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IMPACTS Research Technologies (RT), a division of University Information Technology Services (UITS) and a center in the Pervasive Technology Institute at IU, develops, delivers, and supports advanced technology solutions that enable new possibilities in research, scholarly endeavors, and creative activity at Indiana University and beyond. RT provides services that benefit those in fields ranging from astronomy to zoology. We offer expert consulting, compute and storage resources, and research software, as well as visualization and data services, to meet researchers’ needs. RT complements these efforts with education and technology translation activities to improve the quality of life for people in the IU community, state of Indiana, the nation, and the world.
Find a complete list of RT services to help advance your research and academics at rt.iu.edu/services
Research Technologies Annual Report FY2021
Contents Letter from AVP Matt Link
4–5
Research Technologies by the Numbers
6–9
RT Impact: Indiana University
10–19
RT Impact: The state
20–25
RT Impact: The nation
26–33
RT Impact: The world
34–39
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LETTER FROM MATT LINK, ASSOCIATE VICE PRESIDENT, RESEARCH TECHNOLOGIES This past year was challenging, scary, unpredictable, heartbreaking, and hard on us all. Many of us lost family, friends, and colleagues–for many reasons–and overcame those obstacles with compassion and grace. I want to acknowledge everyone in RT and thank them for always being there to support our mission to serve Indiana University, each other, and our colleagues. I couldn’t be prouder to share some of what we achieved during a truly challenging year. Despite the physical constraints caused by the pandemic, RT continued to support research and scholarly activities with specializations in high performance computing (HPC), consulting, storage, research software, data visualization, and training, allowing RT to foster collaborations across disciplines and campuses. Despite the practical challenges we faced both individually and collectively, there were many bright spots. The Crisis Technologies Innovation Lab, for which RT is a collaborator and I am a co-director, was awarded more than $10M to research best practices for first responders and disaster response that will improve disaster patient care, recovery, and policy implementation. RT was also awarded nearly $700,000 from the National Science Foundation (NSF) to fund the Jetstream cloud computing system’s sixth project year. This brings the total of NSF funding for Jetstream to nearly $14.5M. These funds will allow for
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a seamless transition from Jetstream to Jetstream2, funded by the NSF at $10M, creating continuity. The Jetstream systems provide U.S. researchers with anytime, anywhere access to cloud-based computing and data analysis resources. Through Jetstream, we assisted with the COVID-19 response by participating in the COVID-19 HPC Consortium; sixteen projects used these resources for related research. This included early usage through the Galaxy Gateway for SARS-CoV-2 analysis and provision of resources to the OpenMRS team, which has affected medical records systems and data sharing worldwide. Earlier in the year, with COVID-19 infections still on the rise, RT provided services and resources to help understand and contain the pandemic. The COVID-19 Research Data Commons, or CoRDaCo, is the result of a partnership between the Regenstrief Institute and Indiana University. CoRDaCo uses MDClone software to scrub sensitive patient information from datasets and provide abstracted, synthetic data from COVID-19 mitigation testing, as well as government vital records, to create complete datasets for public health research. RT’s response to the COVID-19 pandemic took other avenues as well. The Advanced Visualization Lab collaborated with units throughout IU to implement a range of technologies to increase engagement and
well-being within the IU community, especially during COVID-necessitated restrictions. Examples include virtual and technology-enhanced components for the Little 500 bike race, graduation ceremonies, Bachelor and Masters of Fine Arts gallery exhibits, and end-of-semester project demonstrations. Similarly, through the IU3D initiative, RT has now digitized more than 100 spaces—including historic buildings, rotating gallery exhibits, research facilities, and schools of study—at five different IU campuses and multiple external sites across Indiana. These digital spaces, while particularly useful in the last year, will continue to be used for student recruitment, virtual exhibits, construction project management, fundraising, fostering cultural understanding, and connecting with alumni. RT has been able to stay ahead of the curve in various areas we support. As COVID-19 shut down in-person training and outreach activities, RT was able to successfully offer training on demand and virtually through platforms like Zoom, Canvas, and Expand. The National Center for Genome Analysis Support team was particularly adept at reaching out to their community and continuing to provide exceptional education and training.
Our high performance compute systems, file systems, and visualization systems have recently undergone upgrades, allowing us to provide the best possible systems for COVID-19 research as well as all the research and educational activities IU aspires to accomplish. In Research Technologies, we remain focused on supporting and enabling all areas of research and scholarly activities as we collectively work to be together again. Last year I ended my letter with the statement: “I look forward to the day that we can all be together again!” I am grateful for all the hard work by IU’s Medical Response Team and our leaders in making the hard choices to bring us all back together–safely. I couldn’t be prouder of Research Technologies and very much look forward to the coming year! Yours,
Matt Link Associate Vice President Research Technologies, Pervasive Technology Institute University Information Technology Services Extended versions of these exceptional highlights can be found here: go.iu.edu/3X0g
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RESEARCH TECHNOLOGIES BY THE NUMBERS HPC Users by Category, 2015-2020 1800 1600 NUMBER OF USERS
1400 1200 1000 800 600 400 200
Graduates
6
2015
2016
Undergrads
Faculty
2017
2018
External researchers
2019 Staff
2020
Group account
Other
$405,838,072
$1,004,092,943
178
FY21 grant dollars
FY21 grant dollars
Departments
supported by RT
for all IU
supported in FY21
one y r e v E fo r
1 COURSE AT TENDANCE 2016–202
500
Course Key Ready, Set, Robots at IU * High Performance Computing IU REDCap National Center for Genome Analysis Support
300
Visualization
NUMBER
OF
AT TENDEE S
400
200
100
2016 Summer
2016 Fall
2017 Spring + Summer
2017 Fall
2018 Spring + Summer
2018 Fall
2019 Spring + Summer **
2019 Fall ***
2020 Spring + Summer
2020 Fall****
2021 Spring + Summer****
S E S S I O N
* Offered during summer only with limited facilities and instructors.
*** NCGAS began offering hybrid "in-person" classes using Expand/Canvas.
** Began offering online/on-demand courses via Expand.
**** All courses were virtual or via Expand/Canvas.
In addition to the attendees noted above, the archived presentations from the FY2021 events had more than 17,000 views on YouTube. An additional 4,000+ views of prior education, outreach, and training activities were also recorded. 7
RESEARCH TECHNOLOGIES BY THE NUMBERS IU’S NEWEST COMPUTE AND S T O R AG E SYS T E M S P R OV I D E up to
more than
10.3 petaFLOPS
112,000
of processing capability
processing cores
up to
more than
768 GB
90 PB
of RAM per
of storage space for
node
research and collaboration
1,870 nodes
more than
2.3 million GPU cores
Compute systems include Quartz, Carbonate, Big Red 3, and Big Red 200. Storage systems include Slate, Slate-Project, Geode, Geode-Project, and the Scholarly Data Archive. 8
The Advanced Visualization Lab (AVL) has provided a total of 611,993,856 pixels of IQ-Wall real estate to the IU community in the last seven years, with 547,627,008 IQ-Wall pixels still in service today. Set end-to-end, all of those pixels would make a line 76 miles long.
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RT IMPACT: INDIANA UNIVERSITY STRENGTHENING CREATIVE RESEARCH IN THE UNIVERSITY COMMUNITY
BRINGING NATIONAL GRANT DOLLARS TO IU
NSF AWARDS $696K FOR JETSTREAM PROJECT YEAR 6 The Pervasive Technology Institute at Indiana University has been awarded nearly $700,000 from the National Science Foundation to fund the Jetstream cloud computing system’s sixth project year. This brings the total of NSF funding for Jetstream to nearly $14.5M. These funds will allow for a seamless transition from Jetstream to Jetstream2, funded by the NSF at $10M, creating continuity. This material is based upon work supported by the National Science Foundation under Grant 2005506. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
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The Crisis Technologies Innovation Lab (CTIL), a Pervasive Technology Institute collaboration between RT and the Luddy School of Informatics, Computing, and Engineering, received two grant awards. NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY, US DEPARTMENT OF COMMERCE AWARD IN EXCESS OF $8M This CTIL grant award will fund a series of prize competitions to foster technology innovations designed to locate first responders inside structures during times of crisis. This work was performed under the following financial assistance award 70NANB21H022 from U.S. Department of Commerce, National Institute of Standards and Technology.
$2.3M GRANT AWARD FROM U.S. ARMY TELEMEDICINE AND ADVANCED TECHNOLOGY RESEARCH CENTER This grant will fund CTIL and three partners to create a Technology in Disaster Environments Learning Accelerator (TLA). The TLA will use data science and performance science to find best practices for improving COVID-19 patient care. It will also provide insights into how technology can be used to improve disaster response and recovery in general. This work was supported by the Office of the Assistant Secretary of Defense for Health Affairs and the Defense Health Agency J9, Research and Development Directorate, through the MTEC - Technology in Disaster Environments (TiDE) program under Award MT21004.001. Opinions, interpretations, conclusions and recommendations are those of the author and are not necessarily endorsed by the Department of Defense.
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SUPPORTING ARTIFICIAL INTELLIGENCE, MACHINE LEARNING, AND GPU COMPUTING EXPLOSIVE IMPACT The Carbonate supercomputer was expanded to include 24 GPU nodes containing a total of 96 NVIDIA V100 GPUs, proving invaluable in both Artificial Intelligence research and more traditional HPC simulation research. For example, Professor Chuck Horowitz (IU Physics) and Assistant Professor Matt Caplan (Illinois State University) have a new theory of how supernovae explode, and they are testing it on Carbonate’s GPUs.
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“Our simulations rely on the massive parallelism of the GPUs, as each nucleus must have its interactions calculated with every other. Without them, this work simply wouldn’t be possible.”
Matt Caplan, assistant professor, Illinois State University
Dr. Sandra Kuebler’s research team employs natural language processing for abusive language detection on social media. Finding abusive posts is increasingly important, but reliable datasets are crucial to creating machine learning approaches. Kuebler’s group investigates questions such as: Can we trust existing datasets to reflect the situation on social media? Do we introduce biases into the datasets by making decisions on how to sample the data? Does the language in abusive posts change over the years? Can we ask users to mark which posts on social media are abusive? Where are the boundaries between abusive and non-abusive posts? Do machine learning approaches pick up on biases from all of those decisions? How do we create unbiased datasets?
“Finding answers to all these questions involves developing and testing a range of models, most of them involving deep neural networks. Our work would not be possible without the high performance computing clusters, and more specifically the Carbonate GPU partition.”
Dr. Sandra Kuebler, Department of Linguistics, College of Arts and Science, IU
In FY21 the Carbonate Deep Learning resource delivered 899,598 core hours and 97,723 GPU hours to users conducting research in disciplines including medical image segmentation, video classification, cybersecurity, genomics, and natural language processing. 13
NEW PERSPECTIVES WITH VISUALIZATION TOOLS ADVANCED VISUALIZATION LAB BRINGS DISPLAY TECHNOLOGIES TO ART INSTALLATION: THE PEOPLE OF IU RT's Advanced Visualization Lab (AVL) facilitated the technical side of The People of IU: a multimodal, interactive installation in Maxwell Hall. Conceived and directed by Professors Susanne Schwibs and Stephanie DeBoer, the collaborative work brings portraits of people from across the university, drawing attention to IU’s collective present and past.
A student-created motion portrait projection diorama at The Cook Center for the Arts
“We were novices with After Effects and learned everything from scratch. Scott Birch helped us whenever we needed and always ended up offering more insight than we even asked for. It was incredibly rewarding to be involved with this project―it’s a unique and fascinating testament to community and collaboration.”
Sam Bowden, undergraduate collaborator for The People of IU: Moving Image Portraits and The Public Screen. 14
DIGITIZING THE GLENN CLOSE COSTUME COLLECTION RT’s Advanced Visualization Lab partnered with the curator of the Sage Collection at the Eskenazi School of Art, Architecture + Design to begin digitizing the vast collection. The COVID-19 shutdown brought to light just how important the digitization of artifacts and one-of-a-kind collections is to enable research to continue, even in the midst of a global pandemic.
“Sage Collection staff were so pleased to partner with the Advanced Visualization Lab to digitally capture some iconic costume and costume elements featured in The Art of the Character: Highlights from the Glenn Close Costume Collection. I look forward to working with the AVL to digitally capture a wide range of fashion and dress objects.”
Kelly Richardson, curator, Sage Fashion Collection
A Glenn Close costume from The Stepford Wives, digitized by the AVL for The Sage Collection at IU
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ADDRESSING INDIANA’S TOUGHEST CHALLENGES IU’s Grand Challenges Program IU’s Grand Challenges Program is a bold commitment to address the issues that impact Indiana and the world. The challenges are split into three categories: the Precision Health Initiative, Prepared for Environmental Change, and Responding to the Addiction Crisis. As these large-scale programs and projects ramp up in size and scope, RT remains committed to providing support to the IU Grand Challenges Program and stands ready to assist with the high performance computing needs that might arise.
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REDCAP OBGYN SCREENING The Hoosier Moms study is part of IU’s Precision Health Initiative Grand Challenges Program, led by the IU School of Medicine. The study, with more than 13,000 data entries, aims to improve understanding of possible genetic links between gestational diabetes and Type 2 diabetes. Flexible and accurate data management, supported by Indiana University’s research survey tool, REDCap, keeps the Hoosier Moms study on track, whether a mom-to-be chooses to join the genetics-based study when she is 8 weeks or 18 weeks along in her pregnancy.
RT has been a significant contributor to IU Grand Challenge projects, specifically providing dedicated storage and shared computational resources to the Precision Health Initiative and the Prepared for Environmental Change projects (using Slate-Project storage, the Scholarly Data Archive, Big Red II+/Big Red 3, and Carbonate systems).
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SUPPORTING A SPECIFIC RESEARCH COMMUNITY IU School of Medicine Center for NeuroImaging (CfN)
CfN enlisted the help of RT to develop Scalable Quality Assurance for Neuroimaging (SQAN), a quality control service to improve PET-based research. Mistakes are difficult for researchers to spot using existing data extraction methods, which can affect the quality of a study’s data. In response, the Scalable Compute Archive (SCA) team developed SQAN.
“Partnering with SCA, we are using SQAN to better understand the timing of the different acquisitions, and we can go back and retroactively apply that data to our data processing stream.”
Dr. Karmen Yoder, professor of radiology and imaging sciences
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“Research of this nature helps to uncover reliable indicators of impairment, which may provide evidence toward previously ConnPipe combines state-of-the-art tools from various image processing packages along with algorithms developed in-house to process complex datasets within one coherent framework. The collaboration of SCA, CfN, and IU School of Medicine researchers has allowed ConnPipe to be significantly improved, allowing the team to make the pipeline faster and more efficient, more modular and adaptable to new techniques, while allowing for better utilization of IU’s vast supercomputing resources.
“XNAT is an enabling technology for our advanced neuroimaging and -omics research on Alzheimer’s disease and related brain disorders. The ability of our IT group to work hand in hand with the SCA greatly facilitates progress.”
undiscovered causal biological and physiological mechanisms underlying the nature of treatment and its side effects.”
Meichen Yu, postdoctoral researcher, CfN
The Scalable Compute Archive took on the management of XNAT, an opensource imaging informatics platform supporting research by the Center for NeuroImaging (CfN) at the IU School of Medicine. The migration involved critical upgrades, including the ability to run the program virtually on a web browser.
Dr. Andrew Saykin, director, CfN and IADRC
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RT IMPACT: THE STATE SERVING INDIANA THROUGH TECHNOLOGICAL INNOVATION
SCAN YOUR WORLD, SHARE YOUR WORLD
Inside the IU South Bend Civil Rights Heritage Center
ENABLING VIRTUAL TOURS ACROSS MULTIPLE IU CAMPUSES Efforts by the IU3D team to digitize buildings and spaces on campus enabled prospective students and their parents to explore IU campuses, even when they weren’t able to visit in person. Take the tour of the IUSB Civil Rights Heritage Center, go to go.iu.edu/3XmF
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“Support from the IU RT team allowed our space to continue thriving by welcoming people virtually where they could not safely come physically. It has been an incredibly useful tool not only for the South Bend community, but communities around the world who now have an opportunity to see and learn from this space like never before.” George Garner, assistant director and curator, Civil Rights Heritage Center, IU South Bend
EXPANDING ACCESS TO CULTURAL HERITAGE RT's IU3D team uses a tool called Matterport to capture cultural heritage spaces in order to provide virtual access to the space and to
“The [IU3D] team created a meaningful and exceptional experience for patrons who visit the Black Cultural Center virtually. The tour offers an intriguing glimpse into the cultural landscape of Purdue. This is an innovative way for the exploration of African American history and exposure to the BCC library and art exhibitions.”
preserve changing exhibits. Renee Thomas, director, Purdue Black Cultural Center
“These captures of physical spaces are certainly important in the midst of a global pandemic, [but] their utility extends beyond this particular moment, offering access to inaccessible spaces for people with disabilities by recreating the physical space and the flow through that space.”
Tassie Gniady, project manager, IU3D
Purdue Black Cultural Center’s keyhole portal, similar to a traditional African village entrance. Go to bit.ly/purdue-bcc to take the virtual tour.
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MAKING RESEARCH TOOLS EASIER TO ACCESS AND USE RT staff strive to enable researchers to reach discovery faster with low barriers to their research. From education and outreach to tools like Research Desktop (RED) and Jetstream, RT makes it easier to access vast amounts of storage and research software, as well as perform fast calculations on IU's supercomputers.
IU’S RED MAKES SUPERCOMPUTING ACCESSIBLE TO A WIDER POOL OF RESEARCHERS AND EDUCATORS RED provides a user-friendly graphical user interface (GUI) for researchers and students unfamiliar with command-line coding who want to use HPC resources. From education and outreach to tools like Research Desktop (RED) and Jetstream, RT makes it easier to access vast amounts of storage and research software, as well as perform fast calculations on IU's supercomputers, to be highly effective in engaging students and researchers who are new to HPC.
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“I have used RED to support undergraduate and graduate education here at IU. As an instructor, I need RED because what I teach often involves the use of technology. RED provides a consistent computing environment for my students.”
Devan Donaldson, assistant professor of information science, IU Bloomington
The White River in Indianapolis
“IU's supercomputing resources have ENABLING DISCOVERY AND ACCURATE PREDICTIONS Predicting a river’s future behavior is critical to preparing communities and ecosystems to handle it. Dan Myers used IU supercomputers, Big Red 3 and Carbonate, to run thousands of models, studying watersheds and verifying that his findings were consistent. His work creating accurate hydrologic models will help inform the design of urban stormwater systems, and help fisheries managers understand what changes will be necessary to adapt to rising water temperatures due to climate change.
allowed us to finish up this study. It took about a year and a half between when we started and when the results were published. But without them, if I were running the models on my desktop computer, I would have hardly made any progress.” Dan Myers, graduate student in the Department of Geography at Indiana University Bloomington
Indiana University researchers and leaders showcased a wave of innovative supercomputing resources and techniques at the Practice and Experience in Advanced Research Computing Conference Series (PEARC20), an annual conference by the Association for Computing Machinery. Plenary speaker David Y. Hancock introduced the XSEDE-funded Jetstream2, one of five innovative HPC systems awarded funding by the National Science Foundation. 23
DATA COLLECTION AND MANAGEMENT MADE EASY Research Electronic Data Capture (REDCap) IU’s Research Electronic Data Capture (REDCap) is a secure web-based platform designed to support data collection and data management for research, operations support, and quality improvement projects. Easy-to-use, intuitive features allow REDCap users to build and manage online surveys and databases with no programming experience required.
FACILITATING AN INTERNATIONAL COVID-19 SYMPTOM SURVEY Throughout the COVID-19 pandemic, the lack of access to virus testing threatened to undermine public health efforts to stop the spread. Researchers at the Regenstrief Institute and Indiana University’s School of Medicine and Fairbanks School of Public Health partnered with REDCap and Microsoft News to develop and launch an international COVID-19 symptom survey.
“The REDCap ETL extension allowed us to merge study data together from all of the various language versions into a single database for analysis. The extension saved our study team a lot of time and effort, and the support we received from Research Technologies was immeasurable.” Brian Dixon, director of Public Health Informatics, Regenstrief Institute
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SUPPORTING A NATION OF ADMINISTRATORS With more than a decade of experience helping administrators from all over the world, IU REDCap’s Technical Lead, Andy Arenson, wins the Most Valuable Person award from a field of administrators across more than 4,000 institutions worldwide. Going above and beyond his commitment to facilitating quality research data, the award honored his fostering of the admin community that supports REDCap for more than a million users worldwide.
Andy Arenson enjoys some downtime with his MVP award.
“Collaboration with the Indiana CTSI [Clinical and Translational Sciences Institute] and IU's Department of Biostatistics and Health Data Science over many years has been instrumental in ensuring RT-managed REDCap dependability in supporting the thousands of projects and users within IU and its many research affiliates.” Bob Davis, the chief data officer of the Indiana State Department of Health
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RT IMPACT: THE NATION ANSWERING THE NATION’S CALL FOR TECHNOLOGICAL ACCESS
ENABLING EASE OF USE AND DELIVERING FAST CALCULATIONS RESEARCH DESKTOP ASSISTS WITH DATA ANALYSIS Colleen Rosales, an environmental science Ph.D. candidate at Indiana University, says radicals― tiny, short-lived, notoriously hard to measure chemical species―play a major role in the chemistry of air pollution. Her research aims to improve the measurement of radicals and build upon science’s understanding of both indoor and outdoor air pollution. To power her calculations using Mathematica software, Rosales uses Indiana University’s Research Desktop (RED), which allows her to expedite data analysis.
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“The graphical interface of RED helps me easily share and show people how to use IU’s supercomputers, from colleagues to undergraduate students.”
Colleen Rosales, Ph.D. candidate in environmental science at Indiana University
“Instead of waiting eight to ten months [for the jobs to complete on a slower machine], I was able to finish my work in a couple of weeks [on Karst and Big Red 3].” Jeff McMullin, assistant professor, Accounting, IU
FAST CALCULATIONS Researchers from IU, University of North Texas, and West Virginia University used IU's Karst and Big Red 3 to perform 18 billion text comparisons in order to determine why companies are using boilerplate risk factor disclosures rather than original, company-specific language as required by federal guidelines.
“By encouraging these types of collaborative relationships, we’re not duplicating work, and we’re The Collaborative Archive & Data Research
creating a more open environment
Environment (CADRE) enables collaboration amongst
and encouraging more data to
researchers across institutions. It also ensures that
be open so that more researchers
researchers can reproduce and replicate each other’s
can work on it, collaborate, and
research. RT's Research Data Services and the Indiana
share work, which in turn should
University Network Science Institute (IUNI) worked
increase reproducibility.”
together, running tests on IU supercomputers like Karst and Carbonate as well as Jetstream, to shorten query times for CADRE from several weeks to just a few minutes, ensuring researchers can perform their
Jaci Wilkinson, head, Discovery and User Experience at Indiana University Libraries
research more efficiently.
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(JET)STREAMING IN THE CLASSROOM AND AROUND THE WORLD REAL-TIME DATA ON JETSTREAM D. Sarah Stamps runs an EarthCube Cloud-Hosted Real-time Data Services (CHORDS) portal for the geosciences on Jetstream virtual servers, enabling her research of an active volcano in Africa to continue in the U.S. Accessible, real-time data facilitated by CHORDS using Jetstream is a critical step in a complicated data-gathering process. Stamps and her team continue to monitor volcanic activity in Tanzania while working from home during the COVID-19 pandemic.
“Using the CHORDS tool in Jetstream for streaming real-time positioning data has allowed my research group to manage a distant network with ease.”
D. Sarah Stamps, assistant professor of geophysics, Virginia Tech Department of Geosciences
This material is based upon work supported by the National Science Foundation under Grant 1445604. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
Ol Doinyo Lengai volcano in Tanzania. Photo: Richard Mortel, CC-BY 2.0
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JETSTREAM IN THE CLASSROOM Doane University, a small university in Crete, Nebraska, used the Jetstream cloud in the computational biology classroom to help students understand the scope of bioinformatics. Before Jetstream, students accessed virtual machines that often took up too much memory on their laptops; now, it’s easy.
“I can just create a virtual machine; everyone logs into the web browser so it’s not using a lot of memory. Jetstream makes it so much easier to get everybody up and running.”
Erin Doyle, professor of biology, Doane University
Bacteria of the genus Neisseria include species which cause gonorrhea and meningitis.
“The students in my team at Spelman [an all-women HBCU] learned to be comfortable with large datasets, analyze them, and to find new avenues to further our research program.”
Jetstream powers the lab of Maira Goytia at Spelman College, where she and undergraduate researchers analyze large sets of transcriptomic and genomic data, to explore the diversity of Neisseria bacteria species. Spelman College is an all-women historically black college/university (HBCU) in Atlanta that benefits greatly from having access to a resource like Jetstream.
Maira Goytia, assistant professor in the Department of Biology at Spelman College 29
SUPPORTING THE HUMANITIES, ARTS, AND SOCIAL SCIENCES
Even researchers and educators in the arts use advanced computing in their work
“Jetstream is easy and accessible for sure, but the technical support has been great. Being able to work with the RT [and Jetstream] team has made this much easier. I have just enough skills to make the right file transfers. And with Jetstream, that’s all I need.” Peter Miksza, Indiana University Jacobs School of Music
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SUPERCOMPUTING IN A MUSIC SCHOOL Aiming to inform both music education researchers and policy makers, Peter Miksza, a professor at the IU Jacobs School of Music, used Jetstream to analyze and host plain-language versions of dense federal data related to music education in the U.S, which has become a resource for both teachers and advocates in the field.
The Distant Reader gateway supplements the traditional reading process by allowing researchers to make sense of a large body of text when there’s too much to process. The Distant Reader uses a dynamic virtual cluster deployed on the Jetstream cloud as well as services like SciGap, Apache Airavata, and OpenStack, supported by PTI Cyberinfrastructure Integration Research Center (CIRC) and RT. The Distant Reader can be helpful to researchers and students in various scholarly situations, from scientists doing a literature review to undergraduates who want a “big picture” understanding of an entire semester’s readings.
EPIDEMIC OUTBREAKS AND REPRESSION DYNAMICS In the COVID-19 era, the IU-led Jetstream cloud system helps researchers determine the relationship between disease and social discord by analyzing data in 48 African countries from 1990 to 2017, found in two datasets: social unrest information from the Social Conflict Analysis Database, and epidemic information in the International Disaster Database.
“The results of this analysis will play an important role in understanding the relationship between communicable diseases and social unrest events in the wake of the COVID-19 global pandemic.” Rebecca Cordell, Ph.D., University of Texas at Dallas
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The National Center for Genome Analysis Support (NCGAS) provides resources for the U.S. biological research community to analyze, understand, and use the vast amount of genomic information now available. A collaborative project between Indiana University and the Pittsburgh Supercomputing Center, a joint computational research center with Carnegie Mellon University and the University of Pittsburgh, NCGAS focuses on transcriptome- and genome-level assembly, phylogenetics, metagenomics, transcriptomics, and community genomics. NCGAS provides consulting services for NSF-funded researchers, education and outreach programs on genome assembly and analysis, and maintains software on IU supercomputers as well as nationally accessible high performance clusters. This material is based upon work supported by the National Science Foundation under Grant 1759906. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
HYBRID APPROACH TO ONLINE INSTRUCTION As the COVID-19 pandemic halted in-person attendance, NCGAS took their R workshop online to serve hundreds of scientists around the world. Using a hybrid approach with pre-recorded video lectures, real-time chat and discussion boards, Jetstream, and step-by-step online instruction in Expand/Canvas, the workshop continued, and attendance grew more than 1,000 percent.
“My favorite part was the video lectures. I have attempted to learn R before on my own using manuals and online courses, but actually ‘sitting’ in a lecture with a real person teaching gave me a few ‘aha’ moments that I had never had before.”
Workshop attendee survey comment 32
BREAKING NEW GROUND IN GENOMIC DATA MINING A collaboration between NCGAS and IU's Center of Excellence for Women & Technology (CEW&T) supported research from a new cohort of talented bioinformation scientists, enabling genomic data mining through the Research Experience for Undergraduates (REU) program.
“There is a lot of data, with multiple layers of research. The NCGAS team was really good at breaking down information about using the software and learning how to use the different programs.”
Christine Campbell, REU program participant from the IU Luddy School of Informatics, Computing, and Engineering
“Working with CEW&T has been a wonderful partnership for NCGAS and for the REU students. The collaboration enables the students professional training through CEW&T and domain skills and experience through NCGAS. We've had several students continue working with us as interns or in other REU programs. And, bonus, one just landed her first industry job!” REU participant Sruthi Ganapaneni receives guidance on presenting her poster from NCGAS staff.
Sheri Sanders, manager and primary investigator, NCGAS
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RT IMPACT: THE WORLD
DELIVERING TRANSFORMATIVE TECHNOLOGY TO THE GLOBAL RESEARCH COMMUNITY
RESPONDING TO A GLOBAL PANDEMIC SUPPORTING INTERNATIONAL RESEARCH EFFORTS Using IU’s Carbonate supercomputer, Josua Aponte-Serrano is part of an international research team that has developed a modular framework for modeling drug effectiveness in treating viral diseases like COVID-19.
“Increased access to powerful computing technologies like Carbonate has broadened the use of complex biomedical models to understand the mechanisms driving the progression of these diseases.” Josua Aponte-Serrano, graduate student researcher, Biocomplexity Institute at Indiana University
Through Jetstream, RT has had a significant impact on COVID-19 response by participating in the COVID-19 HPC Consortium. Projects included early usage through the Galaxy Gateway for SARS-CoV-2 analysis and providing resources to the Open Medical Records System team that has affected medical records systems and data sharing worldwide.
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IUANYWARE EASES THE BURDEN OF LEARNING FROM HOME, EVEN ABROAD
“IUanyWare has allowed
In response to the COVID-19 pandemic, RT's IUanyWare team expanded the reach of the platform to include disciplinespecific software from home, which was previously only available on campus. Speech and Hearing Sciences and the Media School are just two examples of how providing students with access to discipline-specific software has enriched IU students’ experience. IU's remote learning efforts have also reached beyond the borders of the United States, as IUanyWare has provided students who needed to return to their home countries the ability to access software that otherwise might have been unavailable. The IUanyWare team has ensured that during this pandemic, and into the future, students can learn from anywhere.
our professional students to securely access our electronic medical record system remotely, which positively impacted work efficiency and training opportunities for our students.”
Laura Karcher, clinical professor, Speech, Language and Hearing Sciences
FAST, SECURE ACCESS TO COVID-19 DATA “The capabilities of CoRDaCo’s upgraded technologies will not only provide more security, but also will facilitate faster and easier availability to valuable COVID-19 data necessary for IU researchers who are evaluating vast amounts of information and seeking solutions.”
Umberto Tachinardi, M.D., MSc, Regenstrief chief information officer
The COVID-19 Research Data Commons, or CoRDaCo, is the result of a partnership between the Regenstrief Institute and Indiana University. CoRDaCo uses MDClone software to scrub sensitive patient information from datasets and provide abstracted, synthetic data from COVID-19 mitigation testing, as well as government vital records, to create complete datasets for public health research.
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TAKING BIG UNIVERSITY RESOURCES TO SMALLER INSTITUTIONS DATA-DRIVEN ORGANIZATIONS ARE GROWING ORGANIZATIONS Program evaluation—backed by data—has become the norm for grand-scale National Science Foundation projects. Within the Pervasive Technology Institute at IU, Cyberinfrastructure Assessment and Evaluation (CAE) designs studies scaling large and small; conducts interviews, focus groups, and point-of-service surveys; and administers multi-year longitudinal studies. CAE provides analysis of the data and offers recommendations based on that analysis to assist organizations in delivering outstanding value to their stakeholders and improving their growth.
“As organizations look to make data-driven decisions, we help them by envisioning the studies that will get them the data needed to guide day-to-day operations and set long-term strategies.”
Julie Wernert, manager, Cyberinfrastructure Assessment and Evaluation
XCRI and CAE are supported by IU staff through the Extreme Science and Engineering Discovery Environment (XSEDE), funded by the National Science Foundation. This material is based upon work supported by the National Science Foundation under Grant 1548562. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
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LUCILLE LEVELS UP
The campus of Langston University in Langston, OK.
XSEDE's Cyberinfrastructure Resource integration team (XCRI) engaged with Langston University to upgrade their HPC system “Lucille” so students may learn the fundamentals of high performance parallel computing and high throughput distributed computing.
“XCRI is a valuable service for a small institution running a local cluster. This great service can be used by small HPC groups to support struggling centers with limited manpower.”
Dr. Franklin Fondjo Fotou, director of LU Computing Center for Research and Education at Langston University
BUDDY GETS A BOOST XCRI performed a full-week remote build for the University of Central Oklahoma (UCO) on its high performance computing (HPC) system, "Buddy." Buddy provides computational support for projects spanning particle transport, micro-mixing, stochastic modeling, ecological modeling, and bioinformatics and disease spread modeling.
“It was a pleasure working with the XCRI team on our recent rebuild of the Buddy cluster at the University of Central Oklahoma.”
Dr. Evan Lemley of University of Central Oklahoma 37
TWEETING DURING A GLOBAL PANDEMIC
METHODS TO CLASSIFY COVID-19 TWITTER DATA Jetstream enables a self-supervised model to classify COVID-19 tweets in order to provide insights into COVID-19 that have not been investigated. “Public health surveillance and tracking the virus via social media can be a useful digital tool for contact tracing and preventing the spread of the virus. Large volumes of COVID-19 tweets can quickly be processed in real-time to offer information to researchers.”
Brandon Lwowski, Ph.D. student in the Department of Information Technology, AI concentration, at UTSA, and Jetstream Research Experiences for Undergraduates (REU) program participant
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MISINFORMATION ABOUT THE COVID-19 VACCINE Collecting and analyzing between 600,000 and 700,000 Twitter posts a day, the CoVaxxy dashboard tracks and quantifies credible information and misinformation narratives over time. The hope is to encourage the public to be more vigilant about the information they consume on their daily social media feeds in the fight against COVID-19. Various RT services are deployed to aid in this research, including Jetstream, Slate-Project for storage, and the Carbonate supercomputer.
“With Jetstream, it's very easy to set up and we can configure the machines how we want them. We found that it's really useful and powerful because we can essentially set up different machines to do different roles, and we have complete control over the machines ourselves.”
John Bryden, executive director of IU’s Observatory on Social Media
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rt.iu.edu Research Technologies is a division of University Information Technology Services and a center in the Pervasive Technology Institute at Indiana University.
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