Difference between revisions of "20.109(S19): Spring 2019 schedule"

From Course Wiki
Jump to: navigation, search
(Created page with "<div style="padding: 10px; width: 820px; border: 5px solid #0404B4;"> {{Template:20.109(S19)}} Welcome to 20.109! It is our goal to make this class a useful and fun introduc...")
 
 
(87 intermediate revisions by 2 users not shown)
Line 1: Line 1:
−
<div style="padding: 10px; width: 820px; border: 5px solid #0404B4;">
+
<div style="padding: 10px; width: 820px; border: 5px solid #0404B4;">
 
{{Template:20.109(S19)}}
 
{{Template:20.109(S19)}}
  
Line 5: Line 5:
 
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=#0174DF>'''SCHEDULE DETAILS:'''</font color><br>
+
<font color= #27ae60 >'''SCHEDULE DETAILS:'''</font color><br>
−
<font color=#0174DF>'''Lecture times:'''</font color>  T/R 11 - 12 pm (4-149)  <br>
+
<font color= #27ae60 >'''Lecture times:'''</font color>  T/R 11 - 12 pm (32-124)  <br>
−
<font color=#0174DF>'''Laboratory section times:'''</font color>  T/R 1 - 5 pm or W/F 1 - 5 pm (56-322)<br>
+
<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
Line 19: Line 19:
 
|  
 
|  
 
|  
 
|  
−
| T/W Feb 6/7  
+
| T/W Feb 5/6  
−
| [http://be.mit.edu/directory/noreen-lyell NLL]<br>[[Media:Sp18 Orientation lecture.pptx|Orientation Lecture]]
+
| [http://be.mit.edu/directory/noreen-lyell NLL]<br>[[Media:Sp19 Orientation lecture students.pdf| Orientation lecture slides]]
−
| [[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]]
+
| [[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]]
 
|
 
|
 
|--
 
|--
Line 28: Line 28:
 
| 1
 
| 1
 
| 1
 
| 1
−
| R/F Feb 8/9
+
| R/F Feb 7/8
−
| [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:Sp18 20109 M1L1.pdf| M1D1 Lecture]]
+
| [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:20109 M1L1 2019 printout.pdf| M1D1 lecture slides]]
−
| [[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]]
+
| [[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=#0174DF>'''Orientation quiz'''</font color> <br> [[20.109(S18):Homework#Due_M1D1| Homework due]]
+
| <font color= #27ae60>'''Orientation quiz'''</font color> <br> [[20.109(S19):Homework#Due_M1D1| Homework due]]
 
|--
 
|--
 
| 1
 
| 1
 
| 2
 
| 2
−
| T/W Feb 13/14    
+
| T/W Feb 12/13    
−
| [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:Sp18 20109 M1L2 printout-1.pptx| M1D2 Lecture]]
+
| [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:20109 M1L2 2019 printout.pdf| M1D2 lecture slides]]
−
| [[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(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(S18):Homework#Due_M1D2| Homework due]]
+
| [[20.109(S19):Homework#Due_M1D2| Homework due]]
 
|--
 
|--
 
| 1
 
| 1
 
| 3
 
| 3
−
| R/F Feb 15/16  
+
| R/F Feb 14/15  
−
| [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:Sp18 20109 M1L3.pptx| M1D3 Lecture]]
+
| [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:20109 M1L3 2019 printout.pdf| M1D3 lecture slides]]
−
| [[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):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(S18):Homework#Due_M1D3| Homework due]]
+
| [[20.109(S19):Homework#Due_M1D3| Homework due]]
 
|--
 
|--
 
|  
 
|  
 
|  
 
|  
−
| T/W Feb 20/21
+
| T/W Feb 19/20
 
|
 
|
 
| <font color = #0404B4>'''President's day holiday'''</font color>
 
| <font color = #0404B4>'''President's day holiday'''</font color>
Line 56: Line 56:
 
| 1
 
| 1
 
| 4
 
| 4
−
| R/F Feb 22/23
+
| R/F Feb 21/22
−
| [http://be.mit.edu/directory/angela-koehler AK]<br> [[Media:Sp18 20109 M1L4.pptx| M1D4 Lecture]]
+
| [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:20109 M1L4 2019 printout.pdf| M1D4 lecture slides]]
−
| [[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(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=#0174DF>'''Laboratory quiz'''</font color> <br> [[20.109(S18):Homework#Due_M1D4| Homework due]]
+
| <font color= #27ae60>'''Laboratory quiz'''</font color> <br> [[20.109(S19):Homework#Due_M1D4| Homework due]]
 
|--
 
|--
 
| 1
 
| 1
 
| 5
 
| 5
−
| T/W Feb 27/28
+
| T/W Feb 26/27
−
| [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:Sp18 20109 M1L5.pptx| M1D5 Lecture]]
+
| [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:20109 M1L5 2019 prinout.pdf| M1D5 lecture slides]]
−
| [[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(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(S18):Homework#Due_M1D5| Homework due]]
+
| [[20.109(S19):Homework#Due_M1D5| Homework due]]
 
|--
 
|--
 
| 1
 
| 1
 
| 6
 
| 6
−
| R/F Mar 1/2
+
| R/F Feb/Mar 28/1
−
| [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:Sp18 20109 M1L6.pdf| M1D6 Lecture]]
+
| [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:20109 M1L6 2019 printout.pdf| M1D6 lecture slides]]
−
| [[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(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(S18):Homework#Due_M1D6| Homework due]]
+
| [[20.109(S19):Homework#Due_M1D6| Homework due]]
 
|--
 
|--
 
| 1
 
| 1
 
| 7
 
| 7
−
| T/W Mar 6/7
+
| T/W Mar 5/6
−
| [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:Sp18 20109 M1L7.pdf| M1D7 Lecture]]
+
| [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:20109 M1L7 2019 print.pdf| M1D7 lecture slides]]
−
| [[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]]
+
| [[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=#0174DF>'''Laboratory quiz'''</font color> <br> [[20.109(S18):Homework#Due_M1D7| Homework due]]
+
| <font color= #27ae60>'''Laboratory quiz'''</font color> <br> [[20.109(S19):Homework#Due_M1D7| Homework due]]
 
|--
 
|--
 
| colspan="7" |
 
| colspan="7" |
Line 86: Line 86:
 
| 2
 
| 2
 
| 1
 
| 1
−
| R/F Mar 8/9
+
| R/F Mar 7/8
−
| [http://be.mit.edu/directory/noreen-lyell NLL]<br>[[Media:Sp18 M2D1 lecture slides.pdf| M2D1 Lecture]]
+
| [http://be.mit.edu/directory/noreen-lyell NLL]<br>[[Media:Sp19 M2D1 lecture slides.pdf| M2D1 lecture slides]]
−
| [[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(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(S18):Homework#Due_M2D1| Homework due]]
+
| [[20.109(S19):Homework#Due_M2D1| Homework due]]
 
|--
 
|--
 
| 2
 
| 2
 
| 2
 
| 2
−
| T/W Mar 13/14
+
| 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(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(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(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>
+
| [[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 15/16
+
| R/F Mar 14/15
−
| [http://be.mit.edu/directory/ernest-fraenkel EF] <br> [[Media:109 Lecture 180315 2post.pdf| M2D3 Lecture]]
+
| [http://be.mit.edu/directory/ernest-fraenkel EF] <br> [[Media:Sp19 M2 Lecture 1 Unsupervised learning 2 post.pdf| M2D3 lecture slides]]
−
| [[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(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(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>
+
| [[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 20/21
+
| T/W Mar 19/20
−
| [http://be.mit.edu/directory/ernest-fraenkel EF]<br> [[Media:M2D4 lecture RNA-Seq notes 180320.pdf| M2D4 Lecture]]
+
| [http://be.mit.edu/directory/ernest-fraenkel EF]<br>[[Media:Sp19 M2 Lecture 2 RNA Seq 2 post.pdf| M2D4 lecture slides]]
−
| [[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]]
+
| [[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=#0174DF>'''Laboratory quiz'''</font color> <br> [[20.109(S18):Homework#Due_M2D4| Homework due]]
+
| <font color= #27ae60>'''Laboratory quiz'''</font color> <br> [[20.109(S19):Homework#Due_M2D4| Homework due]]
 
|--
 
|--
 
| 2
 
| 2
 
| 5
 
| 5
−
| R/F Mar 22/23
+
| R/F Mar 21/22
−
| [http://be.mit.edu/directory/ernest-fraenkel EF]<br> [[Media:Lecture 3 Big Data to post 2.pdf| M2D5 Lecture]]
+
| [http://be.mit.edu/directory/noreen-lyell NLL]<br>[[Media:Sp19 M2D5 lecture slides.pdf| M2D5 lecture slides]]
−
| [[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(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(S18):Homework#Due_M2D5| Homework due]]
+
| [[20.109(S19):Homework#Due_M2D5| Homework due]]
 
|--
 
|--
 
|  
 
|  
 
|  
 
|  
−
| T/W Mar 27/28
+
| T/W Mar 26/27
 
|   
 
|   
 
| <font color = #0404B4>'''Spring vacation'''</font color>
 
| <font color = #0404B4>'''Spring vacation'''</font color>
−
| [[20.109(S18): M1 Data Summary| <font color=#FF0000>Data summary revision due</font color>]] Mon, Mar 26 at 10 pm
+
| [[20.109(S19): Data Summary| <font color=#FF0000>Data summary revision due</font color>]] Mon, Mar 25 at 10 pm
 
|--
 
|--
 
|  
 
|  
 
|  
 
|  
−
| R/F Mar 29/30
+
| R/F Mar 28/29
 
|   
 
|   
 
| <font color = #0404B4>'''Spring vacation'''</font color>
 
| <font color = #0404B4>'''Spring vacation'''</font color>
Line 135: Line 135:
 
| 2
 
| 2
 
| 6
 
| 6
−
| T/W Apr 3/4
+
| T/W Apr 2/3
−
| Comm Lab<br>
+
| [http://be.mit.edu/directory/ernest-fraenkel EF]<br>[[Media:Sp19 20109 Lecture 3 Big Data 2print.pdf| M2D6 lecture slides]]
−
| [[20.109(S18):Journal club presentations (Day6 and 7)| Journal club I presentations]]<br>
+
| [[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 5/6
+
| R/F Apr 4/5
−
| [http://be.mit.edu/directory/noreen-lyell NLL]<br> [[Media:Sp18 M2D7 lecture slides.pptx| M2D7 Lecture]]
+
| Comm Lab<br>
−
| [[20.109(S18):Journal club presentations (Day6 and 7)| Journal club II presentations]]<br>
+
| [[20.109(S19):Journal club presentations (Day7 and 8)| Journal club I presentations]]<br>
−
| [https://20109s18.blogspot.com/ Blog post due] Sat, Apr 7 at 10 pm <br>
+
| [https://be20109s19classblog.blogspot.com/ Blog post due] Sat, Apr 6 at 10 pm <br>
 
|--
 
|--
 
| 2
 
| 2
 
| 8
 
| 8
−
| T/W Apr 10/11
+
| T/W Apr 9/10
−
| [http://be.mit.edu/directory/ernest-fraenkel EF]<br> [[Media:Sp18 Sequence Motifs 180327 for posting final.pdf| M2D8 Lecture]]
+
| [http://be.mit.edu/directory/ernest-fraenkel EF]<br>
−
| [[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(S19):Journal club presentations (Day7 and 8)| Journal club II presentations]]<br>
−
| [[20.109(S18):Homework#Due_M2D8| Homework due]]
+
|  
 
|--
 
|--
 
| 2
 
| 2
 
| 9
 
| 9
−
| R/F Apr 12/13
+
| R/F Apr 11/12
−
| [http://be.mit.edu/directory/ernest-fraenkel EF]<br> [[Media:Sp18 M2D9 Network lecture to post.pdf| M2D9 Lecture]]
+
| [http://be.mit.edu/directory/ernest-fraenkel EF]<br>
−
| [[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]]
+
| [[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=#0174DF>'''Laboratory quiz'''</font color> <br> [[20.109(S18):Homework#Due_M2D9| Homework due]] <br>  
+
| <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 17/18
+
| 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 19/20
+
| 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(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(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(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
+
| [[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 24/25
+
| 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(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(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(S18):Homework#Due_M3D2| Homework due]]
+
| [[20.109(S19):Homework#Due_M3D2| Homework due]]
−
|--
+
−
| 3
+
−
| 3
+
−
| R/F Apr 26/27
+
−
|[http://be.mit.edu/directory/angela-belcher AB]<br>[[Media:BATTERIES_20.109_2018.pdf | M3D3 Lecture]]
+
−
| [[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]]
+
−
| <font color=#0174DF>'''Laboratory quiz'''</font color> <br> [[20.109(S18):Homework#Due_M3D3| Homework due]]
+
 
|--
 
|--
 
| 3
 
| 3
 
|  
 
|  
−
| T/W May 1/2
+
| 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 3/4
+
| R/F May 2/3
−
| [http://be.mit.edu/directory/angela-belcher AB]<br>[[Media:20.109_TEM_2018.pdf | M3D4 Lecture]]
+
| [http://be.mit.edu/directory/angela-belcher AB]<br>[[Media:20.109_TEM_2019_Spring.pdf| M3D4 lecture slides]]
−
| [[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(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(S18):Homework#Due_M3D4| Homework due]]
+
| [[20.109(S19):Homework#Due_M3D4| Homework due]]
 
|--
 
|--
 
| 3
 
| 3
 
| 5
 
| 5
−
| T/W May 8/9
+
| T/W May 7/8
 
| [http://be.mit.edu/directory/angela-belcher AB]
 
| [http://be.mit.edu/directory/angela-belcher AB]
−
| [[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>
+
| [[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=#0174DF>'''Laboratory quiz'''</font color> <br> [[20.109(S18):Homework#Due_M3D5| Homework due]]
+
| <font color= #27ae60>'''Laboratory quiz'''</font color> <br> [[20.109(S19):Homework#Due_M3D5| Homework due]]
 
|--
 
|--
 
|  
 
|  
 
|  
 
|  
−
| R/F May 10/11
+
| R/F May 9/10
 
|
 
|
−
| [[20.109(S18):Research proposal presentation | Research proposal presentations]]
+
| [[20.109(S19):Research proposal presentation | Research proposal presentations]]
−
| [https://20109s18.blogspot.com/ Blog post due] Sat, May 12 at 10 pm
+
| [https://be20109s19classblog.blogspot.com/ Blog post due] Sat, May 11 at 10 pm
 
|--
 
|--
 
|
 
|
 
|
 
|
−
| T May 15
+
| T May 14
 
|  
 
|  
 
| <font color = #0404B4>'''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>
+
| [[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

20.109(S19): Laboratory Fundamentals of Biological Engineering

Sp19 banner image v2.png

Spring 2019 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 (32-124)
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 5/6 NLL
Orientation lecture slides 		Orientation and laboratory tour
Prelab T/R
Prelab W/F
1 1 R/F Feb 7/8 AK
M1D1 lecture slides 		In silico cloning and confirmation digest of protein expression vector
Prelab T/R
Prelab W/F 		Orientation quiz
Homework due
1 2 T/W Feb 12/13 AK
M1D2 lecture slides 		Purify protein for secondary assays
Prelab T/R
Prelab W/F 		Homework due
1 3 R/F Feb 14/15 AK
M1D3 lecture slides 		Analyze small molecule microarray (SMM) data
Prelab T/R
Prelab W/F 		Homework due
T/W Feb 19/20 President's day holiday
1 4 R/F Feb 21/22 AK
M1D4 lecture slides 		Evaluate protein purity and concentration
Prelab T/R
Prelab W/F 		Laboratory quiz
Homework due
1 5 T/W Feb 26/27 AK
M1D5 lecture slides 		Test protein activity using peptidyl-prolyl cis-trans isomerase assay
Prelab T/R
Prelab W/F 		Homework due
1 6 R/F Feb/Mar 28/1 AK
M1D6 lecture slides 		Confirm ligand binding using differential scanning fluorimetry assay
Prelab T/R
Prelab W/F 		Homework due
1 7 T/W Mar 5/6 AK
M1D7 lecture slides 		Complete data analysis
Prelab T/R
Prelab W/F 		Laboratory quiz
Homework due
2 1 R/F Mar 7/8 NLL
M2D1 lecture slides 		Practice tissue culture techniques and prepare cells for RNA purification
Prelab T/R
Prelab W/F 		Homework due
2 2 T/W Mar 12/13 NLL
M2D2 lecture slides 		Etoposide treat cells for RNA purification
Prelab T/R
Prelab W/F 		Homework due
Data summary draft due Mon, Mar 11 at 10 pm
2 3 R/F Mar 14/15 EF
M2D3 lecture slides 		Purify RNA and practice RNA-seq data analysis methods
Prelab T/R
Prelab W/F 		Homework due
Mini-presentation due Sat, Mar 16 at 10 pm
Blog post due Sun, Mar 17 at 10 pm
2 4 T/W Mar 19/20 EF
M2D4 lecture slides 		Analyze RNA-seq data and prepare for quantitative PCR experiment
Prelab T/R
Prelab W/F 		Laboratory quiz
Homework due
2 5 R/F Mar 21/22 NLL
M2D5 lecture slides 		Perform quantitative PCR experiment and explore additional RNA-seq datasets
Prelab T/R
Prelab W/F 		Homework due
T/W Mar 26/27 Spring vacation Data summary revision due Mon, Mar 25 at 10 pm
R/F Mar 28/29 Spring vacation
2 6 T/W Apr 2/3 EF
M2D6 lecture slides 		Design cell viability experiment and complete RNA-seq data analysis
Prelab T/R
Prelab W/F 		Homework due
2 7 R/F Apr 4/5 Comm Lab
 Journal club I presentations
 Blog post due Sat, Apr 6 at 10 pm
2 8 T/W Apr 9/10 EF
 Journal club II presentations
2 9 R/F Apr 11/12 EF
 Complete data analysis
Prelab T/R
Prelab W/F 		Laboratory quiz
Homework due
T/W Apr 16/17 Patriots' day holiday
3 1 R/F Apr 18/19 AB
M3D1 lecture slides 		Grow phage-based active (cathode) material
Prelab T/R
Prelab W/F
 Homework due
Research article due Sat, Apr 20 at 10 pm
Blog post due Sun, Apr 21 at 10 pm
3 2 T/W Apr 23/24 AB
M3D2 lecture slides 		Purify phage-based active (cathode) material
Prelab T/R
Prelab W/F
 Homework due
3 R/F Apr 25/26 Lecture, but no laboratory
3 3 T/W Apr/May 30/1 AB
 Construct cathode with phage-based active material
Prelab T/R
Prelab W/F 		Laboratory quiz
Homework due
3 4 R/F May 2/3 AB
M3D4 lecture slides 		Visualize phage nanowires using transmission electron microscopy
Prelab T/R
Prelab W/F 		Homework due
3 5 T/W May 7/8 AB Assemble and test batteries
Prelab T/R
Prelab W/F 		Laboratory quiz
Homework due
R/F May 9/10 Research proposal presentations Blog post due Sat, May 11 at 10 pm
T May 14 Feedback and celebratory lunch Mini-report due Mon, May 13 at 10 pm
Retrieved from "http://measurebiology.org/w/index.php?title=20.109(S19):_Spring_2019_schedule&oldid=41458"