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{bio,medical} informatics

Monday, September 09, 2002

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find related articles. powered by google. Genomeweb Urging Researchers to 'Forget the Genome,' Sydney Brenner Sells a Cell Map

"Consistent with his lifelong reputation as a visionary and provocateur, Brenner challenged a crowd of over 250 bioinformaticists gathered at the Wellcome Trust Genome Campus in Hinxton, UK, to "forget the genome."

"The more you annotate the genome, the more you make it opaque," he warned in a keynote speech delivered at the joint Cold Spring Harbor Laboratory/Wellcome Trust Genome Informatics conference on Saturday. "We need to focus on our cells."

Brenner questioned the ability of computational approaches to derive functional knowledge from genomic sequence alone--a "hideously difficult task," he said--because some problems are simply "not soluble or computable." The future, according to Brenner, requires going back to the bench. Old-fashioned data on the biochemistry of the cell would then be used to flesh out the cell map, which would serve as "a framework to think of genomes and their products.""

redux [07.29.02]
find related articles. powered by google. Wired News An Rx for the Pharmaceuticals

"Colin Hill, president and CEO of GNS, said the adoption of modeling will be slow, but even the largest and most stubborn pharmas will soon realize they have to adopt it if they want to compete.

He has seen more success selling pharmas the baby steps toward modeling: tools, such as its Diagrammatic Cell Language, software and database information, rather than actual models."

redux [11.27.00]
find related articles. powered by google. BusinessWeek A Software Model That Fathoms the Human Heart?

"What do a Boeing 777 and the human body have in common? Both are complex systems, dependent on millions of complex parts, whether they be a jet-propelled engine or a pumping organ such as the heart. The big difference: Engineers can design and build highly accurate computer models of the way a Boeing 777 will behave in flight. The human heart? Its complexity has long stymied efforts by researchers intent on turning drug development into a predictive science, much like building airplanes.

But that's changing. A handful of companies are developing software that can model single cells, whole organs, cellular metabolism and toxicology, diseases throughout a patient's body, and even an entire clinical trial."

redux [02.16.01]
find related articles. powered by google. MIT Technology Review Upstream: Biology in Silico

"Computers capable of mimicking life have long been the stuff of sci-fi nightmares - think The Terminator or 2001's HAL 9000. But for researchers struggling to make sense of vast amounts of new biological data, and for drug companies anxious to cut costs and speed development, having accurate computer simulations of living systems is still a dream. To make that dream come true, they are turning to "in silico biology," building computer models of the intricate processes that take place inside cells, organs, and even people. The ultimate goal: an entire organism modeled in silicon, allowing researchers to test new therapies much as engineers "fly" new airplane designs on supercomputers."

redux [05.15.01]
find related articles. powered by google. BioMedNet Cells in cyberspace promise biology real understanding
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""We in physics are used to studying complex systems, but the level of complexity inherent in biological systems ... is way beyond what we have experience dealing with," said Rajagopal, assistant director of research at the Cavendish Laboratory in the University of Cambridge. "Biological systems are much harder to model as they are in highly non-equilibrium states and you not only have to take into account the flow of matter and energy, but also the flow of information!"

He added: "In biology, the whole is greater than the sum of its parts. We have to move on from the "reductionist" towards an "integrationist" approach."

redux [05.15.01]
find related articles. powered by google. HMS Beagle Virtual Cures
[requires 'free' registration]

"For a brief period, supplying the data was enough. More genes meant more potential drug targets. But now the victims of the data flood are crying for help. Companies like Entelos, Inc. (Menlo Park, California) are coming to the rescue by building models that integrate all those data into a single, homeostatic, interconnected whole. The models allow researchers to run virtual drug trials to determine the best drug targets, treatment regimens, and patient populations."

Modelers feel that their time has come. "Leaders in the genomics field are all coming to this realization that model building is becoming the rate-limiting step," says Palsson. "There's a major shift taking place in the biological sciences." Math is back, he says, and "biology is going to become quantitative."

[ 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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