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{bio,medical} informatics

Wednesday, January 16, 2002

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find related articles. powered by google. O'Reilly Network Does Publicly Funded Research Have to Result in Open Source Code?

"A debate is heating up in the academic community over whether software that is generated by publicly funded research must be released with an open source license. The Internet is one example of how releasing research code benefited the public, but the trend seems to be changing now, and universities are more likely to consider the profit opportunity. The Bayh-Dole Act paved the way for the privatization of publicly funded resources, but not everyone is happy with the results.

Against the tide of privatization comes a group of bioinformatics researchers and programmers with an online petition to require that all software created by publicly funded research projects be licensed as open source. They have founded a group and a Web site,, to further this cause.

Here we present two opposing viewpoints on this issue."

redux [01.07.01]
find related articles. powered by google. IT-Analysis Open Source in Bioinformatics

"The Open Source movement is infectious, it seems. It has bubbled up in the field of bioinformatics – gene research software. Gene research is already a burgeoning area of activity, which is predicted to deliver numerous benefits to the health industry. It is also an area where software counts and where universities have managed to prosper from their activities. US universities lodge about 2000 patents each year, many in bioinformatics, and these patents contribute a good deal of revenue – an amount estimated at about $5 billion per annum, or ten percent of their total budgets. Thus Open Source activities in this area are not universally welcomed."

find related articles. powered by google. Salon Public money, private code

"Over the past several years, open-source software development has won high-profile adherents in the business world -- including the likes of IBM and Sun Microsystems. But it has always had its strongest fans in the academic world, where open-source software is seen as a natural extension of the idea that the fruits of academic research should be shared with everyone.

But now some academic programmers on the cutting edge have found that the licensing office is proving a more formidable obstacle to progress than the limits of their imagination and skill."

redux [11.26.01]
find related articles. powered by google. SiliconValley.Com Computer scientists push to publish code powering genetic research

"Before computer whiz Steven E. Brenner accepted his tenure-track research post at the University of California-Berkeley last year, he demanded that the school's intellectual property police leave him alone.

Brenner prevailed. He's now one of the few experts in the emerging field of bioinformatics with the freedom to distribute his work, software used in gene research.

``It's vital to what we do,'' says Brenner, who supports a movement to force universities to allow ``open source'' publishing of gene research software code."

redux [08.18.01]
find related 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 [11.05.01]
find related articles. powered by google. Boston Business Journal Legal issues surround programming bioinformatics

"Computers are supposed to help biotechnology, right? Isn't bioinformatics all the rage right now? Well, it is, but with popularity comes legal questions that many companies don't address until it's too late."

"It seems that many biotech companies don't realize that a computer vendor may have the rights to the software, and ultimately, the work that the biotech companies do.

For example, if a biotech company orders a computer network to help it sequence the genome of yeast, the company may ask the vendor to customize the software it will use to do the sequencing. However, the question is, who owns the right to that customized software--the biotech company or the software programmer?"

redux [08.23.01]
find related 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 [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."

[ 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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