Difference between revisions of "Spring 2014 Synthetic Biology"

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[[Category:CH391L_S13]]
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[[Category:CH391L_S14]]
 
==CH391L: Synthetic Biology (Spring 2014)==
 
==CH391L: Synthetic Biology (Spring 2014)==
  
−
Mondays 2-5 PM  MBB 2.456
+
Mondays 2-5 PM  MBB 2.456<br>
 
Unique #: 53230
 
Unique #: 53230
  
 
Instructors:
 
Instructors:
 
* Prof. Jeffrey Barrick <jbarrick AT cm DOT utexas PERIOD edu>
 
* Prof. Jeffrey Barrick <jbarrick AT cm DOT utexas PERIOD edu>
−
* Dr. Dennis Mishler <jbarrick AT cm DOT utexas PERIOD edu>
+
* Dr. Dennis Mishler <dennis PERIOD mishler AT gmail DOT com>
  
−
Course web page: The course web site on SynBioCyc.org will host course handouts, readings, and assignments.
+
Course web page: This course web site on SynBioCyc.org will host course handouts, readings, and assignments.
  
−
[[Media:CH391_S14_Syllabus.pdf|Course Syllabus]]
+
[http://www.synbiocyc.org/wiki/images/f/f0/CH391L_S14_Syllabus.pdf '''CH391L Spring 2014 Course Syllabus''']
  
−
Previous year's websites:
+
== Motivation ==
 +
 
 +
The purpose of this course is to become familiar with the techniques, biological parts, accomplishments, problems, and challenges of synthetic biology. For the most part, we will focus on ''E. coli'' and yeast.
 +
 
 +
Participants will be expected to individually contribute to SynBioCyc pages describing the history, development, and implementation details of engineered parts and organisms from the scientific literature. As the course progress, students will create a proposal as part of a group with specific experimental and modeling details for using synthetic biology to solve an existing problem with technological or societal impact.
 +
 
 +
== Grading and Assignments ==
 +
 
 +
Coursework will consist of in-class oral presentations on scientific papers or research proposals and a "written" component consisting of Wiki page edits on SynBioCyc. All participants in the course will be expected to provide feedback concerning the content of presentations and the content of Wiki pages.
 +
 
 +
[[CH391L/S14/WikiEditing|Instructions for Wiki Editing]]
 +
 
 +
[[CH391L/S14/Assignments|Class Assignments]]
 +
 
 +
[[CH391L/S14/TopicGradingRubric|Grading Rubric for Wiki Pages, Presentations, and Participation]]
 +
 
 +
[[CH391L/S14/FinalProjectRubric|Grading Rubric for Final Project]]
 +
 
 +
== Previous year's websites ==
 
* [http://openwetware.org/wiki/CH391L/S12 CH391L Synthetic Biology Topics (Spring 2012)]
 
* [http://openwetware.org/wiki/CH391L/S12 CH391L Synthetic Biology Topics (Spring 2012)]
 
* [http://openwetware.org/wiki/CH391L/S13 CH391L Synthetic Biology Topics (Spring 2013)]
 
* [http://openwetware.org/wiki/CH391L/S13 CH391L Synthetic Biology Topics (Spring 2013)]
  
−
Useful links:
+
== Topics ==
−
[http://2012.igem.org 2012 iGEM Competition]
+
−
[http://2013.igem.org 2013 iGEM Competition]
+
−
[http://2014.igem.org 2014 iGEM Competition]
+
  
−
[[CH391L/S14/Users | CH391L Users]]
+
* [[CH391L/S14/Users | List of CH391L/S14 Users]]
 +
* [[:Category:CH391L_S14 | Index of CH391L/S14 pages]]
 +
=== [[CH391L/S14/KeyPapers | Key Papers for the semester]]===
  
−
== Motivation ==
+
=== Week 1: Introduction ===
  
−
The purpose of this course is to become familiar with the techniques, biological parts, accomplishments, problems, and challenges of synthetic biology. For the most part, we will focus on ''E. coli'' and yeast. Participants will be expected to individually contribute to OWW pages describing the history, development, and implementation details of engineered parts and organisms from the scientific literature. Then, they will be expected to create a proposal as part of a group with specific experimental and modeling details for using synthetic biology to solve an outstanding problem with technological or societal impact.
+
* [[CH391L/S14/Introduction | Introduction to Synthetic Biology]]
  
−
== Assignments ==
+
===Week 2: What is a part?===
  
−
Coursework will consist of in-class oral presentations on scientific papers or research proposals and a "written" component consisting of Wiki page edits on OpenWetWare. All participants in the course will be expected to provide feedback concerning the content of presentations and the content of Wiki pages.
+
*[[CH391L/S14/BioBricks | BioBricks and Restriction Enzymes ('''Ella''')]]
 +
*[[CH391L/S14/BiologicalpartsandtheiGEMregistry | Biological Parts and the iGEM Registry ('''Alex''')]]
 +
*[[CH391L/S14/CAD systems | CAD systems '''(Gabo)''']]
  
−
[[CH391L/S13/WikiEditing|Instructions for Wiki Editing]]
+
===Week 3: Assembling the parts===
  
−
[[CH391L/S13/Assignments|Class Assignments]]
+
*[[CH391L/S14/Genome Synthesis | Synthetic Genome '''(Drew)''']]
 +
*[[CH391L/S14/Gibson Assembly | Gibson Assembly '''(Jordan)''']]
  
−
[[CH391L/S13/TopicGradingRubric|Grading Rubric for Wiki Pages, Presentations, and Participation]]
+
===Week 4: Methods of Part Creation, Prospecting, Selection, and Optimization===
 +
* SPEAKER:  Dr. Randy Hughes
 +
*[[CH391L/S14/GFP | GFP (Green Fluorescent Protein) '''(Mindy)''']]
 +
*[[CH391L/S14/Ancestral sequence | Ancestral Sequence Reconstruction '''(Cindy)''']]
  
−
[[CH391L/S13/FinalProjectRubric|Grading Rubric for Final Project]]
+
===Week 5: Parts I: Chassis===
 +
*SPEAKER:  Dr. Chris Yellman spoke about some of the methods used to create large DNA sequences in yeast and the advantages of this organism.
 +
Follow ups on GFP and Ancestral Sequence Reconstruction
  
−
== Topics ==
+
===Week 6: Parts II: Basics of Gene Expression===
 +
*2/24/2014
 +
*[[CH391L/S14/Directed protein evolution | Directed Protein Evolution '''(Nathan)''']]
 +
*[[CH391L/S14/SelectableCounterselectable | Selectable/Counter Selectable Markers ('''Ashley''')]]
 +
*[[CH391L/S14/Biocontainment | Biocontainment '''(Liz)''']]
  
−
== Topics ==
+
* SPEAKER:  Mike Hammerling and ncAA's  <---Moved to....
 +
Tinker Cell in class
  
−
=== Week 1: Introduction ===
+
Catch up day.
  
−
* [[CH391L/S13/Introduction | Introduction to Synthetic Biology]]
+
===Week 7: Parts III: Reporter Genes and Gene Regulation ===
 +
*[[CH391L/S14/StochasticGeneExpression | Stochastic Gene Expression and Noise (Chen) ]]
 +
*[[CH391L/S14/NucleicAcidsRiboswitches | Nucleic Acid Selections and Riboswitches (Dennis)]]
 +
*[[CH391L/S14/Spinach RNA | Spinach RNA (Drew)]]
 +
*[[CH391L/S14/Non-canonical Nucleotides | Non-canonical Nucleotides (Drew)]]
  
−
===Week 2: Making or finding parts/ethics/DIY Biology===
+
===Week 8: Parts IV: Environmental sensing and responses ===
 +
*[[CH391L/S14/QuorumSensing | Quorum Sensing (Mindy)]]
 +
*[[CH391L/S14/MotilityandTaxis | Motility and Taxis (Jorge)]]
 +
*[[CH391L/S14/ApplicationsofOptogenetics | Applications of Optogenetics (Ella)]]
  
−
*[[CH391L/S13/Ethics | Ethics of Synthetic Biology]]
+
===Week 9: Systems I: Circuits===
−
*[[CH391L/S13/DIY_SyntheticBiology | DIY Synthetic Biology]]
+
*[[CH391L/S14/Oscillation | Oscillation (Ashley)]]
−
*[[CH391L/S13/BioBricksAndRegistry | BioBricks and the Registry of Standard Biological Parts]]
+
*[[CH391L/S14/Cellcountingmemory | Cell Counting and memory (Alex)]]
 +
Tinker Cell II:  Group projects
  
−
===Week 3: DNA Assembly===
+
===Week 10: Genome Editing Techniques===
 +
*[[CH391L/S14/MAGE | MAGE (Multiplex Automated Genomic Engineering) (Jordan)]]
 +
*[[CH391L/S14/CRISPR | CRISPR (Gabo)]]
 +
*[[CH391L/S14/PolioGMODualUseEthics | GMOs, Polio Virus, Dual-Use research, and Ethics '''(two people:'''  one undergrad and one grad student) (XXXXXXX)]]  PART I
  
−
*[[CH391L/S13/CAD | CAD in Synthetic Biology]]
+
===Week 11: Systems II: Whole Organisms ===
−
*[[CH391L/S13/DnaAssembly | DNA Assembly: From Genes to Genomes]]
+
April 7th
 +
'''FINAL PROJECT OUTLINES DUE'''
 +
* SPEAKER: Mike Hammerling and Amber-less E. coli
  
−
===Week 4: Chassis Engineering and Making Parts===
+
*[[CH391L/S14/PolioGMODualUseEthics | GMOs, Polio Virus, Dual-Use research, and Ethics '''(two people:'''  one undergrad and one grad student)]]  PART II
  
−
*[[CH391L/S13/CleanGenomes | Minimal "Clean" Genomes]]
+
*[[CH391L/S14/SmallRNAs | Small RNAs in metabolic engineering (Jorge)]]
−
*[[CH391L/S13/In vitro Selection of FNAs | In vitro selection of FNAs]]
+
  
−
===Week 5: Finding and Improving Parts===
+
===Week 12: Systems III: Metabolic Engineering ===
−
*[[CH391L/S13/Ancestral Sequence Reconstruction | Ancestral Sequence Reconstruction]]
+
April 14th
−
*[[CH391L/S13/Metagenomics & Bioprospecting | Metagenomics & Bioprospecting]]
+
*[[CH391L/S14/NitrogenFixationRefactoring | Nitrogen Fixation Refactoring (Nathan)]]
 +
*[[CH391L/S14/Artemisinin | Artemisinin (Liz)]]
 +
*[[CH391L/S14/Bioremediation&caffeinatedcoli | Bioremediation and caffeinated coli (Chen)]]
  
−
===Week 6: Genetic Engineered Technologies===
+
===Week 13: Systems IV: Synthetic Ecologies and Miscellaneous Topics ===
−
*[[CH391L/S13/DirectedProteinEvolution | Directed Protein Evolution]]
+
April 21st
−
*[[CH391L/S13/Optogenetics | Optogenetics]]
+
'''FINAL PROJECTS DRAFTS DUE'''
−
*[[CH391L/S13/Riboswitches | Riboswitches]]
+
* SPEAKER:  Professor Hal Alper
 +
*[[CHE391L/S14/Ethics | Ethics (Ashley)]]
  
−
===Week 7: Communication and Containment ===
+
===Week 14: '''FINAL PROJECT PRESENTATIONS'''===
−
*[[CH391L/S13/QuorumSensing | Quorum Sensing]]
+
−
*[[CH391L/S13/Biocontainment | Biocontainment]]
+
−
*[[CH391L/S13/GeneticMarkers | Selectable Genetic Markers]]
+
  
−
===Week 8: Helpful Microbes ===
+
April 28th
−
*[[CH391L/S13/Algal Biofuels | Algal Biofuels]]
+
−
*[[CH391L/S13/Probiotics | Probiotics]]
+
  
−
===Week 9: Biomedical Applications===
+
AFTER....  May 13th: Revised final projects due
−
*[[CH391L/S13/Synthetic Meats and Organs|Synthetic Meats and Organs]]
+
−
*[[CH391L/S13/Phage Therapy | Phage Therapy]]
+
  
−
===Week 10: Math, Engineering, and Bubbles===
+
[The above date is not correct]
−
*[[CH391L/S13/Gas_Vesicles | Gas Vesicles]]
+
−
*[[CH391L/S13/Refactoring_Operons | Refactoring Operons]]
+
−
*[[CH391L/S13/DNA_Computing | DNA Computing]]
+
  
−
===Week 11: Miscellaneous I ===
+
'''It was announced in class and when meeting with Dennis that final projects are due on Friday, May 9th by 5:00pm.'''
−
*[[CH391L/S13/Genome Editing | Genome Editing]]
+
−
*[[CH391L/S13/Biologically Inspired Materials | Biologically Inspired Materials]]
+
  
−
===Week 12: Miscellaneous II ===
+
If there is some confusion, please e-mail Dennis.
−
*[[CH391L/S13/Cell Scaffolding and Printing | Cell Scaffolding and Printing]]
+
−
*[[CH391L/S13/Metabolic Engineering and Thermophiles | Metabolic Engineering and Thermophiles ]]
+
−
*[[CH391L/S13/Genetic Circuits | Genetic Circuits]]
+
  
−
===Week 13: Miscellaneous III ===
+
[Update: 5/7/2014, 2:30 pm]
−
*[[CHE391L/S13/Mechanosensing | Mechanosensing]]
+
−
*[[CHE391L/S13/Molecular Gastronomy | Molecular Gastronomy]]
+
  
−
=== Ideas for Topics ===
+
== Useful links ==
−
* Use [http://www.copasi.org/tiki-view_articles.php COPASI] to model circuits (like repressilator) and switches, changing parameters to tune behavior.
+
* [http://2012.igem.org 2012 iGEM Competition]
 +
* [http://2013.igem.org 2013 iGEM Competition]
 +
* [http://2014.igem.org 2014 iGEM Competition]

Latest revision as of 19:32, 7 May 2014

Contents

CH391L: Synthetic Biology (Spring 2014)

Mondays 2-5 PM MBB 2.456
Unique #: 53230

Instructors:

  • Prof. Jeffrey Barrick <jbarrick AT cm DOT utexas PERIOD edu>
  • Dr. Dennis Mishler <dennis PERIOD mishler AT gmail DOT com>

Course web page: This course web site on SynBioCyc.org will host course handouts, readings, and assignments.

CH391L Spring 2014 Course Syllabus

Motivation

The purpose of this course is to become familiar with the techniques, biological parts, accomplishments, problems, and challenges of synthetic biology. For the most part, we will focus on E. coli and yeast.

Participants will be expected to individually contribute to SynBioCyc pages describing the history, development, and implementation details of engineered parts and organisms from the scientific literature. As the course progress, students will create a proposal as part of a group with specific experimental and modeling details for using synthetic biology to solve an existing problem with technological or societal impact.

Grading and Assignments

Coursework will consist of in-class oral presentations on scientific papers or research proposals and a "written" component consisting of Wiki page edits on SynBioCyc. All participants in the course will be expected to provide feedback concerning the content of presentations and the content of Wiki pages.

Instructions for Wiki Editing

Class Assignments

Grading Rubric for Wiki Pages, Presentations, and Participation

Grading Rubric for Final Project

Previous year's websites

Topics

Key Papers for the semester

Week 1: Introduction

Week 2: What is a part?

Week 3: Assembling the parts

Week 4: Methods of Part Creation, Prospecting, Selection, and Optimization

Week 5: Parts I: Chassis

  • SPEAKER: Dr. Chris Yellman spoke about some of the methods used to create large DNA sequences in yeast and the advantages of this organism.

Follow ups on GFP and Ancestral Sequence Reconstruction

Week 6: Parts II: Basics of Gene Expression

  • SPEAKER: Mike Hammerling and ncAA's <---Moved to....

Tinker Cell in class

Catch up day.

Week 7: Parts III: Reporter Genes and Gene Regulation

Week 8: Parts IV: Environmental sensing and responses

Week 9: Systems I: Circuits

Tinker Cell II: Group projects

Week 10: Genome Editing Techniques

Week 11: Systems II: Whole Organisms

April 7th FINAL PROJECT OUTLINES DUE

  • SPEAKER: Mike Hammerling and Amber-less E. coli

Week 12: Systems III: Metabolic Engineering

April 14th

Week 13: Systems IV: Synthetic Ecologies and Miscellaneous Topics

April 21st FINAL PROJECTS DRAFTS DUE

Week 14: FINAL PROJECT PRESENTATIONS

April 28th

AFTER.... May 13th: Revised final projects due

[The above date is not correct]

It was announced in class and when meeting with Dennis that final projects are due on Friday, May 9th by 5:00pm.

If there is some confusion, please e-mail Dennis.

[Update: 5/7/2014, 2:30 pm]

Useful links

Retrieved from "https://www.synbiocyc.org/wiki/index.php?title=Spring_2014_Synthetic_Biology&oldid=97228"