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Systems Biology 204: Biomolecular Engineering and Synthetic Biology 2013

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Link to updated website for SysBio204 2014

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://synthetic-biology-class.net, http://sb204.net
  • Poster

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: October 2nd at noon
    • Midterm #2 due: October 22nd (EXTENDED to October 29th at noon)
    • Final project due: November 28 (UPDATED to midnight after Tuesday, 2013 Dec 3)
    • Method of submission: email TA your slides and presentations
  • Midterm and Final Projects


Logistics

  • Instructors: George Church, William Shih, Pamela Silver, Peng Yin
  • Teaching Fellow: Adam Marblestone
  • Meeting time: 2 pm – 3:30 pm, Mon/Wed, Fall 2013
  • Location: Room 521, Wyss Institute, 3 Blackfan circle, Boston, 02115
  • First class on Wednesday Sep 5th.
  • Location: CLSB521
  • No exams
  • Prerequisites: none
  • Grading
    • 20% Participation
    • 40% Midterm projects
    • 40% Final project
  • Harvard course site


Background Info and previous class projects


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.


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