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{bio,medical} informatics

Wednesday, March 21, 2001

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find related articles. powered by google. Conference Bioinformatics Open Source Conference 2001
"The first Bioinformatics Open Source Conference, BOSC2000, convened last August in San Diego, just before ISMB2000. BOSC2001 will take place in Copenhagen on July 19-20, 2001, just before ISMB2001, and concurrent with the BioPathways meeting.

BOSC2000 featured keynote talks by Ewan Birney, Lincoln Stein, and Tim O'Reilly, as well as presentations chosen from submitted abstracts. This year, BOSC will be organized around existing open source bioinformatics projects, providing time for projects to meet personally and also to exchange ideas between projects. The mornings will feature technical talks selected from submitted abstracts. In the afternoons, project groups will be given access to computers and ethernet hubs for collaborative coding, and small across-projects meetings can be organized.

We expect the leaders of most of the major bioinformatics open source projects to be at the meeting, including:

  • Matt Pocock (BioJava)
  • Andrew Dalke (BioPython)
  • Ewan Birney (BioPerl)
  • Jason Stajich (BioPerl and BioCorba)
  • Alan Bleasby (EMBOSS)
  • Chris Mungall (FlyBase)
  • Lincoln Stein (DAS)"
redux [04.28.00]
find related articles. powered by google. Nature Open-source work even more vital to genome project than to software
"We note with dismay and alarm the controversy concerning access, distribution and patenting of the human genome sequence (Nature 404, 317; 2000 & Nature 404, 324; 2000). We wish to point out some analogies between the human genome sequencing efforts and 'open-source' software development, which have implications for the data-release policy of the public sequencing effort."

"The reasons why the Linux project could succeed against commercial wisdom have been analysed by Eric S. Raymond in his book The Cathedral and the Bazaar (O'Reilly, 1999). Most of these findings are of relevance to academic and commercial benefits arising from human genome sequencing." [via]

redux [10.20.00]
find related articles. powered by google. British Medical Journal Medical software's free future
"As computer hardware becomes an ever cheaper commodity with ever increasing power, it is clear that software is the rate limiting step in system development. Software is slippery stuff: its possibilities seem almost limitless, but implementing a system competently is a difficult activity that commands premium rates of pay. A lot of its cost lies in planning, implementing, and monitoring and enforcing exchanges between the parties involved, who might be, for example, a hospital wanting to buy an information system and a system supplier. Such exchanges have high transaction costs. The relationship between an information systems supplier and its clients has, according to transaction cost economists, the quality of "information impactedness": a state in which one of the parties to an exchange is much better informed than the other, and the other cannot achieve information parity, except at great cost.

Even when a system is successfully commissioned, the costs can remain high. Once a customer is "locked into" proprietary software, its makers can demand premium prices, safe in the knowledge that the client would find it even more expensive to change.

It is such forces that have led to the rise of free softwaremost notably the GNU/Linux operating system, which is freely available for download from the internet."

"Free software concepts make particular sense in medicine: although peer review has its problems, medical knowledge is becoming more open, not less, and the idea of locking it up in proprietary systems is untenable. And professional staff should not invest time learning the user interface of proprietary systems that may change, be withdrawn, or be arbitrarily "upgraded" for commercial reasons. Much better instead to invest time on a system licensed under the General Public License that will always be free." [via LinuxMedNews]

redux [07.27.00]
find related articles. powered by google. Informatics Review Open Source Software in Healthcare
"Good software forms seamless connections; as George Orwell said of prose, the best is like a window pane: transparent. The obscurity of commercial binaries is an obstacle to good quality communication between systems. In healthcare, good communication is too important to remain proprietary. Software developers should remain confident that there will always be work for the future in discovering, providing, and adapting applications for organizations, and training people to use them. This, rather than the sharp-suited gouging of Bill Gates wannabees, should become the predominant business model for software in the British NHS. Software engineering will become a profession more like medicine and the law: in which practitioners earn a fair hourly reward for their experience at interpreting, evaluating and applying knowledge from a specialized domain to the benefit of their clients. Current models, which restrict the sharing and development of knowledge, are certainly counterproductive and arguably unethical. Open source is the future: all we have to do is built it."

find related 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."
redux [09.21.00]
find related articles. powered by google. LinuxMedNews Innovation, Open Source and Lessig
"Wayne Wilson on the openhealth-list has a profoundly interesting summary (reprinted here with permission) of a lecture given by Lawrence Lessig, Professor for Entrepreneurial Legal Studies at Harvard. His bio and a collection of his thoughtful articles can be found here. Wilson writes: 'Lessig is a legal scholar and it is not immediately obvious that legal arguments would be appealing to us, but I think they are.' "
find related articles. powered by google. Openhealth The Openhealth list Archive
"The Openhealth mailing list is a place for IT professionals and members of the public who are interested in health care and open source software to gather and discuss the issues of this field. This list is provided as a public service by Minoru Development Corporation. While Minoru staff are participants of the list, they do not direct list content. Areas of discussion include:
- Deployment stories
- Discussion of open source projects and products
- Question and answer
- Open source licences and their applicability to health care
- Authentication and privacy issues for data over the Internet
- Obstacles for open source software in health care ”
find related articles. powered by google. LinuxMedNews LinuxMedNews Open Source Medical Project List
""An army of LinuxMedNews correspondents (me and my Chihuahua Cindy) combed the Internet to form an alphabetized, comprehensive list of medical open source medical projects resulting in 17(!) such projects and many other interesting sites. If your project or site isn't listed, please e-mail. We have opened a new section on medical software companies that support Linux.""

[ 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.


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