Difference between revisions of "20.109(F24):Fall 2024 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.
 +
 +
<font color=  #962c17    >'''SCHEDULE DETAILS:'''</font color><br>
 +
<font color=    #b3351c  >'''Lecture times:'''</font color> Tuesday (T) and Thursday (R) 11 - 12 pm in 16-220<br>
 +
<font color=    #b3351c >'''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=  #962c17  >'''ABSENCE POLICY:'''</font color><br>
 +
<font color=    #b3351c  >'''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=    #b3351c  >'''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
 +
|'''MODULE'''
 +
|'''DATE'''
 +
|'''LECTURER'''
 +
|'''LABORATORY EXPERIMENTS'''
 +
|'''ASSIGNMENTS'''
 +
|--
 +
|
 +
| R/F Sep 7/8 
 +
| [http://be.mit.edu/directory/noreen-lyell NLL] <br> [[Media:Fa23 Orientation lecture student.pdf| Lecture slides]] <br>
 +
| [[20.109(F23):Laboratory tour | Orientation and laboratory tour]]<br> [[Media:Fa23 M0D0 bcm.pdf| T/R prelab]]<br> [[Media:Fa23_M0D0_jz1.pdf| W/F prelab]]
 +
|
 +
|--
 +
| M1D1
 +
| T/W Sep 12/13
 +
| [http://be.mit.edu/directory/bevin-p-engelward BPE] <br>  [[Media:BE109 Fall23 Mod1 Day1 HANDOUT.pdf| Lecture slides]] <br>
 +
| [[20.109(F23):M1D1 | Learn best practices for mammalian cell culture]]<br> [[Media:Fa23 M1D1 bcm.pdf | T/R prelab]] <br> [[Media:Fa23_M1D1_jz.pdf| W/F prelab]]
 +
| <font color= #d57830 >'''Orientation quiz'''</font color> <br> [[20.109(F23):Homework#Due_M1D1|Homework due]]
 +
|--
 +
| M1D2
 +
| R/F Sep 14/15 
 +
| [http://be.mit.edu/directory/bevin-p-engelward BPE] <br> [[Media:BE109 Fall23 Mod1 Day2 HANDOUT.pdf| Lecture slides]]
 +
| [[20.109(F23):M1D2 | Prepare and treat cells for &gamma;H2AX experiment]]<br> [[Media:Fa23 M1D2 bcm marked.pdf |T/R prelab]] <br> [[Media:Fa23_M1D2_jz.pdf | W/F prelab]]
 +
| [[20.109(F23):Homework#Due_M1D2|Homework due]]
 +
|--
 +
| M1D3
 +
| T/W Sep 19/20
 +
| [http://be.mit.edu/directory/bevin-p-engelward BPE] <br> [[Media:BE109 Fall23 Mod1 Day3 HANDOUT.pdf| Lecture slides]]
 +
| [[20.109(F23):M1D3 | Use immunoflourescence staining to assess &gamma;H2AX experiment]]<br> [[Media:Fa23 M1D3 bcm.pdf | T/R prelab]]<br>[[Media:Fa23_M1D3_jz_fixed.pdf | W/F prelab]]
 +
| [[20.109(F23):Homework#Due_M1D3|Homework due]]
 +
|--
 +
|
 +
| R/F Sep 21/22
 +
| BE Comm Lab
 +
| <font color = #a24d0a>'''Career Day holiday'''</font color>
 +
| 
 +
|--
 +
| M1D4
 +
| T/W Sep 26/27
 +
| [http://be.mit.edu/directory/bevin-p-engelward BPE] <br> [[Media:BE109 Fall23 Mod1 Day4 HANDOUT.pdf| Lecture slides]]
 +
| [[20.109(F23):M1D4 | Complete data analysis for &gamma;H2AX experiment]]<br> [[Media:Fa23 M1D4 bcm.pdf | T/R prelab]] <br>[[Media:Fa23_M1D4_jz.pdf | W/F prelab]]
 +
| <font color= #d57830 >'''Laboratory quiz'''</font color> <br> [[20.109(F23):Homework#Due_M1D4|Homework due]]
 +
|--
 +
| M1D5
 +
| R/F Sep 28/29
 +
| [http://be.mit.edu/directory/bevin-p-engelward BPE] <br> [[Media:BE109 Fall23 Mod1 Day5 HANDOUT.pdf| Lecture slides]]
 +
| [[20.109(F23):M1D5 | Treat cells for CometChip assay]]<br> [[Media:Fa23 M1D5 bcm.pdf| T/R prelab]] <br>[[Media:Fa23_M1D5_jz.pdf | W/F prelab]]
 +
| [[20.109(F23):Homework#Due_M1D5|Homework due]] <br> [[20.109(F23):Research talk| <font color =  #227d49 >'''Research talk due'''</font color>]] Sat, Sep 30 at 10 pm
 +
|--
 +
| M1D6
 +
| T/W Oct 3/4
 +
| [http://be.mit.edu/directory/bevin-p-engelward BPE] <br> [[Media:BE109 Fall23 Mod1 Day6 HANDOUT.pdf| Lecture slides]]
 +
| [[20.109(F23):M1D6 | Image and analyze data for CometChip assay]]<br> [[Media:Fa23 M1D6 bcm.pdf | T/R prelab]] <br>[[Media:Fa23_M1D6_jz.pdf | W/F prelab]]
 +
| [[20.109(F23):Homework#Due_M1D6|Homework due]]
 +
|--
 +
| M1D7
 +
| R/F Oct 5/6
 +
| [http://be.mit.edu/directory/bevin-p-engelward BPE] <br>
 +
| [[20.109(F23):M1D7 | Examine experimental data using statistical methods]]<br> [[Media:Fa23 M1D8 nll.pdf| T/R prelab]]<br> [[Media:Fa23 M1D8 nll.pdf| W/F prelab]] <br> [[Media:Fa23 DS discussion.pdf| Data summary discussion]]
 +
| <font color= #d57830 >'''Laboratory quiz'''</font color> <br> [[20.109(F23):Homework#Due_M1D7|Homework due]]
 +
|--
 +
|
 +
| <font color = 999999>T/W Oct 10/11 </font color>
 +
|
 +
| <font color = #a24d0a>'''Indigenous Peoples' Day holiday'''</font color>
 +
| [[20.109(F23):Data Summary| <font color =  #227d49 >'''Data Summary draft due'''</font color>]] Wed, Oct 11 at 10 pm <br> [https://app.slack.com/client/T01KU1VLZQB/C05Q47YG92S Blog post due] Thu, Oct 12 at 10 pm
 +
|--
 +
| M2D1
 +
| R/F Oct 12/13
 +
| [http://be.mit.edu/directory/jacquin-c-niles JCN] <br> [[Media:L01 Intro Drug Discovery 20109 2023-10-12 presented).pdf| Lecture slides]]
 +
| [[20.109(F23):M2D1 |Complete in-silico cloning of protein expression plasmid ]]<br> [[Media:Fa23 M2D1 bcm.pdf | T/R prelab]]<br>[[Media:Fa23_M2D1_jz.pdf | W/F prelab]]
 +
| [[20.109(F23):Homework#Due_M2D1|Homework due]]
 +
|--
 +
| M2D2
 +
| T/W Oct 17/18
 +
| BE Comm Lab <br>
 +
| [[20.109(F23):M2D2 |Perform protein purification protocol]] <br> [[Media:Fa23 M2D2 saw.pdf | T/R prelab]]<br>[[Media:Fa23_M2D2_jz.pdf | W/F prelab]]<br> [[Media:Fa23 JADiscussion nll.pdf| Journal article presentation discussion]]
 +
| [[20.109(F23):Homework#Due_M2D2|Homework due]]
 +
|--
 +
| M2D3
 +
| R/F Oct 19/20
 +
| [http://be.mit.edu/directory/jacquin-c-niles JCN] <br> [[Media:L02 Therapeutic Target Selection 20.109 2023-10-19 (Niles).pdf| Lecture slides]]
 +
| [[20.109(F23):M2D3 |Assess purity and concentration of purified protein]] <br> [[Media:Fa23 M2D3 bcm.pdf | T/R prelab]]<br>[[Media:Fa23_M2D3_jz.pdf | W/F prelab]]
 +
| [[20.109(F23):Homework#Due_M2D3|Homework due]] <br> [[20.109(F23):Data Summary| <font color =  #227d49 >'''Data Summary revision due'''</font color>]] Sat, Oct 21 at 10 pm <br>
 +
|--
 +
|
 +
| T/W Oct 24/25
 +
|
 +
| [[20.109(F23):Journal article presentation| <font color =  #227d49>'''Journal article presentations'''</font color>]]
 +
|
 +
|--
 +
|
 +
| R/F Oct 26/27
 +
|
 +
| [[20.109(F23):Journal article presentation| <font color =  #227d49 >'''Journal article presentations'''</font color>]]
 +
| [https://app.slack.com/client/T01KU1VLZQB/C05Q47YG92S Blog post due] Sat, Oct 28 at 10 pm
 +
|--
 +
| M2D4
 +
| T/W Oct 30/Nov 1
 +
| [http://be.mit.edu/directory/jacquin-c-niles JCN] <br> [[Media:Lecture 03 Choosing an intervention modality 20.109 2023-10-31 (Niles).pdf| Lecture slides]]
 +
| [[20.109(F23):M2D4 |Evaluate protein structures]] <br> [[Media:Fa23 M2D4 bcm.pdf| T/R prelab]] <br> [[Media:Fa23 M2D4 bcm.pdf| W/F prelab]]
 +
| <font color= #d57830 >'''Laboratory quiz'''</font color> <br> [[20.109(F23):Homework#Due_M2D4|Homework due]]
 +
|--
 +
| M2D5
 +
| R/F Nov 2/3
 +
| [http://be.mit.edu/directory/jacquin-c-niles JCN] <br> [[Media:L04 Intro to Screening 1.pdf| Lecture slides]]
 +
| [[20.109(F23):M2D5 |Prepare protein for functional assay]] <br> [[Media:Fa23 M2D5 bcm.pdf | T/R prelab]] <br> [[Media:Fa23 M2D5 bcm.pdf | W/F prelab]]
 +
| [[20.109(F23):Homework#Due_M2D5|Homework due]]
 +
|--
 +
| M2D6
 +
| T/W Nov 7/8
 +
| [http://be.mit.edu/directory/jacquin-c-niles JCN] <br> [[Media:L05 Intro to Screening II Phenotypic Screens (Niles).pdf| Lecture slides]]
 +
| [[20.109(F23):M2D6 |Complete data analysis of functional assay results]] <br> [[Media:Fa23 M2D6 bcm.pdf | T/R prelab]] <br>[[Media:Fa23 M2D6 bcm.pdf | W/F prelab]]
 +
| [[20.109(F23):Homework#Due_M2D5|Homework due]]
 +
|--
 +
|
 +
| <font color = 999999>R/F Nov 9/10 </font color>
 +
|
 +
| <font color = #a24d0a>'''Veterans' Day holiday'''</font color>
 +
|
 +
|--
 +
| M2D7
 +
| T/W Nov 14/15
 +
| [http://be.mit.edu/directory/jacquin-c-niles JCN] <br>
 +
| [[20.109(F23):M2D7 |Organize results and incorporate class data]] <br> [[Media:Fa23 M2D7 bcm.pdf | T/R prelab]] <br> [[Media:Fa23 M2D7 bcm.pdf | W/F prelab]]<br> [[Media:Fa23 RA discussion.pdf|Research article discussion]]
 +
| <font color= #d57830 >'''Laboratory quiz'''</font color> <br> [[20.109(F23):Homework#Due_M2D7|Homework due]]
 +
|--
 +
| M3D1
 +
| R/F Nov 16/17
 +
| [http://be.mit.edu/directory/noreen-lyell NLL]<br>
 +
| [[20.109(F23):M3D1 |Brainstorm ideas for Research proposal presentation]] <br> [[Media:Fa23_M3D1_nll.pdf | T/R prelab]] <br> [[Media:Fa23_M3D1_nll.pdf | W/F prelab]]
 +
| [[20.109(F23):Homework#Due_M3D1|Homework due]]
 +
|--
 +
|
 +
| <font color = 999999>T/W Nov 21/22 </font color>
 +
|
 +
| <font color = #a24d0a>'''Thanksgiving Day holiday'''</font color>
 +
| [[20.109(F23):Research article| <font color =  #227d49 >'''Research article due'''</font color>]]  Mon, Nov 20 at 10 pm <br> [https://app.slack.com/client/T01KU1VLZQB/C05Q47YG92S Blog post due] Tue, Nov 21 at 10 pm
 +
|--
 +
|
 +
| <font color = 999999>R/F Nov 23/24 </font color>
 +
|
 +
| <font color = #a24d0a>'''Thanksgiving Day holiday'''</font color>
 +
|
 +
|--
 +
| M3D2
 +
| T/W Nov 28/29
 +
| [http://be.mit.edu/directory/angela-belcher AB]<br>
 +
| [[20.109(F23):M3D2 |Pitch research proposal presentation ideas ]] <br> [[Media:Fa23 M3D2 nll.pdf|T/R prelab]] <br> [[Media:Fa23_M3D2_jz.pdf|W/F prelab]]
 +
|
 +
|--
 +
| M3D3
 +
| R/F Nov 30/Dec1
 +
| BE Comm Lab
 +
| [[20.109(F23):M3D3 |Develop ideas for Research proposal presentation ]] <br> [[Media:Fa23 M3D3 nll.pdf|T/R prelab]] <br> [[Media:Fa23_M3D3_jz.pdf|W/F prelab]]
 +
| [[20.109(F23):Homework#Due_M3D3|Homework due]]<br>
 +
|--
 +
| M3D4
 +
| T/W Dec 5/6
 +
| [http://be.mit.edu/directory/noreen-lyell NLL] <br>
 +
| [[20.109(F23):M3D4 |Participate in Research proposal peer reviews]] <br>
 +
| [[20.109(F23):Homework#Due_M3D4|Homework due]]
 +
|--
 +
|
 +
| R/F Dec 7/8
 +
|
 +
| [[20.109(F23):Research proposal presentation| <font color =  #227d49 >'''Research proposal presentations'''</font color>]]
 +
| [https://app.slack.com/client/T01KU1VLZQB/C05Q47YG92S Blog post due] Sat, Dec 9 at 10 pm
 +
|--
 +
|
 +
| T Dec 12
 +
| <font color =  #a24d0a>'''Celebration lunch!'''</font color> <br>
 +
| 
 +
|
 +
|}
 +
</div>

Revision as of 13:03, 12 June 2024

20.109(F24): Laboratory Fundamentals of Biological Engineering

Fa24 banner image.png

Fall 2024 schedule        FYI        Assignments        Homework        Class data        Communication        Accessibility

       M1: Genomic integrity        M2: Protein engineering        M3: Project design       


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 16-220
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).

MODULE DATE LECTURER LABORATORY EXPERIMENTS ASSIGNMENTS
R/F Sep 7/8 NLL
Lecture slides
Orientation and laboratory tour
T/R prelab
W/F prelab
M1D1 T/W Sep 12/13 BPE
Lecture slides
Learn best practices for mammalian cell culture
T/R prelab
W/F prelab 		Orientation quiz
Homework due
M1D2 R/F Sep 14/15 BPE
Lecture slides 		Prepare and treat cells for γH2AX experiment
T/R prelab
W/F prelab 		Homework due
M1D3 T/W Sep 19/20 BPE
Lecture slides 		Use immunoflourescence staining to assess γH2AX experiment
T/R prelab
W/F prelab 		Homework due
R/F Sep 21/22 BE Comm Lab Career Day holiday
M1D4 T/W Sep 26/27 BPE
Lecture slides 		Complete data analysis for γH2AX experiment
T/R prelab
W/F prelab 		Laboratory quiz
Homework due
M1D5 R/F Sep 28/29 BPE
Lecture slides 		Treat cells for CometChip assay
T/R prelab
W/F prelab 		Homework due
Research talk due Sat, Sep 30 at 10 pm
M1D6 T/W Oct 3/4 BPE
Lecture slides 		Image and analyze data for CometChip assay
T/R prelab
W/F prelab 		Homework due
M1D7 R/F Oct 5/6 BPE
Examine experimental data using statistical methods
T/R prelab
W/F prelab
Data summary discussion 		Laboratory quiz
Homework due
T/W Oct 10/11 Indigenous Peoples' Day holiday Data Summary draft due Wed, Oct 11 at 10 pm
Blog post due Thu, Oct 12 at 10 pm
M2D1 R/F Oct 12/13 JCN
Lecture slides 		Complete in-silico cloning of protein expression plasmid
T/R prelab
W/F prelab 		Homework due
M2D2 T/W Oct 17/18 BE Comm Lab
Perform protein purification protocol
T/R prelab
W/F prelab
Journal article presentation discussion 		Homework due
M2D3 R/F Oct 19/20 JCN
Lecture slides 		Assess purity and concentration of purified protein
T/R prelab
W/F prelab 		Homework due
Data Summary revision due Sat, Oct 21 at 10 pm
T/W Oct 24/25 Journal article presentations
R/F Oct 26/27 Journal article presentations Blog post due Sat, Oct 28 at 10 pm
M2D4 T/W Oct 30/Nov 1 JCN
Lecture slides 		Evaluate protein structures
T/R prelab
W/F prelab 		Laboratory quiz
Homework due
M2D5 R/F Nov 2/3 JCN
Lecture slides 		Prepare protein for functional assay
T/R prelab
W/F prelab 		Homework due
M2D6 T/W Nov 7/8 JCN
Lecture slides 		Complete data analysis of functional assay results
T/R prelab
W/F prelab 		Homework due
R/F Nov 9/10 Veterans' Day holiday
M2D7 T/W Nov 14/15 JCN
Organize results and incorporate class data
T/R prelab
W/F prelab
Research article discussion 		Laboratory quiz
Homework due
M3D1 R/F Nov 16/17 NLL
 Brainstorm ideas for Research proposal presentation
T/R prelab
W/F prelab 		Homework due
T/W Nov 21/22 Thanksgiving Day holiday Research article due Mon, Nov 20 at 10 pm
Blog post due Tue, Nov 21 at 10 pm
R/F Nov 23/24 Thanksgiving Day holiday
M3D2 T/W Nov 28/29 AB
 Pitch research proposal presentation ideas
T/R prelab
W/F prelab
M3D3 R/F Nov 30/Dec1 BE Comm Lab Develop ideas for Research proposal presentation
T/R prelab
W/F prelab 		Homework due
M3D4 T/W Dec 5/6 NLL
Participate in Research proposal peer reviews
Homework due
R/F Dec 7/8 Research proposal presentations Blog post due Sat, Dec 9 at 10 pm
T Dec 12 Celebration lunch!
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