Difference between revisions of "Spring 2014 Synthetic Biology"

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(Created page with " * Ideas for topics ** Use [http://www.copasi.org/tiki-view_articles.php COPASI] to model circuits (like repressilator) and switches, changing parameters to tune behavior.")
 
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[[Category:CH391L_S13]]
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==CH391L: Synthetic Biology (Spring 2014)==
  
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* Ideas for topics
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Mondays 2-5 PM  MBB 2.456
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Unique #: 53230
 +
 
 +
Instructors:
 +
* Prof. Jeffrey Barrick <jbarrick AT cm DOT utexas PERIOD edu>
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* Dr. Dennis Mishler <jbarrick AT cm DOT utexas PERIOD edu>
 +
 
 +
Course web page: The course web site on SynBioCyc.org will host course handouts, readings, and assignments.
 +
 
 +
[[Media:CH391_S14_Syllabus.pdf|Course Syllabus]]
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Previous year's websites:
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* [http://openwetware.org/wiki/CH391L/S12 CH391L Synthetic Biology Topics (Spring 2012)]
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* [http://openwetware.org/wiki/CH391L/S13 CH391L Synthetic Biology Topics (Spring 2013)]
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Useful links:
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[http://2012.igem.org 2012 iGEM Competition]
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[http://2013.igem.org 2013 iGEM Competition]
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[http://2014.igem.org 2014 iGEM Competition]
 +
 
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[[CH391L/S14/Users | CH391L Users]]
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== Motivation ==
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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.
 +
 
 +
== 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 OpenWetWare. All participants in the course will be expected to provide feedback concerning the content of presentations and the content of Wiki pages.
 +
 
 +
[[CH391L/S13/WikiEditing|Instructions for Wiki Editing]]
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 +
[[CH391L/S13/Assignments|Class Assignments]]
 +
 
 +
[[CH391L/S13/TopicGradingRubric|Grading Rubric for Wiki Pages, Presentations, and Participation]]
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[[CH391L/S13/FinalProjectRubric|Grading Rubric for Final Project]]
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== Topics ==
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== Topics ==
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=== Week 1: Introduction ===
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* [[CH391L/S13/Introduction | Introduction to Synthetic Biology]]
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===Week 2: Making or finding parts/ethics/DIY Biology===
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*[[CH391L/S13/Ethics | Ethics of Synthetic Biology]]
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*[[CH391L/S13/DIY_SyntheticBiology | DIY Synthetic Biology]]
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*[[CH391L/S13/BioBricksAndRegistry | BioBricks and the Registry of Standard Biological Parts]]
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===Week 3: DNA Assembly===
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*[[CH391L/S13/CAD | CAD in Synthetic Biology]]
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*[[CH391L/S13/DnaAssembly | DNA Assembly: From Genes to Genomes]]
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===Week 4: Chassis Engineering and Making Parts===
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*[[CH391L/S13/CleanGenomes | Minimal "Clean" Genomes]]
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*[[CH391L/S13/In vitro Selection of FNAs | In vitro selection of FNAs]]
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===Week 5: Finding and Improving Parts===
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*[[CH391L/S13/Ancestral Sequence Reconstruction | Ancestral Sequence Reconstruction]]
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*[[CH391L/S13/Metagenomics & Bioprospecting | Metagenomics & Bioprospecting]]
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===Week 6: Genetic Engineered Technologies===
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*[[CH391L/S13/DirectedProteinEvolution | Directed Protein Evolution]]
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*[[CH391L/S13/Optogenetics | Optogenetics]]
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*[[CH391L/S13/Riboswitches | Riboswitches]]
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===Week 7: Communication and Containment ===
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*[[CH391L/S13/QuorumSensing | Quorum Sensing]]
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*[[CH391L/S13/Biocontainment | Biocontainment]]
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*[[CH391L/S13/GeneticMarkers | Selectable Genetic Markers]]
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===Week 8: Helpful Microbes ===
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*[[CH391L/S13/Algal Biofuels | Algal Biofuels]]
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*[[CH391L/S13/Probiotics | Probiotics]]
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===Week 9: Biomedical Applications===
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*[[CH391L/S13/Synthetic Meats and Organs|Synthetic Meats and Organs]]
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*[[CH391L/S13/Phage Therapy | Phage Therapy]]
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===Week 10: Math, Engineering, and Bubbles===
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*[[CH391L/S13/Gas_Vesicles | Gas Vesicles]]
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*[[CH391L/S13/Refactoring_Operons | Refactoring Operons]]
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*[[CH391L/S13/DNA_Computing | DNA Computing]]
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===Week 11: Miscellaneous I ===
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*[[CH391L/S13/Genome Editing | Genome Editing]]
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*[[CH391L/S13/Biologically Inspired Materials | Biologically Inspired Materials]]
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===Week 12: Miscellaneous II ===
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*[[CH391L/S13/Cell Scaffolding and Printing | Cell Scaffolding and Printing]]
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*[[CH391L/S13/Metabolic Engineering and Thermophiles | Metabolic Engineering and Thermophiles ]]
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*[[CH391L/S13/Genetic Circuits | Genetic Circuits]]
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===Week 13: Miscellaneous III ===
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*[[CHE391L/S13/Mechanosensing | Mechanosensing]]
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*[[CHE391L/S13/Molecular Gastronomy | Molecular Gastronomy]]
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=== Ideas for Topics ===
 
** Use [http://www.copasi.org/tiki-view_articles.php COPASI] to model circuits (like repressilator) and switches, changing parameters to tune behavior.
 
** Use [http://www.copasi.org/tiki-view_articles.php COPASI] to model circuits (like repressilator) and switches, changing parameters to tune behavior.

Revision as of 19:56, 30 December 2013

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 <jbarrick AT cm DOT utexas PERIOD edu>

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

Course Syllabus

Previous year's websites:

Useful links: 2012 iGEM Competition 2013 iGEM Competition 2014 iGEM Competition

CH391L Users

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 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.

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 OpenWetWare. 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

Topics

Topics

Week 1: Introduction

Week 2: Making or finding parts/ethics/DIY Biology

Week 3: DNA Assembly

Week 4: Chassis Engineering and Making Parts

Week 5: Finding and Improving Parts

Week 6: Genetic Engineered Technologies

Week 7: Communication and Containment

Week 8: Helpful Microbes

Week 9: Biomedical Applications

Week 10: Math, Engineering, and Bubbles

Week 11: Miscellaneous I

Week 12: Miscellaneous II

Week 13: Miscellaneous III

Ideas for Topics

    • Use COPASI to model circuits (like repressilator) and switches, changing parameters to tune behavior.
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