Deepak Chandran

TL;DR: The Synthetic Biology Open Language (SBOL) is described, a proposed data standard for exchanging designs within the synthetic biology community that represents synthetic biology designs in a community-driven, formalized format for exchange between software tools, research groups and commercial service providers.

TL;DR: TinkerCell as mentioned in this paper is a visual modeling tool that supports a hierarchy of biological parts, each part consists of a set of attributes that define the part, such as sequence or rate constants.

TL;DR: The Antimony language provides a way for a researcher to use simple text statements to create, import, and combine biological models, allowing complex models to be built from simpler models, and provides a special syntax for the creation of modular genetic networks.

TL;DR: A number of tools can assist in modifying and understanding cellular metabolic networks, including metabolic reconstruction efforts, network visualization, nucleic acid and protein engineering, metabolic flux analysis, pathway prospecting, post-structural network analysis and culture optimization are presented.

TL;DR: The SBPkb is created as a publically accessible Semantic Web resource for synthetic biology, and RDF technology and SPARQL queries are used to retrieve candidate “promoter” parts that are known to be both negatively and positively regulated.