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

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| [[20.109(F22):Data Summary| Assignment description]]
| [[20.109(F22):Data Summary| Assignment description]]
| Journal club presentation
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| [[20.109(F22):Journal article presentation |Assignment description and article sign-up]]<br>[[Media:JC presentation rubric updatedSu20.pdf| Evaluation rubric (PDF download)]]
| [[20.109(F22):Journal article presentation |Assignment description and article sign-up]]<br>[[Media:JC presentation rubric updatedSu20.pdf| Evaluation rubric (PDF download)]]

Revision as of 19:33, 8 August 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       


You will complete three experimental modules over the course of the semester. The modules differ in both conceptual and technical content and in the ways that your learning will be assessed. Although your laboratory work will be done as partners, several assignments will be submitted individually (as summarized below) and should reflect your personal understanding. Please review the 20.109 statement on collaboration and integrity for details concerning academic honesty in our class. You are highly encouraged to ask the teaching faculty any questions you have about what constitutes appropriate collaboration.

Individual assignments (~60% of final grade):

  • Homework, laboratory notebooks, and quizzes
  • Research talk
  • Journal club presentation
  • Research article

Team assignments (~40% of final grade):

  • Homework
  • Data summary (draft and revision)
  • Research proposal presentation

We appreciate that time management can be difficult and that learning takes place on many time-scales. However, assignments turned in at wildly different times create additional logistical burdens for the Instructors. Therefore, late work (both daily and culminating assignments) will be penalized 1/3 of a letter grade for each day it is late and will not be accepted after a week. We strongly recommend that you plan ahead and and schedule time to complete your work when possible.

We provide equal access to subject 20.109 for students with disabilities, in accordance with the Americans with Disabilities Act (ADA) of 1990. Please see the teaching faculty as soon as possible regarding needed accommodations.

We spend a lot of time together and get to know each other well. Everyone in the 20.109 family needs the support of their peers and instructors. If you find yourself in a situation where more guidance would be appreciated – for example, if you are dealing with a personal or medical issue that is impacting your ability to attend class, complete work, or take an exam – consider visiting Student Support Services ("S cubed"). The deans in S3 will verify your situation, and then discuss with you how to address the missed work. We will not excuse coursework or provide extensions without verification from S3.

Homework Submission Guidelines

  • When submitting assignments online, make sure that your name is in the file name and the document itself. e.g. '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_Blue_DataSummary'
  • Note: Some assignments may indicate a more specific naming scheme than this one. Follow that instead when applicable

Major assignments

All major assignments will be submitted via [XXX].

Assignment % of final grade Links to description and/or rubric
Research talk 5 Assignment description
Data summary 15 Assignment description
Journal article presentation 15 Assignment description and article sign-up
Evaluation rubric (PDF download)
Research article 20 Assignment description
Research proposal presentation 20 Assignment description
Evaluation rubric (PDF download)

Other assignments

In addition to the major assignments listed above, you will complete:

Homework assignments (10% of final grade)

  • All homework assignments will be submitted via [XXX].
  • Homeworks are intended to keep you up to date with the material. Most will directly prepare you for major assessments (e.g., making a draft figure for a report) or lab work (e.g., performing a calculation in advance). The associated points/weighting will vary widely between assignments and will reflect the breadth of the assignment.
  • All homework should be completed individually unless specifically noted.
  • The assignments can be found on the Homework tab and are linked to the Schedule tab to reflect the due date.

Laboratory notebook (5% of final grade)

  • You will record your progress during the semester using Benchling, an electronic notebook. One entry will be evaluated by the teaching faculty once per module.
  • Notebooks will be graded at 10 pm the day following the final day of each module (i.e. at 10 pm on the day after M1D7). Though all entries will be reviewed and a portion of the grade will be based on overall completeness, one entry (to be determined by the teaching faculty) will be assessed more closely and be graded in more detail according to the rubric below.
  1. To develop good archiving practices for the future.
  2. To maintain a one-stop resource to remember what you did each day and record the outcome(s).

You will use an online laboratory notebook to document your work in 20.109. 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.

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.

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.

Though it is not necessary to copy / 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 the URL), 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 h into incubation)
  • unusual observations (e.g. a large number of cells seemed to be floating).

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. So the teaching faculty and TA can find information more easily, you will create one folder for each module and each day will be a separate entry in the appropriate folder.

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.

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.

Grading criteria
Your notebook entries will be examined 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.

Your laboratory notebook entries will be evaluated using the following rubric:

 Laboratory notebook entry component:                                  Points:
                                                                       Complete    Partial      Missing
 Date of experiment (include Module#/Day#) and Title for experiment       1          0.5           0
 Hypothesis or goal / purpose                                             2           1            0
 Protocols (link to appropriate wiki sections)                            1          0.5           0
 Answering questions embedded in wiki sections                            5           3            0
 Observations from demonstrations and video tutorials                     3           2            0
 *Visual details
 *Qualitative information
 *Raw data                                  
 Data analysis                                                            3           2            0
 *Graphs and Tables                          
 Summary and interpretation of data                                       3           2            0
 *What did you learn?
 *How does this information fit into the larger scope of the project?
 Information is clear                                                     2           1            0
 All days represented                                                     5           3            0

Participation (5% of final grade)

The participation will be based on three aspects of the class:

  • Attendance in lecture
  • Active participation in group discussions
  • Contributions to Class blog
  • Progress through laboratory exercises

Active participation

  • You are expected to be an active participant in our 20.109 scientific community. Your student colleagues, the Instructors, and especially your laboratory partner are all your collaborators. They rely on you for timely posting of your data, and for your unique and thoughtful contributions during class.
  • Part of your participation grade will be directly assigned by the Instructors, who will consider whether you asked and/or answered questions during peer presentations, whether you engaged with opportunities to improve your understanding/communication/etc., and whether you promoted a considerate and collaborative class environment.

Contribution to Class blog

  • In addition, the participation grade will be determined by your completing brief reflective blog posts on your 20.109 experience throughout the semester at the [ Class Blog]. Writing these blog posts is intended to provide you with practice writing for an open online community and will be counted separately from other homework. Considering all of the miscommunicated science we see outside of the laboratory, it is important to learn how to effectively communicate your thoughts about both good and not-so-good aspects of your scientific experience. Due dates are included on Schedule tab.
  • Your posts should reflect your experience(s) in 20.109. Many students find it easiest to write about the major assignment / research completed during the module. In particular, students often create entries that detail how they prepared and where they struggled.
  • Class blog posts will not be reviewed for late credit.

Progress through laboratory exercises

  • Lastly, the participation grade will be determined by your efforts toward completing the laboratory exercises. To monitor this, Instructors will check all notebooks at the end of class.
  • Laboratory notebook entries for the day will not be graded on completeness of all of the exercises, rather full credit will be granted if an attempt was made by the student to work through the material for the day. The goal is to ensure students are making use of the allotted laboratory time (which will eliminate excess time needed outside of the class!) and also enable the Instructors to monitor possible sticking points in the material that need to be revisited.
  • Daily laboratory notebook entries will not be reviewed for late credit.

Quizzes (5% of final grade)

  • There are two main purposes for quizzes in 20.109: (1) to refresh your memory about the long-term experiment you are performing, and (2) to provide you with an opportunity to show your technical knowledge decoupled from your communication skills.
  • Questions will be based on content from both lecture and laboratory within a module. Questions will concern fundamentals rather than details. For example, you might be asked to interpret a piece of data, define a major concept, or perform a short calculation.