Difference between revisions of "20.109(S19): Spring 2019 schedule"
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− | <div style="padding: 10px; width: 820px; border: 5px solid # | + | <div style="padding: 10px; width: 820px; border: 5px solid #0404B4;"> |
{{Template:20.109(S19)}} | {{Template:20.109(S19)}} | ||
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Welcome to 20.109! It is our goal to make this class a useful and fun introduction to experiments and techniques in biological engineering. Though there is not time enough 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 experiments and techniques in biological engineering. Though there is not time enough 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= #27ae60 >'''SCHEDULE DETAILS:'''</font color><br> |
− | <font color=# | + | <font color= #27ae60 >'''Lecture times:'''</font color> T/R 11 - 12 pm (32-124) <br> |
− | <font color=# | + | <font color= #27ae60 >'''Laboratory section times:'''</font color> T/R 1 - 5 pm or W/F 1 - 5 pm (56-322)<br> |
{| border=1px | {| border=1px | ||
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| | | | ||
| | | | ||
− | | T/W Feb | + | | T/W Feb 5/6 |
− | | [http://be.mit.edu/directory/noreen-lyell NLL]<br>[[Media: | + | | [http://be.mit.edu/directory/noreen-lyell NLL]<br>[[Media:Sp19 Orientation lecture students.pdf| Orientation lecture slides]] |
− | | [[20.109( | + | | [[20.109(S19):Laboratory tour | Orientation and laboratory tour]]<br>[[Media:Sp19_MOD0_LMMmarked.pdf| Prelab T/R]]<br>[[Media:Sp19 MOD0 nll marked.pdf| Prelab W/F]] |
| | | | ||
|-- | |-- | ||
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| 1 | | 1 | ||
| 1 | | 1 | ||
− | | R/F Feb | + | | R/F Feb 7/8 |
− | | [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media: | + | | [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:20109 M1L1 2019 printout.pdf| M1D1 lecture slides]] |
− | | [[20.109( | + | | [[20.109(S19):In silico cloning and confirmation digest of protein expression vector(Day1) |In silico cloning and confirmation digest of protein expression vector]]<br>[[Media:M1D1_Sp19_LMmarked.pdf| Prelab T/R]]<br>[[Media:Sp19 M1D1 nll marked.pdf| Prelab W/F]] |
− | | <font color=# | + | | <font color= #27ae60>'''Orientation quiz'''</font color> <br> [[20.109(S19):Homework#Due_M1D1| Homework due]] |
|-- | |-- | ||
| 1 | | 1 | ||
| 2 | | 2 | ||
− | | T/W Feb | + | | T/W Feb 12/13 |
− | | [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media: | + | | [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:20109 M1L2 2019 printout.pdf| M1D2 lecture slides]] |
− | | [[20.109( | + | | [[20.109(S19):Purify protein for secondary assays(Day2) |Purify protein for secondary assays]]<br>[[Media:M1D2_Sp19_LMmarked.pdf| Prelab T/R]]<br>[[Media:Sp19 M1D2 nll marked.pdf| Prelab W/F]] |
− | | [[20.109( | + | | [[20.109(S19):Homework#Due_M1D2| Homework due]] |
|-- | |-- | ||
| 1 | | 1 | ||
| 3 | | 3 | ||
− | | R/F Feb | + | | R/F Feb 14/15 |
− | | [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media: | + | | [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:20109 M1L3 2019 printout.pdf| M1D3 lecture slides]] |
− | | [[20.109(S18): | + | | [[20.109(S18):Analyze small microarray data (Day3) | Analyze small molecule microarray (SMM) data]]<br>[[Media:190212_M1D3_Prelab.pdf| Prelab T/R]]<br>[[Media:Sp19 M1D3 nll marked.pdf| Prelab W/F]] |
− | | [[20.109( | + | | [[20.109(S19):Homework#Due_M1D3| Homework due]] |
|-- | |-- | ||
| | | | ||
| | | | ||
− | | T/W Feb | + | | T/W Feb 19/20 |
| | | | ||
| <font color = #0404B4>'''President's day holiday'''</font color> | | <font color = #0404B4>'''President's day holiday'''</font color> | ||
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| 1 | | 1 | ||
| 4 | | 4 | ||
− | | R/F Feb | + | | R/F Feb 21/22 |
− | | [http://be.mit.edu/directory/angela-koehler AK]<br> [[Media: | + | | [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:20109 M1L4 2019 printout.pdf| M1D4 lecture slides]] |
− | | [[20.109( | + | | [[20.109(S19):Evaluate protein purity and concentration (Day4) |Evaluate protein purity and concentration]]<br>[[Media:Sp19_M1D4_Catherine.pdf| Prelab T/R]]<br>[[Media:Sp19 M1D4 nll marked.pdf| Prelab W/F]] |
− | | <font color=# | + | | <font color= #27ae60>'''Laboratory quiz'''</font color> <br> [[20.109(S19):Homework#Due_M1D4| Homework due]] |
|-- | |-- | ||
| 1 | | 1 | ||
| 5 | | 5 | ||
− | | T/W Feb | + | | T/W Feb 26/27 |
− | | [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media: | + | | [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:20109 M1L5 2019 prinout.pdf| M1D5 lecture slides]] |
− | | [[20.109( | + | | [[20.109(S19):Test protein activity using peptidyl-prolyl cis-trans isomerase assay (Day5) |Test protein activity using peptidyl-prolyl cis-trans isomerase assay]]<br>[[Media:Sp19_M1D5_LM_marked.pdf| Prelab T/R]]<br>[[Media:Sp19 M1D5 nll marked.pdf | Prelab W/F]] |
− | | [[20.109( | + | | [[20.109(S19):Homework#Due_M1D5| Homework due]] |
|-- | |-- | ||
| 1 | | 1 | ||
| 6 | | 6 | ||
− | | R/F Mar | + | | R/F Feb/Mar 28/1 |
− | | [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media: | + | | [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:20109 M1L6 2019 printout.pdf| M1D6 lecture slides]] |
− | | [[20.109( | + | | [[20.109(S19):Confirm ligand binding using differential scanning fluorimetry assay (Day6) |Confirm ligand binding using differential scanning fluorimetry assay]]<br>[[Media:Sp19_M1D6_LM_marked.pdf| Prelab T/R]]<br>[[Media:Sp19 M1D6 nll marked.pdf| Prelab W/F]] |
− | | [[20.109( | + | | [[20.109(S19):Homework#Due_M1D6| Homework due]] |
|-- | |-- | ||
| 1 | | 1 | ||
| 7 | | 7 | ||
− | | T/W Mar | + | | T/W Mar 5/6 |
− | | [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media: | + | | [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:20109 M1L7 2019 print.pdf| M1D7 lecture slides]] |
− | | [[20.109( | + | | [[20.109(S19):Complete data analysis (Day7) |Complete data analysis]]<br>[[Media:Sp19_M1D7_LMmarked.pdf| Prelab T/R]]<br>[[Media:Sp19 M1D7 nll marked.pdf|Prelab W/F]] |
− | | <font color=# | + | | <font color= #27ae60>'''Laboratory quiz'''</font color> <br> [[20.109(S19):Homework#Due_M1D7| Homework due]] |
|-- | |-- | ||
| colspan="7" | | | colspan="7" | | ||
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| 2 | | 2 | ||
| 1 | | 1 | ||
− | | R/F Mar | + | | R/F Mar 7/8 |
− | | [http://be.mit.edu/directory/noreen-lyell NLL]<br>[[Media: | + | | [http://be.mit.edu/directory/noreen-lyell NLL]<br>[[Media:Sp19 M2D1 lecture slides.pdf| M2D1 lecture slides]] |
− | | [[20.109( | + | | [[20.109(S19):Practice tissue culture techniques and prepare cells for RNA purification (Day1)| Practice tissue culture techniques and prepare cells for RNA purification]]<br>[[Media:Sp19_M2D1_LMMmarked.pdf| Prelab T/R]]<br>[[Media:Sp19 M2D1 MG nll.pdf| Prelab W/F]] |
− | | [[20.109( | + | | [[20.109(S19):Homework#Due_M2D1| Homework due]] |
|-- | |-- | ||
| 2 | | 2 | ||
| 2 | | 2 | ||
− | | T/W Mar | + | | T/W Mar 12/13 |
− | | [http://be.mit.edu/directory/noreen-lyell NLL]<br> | + | | [http://be.mit.edu/directory/noreen-lyell NLL]<br>[[Media:Sp19 M2D2 lecture slides.pdf| M2D2 lecture slides]] |
− | | [[20.109( | + | | [[20.109(S19):Etoposide treat cells for RNA purification (Day2)| Etoposide treat cells for RNA purification]]<br>[[Media:Sp19 M2D2 LMM.pdf| Prelab T/R]]<br>[[Media:Sp19 M2D2 MG nll.pdf| Prelab W/F]] |
− | | [[20.109( | + | | [[20.109(S19):Homework#Due_M2D2| Homework due]]<br> [[20.109(S19): Data Summary| <font color=#FF0000>Data summary draft due</font color>]] Mon, Mar 11 at 10 pm<br> |
|-- | |-- | ||
| 2 | | 2 | ||
| 3 | | 3 | ||
− | | R/F Mar 15 | + | | R/F Mar 14/15 |
− | | [http://be.mit.edu/directory/ernest-fraenkel EF] <br> [[Media: | + | | [http://be.mit.edu/directory/ernest-fraenkel EF] <br> [[Media:Sp19 M2 Lecture 1 Unsupervised learning 2 post.pdf| M2D3 lecture slides]] |
− | | [[20.109( | + | | [[20.109(S19):Purify RNA and practice RNA-seq data analysis methods (Day3)| Purify RNA and practice RNA-seq data analysis methods]]<br>[[Media:Sp19_M2D3_LMM.pdf| Prelab T/R]]<br>[[Media:Sp19 M2D3 nll marked.pdf| Prelab W/F]] |
− | | [[20.109( | + | | [[20.109(S19):Homework#Due_M2D3| Homework due]] <br> [[20.109(S19): Mini-presentation| <font color=#FF0000>Mini-presentation due</font color>]] Sat, Mar 16 at 10 pm<br>[https://be20109s19classblog.blogspot.com/ Blog post due] Sun, Mar 17 at 10 pm <br> |
|-- | |-- | ||
| 2 | | 2 | ||
| 4 | | 4 | ||
− | | T/W Mar | + | | T/W Mar 19/20 |
− | | [http://be.mit.edu/directory/ernest-fraenkel EF]<br> [[Media: | + | | [http://be.mit.edu/directory/ernest-fraenkel EF]<br>[[Media:Sp19 M2 Lecture 2 RNA Seq 2 post.pdf| M2D4 lecture slides]] |
− | | [[20.109( | + | | [[20.109(S19):Analyze RNA-seq data and prepare for quantitative PCR experiment (Day 4)| Analyze RNA-seq data and prepare for quantitative PCR experiment]]<br>[[Media:Sp19_M2D4_LMM.pdf| Prelab T/R]]<br>[[Media:Sp19 M2D4 nll marked.pdf| Prelab W/F]] |
− | | <font color=# | + | | <font color= #27ae60>'''Laboratory quiz'''</font color> <br> [[20.109(S19):Homework#Due_M2D4| Homework due]] |
|-- | |-- | ||
| 2 | | 2 | ||
| 5 | | 5 | ||
− | | R/F Mar | + | | R/F Mar 21/22 |
− | | [http://be.mit.edu/directory/ | + | | [http://be.mit.edu/directory/noreen-lyell NLL]<br>[[Media:Sp19 M2D5 lecture slides.pdf| M2D5 lecture slides]] |
− | | [[20.109( | + | | [[20.109(S19):Perform quantitative PCR experiment and explore additional RNA-seq datasets (Day5) | Perform quantitative PCR experiment and explore additional RNA-seq datasets]]<br>[[Media:Sp19_M2D5_LMM.pdf| Prelab T/R]]<br> [[Media:Sp19 M2D5 nll marked.pdf| Prelab W/F]] |
− | | [[20.109( | + | | [[20.109(S19):Homework#Due_M2D5| Homework due]] |
|-- | |-- | ||
| | | | ||
| | | | ||
− | | T/W Mar | + | | T/W Mar 26/27 |
| | | | ||
| <font color = #0404B4>'''Spring vacation'''</font color> | | <font color = #0404B4>'''Spring vacation'''</font color> | ||
− | | [[20.109( | + | | [[20.109(S19): Data Summary| <font color=#FF0000>Data summary revision due</font color>]] Mon, Mar 25 at 10 pm |
|-- | |-- | ||
| | | | ||
| | | | ||
− | | R/F Mar | + | | R/F Mar 28/29 |
| | | | ||
| <font color = #0404B4>'''Spring vacation'''</font color> | | <font color = #0404B4>'''Spring vacation'''</font color> | ||
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| 2 | | 2 | ||
| 6 | | 6 | ||
− | | T/W Apr | + | | T/W Apr 2/3 |
− | | | + | | [http://be.mit.edu/directory/ernest-fraenkel EF]<br>[[Media:Sp19 20109 Lecture 3 Big Data 2print.pdf| M2D6 lecture slides]] |
− | | [[20.109( | + | | [[20.109(S19):Design cell viability experiment and complete RNA-seq data analysis (Day6)| Design cell viability experiment and complete RNA-seq data analysis]]<br>[[Media:Sp19_M2D6_LMM.pdf| Prelab T/R]]<br>[[Media:Sp19 M2D6 nll marked.pdf| Prelab W/F]] |
− | | | + | | [[20.109(S19):Homework#Due_M2D6| Homework due]] |
|-- | |-- | ||
| 2 | | 2 | ||
| 7 | | 7 | ||
− | | R/F Apr 5 | + | | R/F Apr 4/5 |
− | | | + | | Comm Lab<br> |
− | | [[20.109( | + | | [[20.109(S19):Journal club presentations (Day7 and 8)| Journal club I presentations]]<br> |
− | | [https:// | + | | [https://be20109s19classblog.blogspot.com/ Blog post due] Sat, Apr 6 at 10 pm <br> |
|-- | |-- | ||
| 2 | | 2 | ||
| 8 | | 8 | ||
− | | T/W Apr | + | | T/W Apr 9/10 |
− | | [http://be.mit.edu/directory/ernest-fraenkel EF]<br> | + | | [http://be.mit.edu/directory/ernest-fraenkel EF]<br> |
− | | [[20.109( | + | | [[20.109(S19):Journal club presentations (Day7 and 8)| Journal club II presentations]]<br> |
− | | | + | | |
|-- | |-- | ||
| 2 | | 2 | ||
| 9 | | 9 | ||
− | | R/F Apr | + | | R/F Apr 11/12 |
− | | [http://be.mit.edu/directory/ernest-fraenkel EF]<br> | + | | [http://be.mit.edu/directory/ernest-fraenkel EF]<br> |
− | | [[20.109( | + | | [[20.109(S19):Complete data analysis (Day9)| Complete data analysis]]<br>[[Media:Sp19_M2D9_LMM.pdf| Prelab T/R]]<br>[[Media:Sp19 M2D9 nll marked.pdf| Prelab W/F]] |
− | | <font color=# | + | | <font color= #27ae60>'''Laboratory quiz'''</font color> <br> [[20.109(S19):Homework#Due_M2D9| Homework due]] <br> |
|-- | |-- | ||
| colspan="7" | | | colspan="7" | | ||
Line 165: | Line 165: | ||
| | | | ||
| | | | ||
− | | T/W Apr | + | | T/W Apr 16/17 |
| | | | ||
| <font color = #0404B4>'''Patriots' day holiday'''</font color> | | <font color = #0404B4>'''Patriots' day holiday'''</font color> | ||
Line 172: | Line 172: | ||
| 3 | | 3 | ||
| 1 | | 1 | ||
− | | R/F Apr 19 | + | | R/F Apr 18/19 |
− | | [http://be.mit.edu/directory/angela-belcher AB]<br> | + | | [http://be.mit.edu/directory/angela-belcher AB]<br>[[Media:20.109_Spring_2019_M3.pdf| M3D1 lecture slides]] |
− | | [[20.109( | + | | [[20.109(S19):Growth of phage-based active (cathode) material (Day1) | Grow phage-based active (cathode) material]]<br>[[Media:Sp19_M3D1_LM.pdf| Prelab T/R]]<br>[[Media:Sp19_M3D1WF_LM.pdf| Prelab W/F]]<br> |
− | | [[20.109( | + | | [[20.109(S19):Homework#Due_M3D1| Homework due]] <br> [[20.109(S19): Research article| <font color=#FF0000>Research article due</font color>]] Sat, Apr 20 at 10 pm <br> [https://be20109s19classblog.blogspot.com/ Blog post due] Sun, Apr 21 at 10 pm |
|-- | |-- | ||
| 3 | | 3 | ||
| 2 | | 2 | ||
− | | T/W Apr | + | | T/W Apr 23/24 |
− | | [http://be.mit.edu/directory/angela-belcher AB]<br> | + | | [http://be.mit.edu/directory/angela-belcher AB]<br>[[Media:BATTERIES20.1092019.pdf| M3D2 lecture slides]] |
− | | [[20.109( | + | | [[20.109(S19):Purify phage-based active (cathode) material (Day2) | Purify phage-based active (cathode) material]]<br>[[Media:Sp19_M3D2_LM.pdf| Prelab T/R]]<br>[[Media:Sp19 M3D2 nll marked.pdf| Prelab W/F]]<br> |
− | + | | [[20.109(S19):Homework#Due_M3D2| Homework due]] | |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | | [[20.109( | + | |
− | + | ||
|-- | |-- | ||
| 3 | | 3 | ||
| | | | ||
− | | | + | | R/F Apr 25/26 |
− | | | + | | |
| <font color = #0404B4>'''Lecture, but no laboratory'''</font color> | | <font color = #0404B4>'''Lecture, but no laboratory'''</font color> | ||
| | | | ||
+ | |-- | ||
+ | | 3 | ||
+ | | 3 | ||
+ | | T/W Apr/May 30/1 | ||
+ | | [http://be.mit.edu/directory/angela-belcher AB]<br> | ||
+ | | [[20.109(S19):Construct cathode with phage-based active material (Day3)| Construct cathode with phage-based active material]]<br>[[Media:Sp19_M3D3_LM.pdf| Prelab T/R]]<br>[[Media:Sp19 M3D3 nll marked.pdf| Prelab W/F]] | ||
+ | | <font color= #27ae60>'''Laboratory quiz'''</font color> <br> [[20.109(S19):Homework#Due_M3D3| Homework due]] | ||
|-- | |-- | ||
| 3 | | 3 | ||
| 4 | | 4 | ||
− | | R/F May | + | | R/F May 2/3 |
− | | [http://be.mit.edu/directory/angela-belcher AB]<br>[[Media:20. | + | | [http://be.mit.edu/directory/angela-belcher AB]<br>[[Media:20.109_TEM_2019_Spring.pdf| M3D4 lecture slides]] |
− | | [[20.109( | + | | [[20.109(S19):Visualize phage nanowires using TEM (Day4)| Visualize phage nanowires using transmission electron microscopy]]<br>[[Media:Sp19_M3D4_LM.pdf| Prelab T/R]]<br>[[Media:Sp19 M3D4 nll marked.pdf| Prelab W/F]] |
− | | [[20.109( | + | | [[20.109(S19):Homework#Due_M3D4| Homework due]] |
|-- | |-- | ||
| 3 | | 3 | ||
| 5 | | 5 | ||
− | | T/W May | + | | T/W May 7/8 |
| [http://be.mit.edu/directory/angela-belcher AB] | | [http://be.mit.edu/directory/angela-belcher AB] | ||
− | | [[20.109( | + | | [[20.109(S19):Assemble and test batteries (Day5) | Assemble and test batteries ]]<br>[[Media:Sp19_M3D5_LM.pdf| Prelab T/R]]<br>[[Media:Sp19 M3D5 nll marked.pdf| Prelab W/F]] |
− | | <font color=# | + | | <font color= #27ae60>'''Laboratory quiz'''</font color> <br> [[20.109(S19):Homework#Due_M3D5| Homework due]] |
|-- | |-- | ||
| | | | ||
| | | | ||
− | | R/F May | + | | R/F May 9/10 |
| | | | ||
− | | [[20.109( | + | | [[20.109(S19):Research proposal presentation | Research proposal presentations]] |
− | | [https:// | + | | [https://be20109s19classblog.blogspot.com/ Blog post due] Sat, May 11 at 10 pm |
|-- | |-- | ||
| | | | ||
| | | | ||
− | | T May | + | | T May 14 |
| | | | ||
| <font color = #0404B4>'''Feedback and celebratory lunch'''</font color> | | <font color = #0404B4>'''Feedback and celebratory lunch'''</font color> | ||
− | | [[20.109( | + | | [[20.109(S19): Mini-report | <font color=#FF0000>Mini-report due</font color>]] Mon, May 13 at 10 pm <br> |
|} | |} | ||
</div> | </div> |
Latest revision as of 19:16, 8 May 2019
Welcome to 20.109! It is our goal to make this class a useful and fun introduction to experiments and techniques in biological engineering. Though there is not time enough 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: T/R 11 - 12 pm (32-124)
Laboratory section times: T/R 1 - 5 pm or W/F 1 - 5 pm (56-322)