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Archive for the 'Open Source' Category

Meet the Nubot: DNA nanotechnology robots

Posted by Christine Peterson on May 11th, 2007

Aharia Nair brings to our attention the new term Nubot, for Nucleic Acid Robots. Wikipedia explains: Nubot is an abbreviation for “Nucleic Acid Robots.” Nubots are synthetic robotics devices at the nanoscale. Representative nubots include the several DNA walkers reported by Ned Seeman’s group at NYU, Niles Pierce’s group at Caltech, John Reif’s group at [...]

Nanotechnology patent problems blamed on unionization

Posted by Christine Peterson on April 9th, 2007

Small Times reports on a meeting held in Oregon among a wide variety of nanotechnology-based business participants, at which many commercialization challenges were discussed. One was difficulties encountered with the U.S. Patent office: Start-ups expressed frustration with the U.S. Patent and Trademark Office (USPTO). Long waits for patent award decisions make it difficult for them [...]

Open source security for nanotechnology

Posted by Christine Peterson on April 5th, 2007

In the long term, we’ll need effective security techniques for advanced nanotechnology-based systems. This will take a while to figure out, so come help us do it at an upcoming open source conference, Penguicon: Open Source-style Security for the Whole Physical World Christine Peterson, Bruce Schneier One of the biggest problems society faces this century [...]

Windows Vista: potential negative impact on nanotechnology

Posted by Christine Peterson on February 12th, 2007

John Walker brings to our attention an apparently distressing set of concerns regarding the new version of Windows, known as Vista, written up by Peter Gutman as A Cost Analysis of Windows Vista Content Protection. Excerpts: The only way to protect the HFS [Hardware Functionality Scan] process therefore is to not release any technical details [...]

Help write open source nanotechnology textbook

Posted by Christine Peterson on January 18th, 2007

Given our interests in both nanotechnology and open source, we are happy to see that Wikibooks has an open-content textbook called The Opensource Handbook of Nanoscience and Nanotechnology. It includes not just text, but also demonstration experiments and media files. This online book was voted Wikibook of the Month for December 2006. Excerpt on molecular [...]

Nanotechnology: Lessons from open source biotech

Posted by Christine Peterson on October 16th, 2006

Roger Brent, director of the Molecular Sciences Institute in Berkeley, is a leader in open source biotech: Putting his patents where his principles are, Dr. Brent’s institute has drafted an “Open Source Policy” which commits to “[making] reagents and methods freely available to the research community.” You can see MSI’s open source policy and a [...]

Open source nanotechnology CAD with distributed computing

Posted by Christine Peterson on September 5th, 2006

News from Howard Lovy, now working with Nanorex: I wanted to make sure you saw this news item about molecular simulation software maker Nanorex acquiring Nano-Hive, developer of a powerful open source tool that speeds up nanoscale simulation through distributed computing. Together, Nanorex’s NanoEngineer-1 and the renamed NanoHive-1 are going to produce faster, better-quality animations. [...]

Open-source research for nanotechnology?

Posted by Christine Peterson on August 1st, 2006

The open-source research model continues to spread, now to biomedical research. An article by Sarah Everts in Chemical & Engineering News explores Open-Source Science, referencing a paper by Matthew Todd titled Open-Source Research—The Power of Us. For an earlier look at whether open source could work for nanotech, see Bryan Bruns’ article Open Sourcing Nanotechnology [...]

Help with collaborative nanoposter development

Posted by Christine Peterson on July 6th, 2006

Alexander Grigorovich-Barsky has designed a large nanotechnology poster (1.2 MB pdf) which attempts to give an overview of the whole topic, from history to today’s work to tomorrow’s atomically-precise manufacturing. An ambitious goal, but he has prudently asked for your help. I already gave him some feedback and, amazingly, the poster has now been re-designed [...]

Good news: Springer launches open access nano journal

Posted by Christine Peterson on July 5th, 2006

In a release titled First nanotechnology journal from a major publisher to offer open access, Springer announced its new journal “Nanoscale Research Letters (NRL), which will be the first nanotechnology journal from a major commercial publisher to publish articles with open access. The new journal provides an interdisciplinary forum for the open communication of scientific [...]

Nanotech: a view from Indonesia

Posted by Christine Peterson on March 1st, 2006

Writing in The Jakarta Post, Indonesia’s leading English language newspaper, is attorney Mohamad Mova Al ‘Afghan. He looks specifically at molecular nanotechnology, which he defines as “the capability to assemble any product than can be designed directly from atoms and molecules.” See the full article, or these excerpts: “The revolution in manufacturing resulting from MNT [...]

Nano-Hive Nanospace Simulator 1.1.0 Released

Posted by RobertBradbury on March 31st, 2005

bhelfrich writes "Nano-Hive version 1.1.0 for win32-x86 is now available for download. *nix distros will be made available in the coming weeks.

This release adds support for running multiple, multi-threaded simulations simultaneously, each able to access multiple Physical Interaction plugins.

We've also added new plugins.

  • MPQC_SClib – This plugin encapsulates the functionality of the Scientific Computing Toolkit (SC) used by the Massively Parallel Quantum Chemistry Program (MPQC).
  • OpenBabelImportExport – This Data Import/Export plugin adds the ability to read and write many new file types by encapsulating the OpenBabel library.
  • SocketsControl – Control Nano-Hive via a TCP socket with this Simulation Control plugin.
  • BondCalculator – This Physical Interaction plugin discovers molecules in the simulation space and specifies bonds to describe them.
  • BasicCellTraverser – This Entity Traversal plugin divides the simulation space up into sub-cells for multi-threaded calculation.

Also included in this release is an alpha version of the HiveKeeper Graphical User Interface for Nano-Hive ( The capabilities of the alpha version includes visualization of the molecular structures even while the simulation is running.

Visit to learn more. Nano-Hive's open source development and distributions are hosted at"

Editors comment — but when will the software be available for non-windows systems? "*nix" distros in coming weeks sounds rather vague.

Open source self-replication?

Posted by RobertBradbury on March 18th, 2005

It would appear that Adrian Bower, a lecturer at the University of Bath, is promoting an open source project for a "Replicating Rapid-Prototyper" that can reproduce not only itself but other macroscale objects.

More on self-replication…

Open source biotech: a model for nanotech?

Posted by Christine Peterson on March 3rd, 2005

Andrew Pollack of the NYT reports: "The open-source movement, which has encouraged legions of programmers around the world to improve continually upon software like the Linux operating system, may be spreading to biotechnology. Researchers from Australia will report in a scientific journal today that they have devised a method of creating genetically modified crops that does not infringe on patents held by big biotechnology companies. They said the technique, and a related one already used in crop biotechnology, would be made available free to others to use and improve, as long as any improvements are also available free. As with open-source software, the idea is to spur innovation through a sort of communal barn-raising effort." I have met the project's leader Richard Jefferson — impressive fellow.–CP

SCALE 3x Plans Panel Discussion on the Future VoIP

Posted by RobertBradbury on January 11th, 2005

Anonymous Coward writes "The Southern California Linux Expo has announced plans to host a panel discussion on the future of open source and voice over IP technologies at SCALE 3x. SCALE 3x, the Third Annual Southern California Linux Expo is the premier grass roots Linux and Open Source conference." More…

VigyaanCD: bio/chemical modeling workbench on PC

Posted by Jim Lewis on April 26th, 2004

PKA writes "Pratul K. Agarwal from Oak Ridge National Laboratory has released VigyaanCD (homepage, mirror). Vigyaan, a Knoppix customization, is an electronic workbench for computational biology and computational chemistry. The user can choose from more than 20 science applications. In addition to bioinformatics software, it provides GROMACS, TINKER for biomolecular modeling and Ghemical, MPQC, PSI3 for quantum chemistry calculations. VigyaanCD is a live Linux CD containing all the software required to boot the PC into workbench environment and is suitable both for beginners (12 demos and tutorials) and experts. Learning computational biology/chemistry has never been easier, so grab the free ISO image from several mirrors around the world and put your PC to work."

Nanotech Intro Class Online

Posted by Jim Lewis on November 10th, 2003

Glenn Fishbine writes "This material was produced as part of a ten hour course designed to introduce the scope of nanotechnology. Use is hereby granted for educational purposes only."

Open Source (Sandia’s DAKOTA app available)

Posted by RichardTerra on April 10th, 2002

Stuart Scott writes "Here is a major engineering application available in source code for anyone. htm It appears to be available in different forms from a Linux application to a massively parallel computer version."

Los Alamos Archive will move to Cornell

Posted by RichardTerra on July 18th, 2001

from the portable-libraries dept.
The Los Alamos E-Print Archive, an "open source" library of scientific papers which is widely credited with revolutionizing the way physical scientists and mathematicians communicate, is moving from the Los Alamos National Laboratory (LANL) in New Mexico to Cornell University. Physicist Paul Ginsparg, who created and maintains the archive, will join the Cornell faculty this fall, and he is bringing the archive with him. It will become a service of Cornell University Library, which has developed several other digital academic resources. Both Ginsparg and library officials express hope that the archive will improve and expand in its new home.

The Los Alamos archive was covered here on nanodot in May 2001 in relation to the movement to establish web-based open public libraries of scientific papers.

nanoTITAN announces nanoML early access release

Posted by RichardTerra on July 17th, 2001

from the NT-design-tools dept.
Rob Bishop writes "nanoTITAN, Inc. is pleased to announce the first early access release of nanoML, a markup language for the description and interchange of nanodevices. nanoML includes the molecular components and structure of a nanodevice — as you might expect — but goes well beyond that to include information about the properties, interoperability, operational characteristics, display, safety, and legal status of nanodevices.
It is our hope that nanoML will accelerate development of molecular nanotechnology by providing a common language for researchers, engineers and other interested parties. Our commitment is to evolve nanoML consistent with the needs of the nanotechnology community and to move toward an open standard. We would greatly appreciate a review of our work so far by the knowledgeable readers of nanodot.
More information can be found at: