Difference between revisions of "20.109(S18): Spring 2018 schedule"
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{{Template:20.109(S18)}} | {{Template:20.109(S18)}} | ||
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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. |
− | '''Lecture:''' T/R 11-12 ( | + | |
− | '''Laboratory | + | <font color=#0174DF>'''SCHEDULE DETAILS:'''</font color><br> |
+ | <font color=#0174DF>'''Lecture times:'''</font color> T/R 11 - 12 pm (4-149) <br> | ||
+ | <font color=#0174DF>'''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 6/7 | | T/W Feb 6/7 | ||
− | | [http://be.mit.edu/directory/noreen-lyell NLL]<br> | + | | [http://be.mit.edu/directory/noreen-lyell NLL]<br>[[Media:Sp18 Orientation lecture.pptx|Orientation Lecture]] |
− | | [[20.109(S18): | + | | [[20.109(S18):Laboratory tour | Orientation and laboratory tour]]<br>[[Media:Sp18 Orientation NLL marked.pdf| T/R Prelab]]<br>[[Media:Sp18 Orientation JB marked.pdf| W/F Prelab]] |
| | | | ||
|-- | |-- | ||
Line 28: | Line 29: | ||
| 1 | | 1 | ||
| R/F Feb 8/9 | | R/F Feb 8/9 | ||
− | | [http://be.mit.edu/directory/angela-koehler AK]<br> | + | | [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:Sp18 20109 M1L1.pdf| M1D1 Lecture]] |
− | | [[20.109(S18):In silico cloning and confirmation digest (Day1) |In silico cloning and confirmation digest]]<br> | + | | [[20.109(S18):In silico cloning and confirmation digest of protein expression vector(Day1) |In silico cloning and confirmation digest of protein expression vector]]<br>[[Media:Sp18 M1D1 nll markedV2.pdf| T/R Prelab]]<br>[[Media:Sp18_M1D1_JB_marked.pdf| W/F Prelab]] |
− | | <font color=# | + | | <font color=#0174DF>'''Orientation quiz'''</font color> <br> [[20.109(S18):Homework#Due_M1D1| Homework due]] |
|-- | |-- | ||
| 1 | | 1 | ||
| 2 | | 2 | ||
| T/W Feb 13/14 | | T/W Feb 13/14 | ||
− | | [http://be.mit.edu/directory/angela-koehler AK]<br> | + | | [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:Sp18 20109 M1L2 printout-1.pptx| M1D2 Lecture]] |
− | | [[20.109(S18):Analyze small microarray data and induce protein expression (Day2) |Complete small | + | | [[20.109(S18):Analyze small microarray data and induce protein expression (Day2) |Complete small microarray analysis and induce protein expression]]<br>[[Media:Sp18 M1D2 nll marked.pdf| T/R Prelab]] and [[Media:Sp18 M1D2 nll lig calc.pdf| ligation calculation]]<br>[[Media:Sp18 M1D2 JB marked.pdf| W/F Prelab]] |
| [[20.109(S18):Homework#Due_M1D2| Homework due]] | | [[20.109(S18):Homework#Due_M1D2| Homework due]] | ||
|-- | |-- | ||
Line 42: | Line 43: | ||
| 3 | | 3 | ||
| R/F Feb 15/16 | | R/F Feb 15/16 | ||
− | | [http://be.mit.edu/directory/angela-koehler AK]<br> | + | | [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:Sp18 20109 M1L3.pptx| M1D3 Lecture]] |
− | | [[20.109(S18):Purify protein (Day3) |Purify protein]]<br> | + | | [[20.109(S18):Purify protein for secondary assays(Day3) |Purify protein for secondary assays]]<br>[[Media:Sp18 M1D3 nll marked.pdf| T/R Prelab]]<br>[[Media:Sp18 M1D3_JB_marked.pdf| W/F Prelab]] |
− | | | + | | [[20.109(S18):Homework#Due_M1D3| Homework due]] |
|-- | |-- | ||
| | | | ||
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| T/W Feb 20/21 | | T/W Feb 20/21 | ||
| | | | ||
− | | <font color = # | + | | <font color = #0404B4>'''President's day holiday'''</font color> |
| | | | ||
|-- | |-- | ||
Line 56: | Line 57: | ||
| 4 | | 4 | ||
| R/F Feb 22/23 | | R/F Feb 22/23 | ||
− | | [http://be.mit.edu/directory/angela-koehler AK]<br> | + | | [http://be.mit.edu/directory/angela-koehler AK]<br> [[Media:Sp18 20109 M1L4.pptx| M1D4 Lecture]] |
− | | [[20.109(S18): | + | | [[20.109(S18):Evaluate protein purity and concentration (Day4) |Evaluate protein purity and concentration]]<br>[[Media:Sp18 M1D4_JBmarkedTR.pdf| T/R Prelab]]<br>[[Media:Sp18 M1D3_JBmarkedWF.pdf| W/F Prelab]]<br>[[Media:Sp18_MethodsTips_JB.pdf| Methods Tips]] |
− | | [[20.109(S18):Homework#Due_M1D4| Homework due]] | + | | <font color=#0174DF>'''Laboratory quiz'''</font color> <br> [[20.109(S18):Homework#Due_M1D4| Homework due]] |
|-- | |-- | ||
| 1 | | 1 | ||
| 5 | | 5 | ||
| T/W Feb 27/28 | | T/W Feb 27/28 | ||
− | | [http:// | + | | [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:Sp18 20109 M1L5.pptx| M1D5 Lecture]] |
− | | [[20.109(S18): | + | | [[20.109(S18):Test protein activity using peptidyl-prolyl cis-trans isomerase assay (Day5) |Test protein activity using peptidyl-prolyl cis-trans isomerase assay]]<br>[[Media:Sp18 M1D5_JBmarkedTR.pdf| T/R Prelab]]<br>[[Media:Sp18 M1D5_JBmarkedWF.pdf| W/F Prelab]] |
− | | | + | | [[20.109(S18):Homework#Due_M1D5| Homework due]] |
|-- | |-- | ||
| 1 | | 1 | ||
| 6 | | 6 | ||
| R/F Mar 1/2 | | R/F Mar 1/2 | ||
− | | [http://be.mit.edu/directory/angela-koehler AK]<br> | + | | [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:Sp18 20109 M1L6.pdf| M1D6 Lecture]] |
− | | [[20.109(S18): | + | | [[20.109(S18):Confirm ligand binding using differential scanning fluorimetry assay (Day6) |Confirm ligand binding using differential scanning fluorimetry assay]]<br>[[Media:Sp18 M1D6 nll.pdf| T/R Prelab]]<br>[[Media:Sp18 M1D6_JB.pdf| W/F Prelab]] |
| [[20.109(S18):Homework#Due_M1D6| Homework due]] | | [[20.109(S18):Homework#Due_M1D6| Homework due]] | ||
|-- | |-- | ||
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| 7 | | 7 | ||
| T/W Mar 6/7 | | T/W Mar 6/7 | ||
− | | [http://be.mit.edu/directory/angela-koehler AK]<br> | + | | [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:Sp18 20109 M1L7.pdf| M1D7 Lecture]] |
− | | [[20.109(S18):Complete data analysis (Day7) |Complete data analysis]]<br> | + | | [[20.109(S18):Complete data analysis (Day7) |Complete data analysis]]<br>[[Media:Sp18_M1D7_nll_marked.pdf| T/R Prelab]]<br>[[Media:Sp18 M1D7_JB.pdf| W/F Prelab]] |
− | | <font color=# | + | | <font color=#0174DF>'''Laboratory quiz'''</font color> <br> [[20.109(S18):Homework#Due_M1D7| Homework due]] |
|-- | |-- | ||
| colspan="7" | | | colspan="7" | | ||
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| 1 | | 1 | ||
| R/F Mar 8/9 | | R/F Mar 8/9 | ||
− | | [http://be.mit.edu/directory/noreen-lyell NLL]<br> | + | | [http://be.mit.edu/directory/noreen-lyell NLL]<br>[[Media:Sp18 M2D1 lecture slides.pdf| M2D1 Lecture]] |
− | | [[20.109(S18): | + | | [[20.109(S18):Practice tissue culture techniques and prepare cells for RNA purification (Day1)| Practice tissue culture techniques and prepare cells for RNA purification]]<br>[[Media:Sp18_M2D1_LMM_marked.pdf| T/R Prelab]]<br>[[Media:Sp18_M2D1_JB_marked.pdf| W/F Prelab]]<br> |
− | | [[20.109( | + | | [[20.109(S18):Homework#Due_M2D1| Homework due]] |
|-- | |-- | ||
| 2 | | 2 | ||
| 2 | | 2 | ||
− | | T/W Mar | + | | T/W Mar 13/14 |
− | | [http://be.mit.edu/directory/ | + | | [http://be.mit.edu/directory/noreen-lyell NLL]<br> |
− | | [[20.109( | + | | [[20.109(S18):Induce DNA damage and apply drug treatments for RNA purification (Day2)| Induce DNA damage and apply drug treatments for RNA purification]]<br>[[Media:Sp18_M2D2_LMM_marked.pdf| T/R Prelab]]<br>[[Media:Sp18_M2D2_JB_marked.pdf| W/F Prelab]] |
− | | | + | | [[20.109(S18):Homework#Due_M2D2| Homework due]]<br> [[20.109(S18): M1 Data Summary| <font color=#FF0000>Data summary draft due</font color>]] Mon, Mar 12 at 10 pm<br> |
|-- | |-- | ||
| 2 | | 2 | ||
| 3 | | 3 | ||
− | | R/F Mar 16 | + | | R/F Mar 15/16 |
− | | [http://be.mit.edu/directory/ | + | | [http://be.mit.edu/directory/ernest-fraenkel EF] <br> [[Media:109 Lecture 180315 2post.pdf| M2D3 Lecture]] |
− | | [[20.109( | + | | [[20.109(S18):Purify RNA and practice RNA-seq data analysis methods (Day3)| Purify RNA and practice RNA-seq data analysis methods]]<br>[[Media:Sp18_M2D3_LMM_marked.pdf| T/R Prelab]]<br>[[Media:Sp18_M2D3_JB_marked.pdf| W/F Prelab]] |
− | | [[20.109( | + | | [[20.109(S18):Homework#Due_M2D3| Homework due]] <br> [[20.109(S18): M1 Mini-presentation| <font color=#FF0000>Mini-presentation due</font color>]] Sat, Mar 17 at 10 pm<br>[https://20109s18.blogspot.com/ Blog post due] Sun, Mar 18 at 10 pm <br> |
|-- | |-- | ||
| 2 | | 2 | ||
| 4 | | 4 | ||
− | | T/W Mar | + | | T/W Mar 20/21 |
− | | [http://be.mit.edu/directory/ | + | | [http://be.mit.edu/directory/ernest-fraenkel EF]<br> [[Media:M2D4 lecture RNA-Seq notes 180320.pdf| M2D4 Lecture]] |
− | | [[20.109( | + | | [[20.109(S18):Analyze RNA-seq data and prepare for quantitative PCR experiment (Day 4)| Analyze RNA-seq data and prepare for quantitative PCR experiment]]<br>[[Media:Sp18_M2D4_CE_marked.pdf| T/R Prelab]]<br>[[Media:Sp18_M2D4_CE_marked2.pdf| W/F Prelab]] |
− | | <font color=# | + | | <font color=#0174DF>'''Laboratory quiz'''</font color> <br> [[20.109(S18):Homework#Due_M2D4| Homework due]] |
|-- | |-- | ||
| 2 | | 2 | ||
| 5 | | 5 | ||
− | | R/F Mar | + | | R/F Mar 22/23 |
− | | | + | | [http://be.mit.edu/directory/ernest-fraenkel EF]<br> [[Media:Lecture 3 Big Data to post 2.pdf| M2D5 Lecture]] |
− | | [[20.109( | + | | [[20.109(S18):Investigate RNA-seq data using public databases (Day5) | Investigate RNA-seq data using public databases]]<br>[[Media:Sp18_M2D5_CE_TRmarked.pdf| T/R Prelab]]<br>[[Media:Sp18_M2D5_CE_WFmarked.pdf| W/F Prelab]] |
− | | | + | | [[20.109(S18):Homework#Due_M2D5| Homework due]] |
|-- | |-- | ||
| | | | ||
| | | | ||
− | | | + | | T/W Mar 27/28 |
| | | | ||
− | | <font color = | + | | <font color = #0404B4>'''Spring vacation'''</font color> |
− | | [[20.109( | + | | [[20.109(S18): M1 Data Summary| <font color=#FF0000>Data summary revision due</font color>]] Mon, Mar 26 at 10 pm |
|-- | |-- | ||
| | | | ||
| | | | ||
− | | | + | | R/F Mar 29/30 |
| | | | ||
− | | <font color = | + | | <font color = #0404B4>'''Spring vacation'''</font color> |
| | | | ||
|-- | |-- | ||
| 2 | | 2 | ||
| 6 | | 6 | ||
− | | T/W Apr | + | | T/W Apr 3/4 |
− | | | + | | Comm Lab<br> |
− | | [[20.109( | + | | [[20.109(S18):Journal club presentations (Day6 and 7)| Journal club I presentations]]<br> |
− | | | + | | |
|-- | |-- | ||
| 2 | | 2 | ||
| 7 | | 7 | ||
− | | R/F Apr 6 | + | | R/F Apr 5/6 |
− | | [http://be.mit.edu/directory/ | + | | [http://be.mit.edu/directory/noreen-lyell NLL]<br> [[Media:Sp18 M2D7 lecture slides.pptx| M2D7 Lecture]] |
− | | [[20.109( | + | | [[20.109(S18):Journal club presentations (Day6 and 7)| Journal club II presentations]]<br> |
− | + | | [https://20109s18.blogspot.com/ Blog post due] Sat, Apr 7 at 10 pm <br> | |
|-- | |-- | ||
| 2 | | 2 | ||
| 8 | | 8 | ||
− | | T/W Apr | + | | T/W Apr 10/11 |
− | | [http://be.mit.edu/directory/ | + | | [http://be.mit.edu/directory/ernest-fraenkel EF]<br> [[Media:Sp18 Sequence Motifs 180327 for posting final.pdf| M2D8 Lecture]] |
− | | [[20.109( | + | | [[20.109(S18):Induce DNA damage and apply drug treatments for cell viability and identification of regulatory motifs in RNA-seq data (Day8)| Induce DNA damage and apply drug treatments for cell viability and identification of regulatory motifs in RNA-seq data]]<br>[[Media:Sp18_M2D8_LM_TRmarked.pdf| T/R Prelab]]<br>[[Media:Sp18_M2D8_JB_WFmarked.pdf| W/F Prelab]] |
− | | | + | | [[20.109(S18):Homework#Due_M2D8| Homework due]] |
|-- | |-- | ||
| 2 | | 2 | ||
| 9 | | 9 | ||
− | | R/F Apr | + | | R/F Apr 12/13 |
− | | [http://be.mit.edu/directory/ | + | | [http://be.mit.edu/directory/ernest-fraenkel EF]<br> [[Media:Sp18 M2D9 Network lecture to post.pdf| M2D9 Lecture]] |
− | | [[20.109(S17): | + | | [[20.109(S17):Complete cell viability assay (Day9)| Complete cell viability assay]]<br>[[Media:Sp18_M2D9_LMM.pdf| T/R Prelab]]<br>[[Media:Sp18_M2D9_JB.pdf| W/F Prelab]] |
− | | <font color=# | + | | <font color=#0174DF>'''Laboratory quiz'''</font color> <br> [[20.109(S18):Homework#Due_M2D9| Homework due]] <br> |
|-- | |-- | ||
| colspan="7" | | | colspan="7" | | ||
Line 164: | Line 165: | ||
| | | | ||
| | | | ||
− | | T/W Apr | + | | T/W Apr 17/18 |
| | | | ||
− | | <font color = # | + | | <font color = #0404B4>'''Patriots' day holiday'''</font color> |
| | | | ||
|-- | |-- | ||
| 3 | | 3 | ||
| 1 | | 1 | ||
− | | R/F Apr 20 | + | | R/F Apr 19/20 |
− | | [http://be.mit.edu/directory/angela-belcher AB]<br> | + | | [http://be.mit.edu/directory/angela-belcher AB]<br> |
− | | [[20.109( | + | | [[20.109(S18):Growth of phage-based active (cathode) material (Day1) | Grow phage-based active (cathode) material]]<br>[[Media:Sp18_M3D1_LMMmarked.pdf| Quiz Review&T/R Prelab]]<br>[[Media: Sp18_M3D1_JBmarked.pdf | Quiz Review&W/F Prelab]] |
− | | [[20.109( | + | | [[20.109(S18):Homework#Due_M3D1| Homework due]] <br> [[20.109(S18): Research article| <font color=#FF0000>Research article due</font color>]] Sat, Apr 21 at 10 pm <br> [https://20109s18.blogspot.com/ Blog post due] Sun, Apr 22 at 10 pm |
|-- | |-- | ||
| 3 | | 3 | ||
| 2 | | 2 | ||
− | | T/W Apr | + | | T/W Apr 24/25 |
− | | [http://be.mit.edu/directory/angela-belcher AB]<br> | + | | [http://be.mit.edu/directory/angela-belcher AB]<br> |
− | | [[20.109( | + | | [[20.109(S18):Purify phage-based active (cathode) material (Day2) | Purify phage-based active (cathode) material]]<br>[[Media:Sp18_M3D2_LMMmarked.pdf| T/R Prelab]]<br>[[Media:Sp18_M3D2_JBmarked.pdf| W/F Prelab]] |
− | | | + | | [[20.109(S18):Homework#Due_M3D2| Homework due]] |
|-- | |-- | ||
| 3 | | 3 | ||
| 3 | | 3 | ||
− | | R/F Apr | + | | R/F Apr 26/27 |
− | |[http://be.mit.edu/directory/angela-belcher AB]<br> | + | |[http://be.mit.edu/directory/angela-belcher AB]<br>[[Media:BATTERIES_20.109_2018.pdf | M3D3 Lecture]] |
− | | [[20.109( | + | | [[20.109(S18):Construct cathode with phage-based active material (Day3)| Construct cathode with phage-based active material]]<br>[[Media:Sp18_M3D3_LMMmarked.pdf| T/R Prelab]]<br>[[Media:Sp18_M3D3_JBmarked.pdf| W/F Prelab]] |
− | | [[20.109( | + | | <font color=#0174DF>'''Laboratory quiz'''</font color> <br> [[20.109(S18):Homework#Due_M3D3| Homework due]] |
|-- | |-- | ||
| 3 | | 3 | ||
| | | | ||
− | | T/W May | + | | T/W May 1/2 |
| | | | ||
− | | <font color = | + | | <font color = #0404B4>'''Lecture, but no laboratory'''</font color> |
| | | | ||
|-- | |-- | ||
| 3 | | 3 | ||
| 4 | | 4 | ||
− | | R/F May | + | | R/F May 3/4 |
− | | [http://be.mit.edu/directory/angela-belcher AB] | + | | [http://be.mit.edu/directory/angela-belcher AB]<br>[[Media:20.109_TEM_2018.pdf | M3D4 Lecture]] |
− | | [[20.109( | + | | [[20.109(S18):Visualize phage nanowires using TEM (Day4)| Visualize phage nanowires using transmission electron microscopy]]<br>[[Media:Sp18_M3D4_LMM_marked.pdf| T/R Prelab]]<br>[[Media:Sp18_M3D4_JB_marked.pdf| W/F Prelab]]<br> |
− | | [[20.109( | + | | [[20.109(S18):Homework#Due_M3D4| Homework due]] |
|-- | |-- | ||
| 3 | | 3 | ||
| 5 | | 5 | ||
− | | T/W May | + | | T/W May 8/9 |
| [http://be.mit.edu/directory/angela-belcher AB] | | [http://be.mit.edu/directory/angela-belcher AB] | ||
− | | [[20.109( | + | | [[20.109(S18):Assemble and test batteries (Day5) | Assemble and test batteries ]]<br>[[Media:Sp18_M3D5_LMM_marked.pdf| T/R Prelab]]<br>[[Media:Sp18_M3D5_JB_marked.pdf| W/F Prelab]]<br> |
− | | <font color=# | + | | <font color=#0174DF>'''Laboratory quiz'''</font color> <br> [[20.109(S18):Homework#Due_M3D5| Homework due]] |
|-- | |-- | ||
| | | | ||
| | | | ||
− | | R/F May | + | | R/F May 10/11 |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
| | | | ||
− | + | | [[20.109(S18):Research proposal presentation | Research proposal presentations]] | |
− | + | | [https://20109s18.blogspot.com/ Blog post due] Sat, May 12 at 10 pm | |
− | + | ||
− | + | ||
− | | [[20.109( | + | |
|-- | |-- | ||
| | | | ||
| | | | ||
− | | | + | | T May 15 |
| | | | ||
− | | <font color = # | + | | <font color = #0404B4>'''Feedback and celebratory lunch'''</font color> |
− | | | + | | [[20.109(S18): Biomaterials engineering mini-report | <font color=#FF0000>Mini-report due</font color>]] Mon, May 14 at 10 pm <br> |
|} | |} | ||
</div> | </div> |
Latest revision as of 02:26, 14 May 2018
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 (4-149)
Laboratory section times: T/R 1 - 5 pm or W/F 1 - 5 pm (56-322)