SC462 Elements of Synthetic Biology: Life 2.0 Fall 2014

Weekly outline

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  • General Information of the Course: SC462 Elements of Synthetic Biology: Life 2.0 Fall 2014

    Please register for the course on Moodle using the password sent to you on your email so that you can submit the assignments etc.

     

  • SC462_CoursePolicy File 368.2KB PDF document
  • Synthetic Biology Wiki URL
  • Bioengineering Wiki URL
  • International Genetically Engineered Machine (iGEM) Wiki URL
  • The Human Genome Project, 3D Animation URL
  • Programming of Life (video) URL
  • DNA - Episode 1 of 5: The Secret of Life - PBS Documentary URL
  • DNA - Episode 2 of 5 - Playing.God - PBS Documentary URL
  • DNA - Episode 3 of 5 - The Human Race - PBS Documentary URL
  • DNA - Episode 4 of 5 - Curing.Cancer - PBS Documentary URL
  • DNA - Episode 5 of 5 - Pandora's Box - PBS Documentary URL
  • James Watson: How we discovered DNA (TED TALK) URL
  • Secrets of the human genome - Eric Lander URL
  • Lectures: Tuesday (11:00 to 11:55), Wednesday (11:00 to 11:55) and Friday (11:00 to 11:55)

    Place: CEP 106

  • Leave Application From for SC462 Life 2.0 URL

    You must fill this if you are unable to come to lecture for reasons beyond your control.

  • News forum
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  28 July - 3 August

  • Introduction and History

    Only 1 Lecture on Friday (August 1, 2014) @ 11:00 to 11:55 (CEP 106) in first week

  • Craig Venter: On the verge of creating synthetic life URL
  • Synthetic Biology: A Primer Video URL
  • Programming Life: The Revolutionary Potential of Synthetic Biology URL
  • Synthetic Biology Explained URL
  • Synthetic Biology - Inventing the Future URL
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  4 August - 10 August

  • Robert Tjian (Berkeley/HHMI) Part 1: Gene regulation: An introduction URL
  • Robert Tjian (Berkeley/HHMI) Part 2: Gene regulation: Why so complex? URL
  • NOVA | Extract Your DNA | PBS URL
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  11 August - 17 August

  • Homework 1 (Due date August 24, 2014) File 53.6KB PDF document
  • Upload Homework 1 (Due Date: August 24, 2014) Assignment (2.2)
  • Introduction to Biology URL
  • Introduction to the Characteristics of life URL
  • Introduction to Genetics URL
  • Life in a Drop of Water URL
  • Proteins URL
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  18 August - 24 August

  • Introduction to Cells URL
  • Seven Wonders of the Microbe World (combined) URL
  • Introduction to Bacteria URL
  • Introduction to Viruses URL
  • How a Virus Works - Great Animation URL
  • Bacteriophage (eaters) video URL
  • Bacteriophage Lambda URL
  • Bacteriophage lambda lysis and lysogeny (video) URL
  • David Baltimore (Cal Tech) Part 1: Introduction to Viruses and HIV URL
  • David Baltimore (Cal Tech) Part 2: Why Gene Therapy Might be a Reasonable Tool for Attacking HIV URL
  • David Baltimore (Cal Tech) Part 3: The Grand Challenge: Engineering Immunity URL
  • How Did Ebola Evolve to Affect Humans? | Through the Wormhole with Morgan Freeman URL
  • Inside Story - Ebola: How far away is a cure? URL
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  25 August - 31 August

  • THE GHOST IN YOUR GENES: HORIZON URL
  • synthetic mosquitoes news URL
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  1 September - 7 September

  • SBOL Designer URL
  • Synthetic Biology Open Language (SBOL) URL
  • A Programming Language for Genetic Engineering of Living Cells URL
  • Software Tools Using SBOL URL
  • GenoCAD URL
  • Notes for lambda phage URL
  • Bacteriophage (Reading material) URL
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  8 September - 14 September

  • Homework 2 (Due date September 14, 2014) File 43.1KB PDF document
  • Homework 2 Upload (September 14, 2014) Assignment (2.2)
  • Construction of a genetic toggle switch in Escherichia coli (original paper) URL
  • A Mathematical Model of a Synthetically Constructed Genetic Toggle Switch URL
  • The genetic toggle switch online solver URL
  • WORLD’S FIRST GENETIC TOGGLE SWITCH URL
  • Modelling and Analysis of a Synthetic Bistable Genetic Switch (Reading Material) URL
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  15 September - 21 September

  • Fill up the form for the selection of project topic for SC462 URL
  • Modular Languages for Systems and Synthetic Biology URL
  • Open Solving Library for ODEs URL
  • Artificial Biochemistry URL
  • Stochastic Pi Machine (SPIM) URL
  • An Introduction to the Pi-Calculus URL
  • Programming in the Pi-Calculus (A Tutorial) URL
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  22 September - 28 September

  • Project areas assigned for SC462 File
  • iGEM Software Page URL
  • A Visual Process Calculus for Biology URL
  • Gene Networks in pi-Calculus URL
  • Efficient, Correct Simulation of Biological Processes in the Stochastic Pi-calculus URL
  • A Compositional Approach to the Stochastic Dynamics of Gene Networks URL
  • Supplementary gene networks examples URL
  • Visual SPiM Tutorial URL
  • Examples in SPiM URL
  • Coupled Chemical Reactions in Stochastic Pi-calculus URL
  • The SPiM Language URL
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  29 September - 5 October

  • Presentation Date schedule File
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  6 October - 12 October

  • No Class on Friday (Oct 10, 2014) due to last minute change in the presentation schedule of team 1. Next presentation will be on October 14, 2014.

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  13 October - 19 October

  • Scribe Notes submission for the project presentation area- Deadline 20 Nov 2014 File
  • Sample Scribe Notes PDF File
  • Sample bib file to cite the references in latex
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  20 October - 26 October

  • Break (No Classes)

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  27 October - 2 November
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  3 November - 9 November
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  10 November - 16 November

  • No Classes (I am away)

  • Upload presentations (ppts) by November 16, 2014 Assignment (2.2)
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  17 November - 23 November

  • Upload Scribe Notes (latex, .bib file etc in zip folder):by Nov 20, 2014 Assignment (2.2)
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  24 November - 30 November

  • Final Exams Week

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  1 December - 7 December
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  8 December - 14 December