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{bio,medical} informatics

Friday, August 04, 2000

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Software Carpentry Internet Groupware for Scientific Collaboration
"The Web was invented so that scientists could use computer networks to collaborate -- that is, exchange documents, discuss them, coordinate work, create and publish collective knowledge. It was, in other words, supposed to be a groupware application.

Despite the popularity of the Web -- or, perhaps, because of that popularity -- it has yet to fulfill that original mission. Today's Web is more like a shotgun marriage of electronic publishing and broadcast television than it is like an engineered solution for group collaboration. True, the Internet empowers today's working scientist in ways only dreamed of even a decade ago. Yet our use of it often remains rooted in pre-Web idioms and habits -- partly because we don't fully exploit today's Internet communication tools, but mainly because we're still missing key tools and infrastructure."

"The goal of Internet groupware should be to reclaim the original vision of the Web as a medium of collaboration. It's no accident that vision arose in a scientific milieu since the enterprise of science is so deeply rooted in collaboration.

This report ends with two final messages. First, we're closer to the two-way Web than we realize. Services such as TimeDance, QuickTopic, Manila, and Meerkat are already making it easier than ever to create and use shared information spaces. They aren't final solutions, but we should use them for all they're worth, and watch for new kinds of collaborative services that are emerging every day. Only by using these services in their current form will we discover, collectively, what they need to evolve into.

Second, the roadmap to the future is coming more sharply into focus. The first-generation Web, though remarkably powerful, is an awkward combination of many different protocols and data formats. The emerging consensus around XML, as a universal way both to interconnect services and to represent many different kinds of information, is the key to a next-generation Web that may finally start to deliver on the collaborative vision of the original. There's nothing magical about XML. It isn't pixie dust. It doesn't, in and of itself, help us collaborate. What will help is messages, documents, applications, and services that all agree on a standard way of representing data -- one that's richer than the line-oriented ASCII we've used so long and so well. That standardization is now occurring. We should welcome it, and we should demand that our tools respect and embrace it."
redux [06.30.00]
Wired Biotech: The Internet, With Soul
"The flood of knowledge that will follow the human genome map will answer many questions, but experts pointed out that some questions just can't be answered, even by unraveling each of the 3.2 billion chemical letters that make us human."

"Nonetheless, [Incyte's CEO Randy] Scott said answers in medicine will come fast. Both Moore's Law and Metcalfe's Law will accelerate the speed of progress in the biotech industry, replicating the growth of the computer and Internet industries.

"The effect of Moore's Law is pretty straightforward," Scott said. Moore's Law, conceived by Gordon Moore, the founder of Intel, maintains that computer power doubles every 18 months. In biology, DNA sequencing rates are doubling every year.

"While you may recognize that the Human Genome Project has been going on for the past ten years, you may not realize that all of the sequencing for the human genome has happened in the last year, and over 50 percent of that just within the last four months," said Scott."

"Metcalfe's Law, Scott said, will help researchers waste less and make discoveries faster. Conceived by Robert Metcalfe who invented the ethernet, the law states that the power of a network increases exponentially with the number of computers connected to it."

Right now up to 80 percent of research is wasted, because graduate students and postdocs repeat past experiments as part of their training, and scientists refuse to share their research until it's published, which can be up to two years after the results are compiled.

"Metcalfe's Law is going to do to biology what the Internet has done to e-commerce," he said. "It's going to connect vast groups of people who previously didn't talk."

"Instead of putzing around in the lab for weeks or months, scientists will search Web-based databases to quickly narrow their ideas and devise experiments that they know they are unique and relevant."
redux [03.29.00]
UIUC Collaboratory for Structural Biology
"The Theoretical Biophysics Group at the University of Illinois is proud to announce the initial public release of BioCoRE, a collaborative research environment. BioCoRE software is freely available for use at the Theoretical Biophysics Group website. BioCoRE development is supported by the NIH National Center for Research Resources.

Modern computational structural biology requires scientists to employ a wide range of tools and techniques to solve complex problems while keeping accurate and complete records of research activities. Additional complications are introduced by the need to effectively engage in interdisciplinary collaborations with geographically dispersed colleagues. The software BioCoRE, a collaborative research environment for molecular modeling and simulations, addresses these challenges."

[ 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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