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{bio,medical} informatics

Friday, April 26, 2002

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find related articles. powered by google. The Seattle Times Creating a 'hothouse' for bioscience research

"When Dr. Leroy Hood sits down to talk about his latest ambition, he takes all of 10 seconds to warm up.

"I think we'll lead the way toward revolutionizing new ways of understanding biology," he said."

"But Hood's enthusiasm these days has been limited by finances. More than two years after an unceremonious exit from the University of Washington, he has been scrounging for money. And his newest vision — using high-speed computers to turn the DNA jumble into something useful for predicting and preventing disease — requires lots of money."

redux [01.19.02]
find related articles. powered by google. O'Reilly Network An Interview with Dr. Leroy Hood

"The integration of bioinformatics with these systems approaches is an integral, essential feature. One of the things that we stress is that in the future it's going to be increasingly important for people in bioinformatics to be intimately associated with data producers, because no matter how smart you are you can't model biological complexity--it's just too complex. The only way we're going to understand it is through the integration of these global experimental observations, together with powerful computational tools for analysis, and ultimately, for modeling.

A mistake that a lot of people in bioinformatics have tended to make is thinking that you can set up a bioinformatics center and it can work in isolation from the biology, and it can study all these great databases and learn lots and lots about biology. In vitro biology and in silico biology are all popular terms, but it isn't true, and it isn't going to be true in the future."

redux [04.18.01]
find related articles. powered by google. The New York Times Approaching Biology From a Different Angle
[requires 'free' registration]

"Systems biology is a loosely defined term, but the main idea is that biology is an information science, with genes a sort of digital code. Moreover, while much of molecular biology has involved studying a single gene or protein in depth, systems biology looks at the bigger picture, how all the genes and proteins interact. Ultimately the goal is to develop computer models that can predict the behavior of cells or organisms, much as Boeing can simulate how a plane will fly before it is built.

But such a task requires biologists to team up with computer scientists, engineers, physicists and mathematicians. The structure of universities makes that difficult, Dr. Hood said."

redux [03.17.01]
find related articles. powered by google. GenomeWeb Beyond Genomics Takes a Gamble on Systems Biology

"When Lee Hood started the Institute for Systems Biology, a project to build an integrated research supercenter for the biological sciences, few doubted the validity of the concept, but many wondered whether the technology existed to make it work.

Now, in a sign that others are also willing to gamble on the idea, systems biology is attracting commercial attention. Beyond Genomics (BG), a startup based in Cambridge, Mass., is attempting to glean medically-relevant information from multiple systems simultaneously, from genes to metabolites, by using software that identifies patterns in these systems caused by disease."

redux [02.26.02]
find related articles. powered by google. MIT Technology Review Systems Biology

"Over the last few years, there’s been an explosion of information in biology. The mapping of the human genome gave biologists unprecedented detail about some 30,000 to 40,000 genes. Efforts are also under way to identify the thousands—and potentially millions—of proteins encoded by those genes. Researchers are now pursuing the next logical step in integrating all this data: systems biology.

The goal is to understand not just the functions of individual genes, proteins and smaller molecules like hormones, but to learn how all of these molecules interact within, say, a cell. Biologists hope to then use this information to generate more accurate computer models that will help unravel the complexities of human physiology and the underlying mechanisms of disease. The biggest payoff: faster development of more-effective drugs."

redux [05.15.01]
find related articles. powered by google. Systems Biology Workbench Development Group Mission

"Our Mission is to develop an integrated, easy-to-use environment, the workbench , which will enable biologists to create, manipulate, display and analyze biological models at molecular, cellular and multicellular levels. We are focusing on biochemical networks including mass action kinetics, metabolic pathways, stochastic simulation, gene expression and regulation."

"One of the key aspects of out project is to facilitate collaboration among existing developers and users of system biology software. We aim to do this by providing an open-source software infrastructure which will enable collaborators to freely use and share each other's computational resources."

redux [07.11.00]
find related articles. powered by google. Biospace.Com Big Picture Biology

"For most of us, formal biology education begins with complex systems--the traditional dissection of a frog in high school biology class is virtually a rite of passage in the U.S.

But the way many people learn about and invest in biotechnology is at the smallest end of the spectrum--the genome, now often described as the "periodic table" of biology. Genomics and all its related buzzwords have been responsible for much of the media attention, government grants, and investment capital heaped on the biotech industry over the past decade.

But just as there is a whole lot of chemistry that happens in between the periodic table and a birthday cake, there is a lot of biology in between the genome and a living organism. With the completion of biology's periodic table within sight, academics and industry players alike are pondering the best way to apply our hard won knowledge.

The only problem is, the path from genome to system seems to get harder the more we learn."

[ 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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