Wednesday, May 31, 2000

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BBC Scientists plan a virtual plant
"A group of plant scientists are calling for a project to understand the biological machinery of a plant in enough detail so that they could construct a 'virtual' plant. "

"The effort is called Project 2010 because by 2010 plant researchers hope to construct a complete "wiring diagram" of all the biological pathways of Arabidopsis.

Dr Chory said, "Ultimately, we hope to create a 'clickable plant.' We want to be able to go to our computers and click on a cell type and understand all the protein-protein interactions."

redux [05.07.00]
Bioinform Academic-Industry Initiative Will Develop Bioinformatics Tools to Model Living Cell
"A team of researchers led by Bob Franza of the University of Washington here is developing bioinformatics tools to create a quantitative model of the living cell.

The Cell Systems Initiative was launched late last year, and thus far has attracted the support of two corporate backers who would like to mine the data it generates to identify new drug targets."

"The goal, according to Franza, is to understand the stages of a cell's development. "How does one stage know when it's supposed to start and stop?" Franza asked. "How do we reconstruct the temporal process?" A complete model of the living cell will need to be understood not as parts, but as components of a continuous system, he said. To that end, the initiative also aims to build a computational infrastructure that can manage the entire dynamic system of data collection and integration."

redux [02.24.00]
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."

Biospace Virtual Drug Development: Start-ups Put Biology in Motion
"One way of animating our growing store of static information is through computer simulation. It is an area that is beginning to emerge slowly in the life sciences, with only a handful of academic and commercial players active in the area. But for a fledging discipline, there is a great variety in the scope of work being undertaken. While academic labs try to create accurate simulations of red blood cells and simple bacteria, the private companies are taking on bolder projects--simulating human organs and even human diseases in their entirety."

Science Revealing Uncertainties in Computer Models
[summary - can be viewed for free once registered]
"Computer simulations give the impression of precision, but they are founded on a raft of assumptions, simplifications, and outright errors. New tools are needed, scientists say, to quantify the uncertainties inherent in calculations and to evaluate the validity of the models. But making uncertainties evident is a tough challenge, as evidenced by several recent workshops.”

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."

The Institute for Systems Biology What is Systems Biology?
"Systems biology is a unique approach to the study of genes and proteins which has only recently been made possible by rapid advances in computer technology. Unlike traditional science which examines single genes or proteins, systems biology studies the complex interaction of all levels of biological information: genomic DNA, mRNA, proteins, functional proteins, informational pathways and informational networks to understand how they work together."