Difference between revisions of "20.109(F22):Homework"

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(Due M1D7)
(Module 1: Genomic instability)
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<font color=red>'''&#9744;'''</font color> Is only information necessary to repeat the experiment included? <br>
 
<font color=red>'''&#9744;'''</font color> Is only information necessary to repeat the experiment included? <br>
 
<font color=red>'''&#9744;'''</font color> Are all descriptions concise and clear? <br>
 
<font color=red>'''&#9744;'''</font color> Are all descriptions concise and clear? <br>
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</p style>
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==Module 1: Drug discovery==
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===Due M2D1===
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*Prepare for the first day of Module 2 by reading the [[20.109(F22):Module 2#Overview | M2 Project overview]] and the [[20.109(F22):M2D1#Introduction |M2D1 Introduction]].
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===Due M2D2===
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*The major verbal assignment in Mod2 is the Journal club presentation.  As part of this assignment you will present a published, peer-reviewed research article to the class.  For this homework, select and review an article for your presentation from the curated lists on the Journal club presentation assignment page.  If you prefer, you can find your own paper and send it to the Instructors for approval.
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<p style="margin-left:100px;">
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Use the checklist below to assist you as you complete this assignment: <br>
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<font color=red>'''&#9744;'''</font color>  Reserve your article on the [[20.109(F22):Journal club presentation|Journal club presentation]] page according to the directions provided under the 'Article selection' header. <br>
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<font color=red>'''&#9744;'''</font color>  Review the abstract and introduction for the selected article. <br>
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<font color=red>'''&#9744;'''</font color>  Submit a brief summary of the selected article that highlights why you think the research is interesting. <br>
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</p style>
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===Due M2D3===
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*For your Journal club presentation, you will only have 10 minutes to present a clear, cohesive story from the data in your selected research article.  Given the number of figures in most research articles it is impossible to show all of the data from your paper in a short presentation.  In this, it is important to identify which figures are the most important to the main conclusion(s) of the research article.  For this homework, read through the paper you selected for the Journal Club presentation and choose the four figures that you think are most important in telling the story presented by the authors.
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<p style="margin-left:100px;">
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To get you started, answer the questions below: <br>
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<font color=red>'''&#9744;'''</font color>  What is the main conclusion of the paper? <br>
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<font color=red>'''&#9744;'''</font color>  What four figures are the most important in supporting the main conclusion? Why? <br>
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<font color=red>'''&#9744;'''</font color>  How do the figures work together to tell a story?  How does this story lead you to the main conclusion of the paper? <br>
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<font color=red>'''&#9744;'''</font color> Hint: you can find the information provided during the Comm Lab workshop on the[[20.109(F22):Communication | Communication]] page for help! <br>
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</p style>
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*The Journal club presentations will occur during the laboratory sessions on Tuesday, November 1st and Thursday, November 3rd for the T/R section and on Wednesday, November 2nd and Thursday, November 4th for the W/F section.  Due to class size, presenters in each section will be divided between the two days by the Instructors. 
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<p style="margin-left:100px;">
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<font color=red>'''&#9744;'''</font color>  To  reserve a presentation date, email Noreen (nllyell@mit.edu) with which day you prefer to present and why. If one of the days becomes oversubscribed then slots will assigned using a lottery. <br>
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</p style>
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===Due M2D4===
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*Your slide deck will be important in your ability to effectively tell the story presented by the authors of your paper.  For this homework you will draft a presentation slide using one of the data figures from the paper you selected that you want to discuss as part of your Journal club presentation.  In addition, include a script for the verbal information that you will deliver when presenting the figure on your slide.
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<p style="margin-left:100px;">
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Use the checklist below to assist you as you complete this assignment: <br>
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<font color=red>'''&#9744;'''</font color> Does the title of your slide convey a concise take-home message about the data shown? <br>
 +
<font color=red>'''&#9744;'''</font color> Do you include data from a single figure of your paper? <br>
 +
<font color=red>'''&#9744;'''</font color> Are you trying to include too much data on a single slide? <br>
 +
<font color=red>'''&#9744;'''</font color> Is all the text from your data figure legible? (especially note the axes text and recreate it if necessary) <br>
 +
<font color=red>'''&#9744;'''</font color> Is there a good balance between figures and text on the slide? (approximately half of each) <br>
 +
<font color=red>'''&#9744;'''</font color> Does the text convey only key information? <br>
 +
<font color=red>'''&#9744;'''</font color> Is your script concise? (i.e. Are you able to convey this information in approximately 1 minute?) <br>
 +
<font color=red>'''&#9744;'''</font color> Does your script contain technically correct scientific information? <br>
 +
<font color=red>'''&#9744;'''</font color> Is the information in your script directly relevant to the data on the slide? <br>
 +
 +
<font color=red>'''&#9744;'''</font color> Hint: you can find the information provided during the Comm Lab workshop on the[[20.109(F22):Communication | Communication]] page for help! <br>
  
 
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</p style>

Revision as of 19:04, 9 September 2022

20.109(F22): Laboratory Fundamentals of Biological Engineering

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Fall 2022 schedule        FYI        Assignments        Homework        Class data        Communication        Accessibility

       M1: Genomic instability        M2: Drug discovery        M3: Project design       


Homework Submission Guidelines

  • When submitting assignments online, make sure that your section information, name, and assignment details are in the file name and included on the document itself. e.g. 'TR_ImaStudent_M1D1' Renaming the file in Stellar itself is not sufficient, as this does not actually affect the file name.
  • For group assignments, submit one copy of the homework and also include your section and team color. e.g. 'TR_Rainbow_M3D2'
  • Note: Some assignments may indicate a more specific naming scheme than this one. Follow that instead when applicable

Module 1: Genomic instability

Due M1D1

  • 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.
  • Complete the following online training courses offered through Environmental Health and Safety (EHS):

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.

Due M1D2

  • The major writing assignment in Mod1 is the Data summary. As part of this assignment you will provide details concerning the relevant background information important for understanding your project. In addition, you will use this information to motivate your specific research question.

To get you started, answer the questions below:
What is your research question?
What important problem is addressed by your research question?
What topics / concepts should be explained to ensure a reader understands why your research question is important?
What experiments / techniques will you use to answer your research question?
Hint: review the information provided on the M1 Project overview for help!

  • 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. To 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 M1D3

  • An important part of scientific research is documenting the details regarding how experiments were performed. To practice this skill, you will work with your laboratory partner to draft a methods section that details the procedures that you completed on M1D1 (specifically, Part 2 and Part 3) and M1D2.

Use the checklist below to assist you as you complete this assignment:
Do you have descriptive subsection headers in a logical order?
Do each of your experimental sections begin with a topic sentence to introduce the purpose of the technique?
Do you write full sentences in passive voice and past tense? (i.e. His-tagged recombinant protein was purified using nickel resin.)
Do all reagents include manufacturer information in parentheses?
Are all abbreviations and acronyms written in full? (if this is the first use of the acronym)
Are all 20.109-specific details omitted? (i.e. do not include "Row A and Row B" or "the experiment was completed by the teaching faculty")
Are all mentions of tubes and water omitted?
Are the most flexible units used? (i.e. concentrations rather than volumes)
Is only information necessary to repeat the experiment included?
Are all descriptions concise and clear?

  • The major verbal assignment in Mod1 is the Research talk. As part of this assignment you will provide a brief, yet detailed, presentation of your results. For this homework, draft an outline of what you will verbally present for your Research talk.

Use the checklist below to assist you as you complete this assignment:
Did you introduce yourself? (No need to mention the class.)
Did you provide an impact statement to give broad context for your work?
Did you provide only appropriate background information to understand the project? (key scientific concepts, essential methods, etc...)
Did you indicate a clear hypothesis/research goal?
Did you discuss specific results using quantitative information?
Did you draw clear conclusions from those results?
Did you specify how those conclusions link back to your hypothesis and impact statement?
Hint: review the information provided on the Research talk page for help!

  • 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. To 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

  • In addition to data figures, scientists use experimental schematics to illustrate the key steps of an experiment to better explain how the data were acquired. For this type of figure the important steps are represented using images and labels while the minor steps are omitted for clarity. To gain experience in this type of figure design you will work with your laboratory partner to craft an experimental schematic that shows the key steps used to complete the γH2AX experiment.

Use the checklist below to assist you as you complete this assignment:
Is your schematic correctly sized (legible, but no more than 1/2 of a 8.5x11" slide)?
Does your schematic include a title below the images that concisely states the figure purpose?
Does your caption concisely define all symbols, jargon, abbreviations, and other relevant information for the schematic?
Does your schematic include only the details needed to understand the main steps in the experiment?
Does your schematic include appropriate images that are not plagiarized from class materials or the wiki?
Is any text in the schematic concise and legible?

  • When tasked with preparing your science for written communication it is often helpful to review articles that present similar types of experiments and results. Through reading the literature that is related to your research you can better understand how to effectively present the data. To assist you in preparing your Data summary assignment, we will discuss a paper published from the Engelward Laboratory.

In preparation for this discussion, read the article and guidelines provided on the M1D4 wiki page.

Due M1D5

  • In scientific communication, data are represented as both figures and in text. For this homework you will craft a data figure from the γ-H2AX results you analyzed.

Use the checklist below to assist you as you complete this assignment:
Did you format your microscopy images? (i.e. more than just copying some microscopy images into your slide)
Does your figure include a take-home title below the image?
Does your figure include a caption with necessary details to interpret the figure?
Does your figure caption begin with a topic sentence?
Does your caption include any unnecessary information (such as methods or interpretation)?
Did you represent the data shown in your figure graphically (if appropriate)?
Is all text in the figure legible (especially axes)?
Is your figure correctly sized (legible, but no more than 1/3 of a 8.5x11" slide)?
Hint: you can find the information provided during the Comm Lab workshop on the Communication page for help!

  • 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. To 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 M1D6

  • Remember that for the Data summary you are presenting your results in an outline format to practice clear and concise writing. In addition, the Data summary is organized such that it is apparent what figures correspond to what text. Specifically, each data slide contains one figure and the bullets that explain the figure. The in-class exercise on M1D5 detailed how to present your results in your Data summary. For this homework, complete the data slide for your protein purity and concentration results.

Use the checklist below to assist you as you complete this assignment:
Did you include an appropriately sized and labeled data figure?
Do you have a concise conclusive title (one with a take-home message)?
Does your figure caption begin with a topic sentence and have the information necessary to interpret the figure?
Does the results section begin with a conclusive title? (This title should be different from the figure title.)
Do you begin the results by providing the overall goal of the experiment(s)?
Do you indicate your expected result?
Do you explain why your result would be correct or incorrect? (i.e. experimental controls)
Do you describe all of the data you show when indicating the result of your experiment? (i.e. all populations on a scatterplot, or all lanes on a gel)
Do you describe the data quantitatively?
Do you draw a conclusion based on the data?
Do you use your last sentence to transition to the next experiment?
Hint: you can find the information provided during the Comm Lab workshop on the Communication page for help!

Due M1D7

  • The final section of your Data summary will discuss the Implications & Future works of your research. In this section the main results are summarized and used to answer the research question. Also, experiments are proposed that will expand upon your results in an effort to address new research questions that are raised by your data.

To get you started, answer the questions below:
What is the main conclusion for your γ-H2AX results?
What is the main conclusion CometChip results?
How do the results answer your research question?
Did you observe any unexpected results or contradictory results?
What follow-up experiments (include at least two!) would be helpful in further addressing your research question?

  • Using feedback to improve your writing is an important step to developing your scientific communication skills. For this homework, work with your laboratory partner to incorporate the feedback you received to revise your methods draft. In addition, include the protocols you used on M1D3.

Use the checklist below to assist you as you complete this assignment:
Do you have descriptive subsection headers in a logical order?
Do each of your experimental sections begin with a topic sentence to introduce the purpose of the technique?
Do you write full sentences in passive voice and past tense? (i.e. His-tagged recombinant protein was purified using nickel resin.)
Do all reagents include manufacturer information in parentheses?
Are all abbreviations and acronyms written in full? (if this is the first use of the acronym)
Are all 20.109-specific details omitted? (i.e. do not include "Row A and Row B" or "the experiment was completed by the teaching faculty")
Are all mentions of tubes and water omitted?
Are the most flexible units used? (i.e. concentrations rather than volumes)
Is only information necessary to repeat the experiment included?
Are all descriptions concise and clear?

Module 1: Drug discovery

Due M2D1

Due M2D2

  • The major verbal assignment in Mod2 is the Journal club presentation. As part of this assignment you will present a published, peer-reviewed research article to the class. For this homework, select and review an article for your presentation from the curated lists on the Journal club presentation assignment page. If you prefer, you can find your own paper and send it to the Instructors for approval.

Use the checklist below to assist you as you complete this assignment:
Reserve your article on the Journal club presentation page according to the directions provided under the 'Article selection' header.
Review the abstract and introduction for the selected article.
Submit a brief summary of the selected article that highlights why you think the research is interesting.

Due M2D3

  • For your Journal club presentation, you will only have 10 minutes to present a clear, cohesive story from the data in your selected research article. Given the number of figures in most research articles it is impossible to show all of the data from your paper in a short presentation. In this, it is important to identify which figures are the most important to the main conclusion(s) of the research article. For this homework, read through the paper you selected for the Journal Club presentation and choose the four figures that you think are most important in telling the story presented by the authors.

To get you started, answer the questions below:
What is the main conclusion of the paper?
What four figures are the most important in supporting the main conclusion? Why?
How do the figures work together to tell a story? How does this story lead you to the main conclusion of the paper?
Hint: you can find the information provided during the Comm Lab workshop on the Communication page for help!

  • The Journal club presentations will occur during the laboratory sessions on Tuesday, November 1st and Thursday, November 3rd for the T/R section and on Wednesday, November 2nd and Thursday, November 4th for the W/F section. Due to class size, presenters in each section will be divided between the two days by the Instructors.

To reserve a presentation date, email Noreen (nllyell@mit.edu) with which day you prefer to present and why. If one of the days becomes oversubscribed then slots will assigned using a lottery.

Due M2D4

  • Your slide deck will be important in your ability to effectively tell the story presented by the authors of your paper. For this homework you will draft a presentation slide using one of the data figures from the paper you selected that you want to discuss as part of your Journal club presentation. In addition, include a script for the verbal information that you will deliver when presenting the figure on your slide.

Use the checklist below to assist you as you complete this assignment:
Does the title of your slide convey a concise take-home message about the data shown?
Do you include data from a single figure of your paper?
Are you trying to include too much data on a single slide?
Is all the text from your data figure legible? (especially note the axes text and recreate it if necessary)
Is there a good balance between figures and text on the slide? (approximately half of each)
Does the text convey only key information?
Is your script concise? (i.e. Are you able to convey this information in approximately 1 minute?)
Does your script contain technically correct scientific information?
Is the information in your script directly relevant to the data on the slide?
Hint: you can find the information provided during the Comm Lab workshop on the Communication page for help!