The main features of GenoCAD can be organized into three main categories. •
Management of genetic sequences: The purpose of this group of features is to help users identify, within large collections of genetic parts, the parts needed for a project and to organize them in project-specific libraries. •
Genetic parts: Parts have a unique identifier, a name and a more general description. They also have a
DNA sequence. Parts are associated with a
grammar and assigned to a parts category such a
promoter,
gene, etc. •
Parts libraries: Collections of parts are organized in libraries. In some cases part libraries correspond to parts imported from a single source such as another
sequence database. In other cases, libraries correspond to the parts used for a particular design project. Parts can be moved from one library to another through a temporary storage area called the cart (analogous to e-commerce shopping carts). •
Searching parts: Users can search the parts database using the
Lucene search engine. Basic and advanced search modes are available. Users can develop complex queries and save them for future reuse. •
Importing/Exporting parts: Parts can be imported and exported individually or as entire libraries using standard file formats (e.g.,
GenBank,
tab delimited,
FASTA,
SBML). •
Combining sequences into genetic constructs: The purpose of this group of features is to streamline the process of combining genetic parts into designs compliant with a specific design strategy. •
Point-and-click design tool: This
wizard guides the user through a series of design decisions that determine the design structure and the selection of parts included in the design. •
Design management: Designs can be saved in the user
workspace. Design statuses are regularly updated to warn users of the consequences of editing parts on previously saved designs. •
Exporting designs: Designs can be exported using standard file formats (e.g.,
GenBank,
tab delimited,
FASTA). •
Design safety: Designs are protected from some types of errors by forcing the user to follow the appropriate design strategy. •
Simulation: Sequences designed in GenoCAD can be simulated to display chemical production in the resulting cell. •
User workspace: Users can personalize their
workspace by adding parts to the GenoCAD database, creating specialized libraries corresponding to specific design projects, and saving designs at different stages of development. ==Theoretical foundation==