Difference between revisions of "20.109(S22):Spring 2022 schedule"
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Welcome to 20.109! It is our goal to make this class a useful and fun introduction to the experiments and techniques used in biological engineering. Though there is not enough time to show you everything needed to do research, after this class you will feel confident and familiar with some fundamental experimental approaches and laboratory protocols. You will develop good habits at the bench, which will increase the likelihood of success in your work and ensure the health and safety of you and your labmates. By the end of the semester, you will also be well-versed in good scientific practices - through your experience with scientific writing, notebook keeping, and orally presenting data and novel ideas. All of us involved in teaching 20.109 hope you will find it a satisfying challenge and an exciting experience that has lasting value. | Welcome to 20.109! It is our goal to make this class a useful and fun introduction to the experiments and techniques used in biological engineering. Though there is not enough time to show you everything needed to do research, after this class you will feel confident and familiar with some fundamental experimental approaches and laboratory protocols. You will develop good habits at the bench, which will increase the likelihood of success in your work and ensure the health and safety of you and your labmates. By the end of the semester, you will also be well-versed in good scientific practices - through your experience with scientific writing, notebook keeping, and orally presenting data and novel ideas. All of us involved in teaching 20.109 hope you will find it a satisfying challenge and an exciting experience that has lasting value. | ||
| − | <font color= | + | <font color= #819081 >'''SCHEDULE DETAILS:'''</font color><br> |
| − | <font color= | + | <font color= #91b391 >'''Lecture times:'''</font color> Tuesday (T) and Thursday (R) 11 - 12 pm in 1-390<br> |
| − | + | <font color= #91b391 >'''Laboratory section times:'''</font color> Tuesday (T) and Thursday (R) 1 - 5 pm or Wednesday (W) and Friday (F) 1 - 5 pm in 56-322<br> | |
| − | <font color= | + | |
| − | + | <font color= #819081 >'''ABSENCE POLICY:'''</font color><br> | |
| − | + | <font color= #91b391 >'''Absences from lecture:'''</font color> Attendance will be recorded for participation points throughout the semester. If absent, student is responsible for all information provided in lecture. <br> | |
| + | <font color= #91b391 >'''Absences from laboratory:'''</font color> Excused absences should be discussed with the Instructors as soon as possible. Because make-up laboratory time is not provided, attendance in another section may be required to complete the necessary experiments. Unexcused absences will result in a 1/3 of a letter grade deduction from the final grade on the major assignment for the module (for example, a B+ would become a B). | ||
{| border=1px | {| border=1px | ||
| Line 20: | Line 21: | ||
|-- | |-- | ||
| | | | ||
| − | | T/W Feb | + | | T/W Feb 1/2 |
| − | | [http://be.mit.edu/directory/noreen-lyell NLL] <br> [[Media: | + | | [http://be.mit.edu/directory/noreen-lyell NLL] <br> [[Media:Sp22 Orientation lecture student.pptx| Lecture slides]] |
| − | | [[20.109( | + | | [[20.109(S22):Laboratory tour | Orientation and laboratory tour]]<br> [[Media:Sp22 M0D0 bcm marked.pdf | T/R prelab]] <br> [[Media:Sp22 M0 nll.pdf| W/F prelab]] |
| | | | ||
|-- | |-- | ||
| Line 28: | Line 29: | ||
|-- | |-- | ||
| M1D1 | | M1D1 | ||
| − | | R/F Feb | + | | R/F Feb 3/4 |
| − | | [http://be.mit.edu/directory/ | + | | [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L1 2022.pdf|Lecture slides]] |
| − | | [[20.109( | + | | [[20.109(S22):M1D1 |Review small molecule microarray (SMM) technology]] <br> [[Media:Sp22 M1D1 bcm marked.pdf | T/R prelab]]<br> [[Media:Sp22 M1D1 jz printFilled.pdf | W/F prelab]] |
| − | | <font color= # | + | | <font color= #819081 >'''Orientation quiz'''</font color> <br> [[20.109(S22):Homework#Due_M1D1|Homework due]] |
|-- | |-- | ||
| M1D2 | | M1D2 | ||
| − | | T/W Feb | + | | T/W Feb 8/9 |
| − | | [http://be.mit.edu/directory/ | + | | [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L2 2022 short.pdf|Lecture slides]] |
| − | | [[20.109( | + | | [[20.109(S22):M1D2 |Examine SMM data collected using TDP43 protein]] <br> [[Media:Sp22 M1D2 bcm marked.pdf | T/R prelab]] <br> [[Media:Sp22 M1D2 jz filled.pdf | W/F prelab]] |
| − | | [[20.109( | + | | [[20.109(S22):Homework#Due_M1D2|Homework due]] |
|-- | |-- | ||
| M1D3 | | M1D3 | ||
| − | | R/F Feb | + | | R/F Feb 10/11 |
| − | | [http://be.mit.edu/directory/ | + | | [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L3 2022.pdf|Lecture slides]] |
| − | | [[20.109( | + | | [[20.109(S22):M1D3 |Induce and purify TDP43 protein]] <br> [[Media:Sp22 M1D3 bcm marked.pdf | T/R prelab]] <br> [[Media: Sp22 M1D3 jz final.pdf | W/F prelab ]] |
| − | | [[20.109( | + | | [[20.109(S22):Homework#Due_M1D3|Homework due]] |
|-- | |-- | ||
| M1D4 | | M1D4 | ||
| − | | T/W | + | | T/W Feb 15/16 |
| − | | [http://be.mit.edu/directory/ | + | | [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L4 2022.pdf|Lecture slides]] |
| − | | [[20.109( | + | | [[20.109(S22):M1D4 |Assess purity and concentration of purified TDP43 protein]] <br> [[Media:Sp22 M1D5 bcm marked.pdf | T/R prelab]] <br> [[Media:Sp22 M1D4 jz print.pdf|W/F prelab]] |
| − | | <font color= # | + | | <font color= #819081 >'''Laboratory quiz'''</font color> <br> [[20.109(S22):Homework#Due_M1D4|Homework due]] |
|-- | |-- | ||
| M1D5 | | M1D5 | ||
| − | | R/F | + | | R/F Feb 17/18 |
| − | | [http://be.mit.edu/directory/ | + | | [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L5 2022.pdf|Lecture slides]] |
| − | | [[20.109( | + | | [[20.109(S22):M1D5 |Perform aggregation assay using TDP43 protein and draft data slide for Data summary]] <br> [[Media:Sp22 M1D5 bcm.pdf|T/R prelab]] <br> [[Media:Sp22 M1D5 jz.pdf|W/F prelab]] |
| − | | [[20.109( | + | | [[20.109(S22):Homework#Due_M1D5|Homework due]] |
|-- | |-- | ||
| | | | ||
| − | | <font color = 999999>T/W | + | | <font color = 999999>T/W Feb 22/23 </font color> |
| − | + | ||
| − | + | ||
| | | | ||
| + | | <font color = #91b391>'''Presidents' day holiday'''</font color> | ||
| + | | [[20.109(S22):Research talk| <font color = #b3251c>'''Research talk due'''</font color>]] Wed, Feb 23 at 10 pm | ||
|-- | |-- | ||
| M1D6 | | M1D6 | ||
| − | | R/F | + | | R/F Feb 24/25 |
| − | | [http://be.mit.edu/directory/ | + | | [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L6 2022.pdf|Lecture slides]] |
| − | | [[20.109( | + | | [[20.109(S22):M1D6 |Learn best practices for mammalian cell culture and seed CAD cells for TDP43-localization experiment]] <br> [[Media:Sp22 M1D6 bcm.pdf |T/R prelab]] <br> [[Media: Sp22 M1D6 jz.pdf | W/F prelab slides]] <br> [https://mit.zoom.us/rec/share/u81JeAamHMCxiZDZhWxhHpZyyInSu1OLjOZaRYA7_jlWf5LJBoo8H-a5P5DwoIMx.4gTyoQXzvOa9UZpm?startTime=1645796510000 W/F prelab video] and [[Media:Sp22 ExpSchem wNotes.pptx|notes for due M1D7 homework]] |
| − | | [[20.109( | + | | [[20.109(S22):Homework#Due_M1D6|Homework due]] |
|-- | |-- | ||
| M1D7 | | M1D7 | ||
| − | | T/W Mar | + | | T/W Mar 1/2 |
| − | | [ | + | | [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L7 2022.pptx|Lecture slides]] |
| − | | [[20.109( | + | | [[20.109(S22):M1D7 |Complete staining for TDP43-localization assay]] <br> [[Media:Sp22 M1D7 bcm marked.pdf | T/R prelab]] <br> [[ Media: Sp22 M1D7 jz.pdf | W/F prelab ]] |
| − | | <font color= # | + | | [[20.109(S22):Homework#Due_M1D7|Homework due]] |
| + | |-- | ||
| + | | M1D8 | ||
| + | | R/F Mar 3/4 | ||
| + | | Comm Lab workshop <br> | ||
| + | | [[20.109(S22):M1D8 |Image TDP43-localization experiment and complete data analysis]] <br> [[Media:Sp22 M1D8 prelab & DS discussion marked.pdf | prelab slides]] [[https://www.dropbox.com/s/km7bbru2ua7s0ih/IMG_0380.MOV?dl=0 T/R prelab video]][[Media:Sp22_M1D8_jz.pdf | W/F prelab]] <br> [https://mit.zoom.us/rec/play/ChMBzMfSwwyJ1G_RrXb0Wk81Fp8TCIpnmhyGcepuXpbzwJaLH_SG-87DHccMJYSp9I4DAXrbIIKzdMr0.bqJBrMSDeMlvQAXo?autoplay=true&continueMode=true&startTime=1646402200000 W/F prelab video] | ||
| + | | <font color= #819081 >'''Laboratory quiz'''</font color> <br> [[20.109(S22):Homework#Due_M1D8|Homework due]] | ||
|-- | |-- | ||
| colspan="6" | | | colspan="6" | | ||
|-- | |-- | ||
| M2D1 | | M2D1 | ||
| − | | | + | | T/W Mar 8/9 |
| − | | [http://be.mit.edu/directory/ | + | | [http://be.mit.edu/directory/noreen-lyell NLL] <br> [[Media:Sp22 M2D1 lecture slides.pdf|Lecture slides]] |
| − | | [[20.109( | + | | [[20.109(S22):M2D1 |Complete in-silico cloning of pdCas9 expression plasmid]] <br> [[Media:Sp22 M2D1 bcm marked.pdf | T/R prelab]] <br> [[Media:Sp22_M2D1_jz.pdf | W/R prelab]] |
| − | | [[20.109( | + | | [[20.109(S22):Homework#Due_M2D1|Homework due]] |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
|-- | |-- | ||
| M2D2 | | M2D2 | ||
| − | | R/F Mar | + | | R/F Mar 10/11 |
| − | | [http://be.mit.edu/directory/ | + | | [http://be.mit.edu/directory/noreen-lyell NLL] <br> [[Media:Sp22 M2D2 lecture slides.pdf|Lecture slides]] |
| − | | [[20.109( | + | | [[20.109(S22):M2D2 |Design gRNA sequence for CRIPSRi system]] <br> [[Media:SP22 M2D2 bcm marked.pdf |T/R prelab]] <br> [[Media:SP22 M2D2 jz.pdf | W/F prelab]] |
| − | | [[20.109( | + | | [[20.109(S22):Homework#Due_M2D2| Homework due]] <br>[[20.109(S22):Data Summary| <font color = #b3251c>'''Data Summary draft due'''</font color>]] Sat, Mar 12 at 10 pm <br> |
|-- | |-- | ||
| M2D3 | | M2D3 | ||
| − | | T/W Mar | + | | T/W Mar 15/16 |
| − | | [http://be.mit.edu/directory/ | + | | [http://be.mit.edu/directory/noreen-lyell NLL] <br> [[Media:Sp22 M2D3 lecture slides.pdf|Lecture slides]] |
| − | | [[20.109( | + | | [[20.109(S22):M2D3 |Clone psgRNA expression plasmid]] <br> [[Media:Sp22 M2D3 bcm marked.pdf | T/R prelab]] <br> [[Media: Sp22_M2D3_jz_pdf.pdf | W/F prelab]] |
| − | | [[20.109( | + | | [[20.109(S22):Homework#Due_M2D3|Homework due]]<br>[https://app.slack.com/client/T01KU1VLZQB/C0323Q19V89 Blog post due] Mon, Mar 14 at 10 pm |
|-- | |-- | ||
| M2D4 | | M2D4 | ||
| − | | R/F | + | | R/F Mar 17/18 |
| − | | [http://be.mit.edu/directory/ | + | | [http://be.mit.edu/directory/noreen-lyell NLL] <br> [[Media:Sp22 M2D4 lecture slides.pdf|Lecture slides]] |
| − | | [[20.109( | + | | [[20.109(S22):M2D4 |Confirm gRNA sequence in psgRNA expression plasmid]] <br> [[Media:Spring2022 M2D4 CZ v2.pdf | T/R Prelab]] [[Media:Sp22 JC presentation.pdf | JC Notes]] <br> [[Media:Spring2022 M2D4 CZ v2.pdf | W/F Prelab]] |
| − | | <font color= # | + | | <font color= #819081 >'''Laboratory quiz'''</font color> <br> [[20.109(S22):Homework#Due_M2D4|Homework due]]<br>[[20.109(S22):Data Summary| <font color = #b3251c>'''Data Summary revision due'''</font color>]] Sun, Mar 20 at 10 pm <br> |
|-- | |-- | ||
| | | | ||
| − | | T/W | + | | <font color = 999999>T/W Mar 22/23 </font color> |
| | | | ||
| − | + | | <font color = #91b391>'''Spring break'''</font color> | |
| | | | ||
|-- | |-- | ||
| | | | ||
| − | | R/F | + | | <font color = 999999>R/F Mar 24/25 </font color> |
| + | | | ||
| + | | <font color = #91b391>'''Spring break'''</font color> | ||
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|-- | |-- | ||
| | | | ||
| − | | | + | | T/W Mar 29/30 |
| | | | ||
| − | | <font color = # | + | | [[20.109(S22):Journal club presentation| <font color = #b3251c>'''Journal club presentations'''</font color>]] |
| | | | ||
| + | |-- | ||
| + | | | ||
| + | | R/F Mar/Apr 31/1 | ||
| + | | | ||
| + | | [[20.109(S22):Journal club presentation| <font color = #b3251c>'''Journal club presentations'''</font color>]] | ||
| + | | [https://app.slack.com/client/T01KU1VLZQB/C0323Q19V89 Blog post due] Fri, Apr 1 at 10 pm | ||
| + | |-- | ||
| + | | M2D5 | ||
| + | | T/W Apr 5/6 | ||
| + | | [http://be.mit.edu/directory/noreen-lyell NLL] <br> [[Media:Sp22 M2D5 lecture slides.pdf|Lecture slides]] | ||
| + | | [[20.109(S22):M2D5 |Prepare for induction of CRISPRi system]] <br> [[Media:Sp22 M2D5 bcm marked.pdf | T/R prelab]] <br> [[Media:Sp22 M2D5 jz.pdf | W/F prelab]] | ||
| + | | [[20.109(S22):Homework#Due_M2D5|Homework due]] | ||
| + | |-- | ||
| + | | M2D6 | ||
| + | | R/F Apr 7/8 | ||
| + | | [http://be.mit.edu/directory/noreen-lyell NLL] <br> [[Media:Sp22 M2D6 lecture slides.pdf|Lecture slides]] | ||
| + | | [[20.109(S22):M2D6 |Complete CRISPRi experiment and measure fermentation products]] <br> [[Media:Sp22 M2D6 bcm marked.pdf | T/R prelab]]<br> [[Media:Sp22_M2D6_jz.pdf | W/F prelab ]] | ||
| + | | [[20.109(S22):Homework#Due_M2D6|Homework due]]<br> | ||
|-- | |-- | ||
| M2D7 | | M2D7 | ||
| − | | | + | | T/W Apr 12/13 |
| − | | [http://be.mit.edu/directory/ | + | | [http://be.mit.edu/directory/noreen-lyell NLL] <br> [[Media:Sp22 M2D7 lecture slides.pdf|Lecture slides]] |
| − | | [[20.109( | + | | [[20.109(S22):M2D7 |Examine features in gRNA-targeted genomic sequences]] <br> [[Media:Sp22 M2D7 bcm marked.pdf | T/R prelab]] <br> [[Media:Sp22 M2D7 jz.pdf | W/F prelab]] |
| − | | <font color= # | + | | [[20.109(S22):Homework#Due_M2D7|Homework due]]<br> |
| + | |-- | ||
| + | | M2D8 | ||
| + | | R/F Apr 14/15 | ||
| + | | Comm Lab workshop <br> | ||
| + | | [[20.109(S22):M2D8 |Organize figures and outline text for Research article]] <br> [[Media:Sp22 RA discussion marked.pdf | prelab]] | ||
| + | | <font color= #819081 >'''Laboratory quiz'''</font color> <br> [[20.109(S22):Homework#Due_M2D8|Homework due]] <br> | ||
|-- | |-- | ||
| colspan="6" | | | colspan="6" | | ||
| + | |-- | ||
| + | | | ||
| + | | <font color = 999999>T/W Apr 19/20 </font color> | ||
| + | | | ||
| + | | <font color = #91b391>'''Patriots' Day holiday'''</font color> | ||
| + | | | ||
|-- | |-- | ||
| M3D1 | | M3D1 | ||
| − | | | + | | R/F Apr 21/22 |
| − | | [http://be.mit.edu/directory/ | + | | [http://be.mit.edu/directory/noreen-lyell NLL]<br> [[Media:Sp22 Drug discovery ethics exercise.pdf|Lecture slides]] |
| − | | [[20.109( | + | | [[20.109(S22):M3D1 |Brainstorm ideas for Research proposal presentation]] <br> [[Media:Sp22 M3D1 bcm.pdf | T/R prelab]] <br> [[Media:Sp22 M3D1 jz.pdf | W/F prelab]] |
| − | | [[20.109( | + | | [[20.109(S22):Homework#Due_M3D1|Homework due]] <br> [[20.109(S22):Research article| <font color = #b3251c>'''Research article due'''</font color>]] Sat, Apr 23 at 10 pm |
|-- | |-- | ||
| + | | | ||
| + | | T/W Apr 26/27 | ||
| + | | [http://be.mit.edu/directory/angela-belcher AB] | ||
| + | | <font color = #819081>'''Research proposal pitches'''</font color> <br> [[Media:Sp22 proposal pitches bcm.pdf | T/R prelab]] <br> [[Media:Sp22 proposal pitches jz_fixed.pdf | W/F prelab]] | ||
| + | | <br> [https://app.slack.com/client/T01KU1VLZQB/C0323Q19V89 Blog post due] Mon, Apr 25 at 10 pm | ||
| + | |-- | ||
| M3D2 | | M3D2 | ||
| − | | R/F Apr 29 | + | | R/F Apr 28/29 |
| − | | | + | | Comm Lab workshop |
| − | | [[20.109( | + | | [[20.109(S22):M3D2 |Develop ideas for Research proposal presentation ]] <br> [[Media:Sp22 M3D2 bcm.pdf | T/R prelab]] <br> [[Media:Sp22 M3D2 jz.pdf | W/F prelab]] |
| − | | [[20.109( | + | | [[20.109(S22):Homework#Due_M3D2|Homework due]]<br> |
|-- | |-- | ||
| M3D3 | | M3D3 | ||
| − | | T/W May | + | | T/W May 3/4 |
| − | | [http://be.mit.edu/directory/ | + | | [http://be.mit.edu/directory/noreen-lyell NLL] <br> [[Media:Sp22 Ethics for research proposals.pdf| Lecture slides]] |
| − | | [[20.109( | + | | [[20.109(S22):M3D3 |Participate in Research proposal peer reviews]] <br> [[Media:Sp22 M3D3 bcm.pdf | T/R prelab]] <br> [[Media:Sp22 M3D3 jz.pdf | W/F prelab]] |
| − | + | | [[20.109(S22):Homework#Due_M3D3|Homework due]] | |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
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| − | + | ||
| − | + | ||
| − | + | ||
|-- | |-- | ||
| | | | ||
| − | | | + | | R/F May 5/6 |
| | | | ||
| − | | [[20.109( | + | | [[20.109(S22):Research proposal presentation| <font color = #b3251c>'''Research proposal presentations'''</font color>]] |
| − | | [ | + | | [https://app.slack.com/client/T01KU1VLZQB/C0323Q19V89 Blog post due] Fri, May 6 at 10 pm |
|-- | |-- | ||
| colspan="6" | | | colspan="6" | | ||
|-- | |-- | ||
| | | | ||
| − | | | + | | T May 10 |
| − | | <font color = # | + | | <font color = #819081>'''Feedback session'''</font color> <br> |
| | | | ||
| | | | ||
|} | |} | ||
</div> | </div> | ||
Latest revision as of 16:41, 4 May 2022
Welcome to 20.109! It is our goal to make this class a useful and fun introduction to the experiments and techniques used in biological engineering. Though there is not enough time to show you everything needed to do research, after this class you will feel confident and familiar with some fundamental experimental approaches and laboratory protocols. You will develop good habits at the bench, which will increase the likelihood of success in your work and ensure the health and safety of you and your labmates. By the end of the semester, you will also be well-versed in good scientific practices - through your experience with scientific writing, notebook keeping, and orally presenting data and novel ideas. All of us involved in teaching 20.109 hope you will find it a satisfying challenge and an exciting experience that has lasting value.
SCHEDULE DETAILS:
Lecture times: Tuesday (T) and Thursday (R) 11 - 12 pm in 1-390
Laboratory section times: Tuesday (T) and Thursday (R) 1 - 5 pm or Wednesday (W) and Friday (F) 1 - 5 pm in 56-322
ABSENCE POLICY:
Absences from lecture: Attendance will be recorded for participation points throughout the semester. If absent, student is responsible for all information provided in lecture.
Absences from laboratory: Excused absences should be discussed with the Instructors as soon as possible. Because make-up laboratory time is not provided, attendance in another section may be required to complete the necessary experiments. Unexcused absences will result in a 1/3 of a letter grade deduction from the final grade on the major assignment for the module (for example, a B+ would become a B).
