Harvard IIC
Science + Computing = Innovation
The B5 star forming region in 13CO as displayed in OsiriX. The color scale represents the intensity of the gas emission.
In a computing landscape filled with web programmers, database developers, and application engineers, the “science” part of computing is often left out or ignored — in fact, a layperson might think there is little difference between “computer science” and “scientific computing.” Scientific computing has become one of the most important disciplines of our time, but unfortunately, much of the scientific community has relegated vital development of new tools for computational science to staff and students rather than collaborating with their peers. Optimally, this work should be a joint effort between the best traditional scientists in the world and the best computer scientists in the world — which is exactly the makeup of the Harvard Initiative in Innovative Computing (IIC).
Alyssa Goodman, Ph.D., Director of the IIC, says, “What we really wanted was peer collaboration. The future of traditional disciplines of science — life sciences, physical sciences, and medicine — depends on advances in computational science in the same way that we depended on instrumentation in the previous century. Science now depends on instrumentation and computation; therefore, people from both backgrounds should work together to solve these problems. Harvard IIC was the outgrowth of this.”
“Computer scientists and scientists can work together as peers, each with their own strengths, to make innovations that nobody has even dreamed of before.”
Disparate Disciplines Unified by Mac OS X
By definition, the Harvard IIC is composed of scientists with vastly varied backgrounds. The group thrives on differing perspectives which lead to novel approaches to both emerging and long-standing problems. A quick read of their project leads jumps from astronomers to biologists, neuroscientists, physicists, psychologists, mathematicians, and of course, computer scientists. It seems far-fetched that this group could agree on anything, but most do agree on one thing — the technology that will help them achieve their goals.”
Goodman says, “I’d say 95% of the people most directly involved with Harvard IIC choose Mac as their primary platform. It is funny; if you walk in here, you would think we were sponsored by Apple.”
The scientific community is unique in that computational research has traditionally been UNIX-based, but the connection between researchers and universities has fostered a Mac-friendly environment for decades. As Apple transitioned to Mac OS X, it quickly became evident to researchers that they no longer needed separate systems to do UNIX-based research and productivity work.
Goodman says, “I have removed my UNIX-only workstation from my desktop — and most of my graduate students have as well. We still use them, but they are in the background, and we use the UNIX interface in the Mac to directly interact with other UNIX hardware and software. Our Systems Engineers also use Macs now even if they don’t open anything but X11. They are usually converts from Linux rather than from UNIX, which has been the most recent migration.”
Astronomical Medicine
The flagship and founding project run by the IIC’s diverse group of scientists is affectionately called Astronomical Medicine. A joint National Science Foundation (NSF) and National Institute of Health (NIH) conference led to a meeting between Alyssa Goodman, Ph.D. and Michael Halle, Ph.D. — an astronomer studying the formation of stars and a computer scientist developing groundbreaking medical imaging software. Goodman had a problem — there was a lack of powerful 3D imaging tools available for the visualization of astronomical data. Halle’s research group had a potential solution — they had been working hard at perfecting a multi-platform open source medical visualization tool, 3D Slicer. Their meeting, combined with Halle’s boyhood penchant for stargazing, gave birth to an idea; Goodman, Halle, and a particularly bright Harvard undergraduate student, Michelle Borkin, would collaborate on an experiment to use 3D Slicer to visualize astronomical data.
Goodman says, “The only way you can understand large volumes of tremendously complex information is to explore it graphically. It allows you to think about things in new ways.”
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At a Glance
The Harvard Initiative in Innovative Computing (IIC) brings scientists together from multiple disciplines to work with their peers in computer science to discover new approaches for solving disparate problems with common threads. Initial advancements include a pilot project to use 3D medical imaging software in astronomical exploration — going as far as navigating the stars using a 3D human head, designed as an interface for brain MRIs.
Apple Solution
In an organization that is defined by diversity, Mac OS X has become a unifying platform for scientists at the Harvard Initiative in Innovative Computing (IIC). Almost every member of the program uses Macs for either development, productivity, remote UNIX access, or as a single do-it-all solution for all of the above.
A Subset of Harvard IIC Projects
The Connectome
To gain a better understanding of mammalian neural circuitry, researchers create a wiring diagram of brain tissue with slices of very high-resolution electronic microscope images which are merged to create a 3D volume. Each image in these multi-Terabyte datasets contains 1014 voxels of information stored in multi-100GB images. Along with the traditional science implications of this study, the Connectome project will study the computational challenges of processing and visualizing massive datasets.
Data-Intensive Science and High-Capacity Scientific Databases
Technology has delivered unprecedented quantities of data to scientists which can be used to better understand the structure of the early universe. The IIC’s scientists are finding new ways to deal with these massive datasets by leveraging multiple computing models including new methods for loosely coupled problems suitable for grid computing, tightly coupled problems not suitable for clusters, and problems which are dependent on massive data storage.
Genepattern and the Virtual Data Center (VDC)
The similarities in statistical analysis of biomedical and social science research have led the IIC to examine the cross-discipline applicability of software design for each field. Scientists are working to combine the capabilities of the Zelig statistical framework for Social Sciences and GenePattern — a genomics analysis application, as a first step to supporting a pipeline of tools and data that will bridge multiple disciplines.
National Virtual Observatory Portal
A Google-like middleware layer connecting archives of Astronomy data including images, spectra, data catalogs and journal catalogs could someday make the possibility of doing “Astronomy by database” a reality. Researchers are building on existing National Virtual Observatory (NVO) tools to unify currently available — but difficult to access data — into an intuitive graphical entry point.
The IC 348 star forming region in 12CO as displayed in OsiriX. The color scale represents the intensity of the gas emission.