A computer-aided
design tool was created for genetic languages to guide the design of biological
systems known as GenoCAD, the
open-source software was developed by researchers at the Virginia
Bioinformatics Institute at Virginia Tech to help synthetic biologists capture
biological rules to engineer organisms that produce useful products or
health-care solutions from inexpensive, renewable materials.
GenoCAD helps researchers in the design of protein
expression vectors, artificial gene networks, and other genetic constructs,
essentially combining engineering approaches with biology.
Synthetic biologists have an increasingly large library of
naturally derived and synthetic parts at their disposal to design and build
living systems. These parts are the words of a DNA language and the
"grammar" a set of design rules governing the language.
GenoCAD is an open-source computer-assisted-design
(CAD) application for synthetic biology. The foundation of GenoCAD is to
consider DNA as a language to program synthetic biological systems. GenoCAD
includes a large database of annotated genetic parts which are the words of the
language. GenoCAD also includes design rules describing how parts should be
combined in genetic constructs. These rules are used to build a wizard
that guides users through the process of designing complex genetic constructs and
artificial gene networks. The same rules are used by the GenoCAD compiler to
maintain the integrity of existing constructs. GenoCAD provides users with data
import and export capabilities using standard formats (FASTA, GenBank, and tab-delimited
text) so that users' personal workspaces can be customized to meet their
specific needs. It has to be expressive enough to allow scientists to generate
a broad range of constructs, but it has to be focused enough to limit the
possibilities of designing faulty constructs.
"Just like software engineers need different languages like
HTML, SQL, or Java to develop different kinds of software applications,
synthetic biologists need languages for different biological
applications," said Jean Peccoud, investigator of the GenoCAD project.
"From its inception, we envisioned GenoCAD as a framework allowing users
to capture their expertise of a particular domain in languages that they could
use themselves or share with others."
The researchers said encapsulating current knowledge by defining
standards will become increasingly important as the number and complexity of
components engineered by synthetic biologists increases.
They propose that grammars are a first step toward the
standardization of a broad range of synthetic genetic parts that could be
combined to develop innovative products.
"Developing a grammar in GenoCAD is a little like writing a
review paper," Purcell said. "You start with the headings and you
progressively dig deeper in the details. At the end of the process, you have a
much better appreciation for what you know and what you don't know about a
particular domain."
Posted By:-
Bioinformatics Department
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