"Pharsight Corporation , a leading provider of software and strategic services for optimizing clinical drug development, recently announced that deCODE genetics, a leading biopharmaceutical company, has become a customer for the Drug Model Explorer (DMX)."
"Daniel L. Hartman, M.D., Senior Vice President of Product Development at deCODE added, "Quantitative modeling and simulation offers a valuable set of approaches to help navigate the myriad trade-offs and complexities that inform key program decisions. We look forward to using DMX to explore model-based results and support the decision-making process for promising therapies in our pipeline.""
DrugResearcher.Com Computational tool uptake dependent on validation issues
"A new report reveals that a lack of validation amongst drug discovery processes has emerged as a major restraint to the uptake and penetration levels of computational biology tools in the drug discovery industry."
"Of the four primary segments - pathway modelling and simulation, tissue modelling and simulation, cellular modelling and simulation as well as disease modelling and simulation - it is the latter, which will have the highest growth potential."redux [09.15.05]
UCSD News Computer Modeling Reveals Hidden Conversations Within Cells
"UCSD biochemists have developed a computer program that helps explain a long-standing mystery: how the same proteins can play different roles in a wide range of cellular processes, including those leading to immune responses and cancer.
Prior to the UCSD team’s findings, which are published in the September 16 issue of the journal Science, many scientists expressed doubts that a computational approach could represent the intricate mechanisms through which cells respond to outside signals. However, the researchers report that their computer model accurately predicts particular behaviors of living cells."
"The computer model comprises 70 equations to account for the behavior of five proteins and three RNA molecules in the “NF-kappaB signaling pathway,” which regulates genes involved in cancer, inflammation, immune function and cell death. Each equation takes into account a different parameter, such as how quickly a protein is synthesized, or how quickly it is degraded."redux [08.22.05]
Bio-IT World Genstruct and Entelos Make Headway on Biological Modeling
"The buzz around biological model-making seems to be growing. Both Genstruct and Entelos, modelers betting on different approaches, announced significant progress points today for themselves and for the systems biology community as a whole.
Founded in 2001, Genstruct achieved the first milestone in a multi-year collaboration with Pfizer, and CEO Keith Elliston says he expects to reach a second milestone in the fall. While Entelos, founded in 1996, ventured outside the drug discovery world by announcing a deal with cosmetics giant Unilever to develop a bi-simulation model for the study of skin allergy."redux [07.24.05]
Genomeweb Harvard Researchers Discuss Systems Biology
"So if what we’re doing is going to become anything more than a kind of niche activity for a small group of computational biologists and become part of working practice then I think we have to solve a number of problems. One, of course, is we have to explain to people what they get out of this that’s different. That’s a very important thing, but let’s leave it for a second. One of the things we have to move away from is this idea that every time I want to study a particular system, I have to build from scratch a kind of monolithic model of it, and not take advantage of the fact that lots of other people will have actually bitten off various different parts of it."redux [03.01.04]
The Scientist Desktop Drug Discovery
[requires 'free' registration]
"Imagine being able to discover the latest blockbuster drug using nothing but a PC and some highly sophisticated software. It's not as far-fetched as it sounds. A growing number of labs--both industrial and academic--are going "in silico," simulating everything from cells to clinical trials. The result is a sea change in pharmaceutical research, with resources once earmarked for bench work now being shunted into central processing unit clock cycles."redux [09.09.02]
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]
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]
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]
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]
BioMedNet Cells in cyberspace promise biology real understanding
[requires 'free' registration]
""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]
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."
“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.”BIOINFORMATICS IN THE 21st CENTURY
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