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Resources

Ethical, Legal, and Social Implications of Synthetic Biology:

The Synthetic Biology Project was established as an initiative of the Foresight & Governance Program of the Woodrow Wilson International Center for Scholars. The Project aims to foster informed public and policy discourse concerning the advancement of synthetic biology - an emerging interdisciplinary field that uses advanced science and engineering to make or re-design living organisms, such as bacteria, so they can carry out specific functions. The Synthetic Biology Project provides independent, rigorous analysis that can inform critical decisions affecting the research, commercialization and use of synthetic biology.

Repositories of Biological Parts:

The JBEI Registry serves as a database of biological "parts" (including proper (though not necessarily standardized) parts, but also plasmids, microbial strains, and most recently Arabidopsis seeds, in collaboration with the Feedstocks Division) and the information associated with them. The JBEI Registry provides advanced search features (such as BLAST sequence queries and field-specific filters), tracks the intellectual property and funding sources associated with each part, and (through web-services) facilitates access to parts distributed across multiple labs. Currently under development, access to machine-readable parts characterization data (of particular importance to BioCAD tools) will soon be available. In addition to the parts database, the platform also offers a suite of integrated tools that provide enhanced feature annotation and sequence editing capabilities (Vector Editor), as well as sequence validation automation. The JBEI Registry Platform software is open source and freely available.

The Registry is a continuously growing collection of genetic parts that can be mixed and matched to build synthetic biology devices and systems. Founded in 2003 at MIT, the Registry is part of the Synthetic Biology community's efforts to make biology easier to engineer. It provides a resource of available genetic parts to iGEM teams and academic labs.

Other:

OpenWetWare is an effort to promote the sharing of information, know-how, and wisdom among researchers and groups who are working in biology and biological engineering. OWW provides a place for labs, individuals, and groups to organize their own information and collaborate with others easily and efficiently. In the process, we hope that OWW will not only lead to greater collaboration between member groups, but also provide a useful information portal to our colleagues, and ultimately the rest of the world.

The BioBricks Foundation (BBF) is a not-for-profit organization founded by engineers and scientists from MIT, Harvard, and UCSF with significant experience in both non-profit and commercial biotechnology research. BBF encourages the development and responsible use of technologies based on BioBrick™ standard DNA parts that encode basic biological functions.

The BIOFAB: International Open Facility Advancing Biotechnology (BIOFAB) was founded in December 2009 as the world's first biological design-build facility. This professionally staffed public-benefit facility was initiated by a grant from the National Science Foundation (NSF) and is led by bioengineers from UC Berkeley and Stanford University. The BIOFAB is operated in partnership with Lawrence Berkeley National Laboratory (LBNL), the BioBricks Foundation (BBF), and the Synthetic Biology Engineering Research Center (SynBERC). BioFab projects will be designed to produce broadly useful collections of standard biological parts that can be made freely available to both academic and commercial users, while also enabling the rapid design and prototyping of genetic constructs needed to support specific needs of partner efforts such as SynBERC Testbeds.

Synthetic Biology Open Language Visual (SBOLv) is a graphical notation that supports biological device development. It provides a formal notation for describing the physical composition of basic parts into composite parts during the development of biological devices. It is targeted for use by biological engineers in forward engineering projects. It encourages and supports model-driven engineering.

With the rise of partification in synthetic biology, there needs to be a formal specification to describe standard biological parts, especially when designing complex devices. The specification needs to be both human-writable and human-readable, a language that raises the level of abstraction where bioengineers can work. Eugene is such a language. Engineering at the part level requires both flexibility and rigidity. Eugene allows the user to mix custom parts with predefined parts from established databases.

The BioCyc collection of Pathway/Genome Databases (PGDBs) provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms. BioCyc PGDBs are generated by software that predicts the metabolic pathway complements of completely sequenced organisms from their genome sequences. Furthermore, BioCyc PGDBs include the results of a number of other computational inference procedures applied to these genomes, including predictions of which genes code for missing enzymes in metabolic pathways, and predicted operons. The BioCyc Web site provides a suite of software tools for database searching and visualization, for omics data analysis, and for comparative genomics and comparative pathway questions.

Systematic construction of single gene knock out mutants of all genes/open reading frames (ORFs) including putative ones has been performed (Baba et al., 2003) by using the Wanner's method (Datsewnko and Wanner, 1997). The mutants are expected to be useful resources not only for the functional analysis of y-genes (genes of unknown functions) but also for the analysis of gene expression profiles based on DNA microarray and other methods. The collection will be termed the "Keio Collection" and will be freely distributed upon request when the construction is completed.

Since 1996, the Saccharomyces Genome Project has revealed the presence of more than 6,000 open reading frames (ORFs) in the S. cerevisiae genome. Approximately one third of these ORFs had no known function four years after their discovery. The goal of the Saccharomyces Genome Deletion Project was to generate as complete a set as possible of yeast deletion strains with the overall goal of assigning function to the ORFs through phenotypic analysis of the mutants.