Harvard:SysBio 204/2016: Difference between revisions

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{{Template:Harvard:SysBio_204_blue|2015}}
 
==Course overview==
*A course focusing on the rational design, construction, and applications of nucleic acid and protein-based synthetic molecular and cellular machinery and systems. Students are mentored to produce substantial term projects.
*Intended for graduate students in Systems Biology, Biophysics, Engineering, Biology and related disciplines. No formal prerequisites. Projects are tailored to each student's strengths and interests.
*Website: http://sb204.net
*Poster: http://openwetware.org/images/e/e0/Sb204.2015.pdf
 
==Midterm and Final==
*There will be two midterms and one final project for this class
**Policy: strict submission deadline, we encourage you to submit your work the night before
**Midterm #1 due: 12pm Monday Oct. 5th (slides, video), and 12pm Monday Oct. 12th (report, sequences)
**Midterm #2 due: 12pm Monday Nov. 2nd (slides, video), and 12pm Monday Nov. 9th (report, sequences)
**Final project due: 12pm Monday Nov. 30th (slides), and 12pm Monday Dec. 7th (report, sequences)
**Method of submission: email slides and presentations to TA and submit them to Dropbox folder shared by TF
*[http://openwetware.org/images/5/5c/SB204_2015-Project-reformat.pdf Midterm and Final Projects (may be updated)]
 
==Logistics==
*Instructors: George Church, William Shih,  Pamela Silver,  Peng Yin
*Teaching Fellow: Josie Kishi (jkishi@g.harvard.edu)
*Meeting time: 2:30 - 4:00 PM, Mon/Wed, Fall 2015
*Location: Room 521, Wyss Institute, 3 Blackfan circle, Boston, 02115
*First class on Wednesday Sep 2nd.
*No exams
*Prerequisites: none
*Grading
**20% Participation
**40% Midterm projects
**40% Final project
* [https://canvas.harvard.edu/courses/6474 Harvard course site]
 
==Example topics for final design project==
*'''miRNA pattern recognition in eukaryotic cells'''
*'''Directed evolution of chemical sensors'''
*'''Nano-breadboards for probing electron transport in proteins'''
*'''Altered genetic codes and amino acid alphabets'''
*'''Modification of proteins for function in harsh environments'''
*'''Automatable assembly of large synthetic genes and circuits'''
*'''Synthetic biology of stem cells and epigenetic reprogramming pathways'''
*'''Structural re-engineering of adenoviruses'''
*'''Artificial chemotactic swimmers'''
*'''Nonequilibrium networks of nano-machines mimicking dynamic instability in the cytoskeleton'''
*'''Recombinase-based multi-state memory in bacteria'''
*'''Exosome manufacturing'''
*'''Self-assembled solar energy harvester based on bio-inorganic nano-antennae for uv-vis'''
*'''Systematic debugging of DNA labeling chemistries by atomic-resolution TEM imaging of DNA origami'''
*'''Transcriptional activation and repression through rational molecular design'''
*'''Tissue engineering scaffold nano-materials'''
*'''Programmable multistep chemical synthesis by templating on catalytic nanostructures'''
*'''Ultra-sensitive signal processing for synthetic biology'''
*'''Antibody 2.0'''
*'''Synthetic nanostructure - virus conjugates'''
*'''Replication of information in synthetic crystals'''
*'''Cheap large-scale production of protein or DNA-based materials'''
*'''Etc. Etc. Etc.'''
 
==Background Info and previous class projects==
*'''BPH242r 2008-2009''' http://openwetware.org/wiki/Biophysics_242r/2009 (Synthetic Biology)
*'''BPH242r 2010-2011''' http://openwetware.org/wiki/Harvard:Biophysics_242r/2011 (Biologically Inspired Molecular Engineering)
*'''SB204 2011-2012''' http://openwetware.org/wiki/Harvard:SysBio_204/2011
**[http://isites.harvard.edu/icb/icb.do?keyword=k83102 Harvard Course Site]
*'''SB204 2012-2013''' http://openwetware.org/wiki/Harvard:SysBio_204/2012
**[http://isites.harvard.edu/icb/icb.do?keyword=k87016 Harvard Course Site]
*'''SB204 2013-2014''' http://openwetware.org/wiki/Harvard:SysBio_204/2013
**[http://isites.harvard.edu/icb/icb.do?keyword=k98865 Harvard Course Site]
*'''SB204 2013-2014''' http://openwetware.org/wiki/Harvard:SysBio_204/2014
**[http://isites.harvard.edu/icb/icb.do?keyword=k106678 Harvard Course Site]

Revision as of 19:55, 20 August 2016

Systems Biology 204: Biomolecular Engineering and Synthetic Biology 2015

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Course overview

  • A course focusing on the rational design, construction, and applications of nucleic acid and protein-based synthetic molecular and cellular machinery and systems. Students are mentored to produce substantial term projects.
  • Intended for graduate students in Systems Biology, Biophysics, Engineering, Biology and related disciplines. No formal prerequisites. Projects are tailored to each student's strengths and interests.
  • Website: http://sb204.net
  • Poster: http://openwetware.org/images/e/e0/Sb204.2015.pdf

Midterm and Final

  • There will be two midterms and one final project for this class
    • Policy: strict submission deadline, we encourage you to submit your work the night before
    • Midterm #1 due: 12pm Monday Oct. 5th (slides, video), and 12pm Monday Oct. 12th (report, sequences)
    • Midterm #2 due: 12pm Monday Nov. 2nd (slides, video), and 12pm Monday Nov. 9th (report, sequences)
    • Final project due: 12pm Monday Nov. 30th (slides), and 12pm Monday Dec. 7th (report, sequences)
    • Method of submission: email slides and presentations to TA and submit them to Dropbox folder shared by TF
  • Midterm and Final Projects (may be updated)

Logistics

  • Instructors: George Church, William Shih, Pamela Silver, Peng Yin
  • Teaching Fellow: Josie Kishi (jkishi@g.harvard.edu)
  • Meeting time: 2:30 - 4:00 PM, Mon/Wed, Fall 2015
  • Location: Room 521, Wyss Institute, 3 Blackfan circle, Boston, 02115
  • First class on Wednesday Sep 2nd.
  • No exams
  • Prerequisites: none
  • Grading
    • 20% Participation
    • 40% Midterm projects
    • 40% Final project
  • Harvard course site

Example topics for final design project

  • miRNA pattern recognition in eukaryotic cells
  • Directed evolution of chemical sensors
  • Nano-breadboards for probing electron transport in proteins
  • Altered genetic codes and amino acid alphabets
  • Modification of proteins for function in harsh environments
  • Automatable assembly of large synthetic genes and circuits
  • Synthetic biology of stem cells and epigenetic reprogramming pathways
  • Structural re-engineering of adenoviruses
  • Artificial chemotactic swimmers
  • Nonequilibrium networks of nano-machines mimicking dynamic instability in the cytoskeleton
  • Recombinase-based multi-state memory in bacteria
  • Exosome manufacturing
  • Self-assembled solar energy harvester based on bio-inorganic nano-antennae for uv-vis
  • Systematic debugging of DNA labeling chemistries by atomic-resolution TEM imaging of DNA origami
  • Transcriptional activation and repression through rational molecular design
  • Tissue engineering scaffold nano-materials
  • Programmable multistep chemical synthesis by templating on catalytic nanostructures
  • Ultra-sensitive signal processing for synthetic biology
  • Antibody 2.0
  • Synthetic nanostructure - virus conjugates
  • Replication of information in synthetic crystals
  • Cheap large-scale production of protein or DNA-based materials
  • Etc. Etc. Etc.

Background Info and previous class projects

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