Tuesday, February 17, 2004

bookmark: connotea :: del.icio.us ::digg ::furl ::reddit ::yahoo::

The Boston Globe The big picture

"Now, quite suddenly, biology is being consumed by a fast-moving intellectual revolution that could profoundly change the course of science -- and medicine -- in the new century. Called "systems biology," it is an audacious attempt to transcend molecular biology and understand organisms as complex interacting systems that are more than the sum of their parts -- that the best way to understand ants, for instance, is to study colonies rather than just the individual insects.

In only a few years, the idea has gone from fringe concept to rallying cry as Harvard, MIT and universities around the world scramble to establish large new systems biology efforts."

redux [02.04.04]
Bio-IT World Catching Up with Leroy Hood on Systems Biology

"Big Pharma is going to be a dinosaur. I think the whole industry is going to be restructured and they'll never be able to get systems biology, so they'll be out of the discovery business. Big Pharma is the worst of silos, even worse than medical schools.

Maybe there are a few like Amgen that'll be flexible enough to really change things. But even there, Roger Perlmutter [executive VP, R&D, Amgen], he's chairman of our board and he still doesn't get systems biology - and he's a really smart guy! See, these guys are too embedded in a billion-dollar-a-year drug [philosophy]. That's exactly the wrong attitude."

redux [01.14.04]
Genomeweb Is Pharma Smart Enough to Do Systems Biology?

"But is big pharma up to the task of using systems biology to transform drug discovery? In spite of efforts like the one at Novartis to create breeding grounds for systems biology, some say that traditional pharmaceutical companies lack the organizational flexibility to make it work. Industry observers say big pharma may be able to integrate data from various biological experiments, or extract patterns from genomic data, but they doubt that systems biology will flourish there. That's because the ultimate goal of systems biology - constructing models of complex biological systems that would enable researchers to predict the outcome of particular experiments - may be beyond the ken of the highly structured behemoths."

MIT News Biology needs a model of complex living systems, Sorger says

"Even with the plethora of existing biological data, Sorger contends that biology is data-poor in "systematically acquired sets of data. All the interesting data in what I work in seems to be missing," he said. "We need to be able to link unstructured data in a systematic way."

"The barrier here is going to be crossed by creativity, not more CPUs," Sorger continued. "The goal is to usher in a systems biology approach without losing the small science that has sustained" the field."

redux [11.01.03]
EE Times Data swell refocuses biotech on systems

"Dealing with the immediate challenge requires a shift to what researchers are calling systems biology, an emerging field of math-based predictive biology."

""I'm up to my eyes in targets," said Ken Kupfer, head of scientific informatics at Bayer's office in Berkeley, Calif. "The time it takes us to develop the depth of understanding we need blows our business models.""

redux [09.22.03]
Bio-IT World GlaxoSmithKline Reveals Ingenuity

"In a further validation of Big Pharma's acceptance of systems biology, GlaxoSmithKline has licensed part of the Ingenuity Pathways Knowledge Base to facilitate genome-wide computational analysis of biological systems underlying disease."

"According to Frank Mara, Ingenuity's senior vice president of marketing, "GSK will be using the Ingenuity Knowledge Base to internally build systems biology applications. Every biotech group out there should pay attention when GSK licenses this thing.""

Genomeweb GSAC Sashays into Savannah, Starts with Systems Biology

"But major challenges remain in the area of systems biology, Hood said. On the academic level, where centers for systems biology and integrative biology are being established, the biggest challenge, according to Hood, is integration. "How do you create a cross disciplinary faculty?," he asked. "How do you put together the high-throughput technology? How do you deal with salary scales of software engineers and engineers so you doint get funneled off to industry?"

And then, while the centers themselves have received abundant funding, there is the issue of how to fund the research. A major challenge remains in getting the funding agencies, especially at the level of study sections, to understand that systems biology is more than "a big fishing expedition.," Hood said. "But we are pushing to get that.""

redux [09.05.03]
Genomeweb Look Who's Blazing the Systems Biology Trail

"With sights set on provoking the next wave of bio developments, schools including Cornell, Duke, MIT, Princeton, Stanford, the University of California, and the University of Michigan have undertaken bold initiatives to foster cross-fertilization among faculty and students of diverse disciplines. With state-of-the-art labs and mod monikers such as Bio-X and QB3, the programs will push scientists to seek interdepartmental solutions to biological questions raised by, among other things, genome data. And their directors - scientists who've had illustrious careers in biology, computational genomics, engineering, genetics, and medicine - are systems biology's new vanguard."

"As David Botstein, director of Princeton's fledgling Lewis-Sigler Institute for Integrative Genomics, notes, "We're in very early days. What we have here is high concept." But if concepts become reality, the training, research, and technologies that flow from these centers will instruct the future of the field that's becoming commonly known as systems biology."

redux [08.21.03]
Computerworld Singapore Beyond bioinformatics

"Some time last year, the "gene bubble" burst when the investment community became disenchanted with the deliverables of genomics, which were not quite as spectacular as promised. Now, a local researcher has predicted that the current hot topic of bioinformatics will not exist within the next ten years. Instead, its position will eventually be usurped by disciplines such as system biology and transcriptome research, which will be the focus for pharmaceutical research in the near future."

"System biology is an emergent field that aims at system-level understanding of biological systems. While system-level understanding has been a long-standing goal of biological sciences, it was only recently that system-level analysis, grounded on discoveries at molecular-level, could be made."

redux [06.24.03]
Bio-IT World BIO2003: Systems biology leading to advances in IT, medicine

"The study of systems biology, the field of research that creates predictive models of complex biological processes, will lead to advances in pharmaceuticals and medical treatment, but also to advances in computer science, a leading systems biologist predicted Monday.

""I think biology is going to give fundamental new insights to IT," Hood said. "Really understanding the evolution of gene regulatory networks is going to provide completely new strategies for how one deals with this horrendous computational problem of taking big programs ... and restructuring them really efficiently so that you don't restructure them simply by adding more onto them.""

redux [04.21.03]
Bio-IT World In Silico Models with Many More Variables

"One of the critical priorities now is to take all the components we can detect, and reconstruct the interaction networks inside cells that underlie biological processes. This type of reconstruction is very tricky: People call it 'integration of heterogeneous databases.' Collating these data files is like stacking playing cards -- each piece of data stands upon, and influences, the reliability of other pieces.

The next priority is then to generate computer models that can be used for simulations -- in silico biology. There are three categories of models we need to build: models for metabolism, DNA regulation, and cell signaling."

redux [02.2.03]
The Scientist Systems Biology: A Pale Beacon For Biotechs
[requires 'free' registration]

"Systems biology, a siren in a sea of dark prospects, has lured investors frustrated with low returns in biotechnology and anxious to set a new course of drug discovery. Institutions have also geared up training programs, but the excitement in the new field has failed to arrest downsizing in the biotech industry."

"Despite the interest of the pharmaceutical industry, prospective systems biologists should think carefully before investing in training in hopes of landing a job in the new field."

redux [03.08.02]
Science Systems Biology: A Brief Overview
[ summary can be viewed for free once registered ]

"To understand biology at the system level, we must examine the structure and dynamics of cellular and organismal function, rather than the characteristics of isolated parts of a cell or organism. Properties of systems, such as robustness, emerge as central issues, and understanding these properties may have an impact on the future of medicine. However, many breakthroughs in experimental devices, advanced software, and analytical methods are required before the achievements of systems biology can live up to their much-touted potential."

redux [02.26.02]
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 [04.05.00]
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."

redux [01.19.02]
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]
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 [07.13.00]
Nature Segmentation in silico

"A new mathematical biology is emerging. Building on experimental data from developing organisms, it uses the power of computational methods to explore the properties of real gene networks."

"Our understanding of gene networks is at an early stage. We perceive their complexity only after it has been filtered by the limitations of the techniques used to study them. Genome databases and DNA-chip technology, which enables huge numbers of genes to be screened for activity, will undoubtedly provide more, and much more complicated, data than anything produced by Drosophila genetics. If a relatively simple gene network such as the segment-polarity system is hard to understand intuitively, we can be certain that modelling will be essential to make sense of the flood of new data.

But this will not be elegant theoretical modelling: rather, it will be rooted in the arbitrary complexity of evolved organisms. The task will require a breed of biologist-mathematician as familiar with handling differential equations as with the limitations of messy experimental data. There will be plenty of vacancies, and, on present showing, not many qualified applicants."

redux [05.15.01]
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]
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."