As informatics pacesetters, IU researchers are affecting knowledge use and transfer across all disciplines
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The work being done by IU Informatics researchers like Larry Yaeger, an artificial intelligence expert, and Mehmet Dalkilic, a bioinformatics specialist in gene networking, is as much about the search for and identification of exacting, quantifiable new tools and methodologies that can empower other scientists as it is about Yaeger or Dalkilic attaining their own unique "Eureka!" moment.
Informatics is the new kid on the academic block and Indiana University, which in 2000 was the first university in the nation to designate a School of Informatics, is that new kid putting its best face forward. With five years of maturation, IU again became an informatics pacesetter, offering the first Ph.D. in the discipline.
In practice, informatics feeds off interdisciplinary opportunity by saddling information technology onto any other discipline, no matter how ancient, that is then willing to run with its applications. And as computing power has accelerated and vast amounts of information have become digitally mobile, the science of providing previously unfathomable amounts of information to needy surgeons, physicists, artists or engineers has taken on phenomenal importance.
"Informatics and computing impact virtually every aspect of daily life," said Bobby Schnabel, dean of the IU School of Informatics. "Faculty and students at the School of Informatics are at the forefront of creating technical innovations in computing and applying them in novel ways to a wide range of fields."
From finding a cure for cancer, as IU bioinformatics researcher Yaoqi Zhou hopes to help do, to insuring that an expanding aging population is afforded maximum safety and happiness in those waning years, as informatics professors Kay Connelly and Kalpana Shankar want to accomplish, informatics applications are now being woven into every discipline and vocation that relies on information. And what discipline or vocation, Connelly or Zhou might ask, wouldn't benefit from easy access to what is realistically becoming a store of unlimited information?
One all-encompassing example of informatics' effects on knowledge use and transfer is the National Science Foundation's TeraGrid, a cyber-infrastructure project designed to accommodate scientific research across the country. Supported by a group of researchers from IU, including some of the founding faculty of the IU School of Informatics, along with 10 other resource provider sites, the TeraGrid is the world's largest and most comprehensive cyber-infrastructure for open scientific research. It holds more than 100 discipline-specific databases while offering more than 250 teraflops of computing power and 30 petabytes of storage.
"It would take 1,000 people doing one calculation per second on an electronic calculator over a period of 30,000 years to do what the TeraGrid can do in one second," said Craig Stewart, executive director of IU's Pervasive Technology Institute. "This is the sort of computing power that is created, in part, by innovations of IU School of Informatics researchers and that is used by those same researchers to enable new discoveries."
Not unlike TeraGrid, the work being done by IU informatics researchers like Larry Yaeger, an artificial intelligence expert, and Mehmet Dalkilic, a bioinformatics specialist in gene networking, is as much about the search for and identification of exacting, quantifiable new tools and methodologies that can empower other scientists as it is about Yaeger or Dalkilic attaining their own unique "Eureka!" moment.
IU President Michael McRobbie drove that philosophy home recently when, during remarks while breaking ground for a new IU Bloomington business incubator where work would be focused on information technology, he touted the importance of making technology more mobile.
"One of this campus' greatest strengths is basic scientific research, as scholars fully and freely explore their research interests. As such, our scholars create a vast reservoir of knowledge and innovation. As a public university, we have a responsibility to transform and mobilize that knowledge and innovation in order to benefit the public," he said. "In essence, this incubator allows us to more efficiently transform the knowledge and innovation gained through basic research into products, services and, ultimately, into jobs that help stimulate local and regional economies."
Frank Tai, Brad Gessler, David Roedl and Will Odom, all recent IU informatics graduates would likely agree that what McRobbie hopes the new incubator will do for Bloomington and the region -- build a path from education to research to jobs -- the School of Informatics has already done for them.
Tai, a 2007 informatics master's degree graduate, left his research in bioinformatics to take a West Coast job at Pixar, the world's cutting-edge special effects movie studio. He's now helping design characters and sets for major motion pictures.
Gessler graduated in 2004 and then found a venture capitalist willing to fund his Chicago-based Poll Everywhere, a startup company that uses cell phone technology and specialized software to do polling at meetings, rather than by renting or buying key pad systems.
And Roedl and Odom, since last year winning the world's premiere student technology competition, Microsoft's Imagine Cup, have gone their separate ways with Odom now a Fulbright Scholar working in Australia and Roedl in Washington, D.C., working for a Nokia-subsidiary as a user experience designer.
From social science and artificial life to cancer and gene research, follow the work of five current informatics researchers through a series of vignettes that connect current research, while accelerated by information technology, to future possibilities:
Larry Yaeger
An 'ecology' called Polyworld: Network science, neural complexities
If the late evolutionary biologist Stephen J. Gould and his longtime counterpart Richard Dawkins could have had a wrestling match over the driven vs. passive evolution of complexity, you could have counted on informatics professor Larry Yaeger to be wedged between them as a fair referee.
"Is it natural selection or is it random?" Yaeger wondered of the two. "It turns out they were both right, sort of, and that they were really arguing from different scales."
But Yaeger's neutral observer status could all change with the ongoing evolution occurring in his second-floor informatics office on East Tenth Street in Bloomington, where Yaeger's simulation of interacting organisms -- with brains specified by neural connection densities, synaptic learning rates and other components of neural complexity -- is ever progressing in a computational ecology he has designed called Polyworld.
Using a "survival of the fittest" scenario to foster evolution within this electronic environment that attempts to mimic the characteristics that influence living organisms, Yaeger sets food-seeking, offspring-bearing populations of color-differentiated, fractal-like creatures out into a world influenced by computer-coded language.
"Network science is pretty much affecting everything today, so if I can make this research useful in that realm it could open up new opportunities for cooperation," he said. "I'm basically doing network science in an artificial nervous system in an effort to better understand different aspects of neural architecture, like what type of architectures give rise to complexity."
With genes built into his creatures, Yaeger and evolution can control the energy used by a creature to give birth, or at a more complex level, determine how many of any given influential neurons might cluster together in order to generate higher level behaviors.
"Environment is not a fixed thing and not all niches are created equal," Yaeger noted. "There are ways for Polyworld to have niches that are the equivalent of thickets or streams, which should help foster speciation, and maybe foster the equivalent of an arms race."
Before coming to IU to resume the study of artificial intelligence and how it might inform evolutionary principles, a project he said had been at the time "lying fallow for 12 years," Yaeger had tread a career path punctuated with fascinating milestones.
Imprinted by a father who as a Pan American Airlines mechanic thought designers were the "coolest," Yaeger studied aerospace engineering while earning a bachelor's degree at Purdue and then an master's degeree on the subject from PolyTechnic Institute of New York. Working for Grumman Aerospace, Rocketdyne and Poseidon Research, he created some of the first-ever flow field simulations for submarines and the space shuttle program.
Through much of the 1980s, having experienced a self-described conscious shift, he worked for Hollywood industries, winning Clio Awards for computer graphics in commercials and generating special effects and providing technical direction and guidance for internationally recognized movies like The Last Starfighter, Labyrinth and Terminator II.
By the time he came to IU in 2004 he had spent almost 20 years at Apple Computer, which he left as an Apple Distinguished Scientist credited with developing, among other things, the company's handwriting recognition software that was used in the Apple Newton and Mac OS X's Inkwell products.
"Today I'm in the process of trying to quantify progress and success in Polyworld, and I believe we've worked out some quantitative measurements using complexity theory," Yaeger said. "With these metrics in place it's possible to monitor progress and better determine how to proceed. And it turns out I can use these measurements to address issues about the growth of complexity over evolutionary time scales, and the relationship between network form and function."
To that end, Yaeger, along with Olaf Sporns, professor of psychological and brain sciences, and fellow informatics professor Alessandro Flammini, have pending a pre-proposal with the National Science Foundation they hope will lead to funding further advances in the effort to connect the essential characteristics of biological brains with information processing in artificial neural networks.
Yaoqi Zhou
Proteins, the work horses of all living things (sometimes they misbehave)
Zhou is working to predict the future. Not the weather, nor the stock market, nor the outcome of the NCAA basketball tournament. For Zhou, predicting the future means recognizing the causes of lung cancer, mad cow disease or cystic fibrosis, and then identifying how to create the drug that might prevent, stop or reverse those diseases. Zhou, director of the bioinformatic graduate program at the SchooI of Informatics at IUPUI, is working to predict how those long chains of amino acids called proteins -- the work horses of all living things that help regulate growth, move oxygen in the bloodstream, even make firefly's glow -- can sometimes misbehave.
"Proteins are one of the most essential components in the cellular machinery of any living organism," said Mathew Palakal, director of the Informatics Research Institute at IUPUI and associate dean of graduate studies and research. "Almost all diseases can be related to the function or malfunction of certain proteins."
The protein hemagglutinin, for example, assists flu viruses in invading the body, while other misbehaving proteins -- in this case those that fold into improper shapes or structures -- are the basis for brain-degenerating diseases like Lou Gehrig's, Parkinson's and Alzheimer's.
So Zhou figures that if you can first understand and then predict through bioinformatic computer simulations and statistical mechanics theories the mechanisms behind protein folding the foundation could be set for creating drugs to address problems, like diseases, that result from protein misfolding.
Pressure on scientists to predict the three-dimensional structure of proteins has never been greater as DNA sequencing efforts like the Human Genome Project have provided huge amounts of data on the amino acid sequences of proteins, which is one of the initial steps in being able to determine protein structure. That sequencing work has outpaced protein structure prediction, a process that could lead to advances in drug design and the creation of new enzymes through biotechnology.
Scientists know protein function is based on shape, and they also know all proteins consist of some combination of only 20 amino acids. The problem is knowing, or predicting, how any sequence of the amino acids will act to develop protein shapes that consist of a beautiful yet not fully understood array of amino acid sidechains, helices and beta sheets.
"In our ongoing quest to discover novel drugs that can cure complex diseases like breast cancer and others, the focus is on discovering personalized drugs that can be more health and cost effective," Palakal said. "An essential ingredient to understand diseases and develop personalized therapies is to discover the underlying biological processes on how proteins fold and interact. Professor Zhou's high profile research is focused on understanding the intricacies surrounding the complex processes that ultimately will lead to new drug discoveries."
That work has been facilitated by an increase in computer power and new algorithms that have allowed Zhou to take a bioinformatic approach, via Zhou's physics background, in developing tools now being used to align protein sequences, predict protein structures and protein stability and predict protein-ligand binding affinities.
In also turns out that experimental physics, Zhou's forte, has provided some of the most important tools for studying proteins, like capturing images at one photo per millisecond of proteins folding using kinetic terahertz absorption spectroscopy. Other protein study techniques using tools first employed by physicists include the use of magnetic resonance and x-ray crystallography, as protein molecules are too small to study with a microscope.
First trained, as he says, "as a theoretical physicist in a chemistry department," at the University of Science and Technology, Anhui, China, Zhou earned a Ph.D. in chemical physics from State University of New York, Stony Brook. He did post-doctoral work in chemical engineering at North Carolina State University for a year before going to Harvard University for five years of post-doctoral work in computational biophysics. He came to IUPUI in 2006.
Zhou has published more than 100 academic papers and book chapters, including seven either already published or slated for publication in 2009.
Kay Connelly and Kalpana Shankar
Studying the ethics of home-based technology in senior health, well-being
It's called everyware. Grandkids chattering competitively over online microphones while in the midst of a Wii video game with their significant elders a thousand miles away. Iraq War amputees rocking a Guitar Hero game modified so the hand-controlled whammy bar is operated with a foot pedal rather than a second hand. Mom gazing over the evening dishwater to the Microsoft Whereabouts Clock that displays, using cell phone technology, where everyone in the family currently is -- work, outdoors, school or home.
It's called everyware, and one of the things informatics researchers Kay Connelly and Kalpana Shankar want to explore are the ethical implications of technology as it becomes more and more embedded in every aspect of life.
"People often think technology is ethically neutral, and it is not at all," said Connelly, an informatics assistant professor whose work involves the implications of technology on the human experience, and if people are willing to compromise values like privacy and autonomy in exchange for things like convenience. "One of the ethical implications we are looking at is with populations considered at-risk and whether we, while trying to make caregivers' lives easier through technology, may also be ignoring important issues of privacy and autonomy of the people being cared for."
Connelly is a co-investigator on the ETHOS Project (Ethical Technology in the Homes of Seniors) with three other professors -- Informatics' Kalpana Shankar and Jean Camp and HPER's Lesa Lorenzen-Huber. Shankar, whose research focuses on the social and ethical dimensions of technology, is also interested in how home-based technologies may be positive or negative influences on quality-of-life issues for the aging.
Funded with $820,000 from the National Science Foundation, the ETHOS project looks at the implications of new technology applications for elders in both independent and assisted living scenarios, including Bloomington's Meadowood Retirement Community.
One example of a new technology in an independent setting that has important privacy issues is a home monitoring system developed by professor Camp that uses cameras, computers and cell phones to photograph front-door visitors. The cameras are triggered by the ringing of the door bell or an opening of the door, sending photos to pre-determined recipients like family members or health care workers. It could be used in the care of in-home Alzheimer's disease patients to detect wandering or as a security device to detect intruders.
Another new technology that is less invasive would be an adaption of the popular interactive Nintendo gaming product Wii. Connelly and Shankar believe that some tweaking or re-design could translate into new quality of life opportunities for the aging.
"One thing we have been working to do is put Wii in Meadowood and then looking at what kind of engagement will happen," Shankar said. "For example, a timid person may just want to sit and watch until their comfort level increases to the point where they may be more willing to engage."
A related component to that research will allow two undergraduate students, Katie O'Donnell and Claire Alvis, to study gaming interactions, conduct interviews with participants and develop Wii games that might be of interest to senior citizens. The project incorporates human-computer interaction, design research, technical implementation and information ethics, and could help lead to a better understanding of user acceptance and involvement patterns, social networking opportunities and cognitive decline.
Funding with a grant from the Computing Research Association Committee on the Status of Women in Computing Research, the undergraduate research experience allows the ETHOS professors an opportunity to address another aspect of technology near and dear to both Connelly and Shankar: increasing the number of young women entering science and technology fields.
"Computing is difficult compared to other studies right off the bat because it is not offered in high school that much," Shankar said. "Computing is one of the least-balanced fields in terms of the ratio of women to men and research points to different things for that, including the perception of what someone in computer science or informatics does. There is research pointing out that when real-world problems are taken up, women find the field more appealing."
Working with Connelly and Shankar, the students will design a Wii game, implement it with senior citizens, gauge its success and then determine whether it might be worth implementing with a competitive component that would allow people to challenge each other. Each step is designed to deliver a two-fold experience for the students of gathering feedback from potential users, and then using that feedback to support game development.
"If the game doesn't work we'll rethink it and see what it needs to look like," Connelly said. "This project is really in its beginnings and right now one of the things we are doing is asking the students to look at just what the universe of opportunities is."
Whatever the results of the undergraduate research project, the data should have value for the ETHOS project and its broader look at everyware, which is also known as ubicomp, a portmanteau for ubiquitous computing and the associated technology appearing more and more in everyday objects and activities.
"A lot of what people are looking at is technology that doesn't look like technology," Shankar said. "We are very concerned in our research group about taking a critical stance and then evaluating the implications of what we do or don't have control over. What are we stuck with? What changes can we make? What values are implicit, emergent, or unexpected in the technologies we create? And how do we maximize good and minimize harm?
Mehmet Dalkilic
Data mining the fruit fly's encrypted genome post-sequencing
When the genetic makeup of the common fruit fly Drosophila melanogaster was sequenced in 2000, it opened up a world of networking opportunities for informatics professor Mehmet "Memo" Dalkilic, although even for a technologically advanced data miner like Dalkilic, it would not be networking in the traditional sense.
Dalkilic recognized the Drosophila sequencing represented an opportunity to use his technology-fueled skill at digging up hidden information submerged in huge amounts of data to look at the newly available information encrypted in the fly's genome. With enough effort one could try to develop a new network based on gene interaction that could be used to draw conclusions about biological processes specific to the fly and possibly a global view of how the genes in any given process function.
"Our goal is to demonstrate that by adopting a logic theoretic framework, large and diverse data sets acquired from studies of a complex metazoan (i.e., the fruit fly) can be integrated to provide a meaningful gene interaction network," said the director of graduate programs at the School of Informatics.
Already knowing that about three-fourths of all human disease genes have a recognizable counterpart within the genetic code of the fruit fly, scientists like Dalkilic are working at a frenzied pace to not only learn what the contribution of each gene is in the genome, but also to be able to measure and model them using data sets. Once complete, scientists might better understand gene relationships, gene function and how information flows through gene protein networks.
Chris Meyer
School of Informatics Ph.D. student Jim Costello studies gene networks in Drosophila melanogaster.
For Dalkilic, along with the assistance of Ph.D. student James Costello, this accruing and networking of genome-scale data is taking shape in the form of Indigene, their project to gather information on the fruit fly's DNA, RNA and associated proteins. They then want to combine that information with known information on which genes cause which phenotypes, or actual traits, in the fly and then devise a theoretical framework to create a meaningful gene interaction network.
"This project leverages two of the areas of life sciences that IU is best known for, that being computation and Drosophila research," Dalkilic said. "Our group has integrated and is mining all the genome-wide data, which is all of the fly's DNA. Through this work, we are unraveling some of the mysteries of the fly, and consequently, its DNA. You know, we're all related."
IU Bloomington has long been an international center for Drosophila research, hosting the National Institutes of Health-funded DNA sequence database FlyBase and the Drosophila Genome Research Center, the most comprehensive research hub on the fruit fly in the world. The Bloomington campus is also home to Thomas Kaufman, IUI Distinguished Professor of biology, considered one of the world's foremost authorities on the fly.
Because Drosophila is one of the most studied organisms, there are staggering amounts of data on the creature and integrating it into a coherent network that can be tested for coherence has been challenging. But Dalkilic has been able to show the complexity of some gene interactions through a computer-designed network where nodes diagrammatically represent genes, and the edges of the network represent genetic functional relationships. The network can then be used to make predictions about other types of genes.
Indigene is also closely tied to another of Dalkilic's core research projects, DDONT, or Data-Drive Ontologies, which seeks to develop a gene ontology for Drosophila. That exhaustive, hierarchical organization of data is being developed using a novel algorithm to uncover new relationships between biological processes and to compare sets of genes.
"This project is timely in that we hope we can use it to make sense of very large corpuses of data," he said.
