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Autodesk , a quirky software start-up in Marin County, north of San Francisco, rose to prominence in the early 1980s because of AutoCAD, its computer-aided design program that was intended for use on personal computers. Over the next decade, AutoCAD became the standard design tool for architects and engineers.

This week at the TED conference in Long Beach, Calif., the company will take the first public step toward translating its computer design approach, which has since spilled over from Hollywood to the Maker movement, into the emerging nanoscale world of synthetic biology and materials.

For the last two years, a small group of software engineers and molecular biologists have been developing a software system for designing at the molecular level at the company’s research laboratory in downtown San Francisco. At the TED conference, Autodesk will introduce “Project Cyborg,” a Web-based software platform for delivering a range of services like molecular modeling and simulation.

The company has quietly begun working with a small group of molecular biologists in the last year. It has not announced when it will commercialize the technology, but it envisions that scientists, engineers and even students and “citizen scientists” will soon be able to use the system on individual projects.

There are still many open questions that nanotechnology needs to surmount, ranging from viability to safety. Autodesk executives and the designers of Project Cyborg believe, however, that they can recreate the thriving commercial ecosystems that the company has now evolved in engineering design at a Lilliputian scale. They foresee nanorobots that will be able to attack cancers and other diseases and a new world of molecular materials, as well as a visualization system for an entire universe beyond the range of the unaided human eye.

“People are only now being introduced to the fact that this form of science is in fact design, and it has the same paradigms and patterns as designing a factory or designing a car, with different nouns and verbs,” said Jeff Kowalski, Autodesk’s chief technology officer. “That’s our objective – to understand how to take 30 years of technology to transform how design is done in the inert world and empower those who are designing in the living world.”

The company will introduce its new nanodesign software vision in two talks to be given by scientists who have been working with the Autodesk research lab. One will be delivered by Skylar Tibbits, an M.I.T. architect and computer scientist who is to discuss biomolecular self-assembly on Tuesday. Jessica Green, a University of Oregon ecologist, is to speak on Thursday about design at the molecular scale.

Autodesk took its first commercial step into biological design last year with a partnership with Organovo Holdings, a San Diego start-up that aims to manufacture human tissues and organs. Autodesk software will be used to control a so-called bioprinter being developed by Organovo. It will initially have pharmaceutical testing applications.

Autodesk is not alone in seeking to build nanoscale design tools, nor the first to try to commercialize molecular design.

Thomas Knight, an M.I.T electrical engineer, introduced the concept of biobricks in 2003. The idea has been to create a library of standard biological parts derived from specific DNA sequences. Ideally they would share a common “interface,” making it possible to use them to construct new biological systems.

A striking example of the potential of molecular design was announced in February 2012 by the Wyss Institute for Biologically Inspired Engineering at Harvard. Two scientists at the institute designed a robotic device from DNA that was intended to seek out specific cells and deliver anticancer therapeutics with remarkable precision. The nanoscale robot is shaped like a clamshell and designed to open when it reaches its target, releasing a specific molecule.

The Autodesk researchers acknowledge they are far from being able to sell commercially robust engineering tools for the nano world. “Right now we don’t even have the notion of digital prototyping in any mature way in biology,” said Carlos Olguin, head of the Autodesk Bio/Nano/Programmable Matter Group. “People really do all of this by trial and error.”

But the company is placing a significant bet that that will not always be the case. If Autodesk is right, it will be a tremendous vindication for K. Eric Drexler, an M.I.T.-trained engineer who in the 1970s began forecasting the emergence of a world engineered by nanoscale machines.