Difference between revisions of "20.109(S21):Homework"

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(Module 2: Screening small molecules)
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==Module 3: Modulating protein activity==
 
==Module 3: Modulating protein activity==
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===Due M3D1===
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===Due M3D2===
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===Due M3D3===
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===Due M3D4===
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===Due M3D5===
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===Wrapping up M3===
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#The [[20.109(S21):Research proposal presentation| Research proposal presentation]] is due by 1 pm on Tuesday, May 18th or Wednesday, May 19th, according to you laboratory section.
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#The [[20.109(S21):Mini-report | Mini report]] is due by 10 pm on Monday, May 24th.
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#Please remember to contribute your reflections, comments, and ideas to the [ Class blog] before 10 pm on Thursday, May 20th.
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#*Note: only three blog posts are required for full credit.

Revision as of 21:52, 22 January 2021

20.109(S21): Laboratory Fundamentals of Biological Engineering

Sp21 banner image v2.png

Spring 2021 schedule        FYI        Assignments        Homework        Communication |        Accessibility

       M1: Antibody engineering        M2: Drug discovery        M3: Protein engineering       


Module 1: Engineering antibodies

Due M1D1

  1. Review the Orientation and laboratory tour exercises to prepare for the Orientation quiz that you and your partner will complete together during at the start of the laboratory session.
  2. Though you will not be completing experiments in the laboratory this semester, please complete the following online training offered through Environmental Health and Safety (EHS). First, it is important that you learn best practices this semester and safety is a major part of this. Second, the training certifications do not expire and will be valid when are able to return to campus for UROP work!
    • Emergency Preparedness (access at this this link)
    • General Chemical Hygiene (access at this link)
    • General Biosafety (access at this link)
    • If you have completed EHS training in a UROP or in another laboratory class, you do not need to repeat the training. Instead submit the certificates of completion or your training record which can be found at "My Training Needs" on Atlas. To access, go to atlas.mit.edu then click the Learning Center tab on the left side of the screen.
  3. Download Benchling onto your computer. You will use this program to maintain your laboratory notebook for the semester.
  4. Prepare for the first day of Module 1 by reading the M1 Project overview and the M1D1 Introduction.

Due M1D2

  1. In class, we will discuss a paper relevant to the material presented in Module 1.
    • To prepare, read the article and assignment details (both are provided on the M1D2 page).
  2. Read through the webinair Keeping a Lab Notebook: Basic Principles and Best Practices provided by the National Institutes of Health. Though not all of the specifications will be adhered to in 20.109, please note the information on slide #9 as this is the basis of the rubric developed to grade your notebook entries this semester.
  3. To prepare for your laboratory session, complete a template for your notebook entry according to the Laboratory notebook guidelines provided on the Assignment tab. You will use these guidelines for every notebook entry you complete in 20.109.
    • Click on the '+' symbol on the left menu bar
    • Click on More-->Template
    • In the "Create Template" dialog box, click "Manage Collections" in the lower left corner.
    • Click on "+ New Collection."
    • Give the collection an appropriate name (e.g. 20.109 Notebook Templates)
    • Create a new template within the newly created collection by typing in the name (e.g. Lab Notebook Entry Template) and press "Create Template."
    • Type in the categories or whatever reminders will help you fill out your lab notebook entry appropriately. It would be wise to base this on the Laboratory notebook guidelines provided as this will ensure the Instructors are able to find the information for grading purposes.
    • Press "Update Information" to save your edits.
    • Now when you want to make a new entry for each lab day, you can make a new entry from this template (When you press the '+' symbol on the top menu bar near your project title, it will give you the option to create an entry from template).
    • See the example entry below for further guidance.
    • Use the Benchling template created above, to generate a Laboratory notebook page for M1D2.
      Fa20 notebook entry template.png

Due M1D3

  1. In scientific communication, data are shown both as figures and in text. For this homework use the data analyzed from the FACS experiment to craft a figure for your Data summary.
    • Carefully consider how to best include the data before you start. Will you summarize the results in a graph / table? How will you organize the data to ensure it is clear to a reader?
    • Remember that all figures must include a title and caption.
    • Review the prelab slides for suggestions and guidance!
  2. The BE Communication Lab is a great resource to keep in mind as you complete your assignments for 20.109. To familiarize you with this resource, you will receive homework points for meeting with a Fellow to discuss an assignment by M1D5.
    • You must schedule your appointment online at the BE Communication Lab homepage. Click "Make an appointment" at the top right corner of the screen. Please review the document linked here to help your prepare for your meeting.

Due M1D4

  1. The major writing assignment in Module 1 is the Data summary. As part of this assignment you will provide details concerning the background information relevant to your research and the motivation for your research. To help you prepare, in this homework you will draft topic sentences that provide the reader with the information necessary for understanding your project. A topic sentence is the first sentence of a paragraph and states and provides context for the subsequent statements in the paragraph.
    • Write 3-5 topic sentences that will be the outline for the Background and Motivation section of your Data summary.
    • Each topic sentence should be supported by a reference from the literature (peer reviewed articles only!). Include the full citation for each article used as a reference and a short description of the key finding(s) in each article.
    • Review the Data summary assignment page and prelab slides for suggestions and guidance!
  2. As part of the major writing assignment in Module 2, you will document the details of the experiments performed in a Methods section. To help you prepare for this task, and to provide you feedback early on, you will draft the Module 1 methods. For this homework, work with your laboratory partner to draft a methods section that details the procedures that were described on M1D2 and M1D3.
    • Review the prelab slides for suggestions and guidance!
  3. The BE Communication Lab is a great resource to keep in mind as you complete your assignments for 20.109. To familiarize you with this resource, you will receive homework points for meeting with a Fellow to discuss an assignment by M1D5.
    • You must schedule your appointment online at the BE Communication Lab homepage. Click "Make an appointment" at the top right corner of the screen. Please review the document linked here to help your prepare for your meeting.

Due M1D5

  1. Submit a short summary (1-2 paragraphs) concerning your meeting with a Fellow from the BE Communication Lab. Including your thoughts on the utility of your meeting and what you learned from the discussion.
    • You must schedule your appointment online at the BE Communication Lab homepage. Click "Make an appointment" at the top right corner of the screen. Please review the document linked here to help your prepare for your meeting.
  2. In scientific communication, data are shown both as figures and in text. For this homework use the data analyzed for the sequence alignment to craft a figure and write the corresponding bullets for your Data summary.
    • Carefully consider how to best include the data before you start. Will you summarize the results in a graph / table? How will you organize the data to ensure it is clear to a reader?
    • Remember that all figures must include a title and caption.
    • Use the questions below to organize the information that should be included in the bullets.
    • Review the prelab slides for suggestions and guidance!
      Sp17 20.109 results-interpretations bullets.png

Due M1D6

  1. Figures serve many functions in scientific communication. In the previous homework you crafted a figure to represent the results of an experiment. Figures are also useful in illustrating the experimental approach, or overview, of a research project. In this type of figure the important experimental steps are represented to highlight the workflow at a high-level. For example, cloning an important plasmid would be represented but the specifics about performing a ligation reaction would not be included.
    • For this homework craft an overview schematic that illustrates the research completed in Module 1.
    • Please note, schematics are figures and should have both a title and a caption.
    • Review the prelab slides for suggestions and guidance!
  2. The major verbal assignment in Module 1 is the Mini-presentation. The Mini-presentation is a short, verbal description of the key components / results of your research project. Furthermore, this assignment is an opportunity to practice your oral communication skills before the Journal Club presentation in Module 2.
    • For this assignment, prepare an outline for your Mini-presentation. You should not submit a script, but rather a bulleted outline of the information you will provide in your presentation.
    • Review the Mini-presentation assignment page and prelab slides for suggestions and guidance!

Due M1D7

  1. The final section of your Data summary will discuss the Implication and Future works of your project. In this section the main findings of the research are summarized and used to answer the research question. Also, experiments are proposed that will expand upon the results in an effort to further answer the research question or perhaps address a new research question raised by your research.
    • For this homework, provide an outline of your summarized results and propose two future experiments.
    • Review the Data summary assignment page and prelab slides for suggestions and guidance!
  2. Incorporate the feedback you received from the Instructors to revise the Methods draft homework you submitted M1D4. As before, work with your laboratory partner to complete this homework.
    • In addition, include the experimental procedures that were discussed M1D4, M1D5, and M1D6 in this revised assignment.

Wrapping up M1

  1. The Data Summary draft is due by 10 pm on Wednesday, March 24th.
  2. The Mini-presentation is due by 10 pm on Sunday, March 28th.
  3. The Data Summary revision is due by 10 pm on Sunday, April 4th.
  4. Please remember to contribute your reflections, comments, and ideas to the [ Class blog] before 10 pm on Monday, March 29th.

Module 2: Screening small molecules

Due M2D1

  1. Prepare for the first day of Module 2 by reading the M2 Project overview and the M2D1 Introduction.

Due M2D2

Due M2D3

Due M2D4

Due M2D5

Due M2D6

Due M2D7

Wrapping up M2

  1. The Research article is due by 10 pm on Sunday, May 2nd.
  2. Please remember to contribute your reflections, comments, and ideas to the [ Class blog] before 10 pm on Saturday, April 10th AND before 10 pm on Monday, May 3rd.

Module 3: Modulating protein activity

Due M3D1

Due M3D2

Due M3D3

Due M3D4

Due M3D5

Wrapping up M3

  1. The Research proposal presentation is due by 1 pm on Tuesday, May 18th or Wednesday, May 19th, according to you laboratory section.
  2. The Mini report is due by 10 pm on Monday, May 24th.
  3. Please remember to contribute your reflections, comments, and ideas to the [ Class blog] before 10 pm on Thursday, May 20th.
    • Note: only three blog posts are required for full credit.