submit particularly successful reports.

Evaluation

The following table describes the features of research papers that are excellent, good, and that need substantial improvement, respectively from left to right. Your own manuscripts will be evaluated with these features in mind. Content

Style