GenoCAD

is an open source

Open source

The term open source describes practices in production and development that promote access to the end product's source materials. Some consider open source a philosophy, others consider it a pragmatic methodology...

 web application

Web application

A web application is an application that is accessed over a network such as the Internet or an intranet. The term may also mean a computer software application that is coded in a browser-supported language and reliant on a common web browser to render the application executable.Web applications are...

 to design DNA construct

DNA construct

A DNA construct is an artificially constructed segment of nucleic acid that is going to be "transplanted" into a target tissue or cell...

s for genetic engineering

Genetic engineering

Genetic engineering, also called genetic modification, is the direct human manipulation of an organism's genome using modern DNA technology. It involves the introduction of foreign DNA or synthetic genes into the organism of interest...

 using a rule-based methodology. GenoCAD is also considered a Computer Assisted Design (CAD) application for synthetic biology

Synthetic biology

Synthetic biology is a new area of biological research that combines science and engineering. It encompasses a variety of different approaches, methodologies, and disciplines with a variety of definitions...

.

Features

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
    DNA sequence
    The sequence or primary structure of a nucleic acid is the composition of atoms that make up the nucleic acid and the chemical bonds that bond those atoms. Because nucleic acids, such as DNA and RNA, are unbranched polymers, this specification is equivalent to specifying the sequence of...
    
    . Parts are associated with a grammar
    Formal grammar
    A formal grammar is a set of formation rules for strings in a formal language. The rules describe how to form strings from the language's alphabet that are valid according to the language's syntax...
    
     and assigned to a parts category such a promoter, gene
    Gene
    A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
    
    , 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
    Sequence database
    In the field of bioinformatics, a sequence database is a large collection of computerized nucleic acid sequences, protein sequences, or other sequences stored on a computer...
    
    . 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
    Lucene
    Apache Lucene is a free/open source information retrieval software library, originally created in Java by Doug Cutting. It is supported by the Apache Software Foundation and is released under the Apache Software License....
    
     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., tab delimited, FASTA
    FASTA
    FASTA is a DNA and protein sequence alignment software package first described by David J. Lipman and William R. Pearson in 1985. Its legacy is the FASTA format which is now ubiquitous in bioinformatics.- History :...
    
    ).
• 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
    Wizard (software)
    A software wizard or setup assistant is a user interface type that presents a user with a sequence of dialog boxes that lead the user through a series of well-defined steps. Tasks that are complex, infrequently performed, or unfamiliar may be easier to perform using a 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
    Workspace
    Workspace is a term used in various branches of engineering and economic development.-Business development:Workspace refers to small premises provided, often by local authorities or economic development agencies, to help new businesses to establish themselves...
    
    . 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
    GenBank
    The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. This database is produced and maintained by the National Center for Biotechnology Information as part of the International Nucleotide Sequence...
    
    , tab delimited, FASTA
    FASTA
    FASTA is a DNA and protein sequence alignment software package first described by David J. Lipman and William R. Pearson in 1985. Its legacy is the FASTA format which is now ubiquitous in bioinformatics.- History :...
    
    ).
• User workspace: Users can personalize their workspace
  Workspace
  Workspace is a term used in various branches of engineering and economic development.-Business development:Workspace refers to small premises provided, often by local authorities or economic development agencies, to help new businesses to establish themselves...
  
   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

GenoCAD is rooted in the theory of formal languages. In particular, the design rules describing how to combine different kinds of parts form context-free grammar

Context-free grammar

In formal language theory, a context-free grammar is a formal grammar in which every production rule is of the formwhere V is a single nonterminal symbol, and w is a string of terminals and/or nonterminals ....

s.

External links

• GenoCAD.org
• Project page on SourceForge
  SourceForge
  SourceForge Enterprise Edition is a collaborative revision control and software development management system. It provides a front-end to a range of software development lifecycle services and integrates with a number of free software / open source software applications .While originally itself...
  
  .