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{bio,medical} informatics

Wednesday, June 11, 2003

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find related articles. powered by google. Bio-IT World Fournier test-drives Pharsight modeling software

"Drug development modeling software supplier Pharsight Corp., Mountain View, Calif., is in the final stages of a trial project at Montreal-based Fournier Pharma Inc. that has already resulted in the maker of treatments for metabolic diseases deciding to cancel a clinical trial, saving perhaps millions of dollars.

Still, Pharsight officials say, Fournier Pharma has not committed to licensing Pharsight's modeling software and services and expanding their use to other projects."

redux [11.24.02]
find related articles. powered by google. Nature: Insight Computational biology

"This Insight presented us with a difficult problem, not in its content -- a collection of reviews showing how sophisticated mathematical concepts have illuminated and continue to illuminate the principles underlying biology at a genetic, molecular, cellular and even organismal level. The problem was what to call it.

In the end we concluded that the unifying strand that runs through all the work described in this Insight was computation, whether it be the production of sophisticated models against which reality is compared, or the subtle analyses that derive patterns and trends from vast and noisy data sets. There are other themes running through the reviews in this Insight, more than you might expect from the titles alone, but 'Computational Biology' it has become."

redux [09.09.02]
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 [12.17.01]
find related articles. powered by google. Fast Company Roche's New Scientific Method

""We used to look at several data points for each experiment," says Louis Renzetti, senior director of discovery pharmacology. "Now there are dozens and dozens." Simply dump all of that data on a scientist's desk, and one of two tragicomic things will happen: Either the scientist will want to pursue every promising lead and will end up like a frazzled amusement-park visitor, or the scientists will refuse to touch the report at all, for fear that she will never be able to make sense of it.

It has taken a while to find the right approach, says James Rosinski, one of Roche's experts in the new field of bioinformatics, which covers the management of genomic data. The key, he says, is for biologists and statisticians to start talking early about how to use data from a GeneChip experiment. "It's iterative," he explains. "We can't just take a one-shot approach and tell the biologists what they ought to be interested in. We have to interact.""

redux [04.05.00]
find related articles. powered by google. HMS Beagle Are Computers Evolving in Biology?
[requires 'free' registration]

"I suspect that although the new enthusiasm for computers in biology is genuine, it overlooks some basic problems in implementation. The basic difficulty, as I see it, is that although biologists use computers, they do not trust everything that comes out of them. It is one thing to use them to print up nice-looking graphs, but it is an entirely different matter to use them to think better."

"Francis Crick was once quoted as saying that no biologist had ever made a discovery using a mathematical model. I would reply that no biologist has ever made a discovery by running an electrophoretic gel. They make discoveries by using their brains. Computers, like all scientific tools, are only as good as the person who uses them. If biologists don't understand how computer models are constructed, they won't know their strengths and limitations. Without some foundation of trust, biologists will be unlikely to utilize or accept this powerful method of data analysis."

[ 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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