Wednesday, September 06, 2000

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UNISCI Nobelist To Lead Web-Based Project On Cell Signaling
"Nobel laureate Dr. Alfred Gilman, chairman of pharmacology at UT Southwestern Medical Center at Dallas, will lead a $10 million-per-year project allowing researchers around the world to pool their efforts in studying one of the biggest unsolved problems in biomedicine -- how cells interact with, or signal, each other."

"Work of these Alliance for Cellular Signaling (AFCS) researchers in the post-genome era ultimately could lead to the development of a "virtual cell" that could be used to test new drugs.”

"When we have a complete virtual cell, it can be used as a drug discovery engine to test drugs on the computer, rather than on cells or animals. It would be a wonderful way to understand what the optimal point would be to place a drug to achieve a specific goal in a specific patient in a specific kind of disease," Gilman said."

"NIGMS has called the AFCS funding "glue grants -- grants to glue together different sorts of people for a common goal," Gilman said. "We actually are gluing together people's brains and their ideas, but the research is not going to be done in their individual labs."

Instead, the researchers will use the Internet as their joint laboratory."

The Alliance for Cellular Signalling General Goals and Statement of Purpose
"The current and pending availability of complete genomic sequences inspires confidence that complex biological phenomena and systems can be understood completely. These feelings are heightened by rapidly expanding capabilities to manipulate gene content and expression in mammalian cells and organisms, detect protein-protein interactions, and quantify the activities of macromolecules in vivo. Such understanding implies the capacity to predict quantitatively the altered behavior of these systems that results from their genetic or environmental (including pharmacological) perturbation. We can envision, rather than simply imagine, the construction of a virtual cell."

The overall goal of the Alliance for Cellular Signaling is to understand as completely as possible the relationships between sets of inputs and outputs in signaling cells that vary both temporally and spatially. The same goal, stated from a slightly different perspective, is to understand fully how cells interpret signals in a context-dependent manner. This will involve identification of all the proteins that comprise the various signaling systems, the assessment of time-dependent information flow through the systems in both normal and pathological states, and finally the reduction of the mass of detailed data into a set of interacting theoretical models that describe cellular signaling."

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 [08.04.00]
Software Carpentry Internet Groupware for Scientific Collaboration
"The Web was invented so that scientists could use computer networks to collaborate -- that is, exchange documents, discuss them, coordinate work, create and publish collective knowledge. It was, in other words, supposed to be a groupware application.

Despite the popularity of the Web -- or, perhaps, because of that popularity -- it has yet to fulfill that original mission. Today's Web is more like a shotgun marriage of electronic publishing and broadcast television than it is like an engineered solution for group collaboration. True, the Internet empowers today's working scientist in ways only dreamed of even a decade ago. Yet our use of it often remains rooted in pre-Web idioms and habits -- partly because we don't fully exploit today's Internet communication tools, but mainly because we're still missing key tools and infrastructure."

"The goal of Internet groupware should be to reclaim the original vision of the Web as a medium of collaboration. It's no accident that vision arose in a scientific milieu since the enterprise of science is so deeply rooted in collaboration.

This report ends with two final messages. First, we're closer to the two-way Web than we realize. Services such as TimeDance, QuickTopic, Manila, and Meerkat are already making it easier than ever to create and use shared information spaces. They aren't final solutions, but we should use them for all they're worth, and watch for new kinds of collaborative services that are emerging every day. Only by using these services in their current form will we discover, collectively, what they need to evolve into.

Second, the roadmap to the future is coming more sharply into focus. The first-generation Web, though remarkably powerful, is an awkward combination of many different protocols and data formats. The emerging consensus around XML, as a universal way both to interconnect services and to represent many different kinds of information, is the key to a next-generation Web that may finally start to deliver on the collaborative vision of the original. There's nothing magical about XML. It isn't pixie dust. It doesn't, in and of itself, help us collaborate. What will help is messages, documents, applications, and services that all agree on a standard way of representing data -- one that's richer than the line-oriented ASCII we've used so long and so well. That standardization is now occurring. We should welcome it, and we should demand that our tools respect and embrace it."