Biological hardware description language

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January 2010:

  • present basic synthbio presentation to select audience at draper. identify ways which synthetic biology can further draper's biomed side.
  • contact profs Weiss and Densmore about possible PhD opportunities

October 2010: take GREs and prepare statement of intent. The statement of intent should be a one page summary of your thesis proposal.

December 2010: apply for grad schools


Ron Weiss, MIT: ask about possible PhD slot and permission to sit in on lectures in the spring

Natalie Kuldell, MIT: ask about possible PhD slot and permission to sit in on lectures in the spring

Doug Densmore, BU: ask about possible PhD slots

Schools to consider






Review Articles

Programming cells: towards an automated 'Genetic Compiler'

Genetic design: rising above the sequence

Genetic parts to program bacteria

The second wave of synthetic biology: from modules to systems

Rule based constraints for the construction of genetic devices

Current tools

TinkerCell: modular CAD tool for synthetic biology

Computational design of synthetic gene circuits with composable parts

Modular modeling of cellular systems with ProMoT/Diva

SYCAMORE—a systems biology computational analysis and modeling research environment

GenoCAD for iGEM: a grammatical approach to the design of standard-compliant constructs

Gene Designer: a synthetic biology tool for constructing artificial DNA segments


GeneDesign 3.0 is an updated synthetic biology toolkit



Systems Biology Markup Language

Main Page

SBML Software Summary

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

LibSBML: an API Library for SBML

Synthetic Biology Simulation Suite

Main Page

SynBioSS: the synthetic biology modeling suite

SynBioSS designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs