http://measurebiology.org/w/index.php?title=20.109(F14):Module_2&feed=atom&action=history20.109(F14):Module 2 - Revision history2024-03-28T09:10:22ZRevision history for this page on the wikiMediaWiki 1.22.3http://measurebiology.org/w/index.php?title=20.109(F14):Module_2&diff=26406&oldid=prevMAXINE JONAS: 1 revision: Transfer 20.109(F14) to HostGator2015-07-29T14:02:35Z<p>1 revision: Transfer 20.109(F14) to HostGator</p>
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</td></tr></table>MAXINE JONAShttp://measurebiology.org/w/index.php?title=20.109(F14):Module_2&diff=26405&oldid=prevNkuldell: /* Module 2 */2014-09-04T14:13:51Z<p><span dir="auto"><span class="autocomment">Module 2</span></span></p>
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==Module 2==<br />
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'''Instructors:''' [http://openwetware.org/wiki/User:Shannon_K._Alford |Shannon Hughes], [http://openwetware.org/wiki/Natalie_Kuldell ], [http://openwetware.org/wiki/User:Noreen_L._Lyell | Noreen Lyell], [http://openwetware.org/wiki/User:AgiStachowiak | Agi Stachowiak]<br><br />
'''TA:''' [http://openwetware.org/wiki/User:Yongjin_Park | YongJin Park]<br><br />
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[[Image:Image M2 20.109(F10).jpg||thumb|left|300 px]] Getting systems that work right out of the box is something that weve come to expect from electrical and mechanical engineers. New car? Get some gas, turn the key and off you go! New digital camera? Charge the battery and then start taking pictures! Biological engineersthough notable in their achievements---have lagged behind in the design and construction of novel systems that work in reliable, scalable, intuitive ways. Biology simply does not always perform as intended. Moreover, tools for the design and testing stages of engineered living systems are not yet robust or standard. In this experimental module well learn to design and tune a biological systemnamely the bacterial photography system in which bacteria serve as pixels in a picture. The picture, though remarkable, is slow to develop, limited to two colors, and low in contrast. To improve the system, well combine some powerful tools from biological science, namely genetics and evolution, with some of the fledgling tools in synthetic biology such as abstraction and standardization of biological parts, to improve and extend the performance of the bacterial photography system. In the process we may also learn something new about the natural systems upon which the engineered one is built. <br />
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[http://www.nature.com/nature/journal/v438/n7067/full/nature04405.html link to bacterial photography paper]<br><br />
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==Lablinks: day by day==<br />
[[20.109(F14): Mod 2 Day 1 Testing an engineered biological system | Day 1: Testing an engineered biological system ]]<br><br />
[[20.109(F14): Mod 2 Day 2 Measuring system performance | Day 2: Measuring system performance ]]<br><br />
[[20.109(F14): Mod 2 Day 3 Tools for system engineering | Day 3: Tools for system engineering ]]<br><br />
[[20.109(F14): Journal Club I| Day 4: Journal Club I]] <br><br />
[[20.109(F14): Mod 2 Day 5 Assessing re-tuned system | Day 5: Assessing re-tuned system ]]<br><br />
[[20.109(F14): Mod 2 Day 6 Readouts of DNA, Protein| Day 6: Readout DNA ]]<br><br />
[[20.109(F14): Mod 2 Day 7 Readout of Protein| Day 7: Readout Protein]]<br><br />
[[20.109(F14):Journal club II (Day8)| Day 8: Journal Club II]]<br><br />
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==Assignments==<br />
[[20.109(F14): System engineering research article| Research Article]]<br><br />
*[[20.109(F14): System engineering research article| Guidelines for this assignment]]<br><br />
*[[Media:How I grade your Research Articles.pdf| Evaluation rubric (PDF download)]]<br />
[[20.109(F14): Journal Club Presentations| Journal Club Presentation, M2D4 or M2D8]]<br><br />
*[[20.109(F14):Guidelines for oral presentations| Guidelines for this assignment]]<br><br />
*[[Media: 20109_Rubric-Oral-Jclub_S12.pdf| Evaluation rubric (PDF download)]]<br />
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==Useful sequence files==<br />
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[[Media:PCph8.str| pCph8]]<br><br />
[[Media:Cph8 ORF seq.docx| Cph8 ORF: sequence]]<br><br />
[[Media:Cph8Translation.pdf| Cph8 ORF: translated]]<br><br />
[[Media:KPLibrary 2014.xlsx| KP mutant library]]<br><br />
[[Media:466-NO296.seq| WT photography DNA, sequenced with NO296]]<br />
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==Notes for Teaching Faculty==<br />
[[20.109(F14): TA notes for module 2| TA notes, mod 2]]</div>Nkuldell