Science for the 21st Century, part 2

robk — Thu, 06 Mar 2008 03:23:00 GMT

With a grounding in what the European Science Initiative is trying to accomplish, and the reasons why, I then stepped across the aisle in the Rainierr/St. Helens room of the Microsoft Conference Center to get a feel for the individual demos on display in the Science for the 21st Century booth.

Leeza Pachepsky is showing Visualizing, Modelling and Analyzing Complex Networks, a project devised by Microsoft Research Cambridge colleague Rich Williams:

"I'm presenting 3-D software for understanding complex networks--in particular, describing who eats who in a ecosystem, as simple as lion seeks antelope, antelope seeks grass. But the real networks are much more complex. This software allows you to run different analyses and also to see what happens if you add or remove a species in an ecosystem. This could help us understand potential changes that climate changes could bring to our ecosystem, or, for example, to construct an artifical ecosystem. The network software is general in the sense that the network analogy and analyses can be applied to many other systems, for example, computing and social networks."

Andrew Phillips discusses Visual Programming of Gene Networks and Biological Pathways, which employs SPiM, functional program code used to constuct graphical representations of biological systems that can be tested in a lab environment.

"Essentially, this stems from a revolution we're seeing in medical research," he says. "Scientists understand more and more molecular details of biological systems, so they're building complicated models, and we're developing a programming language for biology in order to help some of this. We're developing a language that enables a very complicated model to be split up into smaller building blocks that can simulate and analyze these parts of a biological system.

"I'm working with a range of collaborators around the world in building models of biological systems. One of these models is a pathway of the immune system on which we're running simulations. We're basically using techniques from computer science and parallel systems in order to model biological systems and understand reverse-engineering of biological systems."

Robin Freeman is researching Autonomous Monitoring of Vulnerable Ecosystems:

"This allows us to monitor, in real time, changes in organisms within vulnerable environments. We're mining sensor networks, GPS, and a variety of Microsoft software to bring the data back in real time to researchers on their desktop and enable them to both monitor and analyze changes in these vulnerable environments.

"The advantage that gives us is that though we know some things about changes in climate, we don't know how they affect the organmisms in these sensitive environments. An understanding of that, in a variety of different environments, gives us an idea of an early-warning system for ecological changes which we can make to go in and preserve and manage the organisms better."

Martin Calsyn speaks about the DISCOVERY environment, a product of intensive development work by Andreas Heil:

"We now have, with the new age of computational science, an unprecedented demand for computational cycles and resources. Luckily, we have an unprecedented ability for computational cycles and resources. But we have a huge chasm between the users and the resources. What I'm trying to do with the DISCOVERY environment is bridge that chasm. You could boil it down to a cliche by saying less plumbing and more science. We don't want our computational climatoligists, biologists and ecologists to become domain experts in computer science. We want them to spend 80 percent of their time on their work.

"DISCOVERY has a couple of main, featured components. One is clouds, which represent communities. A community is something into which you can put people, resources, and data. By resources, I mean a peer-to-peer collection of computers that form a peer-to-peer grid and use the idle cycles on the computers in your community. We have a workspace, a journal that's replicated in space. Everybody in the community gets a copy, and I can go back in time and make strong statements about the provenance of my data and my visualization results.

"I have the ability to build UI, and when I'm happy with the UI, I have the ability to publish that UI, in the form of a standalone .exe or a Web application, so when I do my peer-reviewed paper, it goes up on the Web. That's DISCOVERY."

Drew Purves, who is leading the Understanding and Predicting Forest Dynamics project wasn't able to make the trip from Cambridge to Redmond for TechFest, but his Web site provides insight:

"Forests harbor around 60 percent of the world’s biodiversity and around half of its terrestrial carbon, so there is an urgent need to predict how forests will respond to continuing anthropogenic perturbations including increased atmospheric CO₂, logging, and land-use change. A new toolbox of techniques for understanding forests--consisting of a new kind of simulation model, new analytical techniques for understanding the model, and new statistical techniques for parameterizing the model using widely available inventory data--is beginning to deliver a fundamentally new, quantitative, and predictive level of understanding of how forests work."

Whew. Forest dynamics, ecosystem modeling, immune-system pathways, complex modeling, tools for computational life sciences. When the European Science Initiative produced its Towards 2020 Science report a couple of years ago, it represented nothing less than a clarion call to the scientific community, and it's fascinating to see how that call is being answered.

Bryan Barnett (left), business manager for Microsoft Research's External Research group, engages in a TechFest chat with Alexander Brändle, head of technology for the European Science Initiative.

Stephen Emmott on 21st Century Science

robk — Thu, 06 Mar 2008 02:07:00 GMT

Next, I wandered over to a mega-booth from Microsoft Research Cambridge called Science for the 21st Century, featuring no fewer than six demos. There was a lot to absorb, so before diving in, I found Stephen Emmott, director of the lab's European Science Initiative, to get a quick overview. In four short minutes, he provided a comprehensive look at his group's motivations and priorities, so I thought it best to stay out of his way and let him explain away:

Stephen Emmott

"All the demos we've got here, the thing that ties them all together is the thing that ties all of our work together, which is our focus on developing new conceptual methods, techniques, and tools for helping scientists model and study complex biological systems.

"Understanding complex natural systems is rapidly becoming the most important and active area of science, certainly for the next 50 years, and the reason for that is because it's where the greatest scientific and societal challenges are: understanding biological systems, living systems. After 50 years of spectacular success in molecular biology, we still don't know how a cell works. And that's going to require building models of complex organisms.

"On the other hand, understanding what's happening to climate change and environmental change ... a lot is known about the physical aspects of climate change to do with carbon, but virtually nothing is known about the other important aspect about what regulates climate change, which is the biosphere, the biological components like the Earth's forests. So we've got the Forest Dynamics project here, which is modeling the relationship between forest dynamics and climate regulation.

"Interestingly, complex natural systems are also where the biggest societal, social, scientific challenges are.The biggest technological, economic opportunities for growth over the next 50 years are also around understading complex natural systems. If we can understand biological systems, it would, in medicine for example, revolutionize our ability to understand and treat disease. And it would probably revolutionize our ability to build novel, biological-based energy sources.

"One of the most efficient users and converters of energy on the planet are plants, and we don't know how they do that. If we understood how they do that, we'd have a big energy- and technological-innovation opportunity.

"The one thing that underpins the proper development of a science of complex natural systems is models and modeling. A lot of data is already known, so it's a question of how you bring all that data together. That's why we focus on complex natural systems, and that's why we focus on modeling and new modeling techniques.

"If we can crack even some of those problems, it would give us enormous insights into how we can think about a model and build much more complex engineered systems, software systems. There's an interesting interplay between understanding and doing science and its impact back on computer science and, naturally, our software engineering. That's the main motivator for everything that we're doing."

TechFest Live! : European Science Initiative

Science for the 21st Century, part 2

Stephen Emmott on 21st Century Science