SynBioFromLeukipposInstitute

Biological design principles for synthetic biology
by Agapakis, Christina Maria, Ph.D., HARVARD UNIVERSITY, 2011, 245 pages; 3462459

Abstract:

The ability to rationally design biological systems holds tremendous promise for applications in medicine, manufacturing, energy, and the environment. As biological complexity and evolution can pose threats to the ease and stability of an engineering approach, emerging principles of biological design have urged abstraction and standardization of biological modules with defined functions. However, the power of biology as a design substrate lies first and foremost in the rich diversity and complexity of evolved biological systems. Instead of flattening and eliminating such diversity, can we instead employ our ever-deepening understanding of processes that drive diversity and evolutionary change as tools for synthetic biology design? This dissertation explores several such design principles and platforms for synthetic biology--protein domains that transfer high-energy electrons, cyanobacteria, plants, and cheese serve as physical platforms, while gene recombination, cellular cooperation, and personalization emerge as conceptual platforms. A more integrated and biological approach to synthetic biology has potential to lead to robust designs with multiple future applications.

Advisor: Silver, Pamela
School: HARVARD UNIVERSITY
Source: DAI-B 72/09, p. , Mar 2012
Source Type: Ph.D.
Subjects: Molecular biology; Biochemistry
Publication Number: 3462459

Has a nice chapter with SynBio resources:

"Synthetic Biology Resources http://www.istl.org/10-spring/internet1.html Provides links to various resources on the internet, including synthetic biology associations, centers of research, ethics, training and educational resources, and journals
Synthetic Biology.net http://www.syntheticbiology.net/index.aspx Portal for professionals in synthetic biology providing information on news, events, products, suppliers, etc., regarding synthetic biology
Synthetic Biology Project http://www.synbioproject.org/ Established as an initiative of the Foresight and Governance Program of Woodrow Wilson International Center for Scholars to foster informed public and policy discourse concerning the advancement of Synthetic Biology
BioBricks Foundation http://bbf.openwetware.org/ Encourages the development and responsible use of technologies based on BioBrick™ standard DNA parts to allow synthetic biologists to program living organisms in the same way a computer scientist can program a computer (see below)
Registry of Standard Biological Parts http://partsregistry.org/Main_Page A collection of genetic parts that can be mixed and matched to build synthetic biology devices and systems
SynBERC Synthetic Biology Engineering Research Center http://www.synberc.org/ Mission is to develop technologies to build biological components and assemble them into integrated systems to perform designed tasks, train engineers for biology, and educate the public on Synthetic Biology
BIOFAB http://www.biofab.org/ Biological design–build facility that aims to produce useful collections of standard biological parts available to academic and commercial users
JBEI Registry https://public.jbeir.org/ Also aims to provide standard DNA parts for Synthetic Biology
GeneDesign http://www.genedesign.org/ Set of web applications that provides public access to a nucleotide manipulation pipeline for Synthetic Biology
SynBioSS Designer http://synbioss.sourceforge.net/ Software suite for the generation, storage, retrieval, and quantitative simulation of synthetic biological networks"

Scientists have claimed that they can build some of the basic components for digital devices out of bacteria and DNA, suggesting a new generation of biological computing devices.