Difference between revisions of "20.109(S18): Spring 2018 schedule"

From Course Wiki
Jump to: navigation, search
 
(107 intermediate revisions by 4 users not shown)
Line 1: Line 1:
 +
<div style="padding: 10px; width: 820px; border: 5px solid #0404B4;">
 
{{Template:20.109(S18)}}
 
{{Template:20.109(S18)}}
−
<div style="padding: 10px; width: 790px; border: 5px solid #0000FF;">
 
  
−
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 -- ones that will increase the likelihood of success in your work and ensure the health and safety of you and those around you. By the end of the semester, you should also be aware of good scientific practice, having had some experience with scientific writing, notebook keeping, and orally presenting data and your 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:'''<br>
+
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 (16-220)  <br>
+
 
−
'''Laboratory sections:'''     T/R 1-5 or W/F 1-5 (56-322)<br>
+
<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
Line 19: Line 20:
 
|  
 
|  
 
| 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):Lab tour | Orientation]]<br>
+
| [[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=#FE2E2E>'''Orientation quiz'''</font color> <br> [[20.109(S18):Homework#Due_M1D1| Homework due]]
+
| <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 microarry analysis and induce protein expression]]<br>
+
| [[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]]
−
| <font color=#FE2E2E>'''Laboratory quiz'''</font color> <br> [[20.109(S18):Homework#Due_M1D3| Homework due]]
+
| [[20.109(S18):Homework#Due_M1D3| Homework due]]
 
|--
 
|--
 
|  
 
|  
Line 50: Line 51:
 
| T/W Feb 20/21
 
| T/W Feb 20/21
 
|
 
|
−
| <font color = #999999>President's day holiday</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):Assess protein purity and concentration (Day4) |Assess protein purity and concentration]]<br>
+
| [[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://koehler-lab.mit.edu/group/people SD]<br>
+
| [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:Sp18 20109 M1L5.pptx| M1D5 Lecture]]
−
| [[20.109(S18):SECONDARY ASSAY D1 (Day5) |SECONDARY ASSAY D1]]<br>
+
| [[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]]
−
| <font color=#FE2E2E>'''Laboratory quiz'''</font color> <br> [[20.109(S18):Homework#Due_M1D5| Homework due]]
+
| [[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):SECONDARY ASSAY D2 (Day6) |SECONDARY ASSAY D2]]<br>
+
| [[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]]
 
|--
 
|--
Line 77: Line 78:
 
| 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=#FE2E2E>'''Laboratory quiz'''</font color> <br> [[20.109(S18):Homework#Due_M1D7| Homework due]]
+
| <font color=#0174DF>'''Laboratory quiz'''</font color> <br> [[20.109(S18):Homework#Due_M1D7| Homework due]]
 
|--
 
|--
 
| colspan="7" |
 
| colspan="7" |
Line 86: Line 87:
 
| 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):Confirm cell lines and practice tissue culture techniques (Day1)| Confirm cell lines and practice tissue culture techniques]]<br>[[Media:Sp17_M2D1_170309_marked.pdf| Prelab T/R]]<br>[[Media:Sp17_M2D1_LMM_1.pdf| Prelab W/F]]
+
| [[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(S17):Homework#Due_M2D1| Homework due]]
+
| [[20.109(S18):Homework#Due_M2D1| Homework due]]
 
|--
 
|--
 
| 2
 
| 2
 
| 2
 
| 2
−
| T/W Mar 14/15
+
| T/W Mar 13/14
−
| [http://be.mit.edu/directory/leona-d-samson LS]<br>Snow day
+
| [http://be.mit.edu/directory/noreen-lyell NLL]<br>
−
| [[20.109(S17):Prepare Western blot and induce DNA damage for quantitative PCR assay (Day2)| Prepare Western blot and induce DNA damage for quantitative PCR assay]]<br>[[Media:Sp17_M2D2_170314_marked.pdf| Prelab T/R]]<br>[[Media:Sp17_M2D2_LMM_1.pdf| Prelab W/F]]
+
| [[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]]
−
| <font color=#04B45F>'''Laboratory quiz'''</font color> <br> [[20.109(S17):Homework#Due_M2D2| Homework due]]<br> [[20.109(S17): M1 Data Summary| Data Summary draft due]] Mon, Mar 13 at 10 pm
+
| [[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 16/17
+
| R/F Mar 15/16
−
| [http://be.mit.edu/directory/leona-d-samson LS] <br> [[Media:FINAL 20.109 Spring 2017 Lectures 2 and 3 (snow day).pdf| M2L2 & L3]]
+
| [http://be.mit.edu/directory/ernest-fraenkel EF] <br> [[Media:109 Lecture 180315 2post.pdf| M2D3 Lecture]]
−
| [[20.109(S17):Purify RNA for quantitative PCR assay and treat cells for survival assay (Day3)| Purify RNA for quantitative PCR assay and treat cells for viability assay]]<br>[[Media:Sp17_M2D3_170316_marked.pdf| Prelab T/R]]<br>[[Media:Sp17_M2D3_LMM_1.pdf| Prelab W/F]]
+
| [[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(S17):Homework#Due_M2D3| Homework due]] <br> [[20.109(S17): M1 Mini-presentation| Mini presentation due]] Sat, Mar 18 at 10 pm
+
| [[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 21/22
+
| T/W Mar 20/21
−
| [http://be.mit.edu/directory/leona-d-samson LS]<br> [[Media:Sp17 M2L4.pdf| M2L4]]
+
| [http://be.mit.edu/directory/ernest-fraenkel EF]<br> [[Media:M2D4 lecture RNA-Seq notes 180320.pdf| M2D4 Lecture]]
−
| [[20.109(S17):Complete cell survival assay and examine transcript levels in response to DNA damage (Day 4)| Complete cell viability assay and examine transcript levels in response to DNA damage]]<br>[[Media:Sp17_M2D4_170320_marked.pdf| Prelab T/R]]<br>[[Media:Sp17_M2D4_LMM_1.pdf| Prelab W/F]]
+
| [[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=#04B45F>'''Laboratory quiz'''</font color> <br> [[20.109(S17):Homework#Due_M2D4| Homework due]]
+
| <font color=#0174DF>'''Laboratory quiz'''</font color> <br> [[20.109(S18):Homework#Due_M2D4| Homework due]]
 
|--
 
|--
 
| 2
 
| 2
 
| 5
 
| 5
−
| R/F Mar 23/24
+
| R/F Mar 22/23
−
| DC
+
| [http://be.mit.edu/directory/ernest-fraenkel EF]<br> [[Media:Lecture 3 Big Data to post 2.pdf| M2D5 Lecture]]
−
| [[20.109(S17):Journal Club I (Day5) | Journal club I]]
+
| [[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]]
 
|--
 
|--
 
|  
 
|  
 
|  
 
|  
−
| <font color = 999999>T/W Mar 28/29</font color>
+
| T/W Mar 27/28
 
|   
 
|   
−
| <font color = 999999>Spring vacation</font color>
+
| <font color = #0404B4>'''Spring vacation'''</font color>
−
| [[20.109(S17): M1 Data Summary| Data Summary revision due]] Mon, Mar 27 at 10 pm
+
| [[20.109(S18): M1 Data Summary| <font color=#FF0000>Data summary revision due</font color>]] Mon, Mar 26 at 10 pm
 
|--
 
|--
 
|  
 
|  
 
|  
 
|  
−
| <font color = 999999>R/F Mar 30/31</font color>
+
| R/F Mar 29/30
 
|   
 
|   
−
| <font color = 999999>Spring vacation</font color>
+
| <font color = #0404B4>'''Spring vacation'''</font color>
 
|  
 
|  
 
|--
 
|--
 
| 2
 
| 2
 
| 6
 
| 6
−
| T/W Apr 4/5
+
| T/W Apr 3/4
−
| [http://be.mit.edu/directory/ernest-fraenkel EF]<br>[[Media:170404 Fraenkel Lecture 1.pdf| M2L6]]
+
| Comm Lab<br>
−
| [[20.109(S17):Practice data analysis methods (Day6)| Practice data analysis methods]]<br>[[Media:Sp17_M2D6_170404_marked.pdf| Prelab T/R]]<br>[[Media:Sp17_M2D6_LMM_1.pdf| Prelab W/F]]
+
| [[20.109(S18):Journal club presentations (Day6 and 7)| Journal club I presentations]]<br>
−
| [http://be20109s17.blogspot.com/ Blog post due] Mon, Apr 3 at 10 pm <br> [[20.109(S17):Homework#Due_M2D6| Homework due]]
+
|
 
|--
 
|--
 
| 2
 
| 2
 
| 7
 
| 7
−
| R/F Apr 6/7
+
| R/F Apr 5/6
−
| [http://be.mit.edu/directory/ernest-fraenkel EF]<br>[[Media:170406 Fraenkel Lecture 2.pdf| M2L7]]
+
| [http://be.mit.edu/directory/noreen-lyell NLL]<br> [[Media:Sp18 M2D7 lecture slides.pptx| M2D7 Lecture]]
−
| [[20.109(S17):Analyze RNA-seq data (Day7) | Analyze RNA-seq data]]<br>[[Media:Sp17_M2D7_170406_marked.pdf| Prelab T/R]]<br>[[Media:Sp17_M2D7_LMM_1.pdf| Prelab W/F]]
+
| [[20.109(S18):Journal club presentations (Day6 and 7)| Journal club II presentations]]<br>
−
| [[20.109(S17):Homework#Due_M2D7| Homework due]]
+
| [https://20109s18.blogspot.com/ Blog post due] Sat, Apr 7 at 10 pm <br>
 
|--
 
|--
 
| 2
 
| 2
 
| 8
 
| 8
−
| T/W Apr 11/12
+
| T/W Apr 10/11
−
| [http://be.mit.edu/directory/leona-d-samson LS] <br> [[Media:THE FINAL 20.109 Spring 2017 Lecture 5.pptx| M2L8]]
+
| [http://be.mit.edu/directory/ernest-fraenkel EF]<br> [[Media:Sp18 Sequence Motifs 180327 for posting final.pdf| M2D8 Lecture]]
−
| [[20.109(S17):Journal Club II (Day8)| Journal club II]]
+
| [[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 13/14
+
| R/F Apr 12/13
−
| [http://be.mit.edu/directory/noreen-lyell NLL]<br>[[Media:Sp17 M2D9 lecture slides.pdf| M2L9]]
+
| [http://be.mit.edu/directory/ernest-fraenkel EF]<br> [[Media:Sp18 M2D9 Network lecture to post.pdf| M2D9 Lecture]]
−
| [[20.109(S17):Examine quantitative PCR results (Day9)| Examine quantitative PCR results]]<br>[[Media:Sp17_M2D9_170413_marked.pdf| Prelab T/R]]<br>[[Media:Sp17_M2D9_LMM_1.pdf| Prelab W/F]]
+
| [[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=#04B45F>'''Laboratory quiz'''</font color> <br> [[20.109(S17):Homework#Due_M2D9| Homework due]] <br> [http://be20109s17.blogspot.com/ Blog post due] Sat, Apr 15 at 10 pm
+
| <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 18/19
+
| T/W Apr 17/18
 
|
 
|
−
| <font color = #999999>Patriots' day holiday</font color>
+
| <font color = #0404B4>'''Patriots' day holiday'''</font color>
 
|
 
|
 
|--
 
|--
 
| 3
 
| 3
 
| 1
 
| 1
−
| R/F Apr 20/21
+
| R/F Apr 19/20  
−
| [http://be.mit.edu/directory/angela-belcher AB]<br>[[Media:20109_M3L1.pptx.pdf | M3L1]] 
+
| [http://be.mit.edu/directory/angela-belcher AB]<br>
−
| [[20.109(S17):Growth of phage materials (Day1) | Grow phage active material]]<br>[[Media:Sp17_M3D1_170420_marked.pdf| Prelab T/R]]<br>[[Media:Sp17_M3D1_LMM_1.pdf| Prelab W/F]]
+
| [[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(S17):Homework#Due_M3D1| Homework due]] <br> [[20.109(S17): Research article| Research article due]] April 22 at 10 pm <br> [http://be20109s17.blogspot.com/ Blog post due] Sun, Apr 23 at 10 pm
+
| [[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 25/26
+
| T/W Apr 24/25
−
| [http://be.mit.edu/directory/angela-belcher AB]<br>[[Media:20109 M3L2.pptx | M3L2]] 
+
| [http://be.mit.edu/directory/angela-belcher AB]<br>
−
| [[20.109(S17):Purify active materials (Day2) | Purify phage active material]]<br>[[Media:Sp17_M3D2_170425_marked.pdf| Prelab T/R]]<br>[[Media:Sp17_M3D2_LMM_1.pdf| Prelab W/F]]
+
| [[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]]
−
| <font color=#04B45F>'''Laboratory quiz'''</font color> <br> [[20.109(S17):Homework#Due_M3D2| Homework due]]
+
| [[20.109(S18):Homework#Due_M3D2| Homework due]]
 
|--
 
|--
 
| 3
 
| 3
 
| 3
 
| 3
−
| R/F Apr 27/28
+
| 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(S17):Cathode construction (Day3)| Construct cathode with phage active material]]<br>[[Media:Sp17_M3D3_170427_marked.pdf| Prelab T/R]]<br>[[Media:Sp17_M3D3_LMM_1.pdf| Prelab W/F]]
+
| [[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(S17):Homework#Due_M3D3| Homework due]]
+
| <font color=#0174DF>'''Laboratory quiz'''</font color> <br> [[20.109(S18):Homework#Due_M3D3| Homework due]]
 
|--
 
|--
 
| 3
 
| 3
 
|  
 
|  
−
| T/W May 2/3
+
| T/W May 1/2
 
|
 
|
−
| <font color = red>Lecture, but no laboratory</font color>
+
| <font color = #0404B4>'''Lecture, but no laboratory'''</font color>
 
|  
 
|  
 
|--
 
|--
 
| 3
 
| 3
 
| 4
 
| 4
−
| R/F May 4/5
+
| 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(S17):TEM (Day4)| Visualize phage nanowires using TEM]]<br>[[Media:Sp17_M3D4_170504_marked.pdf| Prelab T/R]]<br>[[Media:Sp17_M3D4_LMM_1.pdf| Prelab W/F]]
+
| [[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(S17):Homework#Due_M3D4| Homework due]]
+
| [[20.109(S18):Homework#Due_M3D4| Homework due]]
 
|--
 
|--
 
| 3
 
| 3
 
| 5
 
| 5
−
| T/W May 9/10
+
| T/W May 8/9
 
| [http://be.mit.edu/directory/angela-belcher AB]
 
| [http://be.mit.edu/directory/angela-belcher AB]
−
| [[20.109(S17):Battery assembly and testing (Day5) | Assemble and test battery ]]<br>[[Media:Sp17_M3D5_170509_marked.pdf| Prelab T/R]]<br>[[Media:Sp17_M3D5_LMM.pdf| Prelab W/F]]
+
| [[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=#04B45F>'''Laboratory quiz'''</font color> <br> [[20.109(S17):Homework#Due_M3D5| Homework due]]
+
| <font color=#0174DF>'''Laboratory quiz'''</font color> <br> [[20.109(S18):Homework#Due_M3D5| Homework due]]
 
|--
 
|--
 
|  
 
|  
 
|  
 
|  
−
| R/F May 11/12
+
| R/F May 10/11
−
|<font color = red>no lecture</font color>
+
−
| [[20.109(S17):Research proposal presentation| Research proposal presentations]]
+
−
| [http://be20109s17.blogspot.com/ Blog post due] Thu/Fri, May 11/12 at 10 pm
+
−
|--
+
 
|
 
|
−
|
+
| [[20.109(S18):Research proposal presentation | Research proposal presentations]]
−
| T/W May 16/17
+
| [https://20109s18.blogspot.com/ Blog post due] Sat, May 12 at 10 pm
−
|
+
−
| Open office hours
+
−
| [[20.109(S17): Biomaterials engineering mini-report| Mini report due]] Tue/Wed, May 16/17 at 10 pm  
+
 
|--
 
|--
 
|
 
|
 
|
 
|
−
| R May 18
+
| T May 15
 
|  
 
|  
−
| <font color = #00BFFF>'''Feedback and celebratory lunch'''</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

20.109(S18): Laboratory Fundamentals of Biological Engineering

Sp18 banner image v2.png

Spring 2018 schedule        FYI        Assignments        Homework        Class data        Communication
       1. Assessing ligand binding        2. Measuring gene expression        3. Engineering biomaterials              


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)

MODULE DAY DATE LECTURER LABORATORY EXPERIMENTS ASSIGNMENTS
T/W Feb 6/7 NLL
Orientation Lecture 		Orientation and laboratory tour
T/R Prelab
W/F Prelab
1 1 R/F Feb 8/9 AK
M1D1 Lecture 		In silico cloning and confirmation digest of protein expression vector
T/R Prelab
W/F Prelab 		Orientation quiz
Homework due
1 2 T/W Feb 13/14 AK
M1D2 Lecture 		Complete small microarray analysis and induce protein expression
T/R Prelab and ligation calculation
W/F Prelab 		Homework due
1 3 R/F Feb 15/16 AK
M1D3 Lecture 		Purify protein for secondary assays
T/R Prelab
W/F Prelab 		Homework due
T/W Feb 20/21 President's day holiday
1 4 R/F Feb 22/23 AK
M1D4 Lecture 		Evaluate protein purity and concentration
T/R Prelab
W/F Prelab
Methods Tips 		Laboratory quiz
Homework due
1 5 T/W Feb 27/28 AK
M1D5 Lecture 		Test protein activity using peptidyl-prolyl cis-trans isomerase assay
T/R Prelab
W/F Prelab 		Homework due
1 6 R/F Mar 1/2 AK
M1D6 Lecture 		Confirm ligand binding using differential scanning fluorimetry assay
T/R Prelab
W/F Prelab 		Homework due
1 7 T/W Mar 6/7 AK
M1D7 Lecture 		Complete data analysis
T/R Prelab
W/F Prelab 		Laboratory quiz
Homework due
2 1 R/F Mar 8/9 NLL
M2D1 Lecture 		Practice tissue culture techniques and prepare cells for RNA purification
T/R Prelab
W/F Prelab
 Homework due
2 2 T/W Mar 13/14 NLL
 Induce DNA damage and apply drug treatments for RNA purification
T/R Prelab
W/F Prelab 		Homework due
Data summary draft due Mon, Mar 12 at 10 pm
2 3 R/F Mar 15/16 EF
M2D3 Lecture 		Purify RNA and practice RNA-seq data analysis methods
T/R Prelab
W/F Prelab 		Homework due
Mini-presentation due Sat, Mar 17 at 10 pm
Blog post due Sun, Mar 18 at 10 pm
2 4 T/W Mar 20/21 EF
M2D4 Lecture 		Analyze RNA-seq data and prepare for quantitative PCR experiment
T/R Prelab
W/F Prelab 		Laboratory quiz
Homework due
2 5 R/F Mar 22/23 EF
M2D5 Lecture 		Investigate RNA-seq data using public databases
T/R Prelab
W/F Prelab 		Homework due
T/W Mar 27/28 Spring vacation Data summary revision due Mon, Mar 26 at 10 pm
R/F Mar 29/30 Spring vacation
2 6 T/W Apr 3/4 Comm Lab
 Journal club I presentations
2 7 R/F Apr 5/6 NLL
M2D7 Lecture 		Journal club II presentations
 Blog post due Sat, Apr 7 at 10 pm
2 8 T/W Apr 10/11 EF
M2D8 Lecture 		Induce DNA damage and apply drug treatments for cell viability and identification of regulatory motifs in RNA-seq data
T/R Prelab
W/F Prelab 		Homework due
2 9 R/F Apr 12/13 EF
M2D9 Lecture 		Complete cell viability assay
T/R Prelab
W/F Prelab 		Laboratory quiz
Homework due
T/W Apr 17/18 Patriots' day holiday
3 1 R/F Apr 19/20 AB
 Grow phage-based active (cathode) material
Quiz Review&T/R Prelab
Quiz Review&W/F Prelab 		Homework due
Research article due Sat, Apr 21 at 10 pm
Blog post due Sun, Apr 22 at 10 pm
3 2 T/W Apr 24/25 AB
 Purify phage-based active (cathode) material
T/R Prelab
W/F Prelab 		Homework due
3 3 R/F Apr 26/27 AB
M3D3 Lecture 		Construct cathode with phage-based active material
T/R Prelab
W/F Prelab 		Laboratory quiz
Homework due
3 T/W May 1/2 Lecture, but no laboratory
3 4 R/F May 3/4 AB
M3D4 Lecture 		Visualize phage nanowires using transmission electron microscopy
T/R Prelab
W/F Prelab
 Homework due
3 5 T/W May 8/9 AB Assemble and test batteries
T/R Prelab
W/F Prelab
 Laboratory quiz
Homework due
R/F May 10/11 Research proposal presentations Blog post due Sat, May 12 at 10 pm
T May 15 Feedback and celebratory lunch Mini-report due Mon, May 14 at 10 pm
Retrieved from "http://measurebiology.org/w/index.php?title=20.109(S18):_Spring_2018_schedule&oldid=38703"