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Big DataResearch OpportunitiesGrow Exponentially

About the cover:

Dr. Bernie MachenPresident

Dr. David NortonVice President for Research

Board of TrusteesC. David Brown II, Orlando ChairSusan Cameron, Ft. LauderdaleChristopher T. Corr, Lake Lure NCCharles B. Edwards, Ft. MyersJames W. Heavener, Winter ParkMarc Heft, GainesvilleCarolyn K. Roberts, OcalaJason J. Rosenberg, GainesvilleJuliet Murphy Roulhac, PlantationSteven M. Scott, Boca RatonDavid M. Thomas, WindermereCory Yeffet, Gainesville

Explore is published by the UF Office of Research. Opinions expressed do not reflect the official views of the university. Use of trade names implies no endorsement by the University of Florida. 2014 University of Florida. explore.research.ufl.edu

Editor: Joseph M. Kaysjoekays@ufl.edu

Art Director:Katherine Kinsley-Momberger

Design and Illustration: Katherine Kinsley-MombergerPaul MessalNancy Schreck

Writers:Cindy SpenceClaire Baralt

Copy Editor:Andrew Kays

Printing: StorterChilds Printing, Gainesville

Member of the University Research Magazine Associationwww.urma.org

18

Out of the DarknessiDigBio is revealing new research opportunities in long-hidden museum collections.

This 3-D graphical rendering of a petascale computer shows the complexity of current state-of-the-art computing systems and the challenge of developing the computer of the future, which would operate at exascale, performing a quintillion operations per second.

Summer 2014, Vol. 19, No. 2

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UF RisingHuman-centered computing takes off.

Trail Blazers Metabolites map biological processes in all living things.

Vision QuestHarnessing the power of predictive science.

Summer 2014, Vol. 19, No. 2

Some 90 percent of all data that exists today was created in the

last two years, but only half a percent has been analyzed. Big Data represents a big opportunity for science, and the University of Florida is poised to take advantage of it.

UF already has momen-tum in the area. Last year the university unveiled Floridas fastest supercom-puter, known as HiPerGa-tor. It also expanded its data pipeline to allow researchers to share enormous amounts of information at high speed, establishing a level of connectivity with few rivals on university campuses anywhere in the nation. In addition to the investment in infrastructure, UF is recruiting as many as 25 new faculty experts through the UF Rising campaign.

And UF is leveraging the talent already here. In the decade-long iDigBio project, UF researchers are coordi-nating a nationwide effort to digitize up to 1 billion speci-mens in the collections of dozens of museums and uni-versities, with $12 million from the National Science Foundation. Once online, this valuable resource can

unleash waves of discovery, tackling big questions, from the evolutionary paths of species to the future impacts of climate change. As an online resource, it will be open to anyone from a stu-dent interested in dinosaur fossils to a molecular geneti-cist interested in adaptations in a species.

In the $10 million Center for Compressible Multiphase Turbulence, Bala Balachandar and his colleagues are investigating problems of predictive and simulation science using the most powerful computing platforms available. The simulations the team has in mind will require computers so powerful they dont even exist yet. UF scientists, in collaboration with indus-try and NSF, are working on the computer of the future, capable of running the most complex simulations of explosions, volcanic erup-tions and supernovae.

And in the Clinical and Translational Science Institute, a team is study-ing health and disease by following the trails of mol-ecules called metabolites, previously undetectable, but now revealed with increasingly powerful imaging and computing

power. Metabolites convert food into energy and allow communication between cells, tissues and organs. They provide a unique means of studying health. UF launched its South-east Center for Integrated Metabolomics in 2013 with a five-year, $9 million grant from the National Institutes of Health.

The capacity to collect, store and analyze vast troves of information will be essential to scientific inquiry and, in fact, represents a revolution. Instead of asking a question and gathering data, scientists can now look for patterns in data that will help them ask better, bigger questions.

Data itself isnt wisdom. Our researchers tease it out, using computers to take on complex challenges in engi-neering, education, science and health care. We have the computing horsepower and the brainpower to be a national leader in data sci-ence and analytics. Because we already have one of the nations most wide-ranging research portfolios, UF has tremendous potential to use computers to improve peoples lives in numerous ways.

The capacity to collect, store and analyze vast

troves of information will be essential to scientific

inquiry and, in fact, represents a revolution.

Instead of asking a question and gathering

data, scientists can now look for patterns in data

that will help them ask better, bigger questions.

David NortonVice President for Research

4 Summer 2014

Explore 5

Institute of Food and Agricultural Sciences

RESEARCHERS JOIN WITH WATER MANAGEMENT DISTRICT TO STUDY SPRINGS

THE UNIVERSITY OF FLORIDAS Institute of Food and Agricultural Sci-ences is joining forces with two entities as part of a $3 million, three-year contract to provide scientific data to help protect and restore the states springs system. UF/IFAS partners in the effort are the St. Johns River Water Management District, which is funding the project, and UFs Water Institute.

The state of Florida and the St. Johns district have made protection of Floridas springs one of their highest environmental priorities, said Hans G. Tanzler III, the St. Johns districts execu-tive director. This collabo-ration between the district and UF will develop the strong scientific foundation needed to focus resources to achieve the maximum benefit of restoration and protection.

The funding comes from the St. Johns dis-tricts Springs Protection Initiative, which combines science, projects, planning and regulatory programs to reduce nitrate loading and protect spring flows. The partnerships primary focus will be on the Silver Springs springhead and ecosystem, including:

Improving the scien-tific foundation for the

management of nitrates flowing into the springs; Evaluating whether nitrate reduction alone will be sufficient to restore the balance of nature; And assessing the influ-ence of other pollutants and stressors.Scientists will also look at

rainfall and runoff quantity and quality; aquifer storage, flow and spring discharge; nitrate sources, nitrate uptake and nitrate loss in soils and groundwater; how the springs function and algae abundance.

A second system slated for in-depth research will be the Wekiva Springs system in Apopka, which sits at the headwaters of the Wekiva River one of two National Wild and Scenic Rivers in Florida.

Focusing the best water researchers in Florida on this issue will allow us to take the next major step toward the ultimate protection of these jewels in the states crown, said Jack Payne, UF senior vice president for agriculture and natural resources. This collabora-tion will develop the strong scientific foundation needed to restore and protect Flori-das world-class springs.

Florida has one of the largest concentrations of freshwater springs on Earth,

with more than 700 bub-bling up from the states aquifer. There are 96 springs within the SJRWMD, including Silver Springs.

The springs crystal-clear water, which maintains a year-round temperature of 72 degrees, is the source for many of North and Central Floridas rivers and streams, providing habitat for wildlife and fish, including mana-tees, alligators, limpkins, herons and turtles.

Water Institute Director Wendy Graham noted that the program involves 10 Water Institute-affiliated faculty.

The research is lead by K. Ramesh Reddy, chair of the soil and water science department and Ed Lowe, SJRWMDs chief scientist.

Reddy noted that UF has partnered with SJRWMD for four decades on various projects involving manage-ment and restoration of eco-systems within the St. Johns River basin.

Floridas springs serve as living laboratories to provide invaluable opportunities to understand more fully the complex processes regulating the health of these fragile ecosystems, he said.Ramesh Reddy, krr@ufl.edu

Kimberly Moore Wilmoth

FOCUSING THE BEST WATER RESEARCHERS IN FLORIDA ON THIS ISSUE WILL ALLOW US TO TAKE THE NEXT MAJOR STEP TOWARD THE ULTIMATE PROTECTION OF THESE JEWELS IN THE STATES CROWN. JACK PAYNE

BIG DATA Milestones

1956 An IBM 650 CPU, the worlds first mass-produced computer, is installed at the University Statistical Center. It could process 1,000 instructions per second.

6 Summer 2014

GENE THERAPY OFFERS POTENTIAL TO STOP MULTIPLE SCLEROSIS IMMUNE RESPONSE

IN PATIENTS with multiple sclerosis, the body turns on itself, launching an immune system attack that destroys the coating around nerve fibers in the

central nervous system, leaving them exposed

like bare wires. Similar to exposed electrical lines, the unprotected fibers touch and short out, leading to the neurodegenera-

tive effects that are a hallmark of

multiple sclerosis.But what if doctors

could stop the immune response that destroys the protective coating before the disease becomes debilitat-ing? University of Florida researchers have received a $40,000 grant from the National Multiple Sclero-sis Society to test a gene therapy technique in mice that aims to help the body re-establish immune toler-ance in the early stages of the disease.

In previous years, we have learned a lot about how to manipulate toler-ance using gene therapy, said Brad E. Hoffman, an assistant professor of pedi-atrics in the UF College of Medicine. Tolerance is your bodys way of not responding to substances that would otherwise induce an immune response so

you dont have an immune response to everything. In multiple sclerosis, the body loses that ability to distin-guish between self and not-self so it starts to attack its own nervous system cells.

About 2.3 million people worldwide suffer from mul-tiple sclerosis. The disease typically causes problems with vision, fatigue, speech, sensation and mobility. In advanced cases, multiple sclerosis can lead to blind-ness and paralysis.

Typically, gene therapy is used to correct a faulty gene in the body. In this case, researchers will deliver a gene responsible for a brain protein into the liver, via the harmless AAV virus, in hopes that it will spark production of regulatory T cells. These T cells, which suppress the immune system, are crucial because they could effectively shut down the immune attack in the brain. The research-ers are injecting the gene into the liver because the organ filters out unwanted immune responses.

Everything filters through the liver for detoxi-fication, Hoffman said. Because of this, the liver has an innate capacity to induce immune tolerance. We have learned in other gene therapy studies that it is possible for the liver to make cells tolerant to the gene you are putting in.

The UF researchers work is novel because they hope to develop a technique that could be used on a wide number of patients.

Everyone has different types of T regulatory cells and receptors, Hoffman said. By injecting a gene responsible for a brain protein, we are allowing an individuals body to make the specific T regulatory cells it needs.

If it works, this is potentially more clinically feasible, cost-effective and translatable for a large scale.

Although gene therapy has yet to be used to cor-rect autoimmune disorders, the foundations for the study are rooted in research Hoffmans team performed while studying gene therapy for hemophilia. The team was able to induce immune tolerance in mice, and Hoff-man hopes the techniques will help people with mul-tiple sclerosis, too.

Will we be able to cure MS? That would be ideal, but our strategy is more likely to result in suppress-ing the immune response to the nervous system, he said. If you suppress the immune response, you will suppress the neurodegenerative effects and hopefully maintain a higher quality of life.

Brad Hoffman, bhoffman@ufl.edu

April Frawley

College of Medicine

EVERYONE HAS DIFFERENT TYPES OF T

REGULATORY CELLS AND RECEPTORS. BY INJECTING A GENE RESPONSIBLE FOR

A BRAIN PROTEIN, WE ARE ALLOWING AN INDIVIDUALS

BODY TO MAKE THE SPECIFIC T REGULATORY

CELLS IT NEEDS. BRAD E. HOFFMAN

BIG DATA Milestones

1967 An IBM 360/50, which could process 178,000 instructions per second, is installed. On Dec. 6 the UF Computing Center ran 504 jobs, a new record.

Explore 7

G OLD-BASED DRUG FIGHTS BONE CANCER IN PEOPLE AND PETS

College of Veterinary Medicine

A GOLD-BASED drug currently used in human and veterinary medicine to manage certain immune diseases may prove useful in combating osteosarcoma, a devastating bone cancer that affects both dogs and people, University of Florida veterinary researchers report.

By examining an aggressive bone cell line in both species, the research-ers found that the drug, aurothiomalate, commonly known as gold salts, kept cancer cells from forming in the laboratory.

We also were able to demonstrate that the drug slows tumor growth and decreases metastasis when canine bone tumors were created in a mouse model, said Valery Scharf, the studys lead author. A small animal surgery resident at UF, Scharf completed her masters degree last year. The research was the focus of her thesis.

The findings appear in the journal Anti-Cancer Drugs.

This study shows that there is potential promise for the role of gold drugs as a part of bone cancer treat-ment in dogs and potentially in people, although more studies are needed before we can use them in a clinical setting, Scharf said.

Osteosarcoma is the most common primary bone tumor found in dogs and accounts for the

vast majority of cancer-ous tumors around 80 percent in the canine skeleton. The condition occurs most commonly in large-breed dogs that are middle-aged and older. The cancer frequently appears in the front leg, but it can occur in any bone. Dogs with osteosarcoma often show signs of lameness in the affected leg.

Veterinarians typically amputate the affected limb to remove the primary tumor. Dogs can also receive chemotherapy if the cancer has spread. However, some dogs arent candidates for amputation, and the deci-sion to amputate can be dif-ficult for pet owners.

In people, osteosarcoma is rare and also affects the long bones of the body. It typi-cally is diagnosed in people under 25 years of age.

Osteosarcoma is a frus-trating disease, as you can treat the local tumor but the metastasis is something there is no effective means of preventing, Scharf said.

The use of gold com-pounds in human medicine has traditionally been based on golds ability to affect the bodys immune response and anti-inflammatory proper-ties, with the primary use being the management of rheumatoid arthritis. In vet-erinary medicine, gold-based drugs are most commonly used to treat various autoim-mune disorders. In recent

years, however, aurothioma-late has been investigated for its potential effects against certain types of cancer.

The UF study is the first to focus on the drugs effectiveness as a tool for possible canine bone cancer treatment through petri dish tests and in vivo studies in mice.

They found that low doses of the drug signifi-cantly reduced cancer spread to the lungs the site to which osteosarcoma most frequently travels in dogs. High doses reduced micro-scopic spread to the lungs and the incidence of tumor cell clusters within blood vessels.

Further study is needed to better understand how aurothiomalate works against osteosarcoma cancer cells, and to better determine effective dose ranges before extending this research to dogs, the researchers said.

One of the inter-esting things to me in studying oncology and our pets is that their disease often translates to human disease as well, Scharf said. Therefore, research on the animal side can potentially translate to human medicine as well.Valery Scharf, vscharf@ufl.edu

Sarah Carey

Sarah Carey

1972 The UF Computing Center becomes the Northeast Regional Data Center of the State University System of Florida. An IBM 370/165 is installed which could process 1,890,000 instructions per second.

1978 The Florida Computer Crimes Act is passed.

THIS STUDY SHOWS THAT THERE IS POTENTIAL PROMISE FOR THE ROLE OF GOLD DRUGS AS A PART OF BONE CANCER TREATMENT IN DOGS AND POTENTIALLY IN PEOPLE. VALERY SCHARF

8 Summer 2014

SEA SNAKES NEED FRESH WATER FOR DRINKING

College of Liberal Arts and Sciences

ALTHOUGH they spend their lives surrounded by water, sea snakes dehydrate for months at a time, waiting to quench their thirst with fresh water from rainfall, a University of Florida biolo-gist has found.

The finding contradicts the accepted belief that marine vertebrates have evolved to use salt water to meet their water require-ments, said Professor Harvey Lillywhite, whose research appeared in the Proceedings of the Royal Society B, the f lagship bio-logical research journal of the Royal Society.

These snakes refuse to drink salt water, even when dehydrated, Lillywhite said. They need fresh water to survive.

Current physiology textbooks state that marine reptiles drink sea water, dis-tilling the water by excreting excess salt via salt glands. While it is true that they excrete salt, Lillywhite said, no sea snake we have tested drinks sea water.

The findings are the result of three years of field studies of the Yellow-bellied Sea Snake, the most widely distributed pelagic sea snake, which inhabits tropical oceans. Lillywhite and his colleagues also studied the sea snakes in the laboratory.

Both in the field and in the lab, sea snakes shunned salt water, taking a drink only when fresh water was

available. At sea, sips of fresh water depend on rainfall.

Rainfall is less dense than sea water, so it floats on the surface, forming a lens of fresh water. Such layers of water may persist as fresh water or dilute brackish water at the ocean surface for days, but snakes probably drink the rainwater during or shortly after a rainstorm. In lagoons, where sea snakes often are abundant, a fresh water lens might persist longer than one in the open ocean.

The snakes appear to sense rainfall.

We think they almost certainly know that it rains because their behav-ior changes during the approach of a tropical storm as the atmospheric pressure changes, Lillywhite said.

During or after a rain, the snakes, which spend most of their time deeper in the water, surface to take a sip of fresh water. The Yellow-bellied Sea Snake, Lillywhite said, consumes varying quantities, from small amounts up to 25 percent of its body mass when fresh water is available.

The open ocean is a vir-tual desert, especially during the dry season, which can last six or seven months at Gua-nacaste, Costa Rica, where the snakes were studied, Lilly-white said. During that time, sea snakes slowly dehydrate, and lose up to 25 percent of their body mass, a level that would be way past lethal for a human, Lillywhite said.

Lillywhite said diminish-ing rainfall might be the cause of declining popula-tions of sea snakes in some areas, such as drought-stricken Northern Australia, where sea snake populations have declined for 10 years and two local species are thought now to be extinct.

If global climate change causes drought conditions to worsen, sea snakes and other marine vertebrates that depend on rainfall for fresh water could be hurt, Lil-lywhite said. There are more than 60 species of entirely marine sea snakes and eight species of sea kraits that live in the sea but spend some time on shore. Lillywhites study also raises the question of whether other marine spe-cies might depend more on fresh water than previously thought.

An interesting follow-up, he said, would be to study sea turtles which live in salt water and have a broad distribution similar to the pelagic species of sea snake to determine if they depend, even partially, on fresh water.

Understanding the water requirements and drinking behaviors of marine verte-brates could help with con-servation efforts, Lillywhite said. In areas of intensifying drought, they will need to move or die out.Harvey Lillywhite, hblill@ufl.edu

Cindy Spence

WE THINK THEY ALMOST CERTAINLY KNOW THAT IT RAINS BECAUSE THEIR

BEHAVIOR CHANGES DURING THE APPROACH OF A TROPICAL STORM AS THE

ATMOSPHERIC PRESSURE CHANGES.

HARVEY LILLYWHITE

1985 The first laser printers are installed for letter-quality output.

1988 The last card reader is removed. NERDC connects to the Internet.

Explore 9

BURMESE PYTHONS CAN NAVIGATE HOME FROM MILES AWAY

Institute of Food and Agricultural Sciences

IF YOU pick them up and drop them in a new location, most snakes will move rapidly but erratically, often traversing the same terrain before giving up and settling into their new digs.

Burmese pythons arent most snakes.

A team of researchers including scientists from UFs Institute of Food and Agricultural Sciences has discovered that the giant snakes which have invaded and affected the food chain in Everglades National Park and Big Cypress National Preserve can find their way home even when moved more than 20 miles away.

The findings change how researchers understand python behaviors and intellect.

This is way more sophis-ticated behavior than weve been attributing to them, said Frank Mazzotti, a wildlife ecology and conser-vation professor based at the Fort Lauderdale Research and Education Center. Its one of those things where nature makes us go wow. That is truly the significance of this.

In 2006 and 2007, researchers captured 12 pythons and surgically implanted radio transmitters that allowed them to track the snakes movements. As a control group, they returned six of the snakes to the spot

of their capture and turned them loose.

The remaining six snakes were taken to spots ranging from 13 to 22 miles away from where they had been captured and turned loose. To the researchers surprise, the snakes oriented them-selves toward home and maintained their bearings as they traveled.

And although it took between 94 and 296 days for five of the six snakes to get within three miles of home, partly due to it being the snakes dormant season, the reptiles kept that orientation a clear signal to scientists that the snakes have both map and com-pass senses.

The relocated snakes appeared to use local cues at the release site to understand their position relative to home (the map sense), and appeared to use cues along the way (their compass sense) to ensure that they remained on track, although the researchers dont yet know what those cues are: smell, perhaps the stars, light or some kind of mag-netic force.

Mazzotti said its inter-esting for researchers to know that the snakes move purposefully through their environment, but in reality, its not that much help.

It amps up a little bit our concern about the snakes, but given all the

other things we know about pythons, the amount of increasing concern is minor, he said.

The Bur-mese python has been an invasive species in South Florida since about 2000, likely stemming from accidental or purposeful releases by former pet owners. The largest python found in the Everglades area had grown to more than 18 feet.

The snakes suffocate and eat even large animals, such as deer and alligators, and in 2012, a research team that included Maz-zotti found severe declines in python-heavy areas of native animals including raccoons, opossum, bobcats and rabbits.

In 2012, the federal gov-ernment banned the import and interstate trade of four exotic snake species: the Burmese python, the yellow anaconda, and North and South African python.

A link to frequently asked questions: http://www.usgs.gov/faq/categories/10721/4751

Frank Mazzotti, fjma@ufl.edu

Mickie Anderson

A TEAM OF RESEARCHERS, INCLUDING SCIENTISTS FROM UFS INSTITUTE OF FOOD AND AGRICULTURAL SCIENCES, HAS DISCOVERED THAT THE GIANT SNAKES CAN FIND THEIR WAY HOME EVEN WHEN MOVED MORE THAN 20 MILES AWAY.

1989 Wordperfect 4.2 is installed for testing.

1995 IBM scalable POWERparallel SP2 UNIX-based NERSP supercomputer is installed. Nearly 100 28.8 modems are installed.

10 Summer 2014

Institute of Food and Agricultural Sciences

SPACEX DRAGON TAKES UF PLANTS TO SPACE STATION FOR GROWTH STUDIES

A UNIVERSITY OF FLORIDA science project that rocketed to the Interna-tional Space Station on April

18 aboard the SpaceX-3 Dragon is focused, liter-ally, on what it takes for biology to adapt and thrive in space.

The experi-ment by plant molecular biolo-gists Robert Ferl and Anna-Lisa Paul uses small plants as models to understand cellular responses to spaceflight.

This experiment, known as CARA, is a follow-up to research they conducted on the ISS in 2010 which found for the first time that roots display normal movements used to get around rocks and obstacles even when there is no gravity.

The movements, known as waving and skewing, were thought to be due to cellular responses to gravity pulling on roots as they sample their growing surface with touch, Paul said.

But as the images from our experiment started to come down from the Inter-national Space Station in early 2010, it was clear that gravity was not required after all, she said.

Based on the 2010 results, Paul and Ferl wanted to see if, in the absence of

gravity, perhaps the plants were responding to another directional cue, such as the overhead light source inte-grated into the plant growth hardware. Such alternate signal processing by the plant cells would indicate that biology explores unique adaptive strategies when in novel circumstances.

We are intrigued by the numerous light-sensing genes that are expressed specifically in roots in orbit, and the SpaceX-3 experiment further explored the role of these genes in orientation and cellular remodeling, Paul said. It is likely that light plays a more important role in root growth in microgravity than it does on Earth.

And that has big implica-tions for life somewhere other than Earth, Ferl said.

This is telling us that life utilizes special, poten-tially unique signals to adapt to living off planet, he said. This has tremendous implications for the expan-sion of human existence to other worlds, but also richly informs us about the potential for plants to adapt to unusual environmental changes here on Earth.

Ferl and Paul worked with NASA engineers at Glenn Research Center (GRC) in Ohio to adapt the Light Microscopy Module (LMM) for biological appli-cations in order to focus the analysis on the cells that

normally sense gravity in plants.

The LMM is a sophisti-cated fluorescent microscope facility housed on the ISS, with a counterpart at GRC, that has historically been used for physics experi-ments. The plants of the CARA experiment are grown in square petri plates on a nutrient agar matrix, and in this experiment simply attached to the wall of the US module of the ISS. During the course of the CARA experiment the plates were photographed in place with a standard camera, but in addition, the plate containing plants engineered with fluorescent reporters was examined with the LMM to evaluate space-flight-associated changes in the cellular localization of selected genes.

An astronaut inserted the plate into a specially adapted holder on the on-orbit LMM, then Paul and Ferl worked with the GRC engineers to control the use of the microscope telemetri-cally from the ground.

The experiment was sponsored as a research grant to Paul and Ferl by the Center for the Advance-ment of Science in Space (CASIS), the Florida-based national organization responsible for promoting science on the ISS.Rob Ferl, robferl@ufl.edu

Anna-Lisa Paul, alp@ufl.edu

WE ARE INTRIGUED BY THE NUMEROUS LIGHT-

SENSING GENES THAT ARE EXPRESSED SPECIFICALLY IN ROOTS IN ORBIT, AND THE

SPACEX-3 EXPERIMENT FURTHER EXPLORED THE

ROLE OF THESE GENES IN ORIENTATION AND CELLULAR

REMODELING. ANNA-LISA PAUL

1998 UF President John Lombardi announc-es computer requirement for all students.

BIG DATA Milestones

To learn more visit ufspaceplants.blogspot.com

Explore 11

LOBSTER RADAR MAY BE KEY TO BETTER ELECTRONIC SENSORS

McKnight Brain Institute

COULD LOBSTERS help protect soldiers someday? A team of University of Florida researchers says they might.

Dont expect to see battlefields filled with spiny crustaceans on leashes, though. The secret lies in how the clawed creatures locate a specific scent. UF Health researchers and engi-neers say they have identi-fied the neurons involved in that ability call it lobster radar and that discovery may help them develop improved electronic noses to detect landmines and other explosives.

An electronic nose has to recognize an odor and locate its source. Find-ing the source has often been the job of the person handling the electronic nose, said Barry W. Ache, distinguished professor of neuroscience and biology and director of the Center for Smell and Taste in UFs McKnight Brain Institute. To date, the technology has had its drawbacks espe-cially when the nose is used to detect potentially deadly materials that could endan-ger its human handler.

Yuriy V. Bobkov, of the UF Whitney Laboratory for Marine Bioscience, origi-nally discovered a type of olfactory neuron in lobsters that constantly discharges small bursts of electrical pulses, much like radar uses pulses of radio energy to

detect airplanes or thunder-storms. UF researchers spec-ulated that these so-called bursting neurons might cue the crustaceans in on an odors location especially important when they are searching for food or trying to avoid danger.

Odors exist as com-pounds that move through the air or water and settle on olfactory neurons in whiffs. The time between whiffs depends on the dis-tance between the smeller and the source of the smell. Sensing the time intervals allows animals to determine the location of an odor. Thats where bursting olfac-tory neurons from lobsters come in.

To try to solve the mys-tery of how lobsters process sensory information, Jos C. Prncipe and Il Memming Park, of the Computational NeuroEngineering Labora-tory in UFs Department of Electrical and Computer Engineering, took informa-tion gleaned from these cells and created a computational model.

Each bursting cell responds to a whiff at a different frequency, Ache said. Together, the neurons help pinpoint the location of a particular odor. Just as a person can hear a train moving from left to right, a lobsters set of olfactory neurons set the scene for the location of a smell.

By entering the lobster olfactory data into a com-puter model and giving artificial silicon neurons the same features found in the crus-tacean ones, then subjecting the neurons to simu-lated whiffs of odor, the researchers could determine how the bursting neurons function and how they set a scene that tells the animal the source of a smell.

These cells as a popu-lation seem to provide a system for detecting odors in the spatial world, Ache said. We hope not only to learn more about how these systems work, but how that information might be applied to challenges such as electronic noses.

In addition to improv-ing electronic sensors, this finding will help scientists better understand the sense of smell in all animals including humans.

The involvement of bursting sensory neurons in olfactory processing is not unique to the lobster, Bobkov said. Its likely to be a fundamental aspect of olfaction.

The team reported the findings in the Journal of Neuroscience.Barry Ache, bwa@whitney.ufl.edu

Melissa Lutz Blouin

AN ELECTRONIC NOSE HAS TO RECOGNIZE AN ODOR AND LOCATE ITS SOURCE. FINDING THE SOURCE HAS OFTEN BEEN THE JOB OF THE PERSON HANDLING THE ELECTRONIC NOSE.

BARRY W. ACHE

2008 The worlds largest computing grid, pioneered in part by UF researchers, is launched to crunch the mam-moth amounts of data produced by the Large Hadron Collider particle accelerator in Europe.

2013 UF unveils the states most powerful supercomputer, with a peak speed of 150 trillion calculations per second.

Explore 13

Imagine trying to recreate the eruption of Mount St. Helens or the collapse of the World Trade Center.

Sometimes, experiments are not an option, says UF mechanical and aerospace engineering Professor Bala Balachandar.

And even if he could simulate such complex events in the lab, Balachandar says there is currently no computer capable of fully analyzing the f lood of data.

But Balachandar and his team are out to change that, with the sup-port of a five-year, $10 million grant from the National Nuclear Security Administration.

Balachandars field of predictive simulation science is like looking into a crystal ball. It takes the known behavior of atoms and molecules which can be expressed through mathematical equations and applies them to unknown events, like the

chaos of massive explosions natural or man-made.

Its easy to understand why a nucle-ar security agency would be interested in such capabilities, but Balachandar says the practical applications of being able to simulate such complex events go far beyond nuclear devices.

Predictive simulation science grew out of the nuclear test bans of the 1990s. The bans put national nuclear labs in a bind: how do you certify a nuclear warhead is serviceable if you cant test it? Scientists developed computational surrogates for nuclear testing, and in the process found those models useful in studying other complex phenomena that cant be tested in a lab, like supernovae and volcanic eruptions.

Taking a complex process and con-verting it to a computational model is tricky. A model must be detailed enough to account for many variables

so that an accurate prediction can be made. Too much detail, however, and the model collapses under the weight of its own data.

My back-of-the-envelope calcula-tion is not very accurate, Balachan-dar says. On the other hand, if I have an equation for every molecule it would take 100 billion years to pre-dict whats going to happen, and that is not useful. So we have to strike a sweet spot.

In the case of nuclear weapons, Balachandar says, the model should be detailed enough, for example, to tell the President of the United States, You can make a decision based on my simulation, because I trust my answers. Or, if the issue is an impending volcanic eruption, the simulation should be detailed enough that an emergency management offi-cial can decide when and how far to evacuate.

Explore 13Photography by John Jernigan; Illustration by KD Kinsley-Momberger

Harnessing the Power of Predictive Science

By Cindy Spence

14 Summer 2014

Hurricane forecasting is a predic-tive science success story, Balachandar says, noting that 50 years ago hur-ricanes in India caused huge losses of life. A hurricane just last year in India caused fewer than 10 deaths. Balachandar points out that predicting a hurricanes strength at somewhere between category 1 and category 5 is not useful, but a prediction with 95 percent certainty that a hurricane will be category 5 provides information that is useful.

Scientists wont make the deci-sions, but they can give decision-makers an answer they can use in their deliberations.

Simulation allows people to make better decisions, Balachandar says. We reduce the guesswork by bringing in as much physics and computational power as possible.

As a big data challenge, Balachan-dar says, simulating complex phenom-ena is so data intensive that it requires the worlds largest, fastest computers, and then some.

The best computers today operate at petascale, performing a quadrillion a thousand trillion calculations every second. Imagine a desktop com-puter with a quad core; put 250,000 together and you have a million cores, and can do petascale calculations. In the quest for greater precision and speed in simulations, Balachandar says scientists are eyeing the next genera-tion exascale computers.

Which dont exist and wont for many years, says Alan George, the lead computer scientist on the team and a professor of electrical and com-puter engineering.

George and colleagues Herman Lam and Greg Stitt and a team of

students at CHREC, the National Science Foundation Center for High-Performance Reconfigurable Comput-ing at UF, are tackling the problem of computing power for simulation science. Down the hall from Georges office sits the Novo-G, the most powerful reconfigurable computer in the world. The reconfigurability of the Novo-G represents a dramatic departure from the trend of present computer architectures, but even the Novo-G is not exascale.

In the past, science could anticipate the growth of computing power using Moores Law, which forecast that com-puting power would double roughly

every two years. But with petascale computing, a milestone reached five years ago, Moores Law is reaching its limits, making exascale the holy grail of computing, at least for now.

In theory, all youd have to do is string 1,000 petascale machines together and youd have exascale. But youd need one nuclear power plant to run that many machines, Balachandar says, and another nuclear power plant to cool them.

Balachandar and the physics team have all kinds of wonderful ideas about how to make their simulations more accurate, more detailed, more sophisticated, more robust, George

14 Summer 2014

Simulation allows people to make better decisions. We reduce

the guesswork by bringing in as much physics and computational

power as possible. Bala Balachandar

In previous experiments, Balachandar and his collaborators modeled complex multiphase turbulence in an oceanic environment, shown above.

says, so the computer scientists learn how their applications function and try to develop a new computing archi-tecture to support them.

These are very complex simula-tions, and to perform them in a response time shorter than your lifes-pan you need more and more power-ful computers, George says. If you were to look at all the supercomput-ers in the world, thats what most of them are being used to do; some are simulating Earth climate, others are simulating multiphase turbulence, and so on. Supercomputers are widely used to study and solve problems so com-putationally intensive that the most

powerful computers in the world are necessary to do it.

Georges team is charged with the task of studying and evaluating ways to build and use the exascale com-puter of the future what Balachan-dar calls a grand challenge and George says such challenges are natu-ral in computing.

Before exascale was Mount Ever-est, petascale was Mount Everest, and before that terascale, George says. So now exascale is the next big challenge.

The road to exascale computing is fraught with unprecedented dif-ficulties. Pursuing exascale comput-ing in the traditional manner by

connecting a thousand petascale machines doesnt make sense, George says. Each petascale machine costs hundreds of millions of dollars, is as big as a building, and generates so much heat that its cooling bills alone run $1 million a month.

That just doesnt make sense, economically, practically or techni-cally, George says. Because of that, exascale is really opening up new research challenges. How do we design systems in new and better ways than we ever have before?

In the early days of computing, the machine was the main cost. Then software became the main cost. Now,

Explore 15

16 Summer 2014

fastest computer in the world. The one-size-fits-all architecture of a con-ventional computer doesnt change, whether it is used for word processing or sequencing a genome. In recon-figurable computing, the architecture changes to suit the need, and that delivers faster processing at a lower energy cost.

The potential of the Novo-G has drawn interest from more than 30 industry partners.

George points out that the tradi-tional style of expanding computing power has pitfalls. As processors and chips get smaller and more and more are added, the system grows ever more complex, meaning more can go wrong, and then reliability becomes an issue.

All of these things are daunting, George says. Nobody really knows

George says, one day, maybe not too far away, energy may become the dominant cost in computing.

If were already spending a mil-lion dollars a month on utility bills for some of these machines, just imagine what that might be with exascale if we dont find a better way to do things, George says.

George is just the man for the job. As recently as 2004, there wasnt a centralized campus computing infra-structure, but there was a big appetite for it. George chaired a committee that convinced units from all across campus health, agriculture, liberal arts and engineering to pool their resources, and high-performance com-puting at UF took hold.

George moved on to CHREC and reconfigurable computing, and for some applications, the Novo-G is the

the best way to study something that doesnt exist. Balachandar studies things you cant actually build and test, and we are as well.

Balachandar says the point is to co-design: do what can be done at pet-ascale, while developing methods that will work at exascale.

Already, the team is using UFs new HiPerGator computer to develop codes, test them, run cases and fine-tune formulas before hopping on to even more powerful computers at the national labs, and, eventually, the exascale machines of the future.

Traditionally, we scientists work on existing machines and then a new machine comes out and we scramble for three years to change our code to work on the new machine, then guess what. The next machine comes out, and by the time we learn to use that

These are very complex simulations, and to perform them in a response time shorter than your lifespan, you need more and more powerful computers.

Alan George, Gregory Stitt and Herman Lam are tackling the task of developing new computing architectures. Here, they are shown with a 3-D graphical rendering of a petascale machine at the National Science Foundation Center for High-Performance Reconfigurable Computing at UF.

Alan George

16 Summer 2014

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COMPUTING BY THE NUMBERS

one ... so this co-design strategy is a paradigm shift.

Revolutionizing the processing of the gigantic datasets for simulations will lead to discoveries in many other fields as well, Balachandar says.

Were doing something based on a future, non-existent technology, to move science forward, Balachan-dar says. This is great, this is awesome.

Bala BalachandarProfessor of Mechanical & Aerospace Engineeringbalas1@ufl.edu

Alan GeorgeProfessor of Electrical and Computer Engineeringgeorge@hcs.ufl.edu

Related websites:https://www.eng.ufl.edu/ccmt/http://www.chrec.org/

The universities are: University of Florida Stanford University University of Illinois Urbana-Champaign University of Utah Texas A&M University University of Notre Dame

The UF team is: S. Bala Balachandar Alan D. George Raphael T. Haftka Sanjay Ranka Nam-Ho Kim Herman Lam Gregory Stitt Siddharth Thakur Thomas L. Jackson

The University of Florida was chosen for one of the centers in the Predictive Science Academic Alliance Program II (PSAAP II), funded through the National Nuclear Security Administration.

The interdisciplinary teams from six universities will be at the leading edge of computing innovation to address the worlds most complex problems.

CENTERS OF EXCELLENCE

EXASCALE COMPUTINGTWO nuclear power plants are necessary for an exascale computer. One to power and one to cool.

An exascale computer will be 1,000 times FASTER than todays most powerful supercomputer.

A petascale computeris as big as a BARN

$1 Million cooling bill per month

Computing power equal to 250,000 desktop computers

PETASCALE COMPUTING

1,000,0001,000,0001,000,0001,000,0001,000,0001,000,0001,000,0001,000,0001,000,0001,000,0001,000,0001,000,0001,000,0001,000,0001,000,0001,000,0001,000,0001,000,0001,000,0001,000,0001,000,000

MEGAMEGAMEGAMEGAMEGAMEGA

1,000,000,0001,000,000,0001,000,000,0001,000,000,0001,000,000,0001,000,000,0001,000,000,0001,000,000,0001,000,000,0001,000,000,0001,000,000,0001,000,000,0001,000,000,0001,000,000,0001,000,000,0001,000,000,0001,000,000,0001,000,000,0001,000,000,0001,000,000,0001,000,000,0001,000,000,0001,000,000,0001,000,000,0001,000,000,0001,000,000,0001,000,000,0001,000,000,0001,000,000,0001,000,000,0001,000,000,000GIGAGIGAGIGAGIGAGIGA

1,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,0001,000,000,000,000TERATERATERATERATERA

1,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,0001,000,000,000,000,000PETAPETAPETAPETAPETAPETAPETAPETAPETAPETAPETA

1,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,0001,000,000,000,000,000,000EXAEXAEXAEXAEXAEXAEXAEXAEXAEXAEXAEXAEXA

Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power Computing Power OPERATIONS PER SECONDOPERATIONS PER SECONDOPERATIONS PER SECONDOPERATIONS PER SECONDOPERATIONS PER SECONDOPERATIONS PER SECONDOPERATIONS PER SECONDOPERATIONS PER SECONDOPERATIONS PER SECONDOPERATIONS PER SECONDOPERATIONS PER SECONDOPERATIONS PER SECONDOPERATIONS PER SECONDOPERATIONS PER SECONDOPERATIONS PER SECONDOPERATIONS PER SECONDOPERATIONS PER SECONDOPERATIONS PER SECONDOPERATIONS PER SECONDOPERATIONS PER SECONDOPERATIONS PER SECONDOPERATIONS PER SECONDOPERATIONS PER SECONDOPERATIONS PER SECONDOPERATIONS PER SECONDOPERATIONS PER SECONDOPERATIONS PER SECONDOPERATIONS PER SECONDOPERATIONS PER SECONDOPERATIONS PER SECONDOPERATIONS PER SECOND

18 Summer 2014

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arry Page would like to get back to his fishes, the catfish and loaches he studies as a

University of Florida ichthyologist, but first he and his colleagues have some work to do on plant, animal and fossil specimens millions of them.

Page and an army of helpers are on year three of iDigBio, a 10-year, $12 million effort to digitize the biological specimens tucked away in museum collections across the country. He estimates there could be 1 billion nationally, representing the collected knowledge of biological diversity for vast swaths of the planet.

Although it has taken him away from his fishes, the effort already has contributed to his work in an unex-pected way.

A student and I just found a data-base where specimens of a loach have been collected in Pakistan, Page says. We thought these loaches only went as far west as India, but there they were, in Pakistan.

Such moments of discovery can be rare. Scientists can labor long stretches between them, sometimes whole careers without them. But with iDig-Bio, Page says, these aha! moments

iDigBio is revealing new research opportunities in long-hidden museum collectionsBY CINDY SPENCE

could almost be routine; thats what this is all about, and it is happening all the time.

Centuries of knowledge are stored in museum collections around the country, from a fern collected, pressed and labeled hundreds of years ago, to an insect collected just last year. For taxonomists and other scientists, find-ing these specimens can be daunting.

There are specimens that have been around for 100, 200 years, but theyve been in a drawer somewhere, and its hard to know where every-thing is, says Page, the director of iDigBio. If its online, you can touch a button and find in seconds what it might have taken you a lifetime career to know was there.

By the most recent estimate, humans share the Earth with 8.7 mil-lion other life forms. Species are being lost and discovered all the time, but even with all the collected knowl-edge, much, much more remains to be learned. Scientists estimate that 86 percent of land plants and animals and 91 percent of those in the sea have yet to be identified.

Lately, says researcher Pamela Soltis, those discoveries are in specimen drawers.

Most species discoveries are actually made in museums, not in the wild, anymore, says Soltis, who studies molecular systematics and evolutionary genetics as distinguished curator at the Florida Museum of Natural History.

The specimen drawers in most museums are a treasure trove. In most cases, only a tiny fraction of what a museum owns is on display. In storage, sometimes a specimen is overlooked, sometimes not correctly named or well-described. The beauty of keeping it all is that a second look, years later, by a student or a scientist, can uncover an entirely new species. Armed with new methods, like genetic sequencing, new discoveries can be made, or a gap in an evolutionary path filled. Digitizing that informa-tion could speed up the pace of such discoveries. The tree of life, Soltis says, could be way more complex than we think it is.

Theres more information about biodiversity in museum collections than any other place except nature itself, adds Page, but the problem is, its really difficult to get.

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Photography by Kristen Grace

20 Summer 201420 Summer 2014

Scientists who want to examine specimens outside their institution must travel far and wide, generally to several institutions. Alternatively, they can ask for a loan, which means someone at the host institution must pull the speci-mens off shelves, wrap them up, box them and ship them. There are other issues, too, with a loan. The institution receiving a loan must have the facili-ties to properly store it, and of course, things can go wrong in shipping.

Loans, Page says, are never quite satisfying because they leave you won-dering what else might be there. And the most valuable specimens, the pri-mary types the specimens used to validate the name of a species are so precious that often a museum will not loan them at all.

Putting this treasure online opens it to research, education and just plain curiosity. Both the specimen and

the traditional label information are digitized, sometimes along with other information, such as the audio of Cor-nell Universitys bird songs. Using the label data alone, a scientist can pro-duce maps showing, for example, the range of an organism or change in its distribution over time.

The National Science Foundation is funding digitization of museum and university collections to the tune of $100 million over 10 years as part of its Advancing Digitization of Biodiver-sity Collections program, with iDig-Bio coordinating the national effort. So far, 156 collections, representing all 50 states, are participating. Muse-ums and universities are grouped into thematic collections networks, which work together to digitize informa-tion on a particular research topic, for example insects that feed on plants. Museum collections are being added

all the time, most recently the Field Museum in Chicago for its insects and Appalachian State University in North Carolina for its herbarium specimens.

The digitization effort is massive, and thats where citizen scientists can help, Page says. Hobbyists, for example, could input the label data. Two different people would enter the data and a computer would cross refer-ence it, so if theres any discrepancy a specialist would know to take a look at that file.

Already 14 million specimen records and 2 million images are online, accessible from a search portal developed by UFs Advanced Comput-ing and Information Systems Labora-tory (ACIS). The data so far fit into banks of computers the size of two refrigerators in the ACIS lab.

As a big data project, iDigBio cer-tainly qualifies. But Jos A.B. Fortes,

We share the Earth with

8.7 MILLIONOther Life Forms

86% LAND plants & animals91% SEA plants & animals

YETto be identified

1 BILLIONestimated # of biological specimenstucked away in collections nationally

14 MILLIONspecimen records

2 MILLIONspecimen images

ALREADY ONLINE!

iDigBio

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the computing director for iDigBio, says there are issues beyond size. The variety of the data and the differ-ences in how data are recorded and input from institution to institution make it a thorny computing problem. Something as simple as a date can be entered different ways: day first, month first, or year first, using numbers, using names. The storage essentially is a resource problem, one that money solves. The others can be tricky.

There are challenges in the het-erogeneity of the data, heterogeneity of practices and the degree to which different folks feel comfortable with different technologies, says Fortes, an AT&T Eminent Scholar in the Depart-ment of Electrical and Computer Engi-neering and director of the ACIS Lab.

Fortes estimates 15 to 20 times more space will be needed long-term, along with a commitment to upgrad-

ing the equipment. Redundancy, too, is built in to safeguard the data from catastrophes that could wipe out the database. Perhaps the biggest commit-ment and biggest opportunity lies in hosting the data, Fortes says.

The greatest asset in the informa-tion age is data, and thats something that should be the responsibility of an institution of knowledge, like a university. Hosting this data could be a differentiator from one university to the other, Fortes says.

The point of iDigBio is to have the data forever as a resource to do bigger and better things, to enable scientists to answer questions that cannot now be answered.

If you are in a position to do that you clearly have a competitive advan-tage, Fortes says.

Just like having an excellent library is a differentiator, so is data,

Fortes says. If we do it right everyone will come to us. They may not come by walking, they may come through the Internet, but that will enable other things to happen and that will pay for the long-term commitment to host the data.

As rewarding as it is to expand access beyond the traditional realm of museum collections, Soltis also is excited about the novel ways the data can be studied. By using label data where and when a specimen was col-lected locations can be plotted as GPS coordinates to construct models of species distribution based on vari-ables such as temperature or rainfall. That is a much more powerful way of understanding the range of a species, Soltis says.

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Historically, scientists kept their data in field journals like this one from the 1930s, requiring a collaborator to visit a museum or arrange a loan to do research. When the specimen image and collection data go online with iDigBio, the digitized information is available globally, both for research and education.

22 Summer 2014

Recently Soltis and colleagues used the digital label data that exist for about half of Floridas 4,000 spe-cies of plants to construct a model of the effects of climate change on plant communities in Florida.

Based on herbarium records, Soltis and her colleagues plotted each species on a map, then combined the maps to create a picture of plant species diver-sity in Florida today.

Then, using the characteristics that determine the niche of each species for example, temperature, rainfall, soil type the group looked at predictions for those attributes in future climate change scenarios. Her model for 2050 shows an alteration in species distribu-tion as some areas dry out and others become wetter, with an overall loss of plant diversity in Florida, creating challenges for conservation (see map).

This sort of analysis wouldnt be possible at all if we didnt have the digitized data from the museum specimens, Soltis says. We can use the digitized information to find links between evolutionary history, response to climate change and extinction risk.

Soltis points out that her species diversity model was incredibly com-plicated even though it was only in

Florida and only half of the plant spe-cies. Translating it to a larger scale, regionally or nationally, with many more data points makes it a huge data problem because it involves heteroge-neous data: distributions, evolutionary history, possibly genetics. There is talk already of linking iDigBio with Gen-Bank, the national genetic sequence database, creating yet another avenue of inquiry.

The possibilities of linking all these together present a whole new range of opportunities, Soltis said. There are almost no precedents for being able to do that. Big data takes on a unique shape when we think about biodiversity.

Big data projects like iDigBio are changing the past emphasis in sci-ence on hypothesis testing, Soltis says. Sometimes a scientist might not know what to hypothesize, but patterns can emerge from the data and point to a hypothesis to test.

Without access to the data, you might not even know to ask the ques-tion, so I think this whole concept of data-driven science is a really important paradigm shift for us, Soltis says, and I think our biodiversity data are perfect for exploring the bounds of that.

The UF Museum has some of the most comprehensive and widely utilized collections in the world.Most of the museums collections rank among the top 10 nationallyand internationally.

ArchaeologyCaribbean ArchaeologyCeramic Technology LaboratoryEnvironmental Archaeology(Zooarchaeology, Archaeobotany& Archaeopedology)

Florida ArchaeologyHistorical ArchaeologyLatin American ArchaeologySouth Florida Archaeology

EthnographyLatin American EthnographyNorth American Ethnography

Natural SciencesBotany/Herbarium (Plants)Herpetology (Reptiles & Amphibians)Ichthyology (Fishes)Genetic Resources RepositoryLepidoptera (Butterflies & Moths)MammalogyMolecular Systematics & Evolutionary Genetics

Malacology & Invertebrate Zoology (Mollusks & Marine Invertebrates)

Ornithology (Birds)

PaleontologyInvertebrate Paleontology (Inverte-brate Fossils)

Paleobotany & Palynology (Fossil Plants & Pollen)

Vertebrate Paleontology (Vertebrate Fossils)

22 Summer 2014

Museum collections are varied and plentiful, from pinning boxes used for butterfly specimens to jars of fishes and rows of shelves holding mammal bones.

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Page says iDigBio is not only a big data issue, its a dark data issue, too, because so much of the data has been hidden from view.

This is a clear example of bringing the data out of the darkness and into the light, Page says.

The process of shedding light has won over the few institutions that were lukewarm about joining the digitization effort, Page says. Getting funding for collections work some-times is difficult. Its a challenge to convince administrators that a bunch of dead fish in jars has any value, but as more data go online, museums will have an easier time demonstrating the value of their collections.

He says he laughs when people ask what scientists are going to do with all these data. iDigBio, he says, is much more than an exercise in knowledge for the sake of knowledge. The data will be central to exploring climate change, populations, evolution,

extinction, conservation, the number of species that share the planet with us, the very history of life on Earth.

These are huge research questions, so huge that they have been intrac-table, Page says, until now.

I really prefer to just work with fish, but Im more and more excited about this, Page says. The aha! moments, I think, will be happening all the time.

Larry PageCurator of Fisheslpage@flmnh.ufl.edu

Jos A.B. FortesProfessor of Electrical and Computer Engineering and Computer Science fortes@ufl.edu

Pamela SoltisCurator of Molecular Systematics & Evolutionary Geneticspsoltis@flmnh.ufl.edu

Related website:https://www.idigbio.org/

Most species discoveries are

actually made in museums, not

in the wild,anymore.

Pam Soltis Research director for iDigBio

Each of the specimen jar icons throughout this story represents 100 jars in the fish collection at

the Florida Museum of Natural History.

Ichthyology is just one of many collections at UFs museum, and UFs museum is just one of hundreds around the country, where an estimated 1 billion biological specimens are tucked away.

PRESENT

2050

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24 Summer 2014

Every process that happens in our bodies leaves a trail of small molecules called metabolites. A cancer cell starts dividing uncontrollably, it leaves a trail. An athlete injects steroids to improve performance, it leaves a trail. A stroke cuts off blood to a portion of the brain, it leaves a trail.

But until recently the trails were so faint that scientists couldnt see them. Now, through the use of increasingly powerful mass spectrometry and nuclear magnetic resonance, the tell-tale signs of countless processes occur-ring in our bodies are being revealed.

By measuring metabolites, we can get a unique window into health and disease. Metabolites keep everything going. They convert food into energy. They allow cells, tissues and organs to communicate. Theyre the start-ing materials for DNA, proteins and cell membranes, says Arthur S. Edi-son, a professor of biochemistry and molecular biology in the UF College of Medicine.

There are many twists and turns on the road between our DNA and our observable traits from hair color to cancer tumor. Metabolites offer clues to whats occurring along the way.

By identifying which metabolites are present and at what concentration, the emerging science of metabolomics offers a new lens through which sci-entists can assess and understand the state of nutrition, infection, health or disease in an organism, whether human, animal, plant or microbe.

Humans are estimated to have thousands of metabolites, but scien-tists are still at the early stage of iden-tifying and being able to consistently measure them.

The University of Florida is home to one of six centers funded by the National Institutes of Health to spur advances in metabolomics. In 2013, UF launched its Southeast Center for Integrated Metabolomics with a five-year, $9 million NIH grant.

The quest for metabolites typi-cally involves either searching for

specific compounds, known as tar-geted metabolomics, or cataloging all compounds in a sample, called global metabolomics. Databases of identified metabolites are emerging and expand-ing around the world. Scientists use these databases like nature enthusiasts use field guides, with the hope of finding a match or discovering a new metabolite among their data.

The UF center has four closely integrated technical cores that develop and provide services bridging the two technologies most commonly used to generate metabolomics data: mass spectrometry and nuclear magnetic resonance.

Our biggest strength is that we really pulled together the major tech-nologies in a significant way, Edison says. Many groups use one technology or the other. Were going to find better ways to use technologies together.

Edison jointly leads the UF center with Richard A. Yost, a professor and head of analytical chemistry in the UF College of Liberal Arts and Sciences.

Metabolites map biological processes in all living things

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BY CLAIRE BARALT

Photography by John Jernigan; Illustration by KD Kinsley-Momberger

National High Magnetic Field Labora-tory, Ohio State University, the Uni-versity of Georgia, Imperial College London, the University of Geneva and industry partners IROA Technologies and Thermo Fisher Scientific.

Weighing InMetabolites are identified based on

their molecular weight. Mass spectrom-etry is highly sensitive and can detect minute quantities of such compounds. The process starts with a biological sample typically urine or blood. The sample is run through a mass spec-trometer, which separates the sample into its chemical constituents by giving an electric charge to each component. The components then travel different paths through the device so they can be precisely identified and their molecular weight reported.

The UF center provides mass spec-trometry services in collaboration with

Sanford-Burnham, which specializes in targeted metabolomics. UF offers complementary expertise in global metabolomics.

Metabolites are numerous and remarkably diverse in terms of their structures. They display different sizes, polarities, and other properties. We have technology platforms that allow us to generate a broad and comprehen-sive profile of a vast number of unique metabolites, says Stephen Gardell, senior director of scientific resources and an associate professor at Sanford-Burnham. Gardell leads the centers mass spectrometry services with Timothy Garrett, a research assistant professor of pathology, immunology and laboratory sciences in the UF Col-lege of Medicine.

One of the challenges for tradition-al mass spectrometry is that it relies solely on molecular weight to identify the metabolites it detects. The heavier a metabolite is, the more molecular

By measuring metabolites, we

can get a unique window into health and disease.

The new center is part of the UF Clinical and Translational Science Institute, which over the last five years has supported the development of biomedical mass spectrometry at UF. When the NIH funding announce-ment presented an opportunity to integrate and expand metabolomics resources across UF and with external partners, the CTSI provided resources and infrastructure to help create the new center. The centers partners include Sanford-Burnham Medical Research Institute at Lake Nona, the

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ARTHUR EDISON

hum with activity. Shakers the size of tanning beds jostle their incubating inhabitants: worm-like nematodes that serve as model organisms for metabo-lomics experiments. Edison and his team migrate among computers, freez-ers and robots. Ladders lead to the top of two stately magnets processing sam-ples in the National High Magnetic Field Laboratorys Advanced Magnetic Resonance Imaging and Spectroscopy Facility at UF.

Data MiningThe use of different technologies

adds to the complexity of metabolo-mics data. The centers bioinformat-ics core helps ensure high-quality, standardized data regardless of the technology used along with a robust set of tools researchers can use to analyze their data.

The bioinformatics core is led by Lauren McIntyre, a professor of molecular genetics and microbiology in the UF College of Medicine. The core is developing the workflows, infrastructure and automation that will enable the center to process thousands of samples from researchers.

Timothy Garrett

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Glenn Walter

compounds there are that could yield a particular weight.

Imagine trying to guess whats inside a package based only on its weight, but without being able to see its shape or size, or sense what hap-pens when you shake it. Thats where nuclear magnetic resonance comes in. Using NMR is like x-raying the pack-age to see whats inside which, in the case of a metabolite, is atoms. To identify atoms and their location in complex molecules, NMR tracks the spinning of atomic nuclei in response to magnetic fields.

NMR is not as sensitive as mass spectrometry. While mass spectrom-etry can measure thousands of fea-tures, NMR can measure hundreds. The strength of NMR is that it gen-erates separate peaks for every atom type in the molecule, which makes identification of the molecule more straightforward.

If you have an unknown chemical that doesnt match any of the data-bases, you almost always need NMR to get the real atom connectivity. Its close to impossible to get the identity of a new compound with just mass spectrometry. NMR and mass spec-trometry together are an important part of the identification of unknown biomarkers, Edison says.

Not content to make do with the limitations of current technologies, Edisons research group is pioneer-ing the development and use of some of the worlds most sensitive NMR probes.

Edison leads the centers NMR services with Glenn Walter, an associ-ate professor of physiology and func-tional genomics in the UF College of Medicine. The NMR cores facilities

Lauren McIntyre

When were doing it well, it will be almost invisible to everybody, McIntyre says.

But data generated by the UF cen-ter does not all stay at UF. A central tenet of the NIH consortium is that all metabolomics data generated by the six centers with NIH support will be deposited in a national data reposi-tory and coordinating center, which is housed at the University of California, San Diego. The data center is led by Shankar Subramaniam, a professor of bioengineering at UCSD.

Subramaniam outlines five chal-lenges to working with big data that are relevant to biology and his centers work with the metabolomics consortium organizing the data; developing standard ways of naming the data; integrating the data; mak-ing sense of the data once its inte-grated; and ultimately using the data to determine causality.

Making sense of the data involves looking for patterns. With patterns

in biology its not like looking for a needle in a haystack. Its like searching for hay in a haystack. The whole area of data mining and statistical learning from data becomes very important, Subramaniam says.

At the UF center, McIntyres bio-informatics core will help tackle such challenges. She is developing new methods for integrating and modeling metabolomics data, as well as integrat-ing metabolomics data with other omics data.

Metabolomics produces big data, but not on the scale generated by Wal-Mart or Wall Street. Integration with other omics such as genomics, proteomics and transcriptomics will be necessary before scientists can relate metabolites to changes in genes, pro-teins and the regulation of cell behav-ior, and that will cause the data sets to grow dramatically.

One of the advantages we have at UF its a very interdisciplinary and diverse place, Yost says. We have

We have computer

scientists and engineers who

think about big data, scientists

who create instruments

that make big data, and

physicians who use that data to

answer biomedical questions.

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RICK YOST

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computer scientists and engineers who think about big data, scientists who create instruments that make big data, and physicians who use that data to answer biomedical questions.

Erik Deumens is one of those com-puter scientists. Deumens directs UF Research Computing, which serves the UF metabolomics centers data pro-cessing and storage needs. Resources such as UFs HiPerGator supercom-puter and the Internet2 high-speed network connection make it possible for UF researchers to collaborate and compete in the big-data arena.

The Southeast Center for Integrat-ed Metabolomics is bringing together different aspects of peoples metabolism and all kinds of information about health and biochemistry processes. You gather all the data, put it one place and have a chance to look at it from a new point of view. W ere the enabler of that next step, Deumens says.

Noise FiltersInnovation in data generation is a

hallmark of the center at UF. Metabolomics is the ultimate

healthcare platform, but it wont be useful to anyone until you get the time it takes to do it and the time to understand what its telling you down to something reasonable. Thats what the NIH centers are going to do, says Chris Beecher, founder and chief sci-entific officer of IROA Technologies, one of the UF centers partners.

Beecher is developing a technique that is transforming how metabolomics data are generated. Called isotopic ratio outlier analysis, or IROA, it tags all molecules that come from a living sys-tem prior to running samples through a mass spectrometer. Those tags allow scientists to identify all of the signals

idea is that the spatial relationships between metabolites could convey a lot of information with respect to whats happening in an organ, for example. Processing a blood sample can reveal how much glucose or lac-tate is present in the blood, but it doesnt indicate what those levels are in the liver or heart or brain.

Over time, as these new technolo-gies and methodologies are developed, tested and refined, they will become part of the UF centers service offerings for investigators. The center also offers training and pilot funding to help sci-entists access and use its services.

A strong demand for metabolo-mics already is emerging. In its first six months, the center received close to 100 inquiries from investigators at nearly 30 institutions. Investigators are coming to the center with a range of questions for which they hope metab-olomics might yield clues. Projects in discussion are diverse and stimulating. They include looking at the effects of stress during pregnancy on a mother and her fetus; metabolomics approach-es to drug discovery in microbes; studies of the physiology of human pathogens; and studies of metabolic disease in humans and animals.

Were at this wild west stage of trying to figure it out. Im confident this consortium will point the field in a better direction in five years. Every-thing wont be solved, but it will be much clearer what you can do and the importance of it, Edison says.

Arthur S. EdisonProfessor of Biochemistry and Molecular Biologyaedison@ufl.edu

Richard A. YostProfessor of Chemistryryost@chem.ufl.edu

Related website:http://secim.ufl.edu/

from the living system and ignore all of the other noise, or signals from non-living systems that result from the mass spectrometry process a major hurdle in metabolomics.

Innovation is similarly thriving in the UF centers advanced mass spec-trometry core led by Yost. Even amid a spring break void of students, traces of his research groups creative spirit abound. On Yosts table, a bobblehead of Nobel Prize-winning physicist Wolfgang Paul knowingly nods next to a specimen of Pauls handiwork: a quadrupole mass analyzer, four rods neatly bound together.

As it turns out, Yost spent a great deal of time tinkering with the quad-rupole as a graduate student at Michi-gan State University. Together with his advisor Chris Enke, he conceived of the computerized tandem quadrupole mass spectrometer. Scientific reviewers for the National Science Foundation did not believe it would work, but the Office of Naval Research was will-ing to chance that it might. And that chance paid off. Today it is the most common mass spectrometer in the world, with sales of nearly $1 billion each year.

Oftentimes when youre deep in a discipline, there are things you know that are facts, and there are things you think you know that are folklore. And oftentimes the folklore keeps you from moving forward in innovative ways, Yost says.

Yosts lab is devoted to pushing past the folklore to cultivate instru-mentation breakthroughs. His team is now focused on advancing imaging mass spectrometry for tissues. Instead of applying mass spectrometry to the usual urine or blood samples, this technique applies mass spectrometry methods across a section of tissue. The

30 Summer 2014

T he University of Florida has recruited a team of computer scientists with specialties in whats known as human-centered com-puting to help it become a national leader in making computers more secure and more personalized to indi-vidual needs.

Four faculty members, recruited from the same department at Clemson University, are joining the College of Engineerings Department of Com-puter and Information Science and Engineering, known as CISE. This

COLLEGE OF ENGINEERING RECRUITS NATIONAL LEADERS IN EMERGING USER-FRIENDLY FIELD

cluster hire fits into strategies at the college and university levels to expand research into several key areas over the next year.

As our relationship with technol-ogy becomes more pervasive, comfort-able interfaces between humans and computers become more important, said CISE department Chair Paul Gader. Human-centered computing is the frontier where computers begin to recognize what makes each of us unique, and then adapt to offer each of us a more personalized experience.

Bringing this team on board will make UF a leader in ensuring greater accessibility for all human-computer interactions.

The team arrives with a variety of research interests: Juan Gilbert and his team gained national recognition when they devel-oped the technology to make voting more accessible and secure. His elec-tronic voting interface has created a new standard for universal accessibil-ity in elections. Gilbert will be the Andrew Banks Family Preeminence Endowed Chair at UF. Damon Woodard is an expert in biometrics, or identity technology. His work with the U.S. intelligence com-munity includes periocular-based and tightly coupled face/iris recognition systems. The main focus of his current work is the development of techniques that allow machines to establish an individuals identity even when using lower quality or incomplete data. Kyla McMullen specializes in virtual spatial audio, which allows a listener to hear a sound over headphones as though it were coming from a specific point in their immediate environ-ment. She is interested in using this rendering to create more immersive virtual environments, develop assis-tive technology for persons with visual impairments, and to sonify trends in Big Data. Christina Gardner-McCune is a computer science education researcher. She develops interest- and discipline-based computing curriculum and after-school and summer camp

Juan Gilbert

HUMAN-CENTERED COMPUTING BONANZA

Cra

ig M

ahaf

fey

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programming to encourage K-12 stu-dents to enter STEM-related careers. She currently serves on the College Boards development committee for the new Advanced Placement Com-puter Science Principles Exam.

The team brings millions of dol-lars in federal grants to UF and more than a dozen doctoral students. They will be joining CISEs growing HCC team, which includes Benjamin Lok who developed the technology behind local adaptive learning startup Shadow Health and Lisa Anthony and Eakta Jain, both recent doctoral graduates from Carnegie Mellon University who came to UF this year.

If your quality of life has been enhanced by a technology, human-centered computing is probably the reason, said College of Engineering Dean Cammy Abernathy. This team has an excellent reputation for their revolutionary research, their collabora-tion across disciplines, and their wide focus that includes the needs of all members of society. Their addition positions us to have a new center of excellence. We are thrilled to have them.

In addition to this team, CISE is hiring new faculty in areas of Big Data, cyber security, and social net-works, Gader said. Our mission in the department is to improve quality of life and were definitely headed in the right direction.

Juan Gilbert demonstrates an electronic voting system to South Carolina Congressman James Clyburn.

Doctoral student Chris Crawford demonstrates programming to middle school students.

Doctoral student Naja Mack demonstrates an electronic voting system at the Capitol in Washington.

To gain a better understanding of why dementia is more common among people with Parkinsons disease, UF researchers are using MRI images like this to compare the brain tissue of Parkinsons patients with different types of cognitive dif culties. Clinical and health psychology Associate Professor Catherine Price says the research funded by a $2.1 million National Institutes of Health grant may enable researchers to foreshadow the type of impairment, if any, patients will have down the road.

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