SynBERC:MIT: Difference between revisions

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==Proposed topics==
Past and present research topics for synthetic biology working group lunches.  Please add to the list.


#Electronics device families (introduction by TK) - [[SynBERC:MIT/Calendar/2006-9-27]]
#Abstraction hierarchies
##Parts -> Devices -> Systems
##Biological layer model (AC)
#'''DEVICES''': Composability? Device family specification? Interfaces within families?  Interfaces across families?  Eventually parts datasheet?  Eventually standards?
##Transcriptional device families (RS and CAF) - [[SynBERC:MIT/Calendar/2006-10-4]], [[SynBERC:MIT/Calendar/2006-10-11]]
##Post-translational device families  (SS) - [[SynBERC:MIT/Calendar/2007-2-13]]
##Biosynthetic device families (KJP lab) - [[SynBERC:MIT/Calendar/2006-10-18]], [[SynBERC:MIT/Calendar/2006-10-25]]
##Ribozyme device families (AC) - [[SynBERC:MIT/Calendar/2007-1-10]], [[SynBERC:MIT/Calendar/2007-1-17]] and [[SynBERC:MIT/Calendar/2007-1-24]] and [[SynBERC:MIT/Calendar/2007-3-28]]
##Translation device families?
#'''PARTS''': [[SynBERC:MIT/Calendar/2007-2-6]]
##Terminators
##Coding regions
##RBSs
##Promoters
##Composability and characterization - [[SynBERC:MIT/Calendar/2006-11-01]]
#'''CHASSIS''': Why do we want different kinds?  What kinds?  What are the simplest systems that work?
##Minimal chassis
##Mesoplasma florum - [[SynBERC:MIT/Calendar/2006-12-13]]
##E. coli standard strain and rE. coli - [[SynBERC:MIT/Calendar/2006-12-6]]
##Yeast
##Power supply - [[SynBERC:MIT/Calendar/2006-11-15]]
##Vectors - [[SynBERC:MIT/Calendar/2007-1-31]]
#Synthesis technologies
##What is state of the art?
##What are the good ideas?
##How do we get more investment?
##Can the fabs constrain what people synthesize?
#What does the CAD tool look like? - [[SynBERC:MIT/Calendar/2007-7-18]], [[SynBERC:MIT/Calendar/2007-8-1]]
#Human practice
#Differentiation and cell to cell communication.  Development.  Programmed pattern formation.  (Arthur Lander, Radhika)
#[[Synthetic Biology:BioBricks/Standardization|Standards]] (also see talk page)
#Load issues
#*What demands on the chassis are of most concern to us? Replication, transcription, [[Endy:Translation demand|translation]], Enzyme activity?
#**Are we regularly placing high demands on the chassis with our existing systems?
#*What chassis responses to an applied demand are of relevance? Growth rate, protein synthesis capacity?
#**Can we specify a threshold demand level above which the chassis response is so severe as to render the our engineered systems inoperable? 
#Selection against our systems [[SynBERC:MIT/Calendar/2006-12-20]]
##e.g. IS elements are showing up in our devices!
#Statistics of codon pairs (UC Irvine folks)
#iGEM 2010 - [[SynBERC:MIT/Calendar/2006-11-08]]
#Registry 2.0 - [[SynBERC:MIT/Calendar/2007-6-20]]
#Publishing (with CS on Oct 20) - held separately
#Controlled transcriptional termination as an implementation for logic - Chris Anderson
#Designing enzymatic reactions by splitting catalytic activity and substrate specificity potentially by scaffolds - John Dueber? ask Adam Arkin for someone to talk about this
#What is the obvious list of things to do?
##Parts characterization
##How do we get basic tasks done?
#Experience with different parts: RBSs, promoters, terminators - Jen? Chris Anderson? Curt and Hal Alper
#Web of registries - Randy
#Repetitive sequences and potential for recombination - ask Graham Walker, someone in Philadelphia
#Registry of models - Barry and Vincent
#Bacterial counter and how you implement it - Tom or Gerry - [[SynBERC:MIT/Calendar/2007-5-30]]
#How do I get a computer inside my cell? - Tom
#Human practices - Michael Rossi
#Writing DNA - Maia, Farren?, Church lab, Adam Arkin, Sasha and polony sequencing - [[SynBERC:MIT/Calendar/2007-4-3]]
#Noncoding RNAs - Ron Breaker
#Materials - Angie Belcher, Julie Norville - [[SynBERC:MIT/Calendar/2007-5-8]]
#Education in SB - Natalie and Scot and Austin and Michael and Shawn? - [[SynBERC:MIT/Calendar/2007-3-20]], [[SynBERC:MIT/Calendar/2007-5-22]]
##Curriculum
##Workshop implementation
##Materials
##Bootcamp
#Security - are we ok with the current investments in biotechnology? - Drew, Gautam? Phil Sharp and Gerry Fink and Jonathan King and Noam Chomsky and Ed Hammond - [[SynBERC:MIT/Calendar/2007-6-6]], [[SynBERC:MIT/Calendar/2007-6-13]]
#*Must act in the absence of perfect knowledge
#Impact of big pharma and big ag and big energy on our field
#Inteins and Fran Perler from NEB - [[SynBERC:MIT/Calendar/2007-4-10]]
#Brian Baynes and Codon Devices - future of DNA synthesis technology
#Ownership, sharing and innovation - [[SynBERC:MIT/Calendar/2007-5-1]], [[SynBERC:MIT/Calendar/2007-9-26]]
##IP around DNA fabrication technology (synthesis and automated assembly)
##How do we incent contributions?  i.e. documentation of parts in the Registry
##Historical examples around IP
##SynBERC OSI model
##BBF work
#Bioenergy - [[SynBERC:MIT/Calendar/2007-5-15]]
#Please add your topic to the list.


==Room locations for Spring==
==Room locations for Spring==

Revision as of 10:17, 9 September 2010

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SynBERC Research @ MIT

Short summaries of MIT SynBERC research projects.

Lab Video Tours

MIT lab video tours

Synthetic Biology Working Group lunches

Current information about SBWG Lunches is located at SBWGLunches.

Information pre-2010 can be found at SynBERC:SBWGLunchesArchive.


Previous meetings

 


Room locations for Spring

Usually 32-D463 except for the following dates

  • May 7 - 68-180
  • May 28 - no room booked
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