|
|
(69 intermediate revisions by 3 users not shown) |
Line 1: |
Line 1: |
− |
| |
| {{Template:20.109(F16)}} | | {{Template:20.109(F16)}} |
| | | |
| <div style="padding: 10px; width: 790px; border: 5px solid #000FFF;"> | | <div style="padding: 10px; width: 790px; border: 5px solid #000FFF;"> |
| | | |
− | =Working in the lab= | + | =BE Communication Lab resources= |
− | '''<font color = red> Where do we move this "Working in the lab" info?</font color>'''
| + | Throughout the semester you will participate in workshops provided by the instructors from the BE Communication Lab ([mailto:saclarke@mit.edu Sean Clarke] and [mailto:dchien@mit.edu Diana Chien]) that will help you prepare your major communication assignments. The resources provided at these workshops will be posted here! |
− | | + | |
− | [http://openwetware.org/wiki/20.109(F16):General_lab_policy | '''General lab policy''']
| + | |
− | * General dos and don'ts of working in the lab
| + | |
− | | + | |
− | [[20.109(F16):Lab tour | '''Lab tour''']]
| + | |
− | *Familiarize yourself with basic lab equipment and techniques
| + | |
− | | + | |
− | [http://openwetware.org/wiki/20.109(F16):Guidelines_for_working_in_the_tissue_culture_facility | '''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.'''
| + | |
− | *[[Media:2010_EHS_EyeProtectionGuidance.pdf | Eye protection document (PDF download)]]
| + | |
− | *[[Media:2010_EHS_LabCoatGuidance.pdf | Lab coat document (PDF download)]]
| + | |
− | | + | |
− | =Communicating your work=
| + | |
− | ==Resources==
| + | |
− | *[http://be.mit.edu/communicationlab BE Communication Lab]: Make an appointment with a Fellow.
| + | |
− | *[http://libguides.mit.edu/bioleng MIT Libraries Biological Engineering Research Guide]
| + | |
− | **Resources for finding research articles, managing citations, etc.
| + | |
− | **Contact [mailto:hsilver@mit.edu Howard Silver], the MIT Library's biological engineering expert, for personalized help.
| + | |
− | | + | |
− | ==Lab notebook==
| + | |
− | | + | |
− | The purpose of keeping a lab notebook in 20.109 is two-fold:
| + | |
− | #To develop good lab practices for the future.
| + | |
− | #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 [https://evernote.com/ 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'''<br>
| + | |
− | 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'''<br>
| + | |
− | 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'''<br>
| + | |
− | 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'''<br>
| + | |
− | 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:'''
| + | ==Workshop materials== |
| + | Figures and Captions [[File:Figures_workshop_slides_109_16F.pdf]]<br> |
| + | Abstracts and Titles (and Writing Tips) [[File:F2016_20.109_Workshop_2_-_Abstracts_and_Titles_2016_posted.pdf]]<br> |
| + | Journal Club and Oral Presentations [[File:F16_20.109_Workshop_3_-_Journal_Club.pptx]]<br> |
| + | Research Article structure and writing process [[File:F2016_20.109_Workshop_4_Research_Article_final.pptx]]<br> |
| + | Research Proposals [[File:20.109_Workshop_5_-_Proposal_2016F_no_video.pptx]]<br> |
| | | |
− | *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.
| + | To schedule an appointment with a BE Communication Fellow: |
− | *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. | + | *[http://be.mit.edu/communicationlab BE Communication Lab] |
− | *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====
| + | For assistance finding research articles, managing citations, etc: |
− | 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.
| + | *[mailto:hsilver@mit.edu Howard Silver], the MIT Library's biological engineering expert |
| | | |
− | Each time, notebooks will be evaluated by the following rubric:
| + | =Laboratory notebook guidelines= |
| + | The purpose of keeping a laboratory notebook in 20.109 is two-fold: |
| | | |
− | Lab Notebook Evaluation
| + | #To develop good archiving practices for the future. |
− | Date of experiment √- √ √+
| + | #To maintain a one-stop resource to remember what you did each day and record the outcome(s). |
− | Module#/Day# √- √ √+
| + | |
− | Title for experiment √- √ √+
| + | |
− | Brief statement of purpose √- √ √+
| + | |
− | Protocol √- √ √+
| + | |
− | Tables for data entry √- √ √+
| + | |
− | Calculations entered √- √ √+
| + | |
− | Data labeled √- √ √+
| + | |
− | Summary/interpretation √- √ √+
| + | |
− | OVERALL √- √ √+
| + | |
| | | |
− | '''Due dates'''
| + | You will use an online laboratory notebook to document your work in 20.109. [http://benchling.com/ 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. |
| | | |
− | * Module 1, Day 7: either Day 2, 4, or 5 will be collected
| + | 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. |
− | * 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:''' | + | '''Complete'''<br> |
| + | 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. |
| | | |
− | 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
| + | 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 | + | *dilutions and how they were prepared |
− | *Final concentrations (if only stocks are listed) | + | *final concentrations (if only stocks are listed) |
− | *Lot # or date prepared of buffers and other reagents | + | *protocol changes: |
− | **when more than one is available | + | **unexpected delays (''e.g.'' the waterbath was not ready so tubes were kept on ice for one hour) |
− | *Electrophoresis: running voltage and time | + | **unanticipated conditions (''e.g.'' the roller drum was not turned on until ~12 h into incubation) |
− | *Washes: number, volumes | + | *unusual observations (''e.g.'' a large number of cells seemed to be floating). |
− | *Incubation times and temperatures | + | |
| | | |
− | You should also note any unusual changes to the protocol such as
| + | '''Organized'''<br> |
− | *unexpected delays ( waterbath wasn t ready so tubes kept on ice for one hour ),
| + | 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. |
− | *unanticipated conditions ( roller drum found off in AM )
| + | |
− | *unusual observations ( a large number of cells seemed to be floating )
| + | |
| | | |
− | ==Oral presentation==
| + | '''Current'''<br> |
| + | 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. |
| | | |
− | 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 [http://www.insidehighered.com/advice/2010/10/06/delph guidelines] for giving scientific job talks.
| + | '''Permanent'''<br> |
| + | 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. |
| | | |
− | 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.
| + | ====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. |
| | | |
− | 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'''.
| + | Your laboratory notebook entries will be evaluated using the following rubric: |
| | | |
− | In addition to the advice below, you should also consult with the [http://be.mit.edu/communicationlab BE Communication Lab].
| + | 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 |
| | | |
− | '''A few tips'''
| + | =Oral communication guidelines= |
− | *A 10
|