[ExI] Public access to NanoEngineer-1 development repos

Bryan Bishop kanzure at gmail.com
Thu Nov 25 01:22:46 UTC 2010


Hey all,

Some of you may remember NanoEngineer (ne-1), the first open-source nanotech
CAD program. Also, with DNA modeling capabilities much like caDNAno. The
first public release and source code was published in 2008. Now that Nanorex
has shut down, I have converted the subversion repository to git and the
14,000+ commits are now public.

view it here:
http://diyhpl.us/cgit/nanoengineer

or for the hardcore:
git clone git://diyhpl.us/nanoengineer

mailing list (for programmers/nanotech developers)
http://groups.google.com/group/nanoengineer-dev

irc channel: #hplusroadmap on freenode

=== Visuals ===

Renderings and visualization:
http://nanoengineer-1.com/content/index.php?option=com_content&task=view&id=36&Itemid=46

molecular machinery gallery:
http://nanoengineer-1.com/content/index.php?option=com_content&task=view&id=40&Itemid=50

giant poster on structural DNA nanotech:
http://www.somewhereville.com/rescv/nanorex_dnaposter_0_33_scaled.jpg
larger versions: http://www.somewhereville.com/?page_id=10

=== Historical deets ===

You can find remnants of Nanorex on the web here:
http://www.nanoengineer-1.com/

And the wiki (which may or may not be soon deprecated):
http://www.nanoengineer-1.net/mediawiki/index.php?title=Main_Page

Here are some of the original announcements from 2008:

"NanoEngineer-1 software for CAD/CAM with structural DNA"
http://nextbigfuture.com/2008/04/nanoengineer-1-software-for-cadcam-with.html

"Do-it-yourself nanotechnology objects from DNA"
https://www.foresight.org/d/nanodot/?p=2710

This was some of the original text from Nanorex describing what they were
doing:

"""
Our mission is to support the design and development of advanced nanosystems

Self-assembled atomically precise nanosystems hold great promise in many
areas, both experimental and practical. Among the products will be systems
that help researchers build more advanced systems. We expect structural DNA
nanotechnology to play a central role in next-generation nanosystems.

Our mission is to support the design and development of advanced nanosystems
through computational tools. In all areas of technology, tools for design
and modeling help researchers to solidify their ideas into concrete
representations and to evaluate and revise them. This speeds the cycle of
design, fabrication, and testing at the center of the development process.
Structural DNA nanotechnology (SDN) will be no exception.

DNA structures can provide frameworks for next-generation nanosystems

Three lines of research are converging to create a capability for systematic
design of complex, atomically precise nanosystems. SDN has a crucial role in
this prospective development.

Special structures

The first line of research is the development of a wide range of atomically
precise functional components -- organometallic complexes, magic-size
quantum dots, nanotubes and fibers, engineered surfaces, and so forth. These
have functions ranging from chemical catalysis to electro-optical
transduction to structural support. This wide range of functions, however,
is offset by a major limitation: each of these functional components is a
special structure, either unique or part of a small family, not a member of
a designable class of billions of possible structures. This limitation makes
it almost impossible to design components that will self-assemble to form
complex, atomically precise systems. By themselves, these special structures
are simply too constrained to provide the necessary diversity of selectively
complementary surfaces.

Engineered proteins

The second line of research is the development of polymers made from a
diverse set of monomers that fold to make specific 3D structures. Protein
engineering is the advanced technology of this sort, and it has progressed
to the point where researchers routinely design novel structures that are
more stable than those found in nature. Artificial and natural examples show
that proteins can perform a wide range of functions, and can bind proteins,
nucleic acids, and an enormous range of other atomically precise structures,
both biological and non-biological. Proteins therefore provide a solution to
the problem of assembling the special, highly functional structures
discussed above. Protein molecules can be effective structures: they have
strengths and stiffnesses like those of epoxies, polycarbonates, and other
engineering polymers. However, these useful properties are offset by a slow
design, fabrication, and testing cycle (several months) and by the small
size of individual proteins (a few nanometers). They are attractive as
components and linkers, but less attractive as a way to combine components
to make large systems.

Structural DNA

The third line is SDN itself, which now can be used to implement a large
growing range of structures on a scale of tens to thousands of nanometers.
Like proteins, but unlike the special, highly functional structures, DNA is
a modular system that can be used to make a set of structures of
combinatorial size, with billions of possible design choices for strands
just a few nanometers long. Unlike proteins, DNA structures can be made with
a fast design, fabrication, and testing cycle (no more than a few days, in
some instances), and they can easily be thousands of times larger in volume.
They can provide specific binding sites for proteins or DNA-tagged
structures, holding hundreds or thousands of components in specific spatial
geometries.

These lines of development are complementary, the first providing diverse
elements of high functionality, the second providing components that can
bind them precisely, and the third providing structures that can organize
them in large numbers to form complex patterns. The resulting ability to
build modular composite nanosystems opens the door to an as-yet unimaginable
range of experimental and practical applications. SDN plays a vital role in
this prospect: it is literally what holds it all together.
Structural DNA nanotechnology is a point of high leverage for computational
tools

DNA structures are a good target for computer-aided design tools. They are
regular enough that they can be designed and using relatively abstract
representations, yet complex enough that computer support for visualization
is essential. With DNA as a medium, designers can arrange and rearrange
parts in a systematic way, much as they would in designing conventional
macroscopic objects.

Special structures, by contrast, leave little scope for design, and while
proteins have enormous scope for design, the process has special
difficulties. Where a designer can rearrange DNA strands by following simple
rules, relying on the regularities of helical structure and paired bases, a
protein designer must use a computational search process to find
combinations of side chains that fit together. This makes even the simplest
design steps more difficult to plan and implement.

The development of modular composite nanosystems will require computational
support for designs that include special structures and proteins, and some
support may be possible at an early date. SDN design is the natural starting
point, however, and is a rich field in itself.

An open-source framework will enable collaborative development of software
tools

The growing SDN community has developed many software tools, and will
develop many more in the years to come. Nanorex is developing open-source
software that provides tools for visualization, modeling, and manipulation
of DNA structures, and that provides interfaces for integrating these
capabilities with existing and future software tools developed within the
SDN community.

Because the core software is open source (NanoEngineer-1 is under GPL), all
participants can be confident that it won't become expensive, and that any
team that is working to extend it must continue to satisfy the broader
community. Nanorex can't take down the project by failing, going bad, or
trying to squeeze money out of the software itself -- in the worst case, the
work would simply continue under new leadership.

Researchers will want to keep control of the tools they create, both to
ensure their quality and to get proper credit when they are used. These
tools can be treated as distinct open-source projects, giving researchers
full control of the content of software that appears under their names. User
interface conventions in NanoEngineer-1 will give clear credit to the
creator of a tool when it is used. Rather than absorbing contributions and
making them invisible, the project will offer researchers a new distribution
channel that can make their work better known, better supported, and more
widely used.

Our mission is to support the design and development of advanced
nanosystems, and we see SDN is a central part of that development. No single
research group or company could possibly provide all the necessary tools, so
the choice is whether to have a jumble of incompatible pieces of software,
each implementing a limited user interface, or to find a way to bring these
tools together to form a more integrated system with powerful capabilities.
We think that the general approach described here will enable the second,
superior option. The approach itself, of course, is also open to
contributions and revision by the community of users and contributors in the
SDN research community.
"""

I'll also be re-deploying bugzilla and a few other infrastructure items
(nightly builds, etc.) in the coming weeks.

- Bryan
http://heybryan.org/
1 512 203 0507
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