Difference between revisions of "20.109(F10):Module 2"

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==Module 2==
 
==Module 2==
  
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'''Instructors:''' [[Natalie Kuldell]], [[Nate Tedford]]
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'''Instructors:''' [http://openwetware.org/wiki/Natalie_Kuldell ], [http://openwetware.org/wiki/Nate_Tedford ]
  
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'''TA:'''
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'''TA:'''[http://openwetware.org/wiki/User:Mark_B._Smith | Mark Smith] <br>
  
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[[Image:Image M2 20.109(F10).jpg|200 px]]
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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.  
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Getting systems that work right out of the box is something that we’ve 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 engineers—though 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 we’ll learn to design and tune a biological system—namely 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, we’ll 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.  
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==Lablinks: day by day==
 
==Lablinks: day by day==
 
[[20.109(F10): Mod 2 Day 1 Testing an engineered biological system | Day 1: Testing an engineered biological system ]]<br>
 
[[20.109(F10): Mod 2 Day 1 Testing an engineered biological system | Day 1: Testing an engineered biological system ]]<br>
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[[20.109(F10): Mod 2 Day 2 Measuring system performance | Day 2: Measuring system performance ]]<br>
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[http://openwetware.org/wiki/20.109(F10):_Mod_2_Day_2_Measuring_system_performance  | Day 2: Measuring system performance ]<br>
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[[20.109(F10): Mod 2 Day 3 Tools for system engineering | Day 3: Tools for system engineering ]]<br>
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[http://openwetware.org/wiki/20.109(F10):_Mod_2_Day_3_Tools_for_system_engineering  | Day 3: Tools for system engineering ]<br>
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[[20.109(F10): Journal Club I| Day 4: Journal Club I]] <br>
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[http://openwetware.org/wiki/20.109(F10):_Journal_Club_I | Day 4: Journal Club I] <br>
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[[20.109(F10): Mod 2 Day 5 Assessing re-tuned system | Day 5: Assessing re-tuned system ]]<br>
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[http://openwetware.org/wiki/20.109(F10):_Mod_2_Day_5_Assessing_re-tuned_system  | Day 5: Assessing re-tuned system ]<br>
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[[20.109(F10): Mod 2 Day 6 Readouts of DNA, Protein| Day 6: Readout DNA, Protein ]]<br>
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[http://openwetware.org/wiki/20.109(F10):_Mod_2_Day_6_Readouts_of_DNA,_Protein | Day 6: Readout DNA ]<br>
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[[20.109(F10): Journal Club II| Day 7: Journal Club II]]<br>
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[[20.109(F10): Mod 2 Day 7 Readout of Protein| Day 7: Readout Protein]]<br>
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[http://openwetware.org/wiki/20.109(F10):_Journal_Club_I I| Day 8: Journal Club II]<br>
  
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[[20.109(F10):System engineering research article guidelines| System engineering research article guidelines]]<br>
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[[20.109(F10): System engineering research article| System engineering research article guidelines]]<br>
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==Useful sequence files==
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[[Media:PCph8 DNA sequence from Jeff Tabor.docx| pCph8 plasmid sequence]]<br>
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[[Media:Cph1-EnvZ DNAseq.docx| Cph8 ORF: DNA sequence]]<br>
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[[Media:Cph8 Translated.txt| Cph8 ORF: translated]]<br>
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[[Media:BuildingK+Library.xls| K+ mutant library]]<br>
  
 
==Notes for Teaching Faculty==
 
==Notes for Teaching Faculty==
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[[20.109(F09): TA notes for module 2| TA notes, mod 2]]<br>
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[http://openwetware.org/wiki/20.109(F10):_TA_notes_for_module_2 | TA notes, mod 2]
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[[20.109(F10): TA notes for module 2| TA notes, mod 2]]
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Latest revision as of 21:00, 28 July 2015


20.109(F10): Laboratory Fundamentals of Biological Engineering

Homepage imageidea F10.jpg

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DNA Engineering        System Engineering        Biomaterials Engineering              

Module 2

Instructors: [1], [2]

TA:| Mark Smith

Image M2 20.109(F10).jpg
Getting systems that work right out of the box is something that we���ve 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 engineers���though 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 we���ll learn to design and tune a biological system���namely 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, we���ll 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.


Lablinks: day by day

Day 1: Testing an engineered biological system
| Day 2: Measuring system performance
| Day 3: Tools for system engineering
| Day 4: Journal Club I
| Day 5: Assessing re-tuned system
| Day 6: Readout DNA
Day 7: Readout Protein
I| Day 8: Journal Club II

System engineering research article guidelines

Useful sequence files

pCph8 plasmid sequence
Cph8 ORF: DNA sequence
Cph8 ORF: translated
K+ mutant library

Notes for Teaching Faculty

| TA notes, mod 2
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