Difference between revisions of "Talk:20.109(S13): Spring 2013 schedule"
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(New page: {{Template:20.109(S13)}} <div style="padding: 10px; width: 640px; border: 5px solid #99FF66;"> TEMP AGI <center> {| border=1px |'''MODULE''' |'''DAY''' |'''DATE''' |'''LECTURER''' |'''T...) |
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| − | <div style="padding: 10px; width: | + | <div style="padding: 10px; width: 540px; border: 5px solid #99FF66;"> |
| − | + | '''Lecture:''' T/R 11-12 (4-237) <br> | |
| + | '''Lab:''' T/R 1-5 or W/F 1-5 (56-322)<br> | ||
| + | '''People:''' Instructor and student web pages may be found at the linked [[20.109(S13):People | '''People''']] page. | ||
| + | |||
| + | Welcome to 20.109! For some of you this will be the first time in a research lab and for others it will not; either way, it is our goal to make this class a useful and fun introduction to experiments and techniques in biological engineering. There is not time enough to show you everything you’ll need to know if you go on to do research, but after taking this class you should feel confident and familiar with some fundamental experimental approaches and lab 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 report writing, notebook keeping, and publicly 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. | ||
| + | |||
| + | '''ASSIGNMENT OVERVIEW''' | ||
| + | |||
| + | You will perform three series of experiments (hereafter “modules”) over the course of the semester. The modules differ in both conceptual and technical content, and in the ways that your learning will be assessed. Links to the experiments and assignments are provided below. | ||
| + | |||
| + | Although your lab work will be done in pairs, <font color = CC0000>'''most assignments will be submitted individually (as summarized below) and should reflect your personal understanding.'''</font color> Please read the 20.109 [[20.109(S13):Statement on collaboration and integrity | '''statement on collaboration and integrity''']] for more detail about academic honesty in our class. You are encouraged to ask the teaching faculty any questions you have about what constitutes appropriate collaboration. | ||
| + | |||
| + | *Individual assignments (60% of grade): all lab notebooks, quizzes, and homeworks (unless otherwise noted in directions); Module 1 primer design summary and journal club presentation; Module 2 research article. | ||
| + | *Team assignments (40% of grade): Module 1 laboratory report (draft and revision), Module 3 data summary, and Module 3 research proposal. | ||
| + | |||
| + | We appreciate that time management can be a difficult skill to develop, and that learning takes place on many time-scales. However, assignments turned in at wildly disparate times create additional logistical burdens for the teaching faculty. <font color= CC0000><b>Therefore, late work (both daily and culminating assignments) will be penalized 1/3 of a letter grade for each day late and will not be accepted after a week.</b></font color> We strongly recommend that you plan ahead and space out your work when possible. | ||
| + | |||
| + | We will endeavor to provide equal access to subject 20.109 for students with disabilities, in accordance with the Americans with Disabilities Act (ADA) of 1990. Please see the teaching faculty as soon as possible regarding needed accommodations. | ||
| + | |||
| + | '''SCHEDULE''' | ||
<center> | <center> | ||
| Line 10: | Line 29: | ||
|'''DAY''' | |'''DAY''' | ||
|'''DATE''' | |'''DATE''' | ||
| − | |||
| − | |||
|'''LAB''' | |'''LAB''' | ||
| − | |||
|-- | |-- | ||
| − | | | + | | N/A 0 |
| | | | ||
| Tue/Wed Feb 5/6 | | Tue/Wed Feb 5/6 | ||
| − | |||
| − | |||
| [[20.109(S13):Lab tour | Orientation]] | | [[20.109(S13):Lab tour | Orientation]] | ||
| − | |||
|-- | |-- | ||
| − | | colspan=" | + | | colspan="4" | |
|-- | |-- | ||
| 1 | | 1 | ||
| 1 | | 1 | ||
| Thur/Fri Feb 7/8 | | Thur/Fri Feb 7/8 | ||
| − | |||
| − | |||
| [[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]] | ||
| − | |||
|-- | |-- | ||
| 1 | | 1 | ||
| 2 | | 2 | ||
| Tue/Wed Feb 12/13 | | Tue/Wed Feb 12/13 | ||
| − | |||
| − | |||
| [[20.109(S13):DNA extraction (Day2)| DNA extraction]] | | [[20.109(S13):DNA extraction (Day2)| DNA extraction]] | ||
| − | |||
|-- | |-- | ||
| 1 | | 1 | ||
| 3 | | 3 | ||
| Thur/Fri Feb 14/15 | | Thur/Fri Feb 14/15 | ||
| − | |||
| − | |||
| [[20.109(S13):PCR and paper discussion (Day3)| PCR and paper discussion]] | | [[20.109(S13):PCR and paper discussion (Day3)| PCR and paper discussion]] | ||
| − | |||
|-- | |-- | ||
| − | + | ! colspan="3" | President's Day Feb 18 | |
| − | + | ||
| − | ! colspan=" | + | |
| '''No lab Feb 19 or Feb 20''' | | '''No lab Feb 19 or Feb 20''' | ||
|-- | |-- | ||
| Line 57: | Line 59: | ||
| 4 | | 4 | ||
| Thur/Fri Feb 21/22 | | Thur/Fri Feb 21/22 | ||
| − | |||
| − | |||
| [[20.109(S13):DNA cloning (Day4)| DNA cloning]] | | [[20.109(S13):DNA cloning (Day4)| DNA cloning]] | ||
| − | |||
|-- | |-- | ||
| 1 | | 1 | ||
| 5 | | 5 | ||
| Tue/Wed Feb 26/27 | | Tue/Wed Feb 26/27 | ||
| − | |||
| − | |||
| [[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]] | ||
| − | |||
|-- | |-- | ||
| 1 | | 1 | ||
| 6 | | 6 | ||
| Thur/Fri Feb 28/ Mar 1 | | Thur/Fri Feb 28/ Mar 1 | ||
| − | |||
| − | |||
| [[20.109(S13):Journal club I (Day6)| Journal club I]] | | [[20.109(S13):Journal club I (Day6)| Journal club I]] | ||
| − | |||
|-- | |-- | ||
| 1 | | 1 | ||
| 7 | | 7 | ||
| Tue/Wed Mar 5/6 | | Tue/Wed Mar 5/6 | ||
| − | |||
| − | |||
| [[20.109(S13):Phylogenetic analysis (Day7)| Phylogenetic analysis]] | | [[20.109(S13):Phylogenetic analysis (Day7)| Phylogenetic analysis]] | ||
| − | |||
|-- | |-- | ||
| 1 | | 1 | ||
| 8 | | 8 | ||
| − | | Thur/Fri Mar 7/8 | + | | Thur/Fri Mar 7/8, '''No lecture today''' |
| − | + | ||
| − | + | ||
| [[20.109(S13):Journal club II (Day8)| Journal club II]] | | [[20.109(S13):Journal club II (Day8)| Journal club II]] | ||
| − | |||
|-- | |-- | ||
| − | | colspan=" | + | | colspan="4" | |
|-- | |-- | ||
| 2 | | 2 | ||
| 1 | | 1 | ||
| Tue/Wed Mar 12/13 | | Tue/Wed Mar 12/13 | ||
| − | + | |[[20.109(S13):Design mutant (Day1)| Design mutant]]<br><font color = CC0000><b>Module 1 Draft Due</b></font color><br> | |
| − | + | ||
| − | |[[20.109(S13):Design mutant (Day1)| Design mutant | + | |
| − | + | ||
|-- | |-- | ||
| 2 | | 2 | ||
| 2 | | 2 | ||
| Thur/Fri Mar 14/15 | | Thur/Fri Mar 14/15 | ||
| − | |||
| − | |||
|[[20.109(S13):Site-directed mutagenesis (Day2)| Site-directed mutagenesis]] | |[[20.109(S13):Site-directed mutagenesis (Day2)| Site-directed mutagenesis]] | ||
| − | |||
|-- | |-- | ||
| 2 | | 2 | ||
| 3 | | 3 | ||
| Tue/Wed Mar 19/20 | | Tue/Wed Mar 19/20 | ||
| − | + | |[[20.109(S13):Bacterial amplification of DNA (Day3)| Bacterial amplification of DNA]]<br><font color = CC0000><b>Module 1 Primer Summary Due</b></font color> | |
| − | + | ||
| − | |[[20.109(S13):Bacterial amplification of DNA (Day3)| Bacterial amplification of DNA | + | |
| − | + | ||
|-- | |-- | ||
| 2 | | 2 | ||
| 4 | | 4 | ||
| Thur/Fri Mar 21/22 | | Thur/Fri Mar 21/22 | ||
| − | |||
| − | |||
|[[20.109(S13):Prepare expression system (Day4)| Prepare expression system]] | |[[20.109(S13):Prepare expression system (Day4)| Prepare expression system]] | ||
| − | |||
|-- | |-- | ||
| − | + | ! colspan="3" | Spring Break Mar 25-29 | |
| − | + | ||
| − | ! colspan=" | + | |
| '''No lab all week''' | | '''No lab all week''' | ||
|-- | |-- | ||
| Line 136: | Line 109: | ||
| 5 | | 5 | ||
| Tue/Wed Apr 2/3 | | Tue/Wed Apr 2/3 | ||
| − | |||
| − | |||
|[[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]] | ||
| − | |||
|-- | |-- | ||
| 2 | | 2 | ||
| 6 | | 6 | ||
| Thur/Fri Apr 4/5 | | Thur/Fri Apr 4/5 | ||
| − | + | |[[20.109(S13):Purify protein (Day6)| Purify protein]]<br><font color = CC0000><b>Module 1 Revision Due</b></font color><br> | |
| − | + | ||
| − | |[[20.109(S13):Purify protein (Day6)| Purify protein | + | |
| − | + | ||
|-- | |-- | ||
| 2 | | 2 | ||
| 7 | | 7 | ||
| Tue/Wed Apr 9/10 | | Tue/Wed Apr 9/10 | ||
| − | |||
| − | |||
|[[20.109(S13):Characterize protein expression (Day7)| Characterize protein expression]] | |[[20.109(S13):Characterize protein expression (Day7)| Characterize protein expression]] | ||
| − | |||
|-- | |-- | ||
| 2 | | 2 | ||
| 8 | | 8 | ||
| Thur/Fri Apr 11/12 | | Thur/Fri Apr 11/12 | ||
| − | |||
| − | |||
|[[20.109(S13):Assess protein function (Day8)| Assess protein function]] | |[[20.109(S13):Assess protein function (Day8)| Assess protein function]] | ||
| − | |||
|-- | |-- | ||
| − | + | ! colspan="3" | Patriot's Day April 15-16 | |
| − | + | ||
| − | ! colspan=" | + | |
| '''No lab Apr 16 or Apr 17''' | | '''No lab Apr 16 or Apr 17''' | ||
|-- | |-- | ||
| − | | colspan=" | + | | colspan="4" | |
|-- | |-- | ||
| 3 | | 3 | ||
| 1 | | 1 | ||
| Thur/Fri Apr 18/19 | | Thur/Fri Apr 18/19 | ||
| − | |||
| − | |||
| [[20.109(S13):Design experiment (Day1)| Design experiment]] | | [[20.109(S13):Design experiment (Day1)| Design experiment]] | ||
| − | |||
|-- | |-- | ||
| 3 | | 3 | ||
| 2 | | 2 | ||
| Tue/Wed Apr 23/24 | | Tue/Wed Apr 23/24 | ||
| − | + | | [[20.109(S13):Initiate cell culture (Day2)| Initiate cell culture]]<br><font color = CC0000><b>Module 2 Report Due MONDAY APRIL 22 by 5 pm for all.</b></font color><br> | |
| − | + | ||
| − | | [[20.109(S13):Initiate cell culture (Day2)| Initiate cell culture | + | |
| − | + | ||
|-- | |-- | ||
| 3 | | 3 | ||
| 3 | | 3 | ||
| Thur/Fri Apr 25/26 | | Thur/Fri Apr 25/26 | ||
| − | |||
| − | |||
| [[20.109(S13):Testing cell viability (Day3)| Testing cell viability]] | | [[20.109(S13):Testing cell viability (Day3)| Testing cell viability]] | ||
| − | |||
|-- | |-- | ||
| 3 | | 3 | ||
| 4 | | 4 | ||
| Tue/Wed Apr 30/May 1 | | Tue/Wed Apr 30/May 1 | ||
| − | |||
| − | |||
| [[20.109(S13):Preparing cells for analysis (Day4)| Preparing cells for analysis]] | | [[20.109(S13):Preparing cells for analysis (Day4)| Preparing cells for analysis]] | ||
| − | |||
|-- | |-- | ||
| 3 | | 3 | ||
| 5 | | 5 | ||
| Thur/Fri May 2/3 | | Thur/Fri May 2/3 | ||
| − | |||
| − | |||
| [[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]] | ||
| − | |||
|-- | |-- | ||
| 3 | | 3 | ||
| 6 | | 6 | ||
| Tue/Wed May 7/8 | | Tue/Wed May 7/8 | ||
| − | |||
| − | |||
| [[20.109(S13):Transcript-level analysis (Day6)| Transcript-level analysis]] | | [[20.109(S13):Transcript-level analysis (Day6)| Transcript-level analysis]] | ||
| − | |||
|-- | |-- | ||
| 3 | | 3 | ||
| 7 | | 7 | ||
| Thur/Fri May 9/10 | | Thur/Fri May 9/10 | ||
| − | + | | [[20.109(S13):Protein-level and wrap-up analysis (Day7)| Protein-level and wrap-up analysis]]<br><font color = CC0000><b>Module 3 Summary Due</b></font color><br> | |
| − | + | ||
| − | | [[20.109(S13):Protein-level and wrap-up analysis (Day7)| Protein-level and wrap-up analysis | + | |
| − | + | ||
|-- | |-- | ||
| 3 | | 3 | ||
| 8 | | 8 | ||
| Tue/Wed May 14/15 | | Tue/Wed May 14/15 | ||
| − | |||
| − | |||
| [[20.109(S13):Student presentations (Day8)| Student presentations]] | | [[20.109(S13):Student presentations (Day8)| Student presentations]] | ||
| − | |||
| − | |||
| − | |||
|-- | |-- | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
|} | |} | ||
</center> | </center> | ||
| − | |||
Latest revision as of 13:48, 29 July 2015
Lecture: T/R 11-12 (4-237)
Lab: T/R 1-5 or W/F 1-5 (56-322)
People: Instructor and student web pages may be found at the linked People page.
Welcome to 20.109! For some of you this will be the first time in a research lab and for others it will not; either way, it is our goal to make this class a useful and fun introduction to experiments and techniques in biological engineering. There is not time enough to show you everything you’ll need to know if you go on to do research, but after taking this class you should feel confident and familiar with some fundamental experimental approaches and lab 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 report writing, notebook keeping, and publicly 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.
ASSIGNMENT OVERVIEW
You will perform three series of experiments (hereafter “modules”) over the course of the semester. The modules differ in both conceptual and technical content, and in the ways that your learning will be assessed. Links to the experiments and assignments are provided below.
Although your lab work will be done in pairs, most assignments will be submitted individually (as summarized below) and should reflect your personal understanding. Please read the 20.109 statement on collaboration and integrity for more detail about academic honesty in our class. You are encouraged to ask the teaching faculty any questions you have about what constitutes appropriate collaboration.
- Individual assignments (60% of grade): all lab notebooks, quizzes, and homeworks (unless otherwise noted in directions); Module 1 primer design summary and journal club presentation; Module 2 research article.
- Team assignments (40% of grade): Module 1 laboratory report (draft and revision), Module 3 data summary, and Module 3 research proposal.
We appreciate that time management can be a difficult skill to develop, and that learning takes place on many time-scales. However, assignments turned in at wildly disparate times create additional logistical burdens for the teaching faculty. Therefore, late work (both daily and culminating assignments) will be penalized 1/3 of a letter grade for each day late and will not be accepted after a week. We strongly recommend that you plan ahead and space out your work when possible.
We will endeavor to provide equal access to subject 20.109 for students with disabilities, in accordance with the Americans with Disabilities Act (ADA) of 1990. Please see the teaching faculty as soon as possible regarding needed accommodations.
SCHEDULE
| MODULE | DAY | DATE | LAB |
| N/A 0 | Tue/Wed Feb 5/6 | Orientation | |
| 1 | 1 | Thur/Fri Feb 7/8 | Context-setting and primer design |
| 1 | 2 | Tue/Wed Feb 12/13 | DNA extraction |
| 1 | 3 | Thur/Fri Feb 14/15 | PCR and paper discussion |
| President's Day Feb 18 | No lab Feb 19 or Feb 20 | ||
|---|---|---|---|
| 1 | 4 | Thur/Fri Feb 21/22 | DNA cloning |
| 1 | 5 | Tue/Wed Feb 26/27 | DNA sequencing and primer analysis |
| 1 | 6 | Thur/Fri Feb 28/ Mar 1 | Journal club I |
| 1 | 7 | Tue/Wed Mar 5/6 | Phylogenetic analysis |
| 1 | 8 | Thur/Fri Mar 7/8, No lecture today | Journal club II |
| 2 | 1 | Tue/Wed Mar 12/13 | Design mutant Module 1 Draft Due |
| 2 | 2 | Thur/Fri Mar 14/15 | Site-directed mutagenesis |
| 2 | 3 | Tue/Wed Mar 19/20 | Bacterial amplification of DNA Module 1 Primer Summary Due |
| 2 | 4 | Thur/Fri Mar 21/22 | Prepare expression system |
| Spring Break Mar 25-29 | No lab all week | ||
| 2 | 5 | Tue/Wed Apr 2/3 | Induce protein and evaluate DNA |
| 2 | 6 | Thur/Fri Apr 4/5 | Purify protein Module 1 Revision Due |
| 2 | 7 | Tue/Wed Apr 9/10 | Characterize protein expression |
| 2 | 8 | Thur/Fri Apr 11/12 | Assess protein function |
| Patriot's Day April 15-16 | No lab Apr 16 or Apr 17 | ||
| 3 | 1 | Thur/Fri Apr 18/19 | Design experiment |
| 3 | 2 | Tue/Wed Apr 23/24 | Initiate cell culture Module 2 Report Due MONDAY APRIL 22 by 5 pm for all. |
| 3 | 3 | Thur/Fri Apr 25/26 | Testing cell viability |
| 3 | 4 | Tue/Wed Apr 30/May 1 | Preparing cells for analysis |
| 3 | 5 | Thur/Fri May 2/3 | Initiating transcript and protein assays |
| 3 | 6 | Tue/Wed May 7/8 | Transcript-level analysis |
| 3 | 7 | Thur/Fri May 9/10 | Protein-level and wrap-up analysis Module 3 Summary Due |
| 3 | 8 | Tue/Wed May 14/15 | Student presentations |
