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{bio,medical} informatics

Tuesday, May 09, 2006

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find related articles. powered by google. Genomics and Proteomics Open Source Bioinformatics

"Launched in 1998, BOI embraced the ideals of the open-source movement to combat restrictive, if not elitist, working conditions imposed by the cost of scientific progress rendered proprietary. (For this article "open source" is defined as freely available software, data sets, or computing capacity.)

"When I got into this field in 1995," says Bizzaro, "software as well as biological data were being patented at an alarming rate. Computational tools could run hundreds of thousands of dollars, requiring institutional licenses that only the better-endowed academic institutions could afford." Out of this frustration and almost a sense of isolation, the idea of shared bioinformatics resources evolved. "I created an environment—an online community where myself and others, those of us who didn't have a local group—could meet and share information."

The result was not so much a community tool chest as an archive of achievement."

redux [03.20.06]
find related articles. powered by google. The OpenScience Project How to make money from Open Source scientific software

"So, I’m left with a dilemma. I want this company to do well, to hire more of my students in the future, and to continue to produce high quality code. I also want the codes that we use in my field to be available for skeptical review. So today, I’m starting a set of posts in which I’ll try to hash out the following question: How can people make money from open source scientific software?

The question has been asked (and answered) many times before in non-scientific fields, and some of the answers that might work for a piece of commodity software (like a database) might not work so well for highly-specialized software. Over the next few days, I’ll lay out a set of common strategies from non-scientific fields to figure out if any of these strategies might work in the sciences."

redux [06.10.04]
find related articles. powered by google. The Economist An open-source shot in the arm?

"The open-source model is a good way to produce software, as the example of Linux shows. Could the same collaborative approach now revitalise medical research too?"

"In fact, open-source approaches have emerged in biotechnology already. The international effort to sequence the human genome, for instance, resembled an open-source initiative. It placed all the resulting data into the public domain rather than allow any participant to patent any of the results. Open source is also flourishing in bioinformatics, the field in which biology meets information technology. "

redux [05.13.04]
find related articles. powered by google. Bio-IT World Expert: Open Source Development Models Fall Flat

"Typical open source project development strategies work well for free software but don't flourish in commercial settings, according to one expert."

"Specifically, [Professor Jim Herbsleb of Carnegie Mellon University's International School of Computer Science] looked at cases where many developers from all over the world would successfully collaborate and coordinate to work on one piece of software. While looking at this, he also examined why this distributed development model has not thrived in industry. In fact, Herbsleb found that it takes companies more than twice as long to develop software in disparate locations than in one location."

redux [03.31.04]
find related articles. powered by google. LinuxWorld Open source appeals to bioinformatics

"Australia's bioinformatics industry will increasingly rely on open source software as researchers look for inexpensive point solutions that are not just a "black box", according to delegates at an Australian Technology Park Innovations bioinformatics symposium in Sydney.

Sydney University senior lecturer in bioinformatics, Dr Bret Church, said open source is undoubtedly the founding stone of bioinformatics.

"We love it," Dr Church said. "It is made for research, and there was plenty out there when bioinformatics came along. On the way to solutions, and while exploring possibilities and avenues, open source code tends to play a leading role.""

redux [12.18.03]
find related articles. powered by google. Bio-IT World 3rd Millennium Goes 'Open Source'

"3rd Millennium wants to cash in on the software it spent seven years developing for various government and commercial clients - by giving it away free.

The Waltham, Mass.-based informatics consultancy and services firm has released its Data Centric Knowledge Management System for biotech and drug R&D under a GNU general public license (GPL)."

"The company is betting that, of those life science organizations deploying the software, some will want to buy support and maintenance contracts."

redux [11.20.02]
find related articles. powered by google. IBM developerworks Open source in the biosciences

"Until recently, open source has often appeared to bioscientists as some sort of novelty, or, worse, a threat to IP protection. In the last few years, though, solid achievements in clustering, genomic data management, Web publication, and scores of specific "vertical" applications have established open source as a serious technical alternative.

Big Pharma and other biosciences are just starting to realize how open source can systematically cut costs, improve security, allow their own workers to shift attention back to their "core competences" from proprietary IT expertise, and even promote better science. We're in the midst of a dramatic evangelical movement that teaches better ways for open source IT to support bioscientific goals. Perhaps the most consequential shift is that participants have begun to understand that standards-based open source can enhance biosciences' fundamental values. These are exciting times for open source bioinformatics."

redux [09.30.02]
find related articles. powered by google. Genomeweb Is Bioinformatics--and Open-Source Software--in ABI's Future?

"Brenner, for example, stressed that while open sourcing "has potential in a generic sort of way," success depends on the operational and business models of specific companies.

Even considering a move to open sourcing can meet with resistance. "All of the instrument companies were brought up in closed-source shops, so they would have to change this fundamental attitude," explained Hood."

find related articles. powered by google. Bio-IT World Open Source: Not Yet a Closed Case

"THE OPEN SOURCE MOVEMENT has gained significant momentum of late, particularly within the bioinformatics field. While open source licenses vary widely, distribution of open source software typically requires delivery of both the object code and the source code. Most commercial software is delivered only in object code form, which is not easily read and modified by programmers.

The decision of whether to use open source software requires a careful analysis of various factors. In the right situations, open source software can be an excellent choice. In other cases, it can be disastrous."

redux [08.21.02]
find related articles. powered by google. Genomeweb How Good is Greed for Open-Source Bioinformatics?

"Want to make money from open-source bioinformatics? As long as it's not too much you might be OK.

This was the verdict of a panel of academics and business executives who had convened last week to talk broadly about open-source bioinformatics. But the discussion, which took place at the IEEE Computer Society bioinformatics conference at Stanford University, frequently veered to whether one could, or even should, make money from it.

The answer was a resounding maybe."

redux [01.16.02]
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."

[ 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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