Working in the lab

Where do we move this "Working in the lab" info?

General lab policy

• General dos and don'ts of working in the lab

Lab tour

• Familiarize yourself with basic lab equipment and techniques

Guidelines for working in the tissue culture facility

• Procedures for doing tissue culture work

Links to guidelines on using personal protective equipment, developed by the Environmental Health and Safety Office at MIT.

• Eye protection document (PDF download)
• Lab coat document (PDF download)

Communicating your work

How to maintain a good lab notebook

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 20.109 teaching assistants will examine your notebook pages for a specific day once per module. You will not know in advance which day will be collected. For example, on Module 2/Day 7, the notebook pages summarizing Module 2/Day 2, Day 3, or Day 4 might be collected.

Each time, notebooks will be evaluated by the following rubric:

 Lab Notebook				Evaluation
 Date of experiment			√-	√	√+
 Module#/Day#		        	√-	√	√+
 Title for experiment			√-	√	√+
 Brief statement of purpose		√-	√	√+
 Protocol		        	√-	√	√+
 Tables for data entry			√-	√	√+
 Calculations entered			√-	√	√+
 Data labeled		        	√-	√	√+
 Summary/interpretation           	√-	√	√+	
 OVERALL    			        √-	√	√+

Due dates

• Module 1, Day 7: either Day 2, 4, or 5 will be collected
• Module 2, Day 7: either Day 2, 3, or 4 will be collected
• Module 3, Day 5: either Day 1, 2, or 4 will be collected

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)
• Lot # or date prepared of buffers and other reagents
  • when more than one is available
• Electrophoresis: running voltage and time
• Washes: number, volumes
• Incubation times and temperatures

You should also note any unusual changes to the protocol such as

• unexpected delays (“waterbath wasn’t ready so tubes kept on ice for one hour”),
• unanticipated conditions (“roller drum found off in AM”)
• unusual observations (“a large number of cells seemed to be floating”)

How to give a good oral presentation

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

How to communicate your data in the form of a research article