snowdeal logo

archives archives

{bio,medical} informatics

Thursday, August 23, 2001

bookmark: connotea :: ::digg ::furl ::reddit ::yahoo::

find rt skeptics saw something entirely different in today's announcement. One fund manager, an Humelated articles. powered by google. Stanford Medical Informatics Preprint Archive Open Source Initiatives in Bioinformatics

"This report outlines recent activity in open source software development within the discipline of bioinformatics. I present the relevant highlights of two bioinformatics meetings held in July 2001 in Copenhagen, Denmark: the Bioinformatics Open Source Conference and the Intelligent Systems for Molecular Biology Conference. The report also describes a large number of projects and groups important to bioinformatics open source software development. The appendices include meeting programs, the currently accepted definition of open source software, and descriptions of important online biological data sources."

redux [08.18.01]
find rt skeptics saw something entirely different in today's announcement. One fund manager, an Humelated articles. powered by google. GenomeWeb Legal Pitfalls of Free Bioinformatics Software May Loom Large

"Steve Brenner, assistant professor and leader of a computational genomics research group at the University of California, Berkeley, said he fears that many academic bioinformaticists are unaware of a legal risk they face on a daily basis: contributing to open source software projects without explicit permission from their institutions.

While many employers have clauses in their employment contracts that restrict the creation and use of open source software, bioinformatics programmers at universities are often not as attuned to copyright issues as their industry counterparts. This fact, Brenner said, raises the possibility that a good portion of biological open source software is currently being produced illegally."

"The issue seems to be coming to a head in the academic world now, as more universities are exploiting the revenue stream made possible by their copyright and patent holdings. ?If you?re a software developer, the university holds rights to your software, but if you?re an English professor or Law professor and publish a book, they?re not the least bit interested in copyright,? said Thomas Field, an attorney at the Franklin Pierce Law Center affiliated with the Association of University Technology Managers."

redux [05.09.01]
find rt skeptics saw something entirely different in today's announcement. One fund manager, an Humelated articles. powered by google. IEEE Spectrum Open-Source Biology And Its Impact on Industry

"The toolbox of biochemistry, the parts list--"the kernel," to stretch the software analogy--is shared by all organisms on the planet. In general, organisms differ from one another because of their order of gene expression or because of relatively subtle perturbations to protein structures common to all forms of terrestrial life. That is, innovation in the natural world in some sense has always followed the idea of a service and flow economy. If the environment is static, only when an organism figures out how to use the old toolbox to provide itself, or another organism, with a new service is advantage conferred.

The analogy to future industrial applications of biology is clear: When molecular biologists figure out the kernel of biology, innovation by humans will consist of tweaking the parts to provide new services. Because of the sheer amount of information, it is unlikely that a single corporate entity could maintain a monopoly on the kernel. Eventually, as design tasks increase in number and sophistication, corporations will have to share techniques and this information will inevitably spread widely, reaching all levels of technical ability--the currency of the day will be innovation and design. As with every other technology developed by humans, biological technology will be broadly disseminated."

Technology based on intentional, open-source biology is on its way, whether we like it or not, and the opportunity it represents will just begin to emerge in the next 50 years."

redux [03.04.01]
find rt skeptics saw something entirely different in today's announcement. One fund manager, an Humelated articles. powered by google. The Washington Monthly Reboot! How Linux and open-source development could change the way we get things done

"Imagine a scale with all the advantages of a proprietary model on the left and all the advantages of an open-source model on the right. Pretend everybody who wants to solve a problem or build a project has a scale like this. If it tips to the left, the proprietary model is chosen; if it tips to the right, the open model is chosen. Now, as connectivity increases with the Internet, and computer power increases exponentially, more and more weight accumulates on the right. Every time computer power increases, another household gets wired, or a new simulator is built online, a little more weight is added to the right. Having the example of Linux to learn from adds some more weight to the right; the next successful open-source project will add even more.

"Perhaps the next boom in open source will come from the law; perhaps from drug X; perhaps it will be something entirely different. Although it's difficult to tell, it is quite likely that the scale is going to tip for some projects and that there will be serious efforts at open-source development in the next decade. Moreover, it's quite likely some of these projects will work."

[ rhetoric ]

Bioinformatics will be at the core of biology in the 21st century. In fields ranging from structural biology to genomics to biomedical imaging, ready access to data and analytical tools are fundamentally changing the way investigators in the life sciences conduct research and approach problems. Complex, computationally intensive biological problems are now being addressed and promise to significantly advance our understanding of biology and medicine. No biological discipline will be unaffected by these technological breakthroughs.


[ search ]

[ outbound ]

biospace / genomeweb / bio-it world / scitechdaily / biomedcentral / the panda's thumb / / nodalpoint / flags and lollipops / on genetics / a bioinformatics blog / andrew dalke / the struggling grad student / in the pipeline / gene expression / free association / pharyngula / the personal genome / genetics and public health blog / the medical informatics weblog / linuxmednews / nanodot / complexity digest /

eyeforpharma /

nsu / nyt science / bbc scitech / newshub / biology news net /

informatics review / stanford / bmj info in practice / bmj info in practice /

[ schwag ]

look snazzy and support the site at the same time by buying some snowdeal schwag !

[ et cetera ]

valid xhtml 1.0?

This site designed by
Eric C. Snowdeal III .
© 2000-2005