20.109(S13): Spring 2013 schedule

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===Table view with links===
<center>
<center>
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| [[20.109(S13):Lab tour | Orientation]]
| [[20.109(S13):Lab tour | Orientation]]
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| *[[Media:20.109 OrientLect(S13).pdf | Introductory Lecture (PDF)]] <br>*[[Media:S13_Orient_Pre-Lab-ANS.pdf | Intro Pre-Lab, T/R]]
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| *[[Media:20.109 OrientLect(S13).pdf | Introductory Lecture (PDF)]] <br>*[[Media:S13_Orient_Pre-Lab-ANS.pdf | Intro Pre-Lab, T/R]]<br>*[[Media:M1D0_SKH_prelab_final.pdf | Intro Pre-Lab, W/F]]
|--
|--
| colspan="7" |
| colspan="7" |
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| Thur/Fri Feb 7/8
| Thur/Fri Feb 7/8
| [http://web.mit.edu/be/people/runstadler.shtml JR]
| [http://web.mit.edu/be/people/runstadler.shtml JR]
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|  
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| [[User:Ian_Tay |Ian]]
| [[20.109(S13):Context-setting and primer design (Day1)| Context-setting and primer design]]
| [[20.109(S13):Context-setting and primer design (Day1)| Context-setting and primer design]]
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|
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|*[[Media:20109_S13-M1Lec1_Runstadler.pdf | M1D1 Lecture]] <br>*[[Media:S13_M1D1-ANS.pdf | T/R Pre-Lab]]<br>*[[Media:M1D1_lab_SKH.pdf | W/F Pre-Lab]]
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| Tue/Wed Feb 12/13  
| Tue/Wed Feb 12/13  
| [http://web.mit.edu/be/people/runstadler.shtml JR]
| [http://web.mit.edu/be/people/runstadler.shtml JR]
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|  
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| [[User:Ian_Tay |Ian]]
| [[20.109(S13):DNA extraction (Day2)| DNA extraction]]
| [[20.109(S13):DNA extraction (Day2)| DNA extraction]]
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|
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|*[[Media:20109_S13-M1Lec2_Runstadler.pdf | M1D2 Lecture]] <br>*[[Media:S13_M1D2-ANS.pdf | T/R Pre-Lab (green text added later)]]<br>*[[Media:M1D2_lab_SKH_final.pdf | W/F Pre-Lab]]<br>[[Media:20.109_SP13_Roldan.pdf | T/R WAC talk]]<br>[[Media:20.109S13INTROmpo.pdf | W/F WAC talk]]
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| 1
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| Thur/Fri Feb 14/15
| Thur/Fri Feb 14/15
| [http://web.mit.edu/be/people/runstadler.shtml JR]
| [http://web.mit.edu/be/people/runstadler.shtml JR]
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|  
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| [[User:Ian_Tay |Ian]]
| [[20.109(S13):PCR and paper discussion (Day3)| PCR and paper discussion]]
| [[20.109(S13):PCR and paper discussion (Day3)| PCR and paper discussion]]
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|
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|*[[Media:20109_S13-M1Lec3_Runstadler.pdf | M1D3 Lecture]] <br>*[[Media:S13_M1D3-ANS.pdf | T/R Pre-Lab]]<br>*[[Media:M1D3_lab_SKH_final.pdf | W/F Pre-Lab]]
|--
|--
|
|
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| Thur/Fri Feb 21/22
| Thur/Fri Feb 21/22
| [http://web.mit.edu/be/people/runstadler.shtml JR]
| [http://web.mit.edu/be/people/runstadler.shtml JR]
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|  
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| [[User:Ian_Tay |Ian]]
| [[20.109(S13):DNA cloning (Day4)| DNA cloning]]
| [[20.109(S13):DNA cloning (Day4)| DNA cloning]]
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|
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|*[[Media:20109_S13-M1Lec4_Runstadler.pdf | M1D4 Lecture]] <br>*[[Media:S13_M1D4-ANS.pdf | T/R Pre-Lab]]<br>*[[Media:M1D4_SKH.pdf | W/F Pre-Lab]]
|--
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| 1
| 1
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| Tue/Wed Feb 26/27  
| Tue/Wed Feb 26/27  
| [http://web.mit.edu/be/people/runstadler.shtml JR]
| [http://web.mit.edu/be/people/runstadler.shtml JR]
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|  
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| [[User:Ian_Tay |Ian]]
| [[20.109(S13):DNA sequencing and primer analysis (Day5)| DNA sequencing and primer analysis]]
| [[20.109(S13):DNA sequencing and primer analysis (Day5)| DNA sequencing and primer analysis]]
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|
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|*[[Media:20109_S13-M1Lec5_Runstadler.pdf | M1D5 Lecture]] <br>*[[Media:S13_M1D5-ANS.pdf | T/R Pre-Lab]]<br>*[[Media:M1D5_SKH_Final.pdf | W/F Pre-Lab]]
|--
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| 1
| 1
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| Thur/Fri Feb 28/ Mar 1
| Thur/Fri Feb 28/ Mar 1
| [http://web.mit.edu/be/people/runstadler.shtml JR]
| [http://web.mit.edu/be/people/runstadler.shtml JR]
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|  
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| [[User:Ian_Tay |Ian]]
| [[20.109(S13):Journal club I (Day6)| Journal club I]]
| [[20.109(S13):Journal club I (Day6)| Journal club I]]
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|*[[Media:20109_S13-M1Lec6_Runstadler.pdf | M1D6 Lecture]]
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| 1
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| Tue/Wed Mar 5/6  
| Tue/Wed Mar 5/6  
| [http://web.mit.edu/be/people/runstadler.shtml JR]
| [http://web.mit.edu/be/people/runstadler.shtml JR]
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|  
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| [[User:Ian_Tay |Ian]]
| [[20.109(S13):Phylogenetic analysis (Day7)| Phylogenetic analysis]]
| [[20.109(S13):Phylogenetic analysis (Day7)| Phylogenetic analysis]]
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|
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|*[[Media:20109_S13-M1Lec7_Runstadler.pdf | M1D7 Lecture]] <br>*[[Media:S13_M1D7-ANS.pdf | T/R Pre-Lab]]<br>*[[Media:M1D7_SKH_Final.pdf | W/F Pre-Lab]]
|--
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| 1
| 1
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| [[User:Mark_Mimee |MM]]
| [[User:Mark_Mimee |MM]]
|[[20.109(S13):Design mutant (Day1)| Design mutant]]
|[[20.109(S13):Design mutant (Day1)| Design mutant]]
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|<br><font color = CC0000><b>Module 1 Draft Due</b></font color><br>
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|*[[Media:20109_S13-M2Lec1_Jasanoff.pdf | M2D1 Lecture]] <br>*[[Media:S13_M2D1-ANS.pdf | T/R Pre-Lab]]<br>*[[Media:M2D1_SKH_Final.pdf | W/F Pre-Lab]]<br><font color = CC0000><b>Module 1 Draft Due</b></font color><br>
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|[[User:Mark_Mimee |MM]]
|[[User:Mark_Mimee |MM]]
|[[20.109(S13):Site-directed mutagenesis (Day2)| Site-directed mutagenesis]]
|[[20.109(S13):Site-directed mutagenesis (Day2)| Site-directed mutagenesis]]
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|
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|*[[Media:20109_S13-M2Lec2_Jasanoff.pdf | M2D2 Lecture]] <br>*[[Media:S13_M2D2-ANS.pdf | T/R Pre-Lab]]<br>*[[Media:M2D2_SKH_Final.pdf | W/F Pre-Lab]]
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| 2
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| [[User:Mark_Mimee |MM]]
| [[User:Mark_Mimee |MM]]
|[[20.109(S13):Bacterial amplification of DNA (Day3)| Bacterial amplification of DNA]]
|[[20.109(S13):Bacterial amplification of DNA (Day3)| Bacterial amplification of DNA]]
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|
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|*[[Media:20109_S13-M2Lec3_Jasanoff.pdf | M2D3 Lecture]] <br>*<font color = CC0000><b>Module 1 Primer Summary Due</b></font color><br>*[[Media:S13_M2D3-ANS.pdf | T/R Pre-Lab]]<br>*[[Media:M2D3_SKH_Final.pdf | W/F Pre-Lab]]
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| 2
| 2
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|[[User:Mark_Mimee |MM]]
|[[User:Mark_Mimee |MM]]
|[[20.109(S13):Prepare expression system (Day4)| Prepare expression system]]
|[[20.109(S13):Prepare expression system (Day4)| Prepare expression system]]
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|
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|*[[Media:20109_S13-M2Lec4_Jasanoff.pdf | M2D4 Lecture]] <br>*[[Media:S13_M2D4-ANS.pdf | T/R Pre-Lab]]<br>*[[Media:M2D4_SKH_Final.pdf | W/F Pre-Lab]]
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| [[User:Mark_Mimee |MM]]
| [[User:Mark_Mimee |MM]]
|[[20.109(S13):Induce protein and evaluate DNA (Day5)| Induce protein and evaluate DNA]]
|[[20.109(S13):Induce protein and evaluate DNA (Day5)| Induce protein and evaluate DNA]]
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|*[[Media:20109_S13-M2Lec5_Jasanoff.pdf | M2D5 Lecture]] <br>*[[Media:S13_M2D5-ANS.pdf | T/R Pre-Lab]]<br>*[[Media:M2D5_SKH_final.pdf | W/F Pre-Lab]]
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| 2
| 2
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| Thur/Fri Apr 4/5
| Thur/Fri Apr 4/5
| [http://web.mit.edu/be/people/jasanoff.shtml AJ]  
| [http://web.mit.edu/be/people/jasanoff.shtml AJ]  
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|
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|[[User:Mark_Mimee |MM]]
|[[20.109(S13):Purify protein (Day6)| Purify protein]]
|[[20.109(S13):Purify protein (Day6)| Purify protein]]
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|<br><font color = CC0000><b>Module 1 Revision Due</b></font color><br>
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|*[[Media:20109_S13-M2Lec6_Jasanoff.pdf | M2D6 Lecture]] <br>*[[Media:S13_M2D6-ANS.pdf | T/R Pre-Lab]]<br>*[[Media:M2D6_SKH.pdf | W/F Pre-Lab]]<br><font color = CC0000><b>Module 1 Revision Due</b></font color><br>
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| 2
| 2
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| [[User:Mark_Mimee |MM]]
| [[User:Mark_Mimee |MM]]
|[[20.109(S13):Characterize protein expression (Day7)| Characterize protein expression]]
|[[20.109(S13):Characterize protein expression (Day7)| Characterize protein expression]]
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|
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|*[[Media:20109_S13-M2Lec7_Jasanoff.pdf | M2D7 Lecture]] <br>*[[Media:S13_M2D7-ANS.pdf | T/R Pre-Lab]]<br>*[[Media:M2D7_SKH_Final.pdf | W/F Pre-Lab]]
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|[[User:Mark_Mimee |MM]]
|[[User:Mark_Mimee |MM]]
|[[20.109(S13):Assess protein function (Day8)| Assess protein function]]
|[[20.109(S13):Assess protein function (Day8)| Assess protein function]]
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|*[[Media:20109_S13-M2Lec8_Jasanoff.pdf | M2D8 Lecture]] <br>*[[Media:S13_M2D8-ANS.pdf | T/R Pre-Lab]]<br>*[[Media:M2D8_SKH_Final.pdf | W/F Pre-Lab]]
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| [[20.109(S13):Design experiment (Day1)| Design experiment]]
| [[20.109(S13):Design experiment (Day1)| Design experiment]]
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| *[[Media:20109_S13-M3Lec1_Stachowiak.pdf | M3D1 Lecture]] <br>*[[Media:S13_M3D1-ANS.pdf | T/R Pre-Lab]]<br>*[[Media:M3D1_SKH_Final.pdf | W/F Pre-Lab]]
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| [[20.109(S13):Initiate cell culture (Day2)| Initiate cell culture]]
| [[20.109(S13):Initiate cell culture (Day2)| Initiate cell culture]]
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| <br><font color = CC0000><b>Module 2 Report Due MONDAY APRIL 22 by 5 pm for all.</b></font color><br>
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| *[[Media:20109_S13-M3Lec2_Stachowiak.pdf | M3D2 Lecture]] <br><font color = CC0000><b>Module 2 Report Due MONDAY APRIL 22 by 5 pm for all.</b></font color><br>
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| Thur/Fri Apr 25/26
| Thur/Fri Apr 25/26
| [[User:AgiStachowiak | ANS]]
| [[User:AgiStachowiak | ANS]]
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| *[[Media:20109_S13-M3Lec3_Stachowiak.pdf | M3D3 Lecture]] <br>
| [[20.109(S13):Testing cell viability (Day3)| Testing cell viability]]
| [[20.109(S13):Testing cell viability (Day3)| Testing cell viability]]
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| [[20.109(S13):Preparing cells for analysis (Day4)| Preparing cells for analysis]]
| [[20.109(S13):Preparing cells for analysis (Day4)| Preparing cells for analysis]]
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| *[[Media:20109_S13-M3Lec4_Stachowiak.pdf | M3D4 Lecture]] <br>*[[Media:S13_M3D4-ANS.pdf | T/R Pre-Lab]]<br>* [[Media:M3D4_SKH_Final.pdf | W/F Pre-Lab]]
|--
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| [[20.109(S13):Initiating transcript and protein assays (Day5)| Initiating transcript and protein assays]]
| [[20.109(S13):Initiating transcript and protein assays (Day5)| Initiating transcript and protein assays]]
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| *[[Media:20109_S13-M3Lec5_Stachowiak.pdf | M3D5 Lecture]] <br>*[[Media:S13_M3D5-ANS.pdf | T/R Pre-Lab]]<br>* [[Media:M3D5_SKH_Final.pdf | W/F Pre-Lab]]
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| [[20.109(S13):Transcript-level analysis (Day6)| Transcript-level analysis]]
| [[20.109(S13):Transcript-level analysis (Day6)| Transcript-level analysis]]
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| *[[Media:20109_S13-M3Lec6_Stachowiak.pdf | M3D6 Lecture]] <br>*[[Media:S13_M3D6-ANS.pdf | T/R Pre-Lab]]<br>* [[Media:M3D6_SKH_Final.pdf | W/F Pre-Lab]]
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| [[20.109(S13):Protein-level and wrap-up analysis (Day7)| Protein-level and wrap-up analysis]]
| [[20.109(S13):Protein-level and wrap-up analysis (Day7)| Protein-level and wrap-up analysis]]
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| <br><font color = CC0000><b>Module 3 Summary Due</b></font color><br>
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| Lecture: [http://openwetware.org/images/d/d5/Mod4_presentations.pdf on Atissa's page] <br>*[[Media:S13_M3D7-ANS.pdf | T/R Pre-Lab]]<br>* [[Media:M3D7_SKH_Final.pdf | W/F Pre-Lab]]<br><font color = CC0000><b>Module 3 Summary Due</b></font color><br>
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| No lab session. Evaluations during lecture, then celebratory lunch, room/time TBD
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| No lab session. Meet in '''56-614''' from 11am-1pm: feedback/discussion about class, then celebratory lunch etc.
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</center>
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<br style="clear:both;"/>
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===Google calendar view===
 +
 +
I have decided to invite you all to the calendar instead of embedding it here, due to color-coding of assignments not being transferred upon embedding. Please let me know if you did not receive an invitation.
 +
 +
So far quiz dates and major assignments are included. Soon dates for lab notebooks and reflections will be included, along with links to homework assignments.
 +
 +
Correction: I will embed (for those who want privacy), and also invite (for those who want to use their gmail accounts).
 +
 +
<html><iframe src="https://www.google.com/calendar/embed?src=89c4e1q4e1kcncrq5s08qrqk9o%40group.calendar.google.com&ctz=America/New_York" style="border: 0" width="800" height="600" frameborder="0" scrolling="no"></iframe> </html>

Current revision

20.109(S13): Laboratory Fundamentals of Biological Engineering

Home        Schedule Spring 2013        Assignments       
DNA Engineering        Protein Engineering        Cell Engineering              

Table view with links

MODULE DAY DATE LECTURER TA LAB NOTES
Tue/Wed Feb 5/6 ANS Orientation * Introductory Lecture (PDF)
* Intro Pre-Lab, T/R
* Intro Pre-Lab, W/F
1 1 Thur/Fri Feb 7/8 JR Ian Context-setting and primer design * M1D1 Lecture
* T/R Pre-Lab
* W/F Pre-Lab
1 2 Tue/Wed Feb 12/13 JR Ian DNA extraction * M1D2 Lecture
* T/R Pre-Lab (green text added later)
* W/F Pre-Lab
T/R WAC talk
W/F WAC talk
1 3 Thur/Fri Feb 14/15 JR Ian PCR and paper discussion * M1D3 Lecture
* T/R Pre-Lab
* W/F Pre-Lab
President's Day Feb 18 No lab Feb 19 or Feb 20
1 4 Thur/Fri Feb 21/22 JR Ian DNA cloning * M1D4 Lecture
* T/R Pre-Lab
* W/F Pre-Lab
1 5 Tue/Wed Feb 26/27 JR Ian DNA sequencing and primer analysis * M1D5 Lecture
* T/R Pre-Lab
* W/F Pre-Lab
1 6 Thur/Fri Feb 28/ Mar 1 JR Ian Journal club I * M1D6 Lecture
1 7 Tue/Wed Mar 5/6 JR Ian Phylogenetic analysis * M1D7 Lecture
* T/R Pre-Lab
* W/F Pre-Lab
1 8 Thur/Fri Mar 7/8 NO LECTURE TODAY Journal club II
2 1 Tue/Wed Mar 12/13 AJ MM Design mutant * M2D1 Lecture
* T/R Pre-Lab
* W/F Pre-Lab
Module 1 Draft Due
2 2 Thur/Fri Mar 14/15 AJ MM Site-directed mutagenesis * M2D2 Lecture
* T/R Pre-Lab
* W/F Pre-Lab
2 3 Tue/Wed Mar 19/20 AJ MM Bacterial amplification of DNA * M2D3 Lecture
*Module 1 Primer Summary Due
* T/R Pre-Lab
* W/F Pre-Lab
2 4 Thur/Fri Mar 21/22 AJ MM Prepare expression system * M2D4 Lecture
* T/R Pre-Lab
* W/F Pre-Lab
Spring Break Mar 25-29 No lab all week
2 5 Tue/Wed Apr 2/3 AJ MM Induce protein and evaluate DNA * M2D5 Lecture
* T/R Pre-Lab
* W/F Pre-Lab
2 6 Thur/Fri Apr 4/5 AJ MM Purify protein * M2D6 Lecture
* T/R Pre-Lab
* W/F Pre-Lab
Module 1 Revision Due
2 7 Tue/Wed Apr 9/10 AJ MM Characterize protein expression * M2D7 Lecture
* T/R Pre-Lab
* W/F Pre-Lab
2 8 Thur/Fri Apr 11/12 AJ MM Assess protein function * M2D8 Lecture
* T/R Pre-Lab
* W/F Pre-Lab
Patriot's Day April 15-16 No lab Apr 16 or Apr 17
3 1 Thur/Fri Apr 18/19 ANS Design experiment * M3D1 Lecture
* T/R Pre-Lab
* W/F Pre-Lab
3 2 Tue/Wed Apr 23/24 ANS Initiate cell culture * M3D2 Lecture
Module 2 Report Due MONDAY APRIL 22 by 5 pm for all.
3 3 Thur/Fri Apr 25/26 ANS * M3D3 Lecture
Testing cell viability
3 4 Tue/Wed Apr 30/May 1 ANS Preparing cells for analysis * M3D4 Lecture
* T/R Pre-Lab
* W/F Pre-Lab
3 5 Thur/Fri May 2/3 ANS Initiating transcript and protein assays * M3D5 Lecture
* T/R Pre-Lab
* W/F Pre-Lab
3 6 Tue/Wed May 7/8 ANS Transcript-level analysis * M3D6 Lecture
* T/R Pre-Lab
* W/F Pre-Lab
3 7 Thur/Fri May 9/10 ANS Protein-level and wrap-up analysis Lecture: on Atissa's page
* T/R Pre-Lab
* W/F Pre-Lab
Module 3 Summary Due
3 8 Tue/Wed May 14/15 ANS Student presentations
Thur May 16 No lab session. Meet in 56-614 from 11am-1pm: feedback/discussion about class, then celebratory lunch etc.


Google calendar view

I have decided to invite you all to the calendar instead of embedding it here, due to color-coding of assignments not being transferred upon embedding. Please let me know if you did not receive an invitation.

So far quiz dates and major assignments are included. Soon dates for lab notebooks and reflections will be included, along with links to homework assignments.

Correction: I will embed (for those who want privacy), and also invite (for those who want to use their gmail accounts).

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