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 [...]
Archive for the 'Open Source' Category
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. [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 (http://www.nano-hive.org/hivekeeper/). The capabilities of the alpha version includes visualization of the molecular structures even while the simulation is running.
Editors comment — but when will the software be available for non-windows systems? "*nix" distros in coming weeks sounds rather vague.
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…
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
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…
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."
Stuart Scott writes "Here is a major engineering application available in source code for anyone. http://www.sandia.gov/media/NewsRel/NR2002/DAKOTA. htm It appears to be available in different forms from a Linux application to a massively parallel computer version."
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.
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:
The New York Times ran a special supplement on E-Business (13 June 2001) that included a number of interesting articles, including an interview with open source advocate Tim O'Reilly ("Making Programs Like Water: Free and Transparent", by K. Hafner) and an article on distributed software ("Software's Next Leap Is Out of the Box", by J. Markoff).
from the ideas-in-the-marketplace dept.
An article in the New York Times recaps the latest in the ideological war of words (and actions) between Microsoft and the Open Source/Free Software movement ("New Economy: Open-Source Movement Advances", by L. Flynn, 4 June 2001).
According to the article, "Microsoft has reason for concern, particularly where corporate clients are concerned. Despite the company's efforts to curb the movement, support for open-source software continues to grow here and abroad, led primarily by I.B.M."
The article also quotes a piece by Eben Moglen, a law professor at Columbia and general counsel for the Free Software Foundation: "Microsoft, which used to say all the time that the software business was ruthlessly competitive, is now matched against a competitor whose model of production and distribution is so much better that Microsoft stands no chance of prevailing in the long run. They're simply trying to scare people out of dealing with a competitor they can't buy, can't intimidate and can't stop." Moglenís comments were written in response to a speech in May 2001 by Craig Mundie, a senior vice president at Microsoft
from the fewer-lawyers-more-engineers dept.
San Jose Mercury News business columnist Dan Gillmor's May 4, 2001 column describes Foresight's PriorArt.org disclosure website, a joint project with IP.com. Dan writes: "Open-source programmers want to ensure that their work remains in the public domain. But some fear that private companies will take their good ideas and turn them into proprietary products — and even patent other people's work…It costs a bundle to challenge even a blatantly bad patent. If this site causes companies to hire fewer lawyers and more engineers, it will be a terrific enhancement to the intellectual-property field." See also earlier controversy.
from the time-to-think-hard dept.
Foresight's new open source disclosure website, PriorArt.org, is generating controversy. Some complain that it's too "anti-patent", while others are concerned that it may have pro-patent effects. About the latter: there are two specific concerns raised by Richard Stallman that merit attention. Read more to see the pros and cons described, and then give your views. At the end of the Read More section are some quotes from people who currently see the project as a good idea (Jeff "Hemos" Bates, Brian Behlendorf, Lawrence Lessig, Eric Raymond, Lawrence Rosen). You may want to read this general description of the project first. This is a serious issue, folks, and merits serious thought and participation.
from the feeling-the-heat dept.
An article in the New York Times ("Microsoft Is Set to Be Top Foe of Free Code", by John Markoff, 3 May 2001) describes Microsoftís attempts to counter the growing global open-source software movement.
According to the article, "Microsoft is preparing a broad campaign countering the movement to give away and share software code, arguing that it potentially undermines the intellectual property of countries and companies. At the same time, the company is acknowledging that it is feeling pressure from the freely shared alternatives to its commercial software . . . [The campaign is] an effort by Microsoft to raise questions about the limits of innovation inherent in the open-source approach and to suggest that companies adopting the approach are putting their intellectual property at risk." A particular target of the company, according to quotes from Microsoft executives, will be the General Public License (GPL) distribution model that is favored by many open source advocates.