Microsoft Research funds genome-related computing work

Microsoft Research announced it will support a number of genome-related research projects as part of its Computational Challenges of Genome Wide Association Studies (GWAS) program. Funding places emphasis on data access and visualitzation tools for scientists working to map the human genome.

 

Among the supported work: Purdue University researches gained support for an effort to build an Interactive Software System for Integrating Clinical Genotyping With Prescription Drug Safety Assurance.

 

Also, the Translational Genomics Research Institute, will work on combining data generated in genome research via a universal data format that would accommodate multiple vendor  platforms into a single file and software library. Johns Hopkins Hospital will work the genes responsible for  Amyotrophic Lateral Sclerosis (ALS) by studying 489 Finnish ALS cases.

 

University of California, San Diego; Division of Computer Science, and the University of California, Berkeley; will look into “Pathway-Based Association: for genome studies. They will look to explain the associations captured by GWAS in terms of known gene and protein interactions by developing computational tools that help explain linkages between signaling, regulatory and  metabolic pathways to the genes that are associated with a disorder.

 

Among other work supported by Microsoft, the University of the Republic of Uruguay; Pasteur Institute at Montevideo will work to define biologiy-oriented data-quality properties.

 

Scientists Explore Human Gene Pool With Help From Microsoft Research – Microsoft, April 18, 2008

 

 

Grid tackles patient outcomes

IBM and several universities have banded together to form a collaborative research effort to create diagnostic tools for predicting cancer patients’ response to treatment.

 

The primary objective of the center is to develop pattern recognition algorithms that can compare data in digitally archived cancer specimens, radiology images and proteomic and genomic data. As such, this effort recalls other IBM-Academic Grid efforts that try to tap data bases of patient outcomes and tests.

 

In the effort, Reuters will address computational and distributed computing issues at the system and application levels. CINJ and Rutgers will develop suitable machine learning, image processing and pattern recognition methods. The NSF will work on autonomic systems and applications. Among other things, IBM is going to provide a pretty psychedelic Grid.

 

 IBM and University Researchers to Develop Research Tools to Improve Cancer Patient Outcomes – IBM.com

From xConomy: BASF bread for polymers; Poitras funds for depression roots study

Read Wade Roush on Boston-area boffin doings. New funds at the McGovern Institute for Brain Research [from MIT alumnus James Poitras and wife Patricia] will go to support research into the genetic and environmental roots of depression. Meanwhile, at Harvard, BASF will find research into building polymer structures that could deliver active-ingredient molecules to specific places in the body. Each of the fundings is pegged at $20 million.

This and more at Xconomy.com

Freeman Dyson Biology on NYRB.com: Woese for the wear

Freeman Dyson writes in the Jul 19 2007 NYRB, “our Biotech Future”; and discusses biology which is ‘bigger than physics’ now in a number of ways. Well, the first premise is true enough. But, as he notes, it is accepted wisdom. Let’s get into which is not accepted and which is not wise, ok? He then starts to discuss genetic engineering, which he indicates is moving now from centrally controlled development to disbursed open system development, and he suspects that the real advances will be on their way now as the same everyday folks who managed, over many eras, to create new types of dog and plant breeds, will be able to work their democratic magic directly on genes soon, moving to the lab what once took place in the hot house or the kennel.

Dyson worked in the company of John von Neumann in the distant past -  after all, John von left our midst in the 1950s -  and he saddles the long-departed Neumann  with blinkers [‘Blinkered vision”] – with the “vision of computers as large centralized facilities.” [Does von Neumann’s late innings’ interest in cellular automata count for anything?] You might think that this infers that Freeman in the 1950s could see what was coming in computers and biology, or at least that von Neumann didn’t see it. Doesn’t this seem a bit unfair? Is a score being settled?

JvN failed to see says Freeman that small and domesticated would be the evolution rather than “big and centralized.” That’s part one.

From there he goes on to talk about Carl Woese and “A new Biology for a New Century” in which he posits the brewing cross breeder wave with the imagined primordial soup of Woese, before the bacteria struck off on its own, began to specialize, before the first species, when all the bits used to intermingle. Hold on to your hats folks, because those funky days are back again. Maybe.

The bit of usefulness here in an largely charming piece is that Freeman explores the notion that reductionist science has reached a deadend, or, to be more faithful, has reached a point where it needs a serious adjunct arm dedicated to holistic system technology. Some of the parts are worth more than the hole.

The piece ends with a bit of a brickbat cast at the Green folks who don’t endorse Green Technology. Freeman Dyson says ‘if the technology is developed carefully and deployed with sensitivity to human feelings, it is like to be accepted by most of the people who will be affected by it.”  But let us face it, the whole antiFrankenfoods movement makes perfect sense as Monsanto and its buddies just darkly at night without much public forum started bringing the genetic engineered produce online. What where has changed? The Monsanto fate should be studied closely, and maybe some one will learn how to behave better. In the mean time, the question is: When the hell was there evey a time when a technology was carefully deployed with sensitivity to human feelings?

Meanwhile one important Freeman question goes begging. How long will it take us to grow plants with silicon leaves?

But dont take my word, read it yourself:
http://www.nybooks.com/articles/20370
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