October 19, 2010

Cloud-Driven Tools from Microsoft Research Target Earth, Life Sciences

Nicole Hemsoth

Following its eScience Workshop at the University of California, Berkeley last week, Microsoft made a couple of significant announcements to over 200 attendees about new toolsets available to aid in ecological and biological research.

At the heart of its two core news items is a new ecological research tool called MODISAzure coupled with the announcement of the Microsoft Biology Foundation, both of which are tied to Microsoft’s Azure cloud offering, which until relatively recently has not on the scientific cloud computing radar to quite the same degree as Amazon’s public cloud resource.

While the company’s Biology Foundation announcement is not as reliant on the cloud for processing power as much as it supplies a platform for collaboration and information-sharing, the ecological research tool provides a sound use case of scientific computing in the cloud. All of the elements for what is useful about the cloud for researchers is present: dynamic scalability, processing power equivalent or more powerful than local clusters, and the ability for researchers to shed some of the programming and cluster management challenges in favor of on-demand access.

MODISAzure and Flexible Ecological Research

Studies of ecosystems, even on the minute, local scale are incredibly complex undertakings due to the fact that any ecosystem is comprised of a large number of elements; from water, climate and plant cycles to external influences, including human interference, the list of constituent parts that factor into the broader examination of an ecosystem seems almost endless. Each element doubles onto itself, forming a series of sub-factors that must be considered — a task that requires supercomputer assistance, or at least used to.

Last week at its annual eScience Workshop, Microsoft Research teamed up with the University of California, Berkeley to announce a new research tool that simplifies complex data analysis that creators claim will focus on “the breathing of the biosphere.” Notice how the word “breathing” here implies that there will be a near real-time implication to the way data is collected and analyzed, meaning that researchers will be able to see the ecosystem as it exists in each moment — or as it “breathes” or exists in a particular moment.

In order to monitor the breathing of a biosphere, data from satellite images from the over 500 FLUXNET towers are analyzed in minute detail, often down to what the team describes as a single-kilometer-level, or, if needed, on a global scale. The FLUXNET towers themselves, which are akin to a network of sensor arrays that measure fluctuations in carbon dioxide and water vapor levels, can provide data that can then be scaled over time, meaning that researchers can either get a picture of the present via the satellite images or can take the data and look for patterns that stretch back over a ten-year period if needed.

It is in this flexibility of timelines that researchers have to draw from that the term “breathing” comes into play. According to Catharine van Ingen, a partner architect on the project from Microsoft Research, “You see more different things when you can look big and look small. The ability to have that kind of living, breathing dataset ready for science is exciting. You can learn more and different things at each scale.”

To be more specific, as Microsoft stated in its release, the system “combines state-of-the-art biophysical modeling with a rich cloud-based dataset of satellite imagery and ground-based sensor data to support carbon-climate science synthesis analysis on a global scale.”

This system is based on MODISAzure, which Microsoft describes as a “pipeline for downloading, processing and reducing diverse satellite imagery.” This satellite imagery, which is collected from the network of FLUXNET towers, employs the Windows Azure platform to gain the scalable boost it needs to deliver the results to researchers’ desktops.

What this means, in other words, is that in theory, scientists studying the complex interaction of forces in an ecosystem and would otherwise rely on supercomputing capacity to handle such tasks, are now granted a maintenance- and hassle-free research tool via the power of Microsoft’s cloud offering.

Like a range of HPC on-demand resources, virtualized or otherwise, this means that scientists are able to shed the responsibility and difficulty of managing their own cluster or other large resource and instead can tap into the power of the cloud to remove the complexity and secure access to scalable, on-demand resources.

As mentioned earlier, part of what makes ecosystem research such an intricate process is that it relies on sharing and collaboration across disciplines along with effective ways to synthesize and then analyze the data in a way that’s relevant for specific purposes. According to Microsoft, “this approach enables scientists from different disciplines to share data and algorithms, helping them better understand and visualize how ecosystems behave as climate change occurs.”

Bringing Scientific Cloud Use Cases to Bear

Microsoft has been steadily reaching out to the scientific community with its Technical Computing initiative and push to its Azure cloud offering. During its eScience Workshop at Berkeley last week, the company also announced the Microsoft Biology Foundation (MBF), which is being made available to scientists in the areas of bioinformatics and general biology. In essence, this is a toolkit to help scientists share and access vital resources, computational and otherwise.

According to Microsoft, “This programming-language-neutral bioinformatics toolkit was built as an extension to the .NET framework [and] serves as a library of commonly used bioinformatics functions. MBF implements a range of parsers for common bioinformatics file formats; a range of algorithms for manipulating DNA, RNA and protein sequences and a set of connectors to biological Web services as the National Center for Biotechnology Information BLAST.”

During the MBF announcement, Microsoft stated that several universities and enterprises were already using MBF as a foundation for a number of experimental initiatives that would better equip scientists and clinicians with what they needed to leap key technological barriers and come up with better ways of researching and developing biological data-driven initiatives.

Although the news does not emerge daily, or sometimes even weekly, there are some fully functional cloud computing experiments and full-fledged initiatives underway at a number of institutions and companies, particularly in the biosciences. UC Berkeley is a hotbed of scientific cloud experimentation and this particular project brings Microsoft with its Azure platform into play, which in the case of Berkeley, is not always as prevalent press-wise as their work with Amazon’s cloud.

While life sciences companies and bioinformatics are the areas that seem to garner the most attention, in part because some of the analytics applications are often ideal workloads to shuffle out to public cloud providers since they do not require snappy low-latency networking and are often “bursty” in nature (i.e., the need for such processing fluctuates wildly), it is no surprise that cloud providers are making big noise about their work in scientific computing — especially in the biological realm.

This latest branch out into the environmental and ecological end of the spectrum, both with its MBF and MODISAzure announcement, brings Microsoft a few steps closer to becoming a real contender for AWS on the scientific cloud front. While there are Azure use cases for science and research, since Microsoft’s offering is a bit younger than AWS, it hasn’t received quite the same level of glory.

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