Harvard:SysBio 204/2012

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: Wed. Oct. 3, 12pm
  • Midterm #2 due: Mon. Oct. 22, 12pm
  • Final project due: Wed. Nov. 28, 2am
  • Method of submission: email TA your slides and presentations
• Midterm and Final Projects

Logistics

• Instructors: George Church, William Shih, Pamela Silver, Peng Yin
• Meeting time: 2 pm – 3:30 pm, Mon/Wed, Fall 2012
• 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

• 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 (Biologically Inspired Molecular Engineering)
  • 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.

Recent changes

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24 April 2019

			23:19		Desireegonzalez Week 12‎‎ (2 changes | history) . . (+601)‎ . . [Desireegonzalez‎ (2×)]
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			16:04		BIOL478/S19:Microarray Data Analysis‎‎ (10 changes | history) . . (+810)‎ . . [Kam D. Dahlquist‎ (10×)]
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					11:46 (cur | prev) . . (+656)‎ . . Kam D. Dahlquist (talk | contribs) (→‎Visualizing Your Gene Regulatory Network with GRNsight: add list of files)
					11:41 (cur | prev) . . (-19)‎ . . Kam D. Dahlquist (talk | contribs) (→‎Identifying regulatory transcription factors responsible for observed changes in gene expression (step 10): clarified a couple of things)
					11:38 (cur | prev) . . (+32)‎ . . Kam D. Dahlquist (talk | contribs) (→‎Visualizing Your Gene Regulatory Network with GRNsight: mention grid layout)
					11:36 (cur | prev) . . (-2)‎ . . Kam D. Dahlquist (talk | contribs) (→‎Comparing results with known data (step 7): elevating heading level)
					11:36 (cur | prev) . . (0)‎ . . Kam D. Dahlquist (talk | contribs) (→‎Clustering and GO Term Enrichment with stem (steps 7-8): changings step number)
					11:35 (cur | prev) . . (+7)‎ . . Kam D. Dahlquist (talk | contribs) (→‎Comparing results with known data: elevating level)
					11:34 (cur | prev) . . (-9)‎ . . Kam D. Dahlquist (talk | contribs) (→‎Clustering and GO Term Enrichment with stem (steps 7-8): change ASH1 to HMO1, uncomment YEASTRACT/GRNsight)

23 April 2019

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(User creation log) . . User account CoryCasikenquirm (talk | contribs) was created by Yar (talk | contribs) and password was sent by email ‎

			16:52		(Upload log)‎ . . [Angela C Abarquez‎ (2×)]
					16:52 . . Angela C Abarquez (talk | contribs) uploaded File:AA chemostat 2nutrient script.m.zip ‎(script MATLAB file)
					16:49 . . Angela C Abarquez (talk | contribs) uploaded File:AA chemostat 2nutrient dynamics.m.zip ‎(Matlab dynamics file)