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Connecting Researchers in Sharing and Re-Use of Research Data and Software: University of California Office of the President

Sponsor: University of California, Office of the President, Oakland

Guenter Waibel

[email protected] (Principal Investigator)

ABSTRACT

Open science practices have gained widespread adoption, globally, with the help of federal funding and publisher policies, as well as the increasing visibility and growing awareness of the value of sharing work. This has been largely evident in light of the current COVID19 pandemic, with data sharing driving many areas of research, and open software resources must evolve to meet the needs of researchers. To meet the emerging demands and growing requirements of the research community who need support for both data and software sharing, Dryad and California Digital Library partnered in 2018 and Dryad and Zenodo partnered in 2019. These partnerships have allowed for the three organizations to re-think the data and publishing processes, explore ways for data curation, software preservation, and for output re-use to be tied together more seamlessly.

This project is a one-day, invitational workshop bringing together researchers and adjacent community members with diverse backgrounds to discuss needs, challenges, and priorities for re-using research data and software. The goal of the meeting is to develop pathways for consistent engagement with individuals and groups across the diverse scientific disciplines in order to be connected with and responsive to researchers’ needs and goals. Meeting topics include dataset re-use, deposition guidance, curation standards and requirements, integrations and relationships between data and code, and advocacy and adoption. The anticipated outputs are a set of requirements and needs to better enable data and software sharing and re-use.

Virtual Reality Research

Digitization TCN: Collaborative Research: Capturing California's Flowers: using digital images to investigate phenological change in a biodiversity hotspot: San Diego Society of Natural History

Layla Aerne Hains

[email protected]

Flowering time is an important biological phenomenon, affecting human societies through its effects on agricultural crops, pollinators, pests, and biodiversity. Given the sensitivity of flowering times to climatic conditions, a thorough understanding of how plants respond to changing environments is necessary for predicting the consequences for pollinators, herbivores, parasites, and plant populations. A record of historical flowering times is found within the nation's herbaria. This award establishes a thematic collection network (TCN) dedicated to understanding flowering time shifts in the California flora. California has the most diverse native flora of any state in the U.S., containing more than one-third of all U.S. plant species. The state is a biodiversity hotspot due to the high number of endemic species that are also threatened. The Capturing California's Flowers (CCF) TCN will record flowering times from and create images of over 900,000 herbarium specimens from the oldest records, the most diverse families, and most threatened families in California. Twenty-two institutions spanning the state, including public universities, state agencies, museums, and botanic gardens, will participate in these efforts. This project will generate data that will increase our understanding of flowering time shifts – a critical need for agriculturalists, conservation biologists, plant taxonomists, land managers, and wildlife biologists.<br/><br/>Digitization of each specimen in the CCF TCN will result in a high-resolution image, a databased record of collection metadata, a georeferenced point, and the reproductive status of the specimen. New tools will be developed for the public to search and display phenological data through a Symbiota portal interface. The CCF TCN will develop novel data standards for capturing and sharing trait data from specimens. Building on already successful national and regional programs, the CCF TCN will partner with schools, universities, botanical clubs, and the general public to crowd source phenological measurements through online expeditions, workshops, new college courses, and K-12 educational programs. The CCF TCN will provide a historical record of plants currently being monitored through the National Phenology Network and other regional programs. Finally, this award will expand efforts to train the "next generation" of museum curators, collectors, and researchers. This award is made as part of the National Resource for Digitization of Biological Collections through the Advancing Digitization of Biological Collections program, and all data resulting from this award will be available through the national resource (iDigBio.org).<br/><br/>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

Virtual Reality Research

Collaborative Research: ABI Innovation: Algorithms for recovering root architecture from 3D imaging: Saint Louis University

David Letscher

[email protected]

Roots, the "hidden" half of the plant, play many critical roles in the plant's development such as the uptake of water and nutrients, providing anchorage, and stabilizing the soil. These functions, in turn, are closely associated with the root architecture. Quantifying root architecture is not only a fundamental aspect of plant science but is a critical component in crop breeding for sustainable agriculture. Recent advances in 3D imaging (e.g., CT and MRI) have made it possible to capture 3D root structures in natural growing environments and monitor their growth over time. Unfortunately, the potential of the imaging techniques has been largely held back by the lack of effective computational tools for interpreting the images and distilling biological insights. This project, to be conducted by a group of computer scientists, mathematicians, and biologists across three institutes in the St. Louis region, aims at developing efficient and robust computational methods for automated analysis of root architecture from 3D images. The research looks a step ahead of the current cutting edge phenotype data collection, to how we will derive accurate representations of growing root systems, and therefore gain insight into the plant phenome. The team is committed to providing training to more than ten students over the course of the project, leveraging the existing NSF REU programs at two of the institutes. The team will pursue outreach activities not only within the research communities but also locally in the St. Louis area with a focus on grade schools.<br/><br/>Deriving root architecture from 3D images involves a number of technically challenging tasks, including inferring individual roots from a segmented image, reconstructing their branching structure, and tracking the architecture in a time series of segmented images. This research draws from, and extends upon, methods from computer graphics and computational geometry to address these tasks. Specifically, the research will develop three novel classes of methods. Given a noise-ridden root segmentation, the first class of methods produces a curve skeleton that captures the topology and branching structure of the root system. The second class then uses the curve skeleton to automatically infer architectural components such as the root hierarchy and types. The third class improves the accuracy of the algorithms in the 1rst two classes by utilizing a sequence of segmentations and further annotates the root architecture with a time function. These algorithms enable the extraction of detailed root traits for root phenotyping, and both the algorithms and traits will be evaluated by a suite of representative real-world imaging data.<br/>Besides the design of automatic algorithms, a graphical software will be prototyped that offers fast and interactive means to inspect and edit the results produced by the algorithms. The software will be tested by biologists in the team and freely distributed to the research community.<br/><br/>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

Virtual Reality Research

The Formation, Evolution, and Fate of Multiple Star Systems: University of Oklahoma Norman Campus

John Tobin

[email protected]

Stars are born within clouds of dense gas that collapse under their own gravity. Sometimes solitary stars form, like our own Sun. But, stars also commonly form in binary or multiple star systems that are bound by gravity. It remains unknown how most of these binary stars form. One way that they may form is within the disk of gas and dust that forms around the newborn star. They may also first form separately and later become bound due to their own mutual gravity. The number of<br/>forming binary systems, their separations, and the environment that the binary stars formed within must be examined to understand why they are so common.<br/><br/>The investigators seek to understand formation of binary stars, by finding and examining previously unknown newborn binary stars. These newborn stars will be observed with the NSF's Very Large Array (VLA) and the Atacama Large Millimeter/submillimeter Array (ALMA) radio telescopes. These high-resolution observations will discover binary stars forming with separations smaller than the size of our own Solar System. They will show where binary stars form, how they most likely formed, and if they will remain in a binary system throughout their lives. This project will help reveal how often Solar Systems like our own form around a single star. As part of this project, radio astronomy will be integrated into undergraduate and graduate education at the University of Oklahoma. Lab activities using the local 3-meter radio telescope will be designed to fulfill educational goals at multiple levels. Collaboration with local high schools will also enable them to conduct radio astronomy observations from their classroom.<br/><br/>The investigators will conduct a systematic search for multiple stars. The investigators will analyze surveys of the Orion and Perseus star forming regions, sampling over 400 proto-stars in total, achieving better than 30 Astronomical Unit resolution. The companion separation distributions between Orion and Perseus will be compared between themselves and with the distributions measured for field stars using statistical tests. For a subset of the systems, molecular line imaging from ALMA will be used to verify that the disks are Keplerian and to measure the masses of the proto-stars and estimate their mass ratios. Finally, even if systems lack a companion, but have a clear disk, their likelihood of later fragmentation will be assessed. In addition to this census, their formation conditions will be characterized and the potential for companion formation will be estimated. The investigators will create a clearer picture of multiplicity at the time of early star formation and how the distribution of multiple stars must change as the stellar systems mature to the main sequence.<br/><br/>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

Virtual Reality Research

Supporting Science Students through Scholarships, Academic and Social Activities, and Reflective Journaling: Joliet Junior College

Andrew Morrison

[email protected]

With funding from the National Science Foundation's Scholarships in Science, Technology, Engineering and Mathematics (S-STEM) program, this project at Joliet Junior College is designed to address the ever-increasing need in Illinois and surrounding areas for highly qualified STEM professionals. It will add to the local, regional, and national understanding of learning as it enhances student retention, performance, graduation, and peer support networks. A structured research study will be used to determine the impact of course specific tutoring, mentoring, and reflective journaling among students in STEM courses. The project will also assess and track the metacognitive skills that students use to advance their scientific thinking. Data reflecting the activities will be used to improve the program for all participants, as well as inform the academic community through conference papers and presentations at national and regional conferences. Each of these areas will be evaluated by an external evaluator using surveys, rubrics, and performance in specific courses to gather both quantitative and qualitative information about the project. Due to the demographics of the institution and the targeted recruitment of women and other underrepresented groups from both high schools and the college, the project will help to diversify the workforce.<br/><br/>To increase the number of academically talented students with demonstrated financial need who begin and complete a STEM program of study, the college will integrate scholarships and academic support with STEM faculty mentoring, reflective journaling, social cohorts, hands-on experiential learning through relevant research projects, and exposure to industry leaders and topics to provide scholars a pathway to success in STEM fields. Involvement in STEM classes, increased faculty mentoring geared to specific student needs, and reflective journals will encourage students to embrace the STEM community and find their own identity within it, while simultaneously learning how to mentor the next generation of scientists. Information gathered during classes, mentoring, reflective journals, student evaluations will inform the wider STEM community at the college, as well as increase awareness of student group building within the college student academic and support programs.

Virtual Reality Research

Collaborative Research: Nanofluidics Enabled Attenuation of Dynamic Impacts and Stress Waves: University of Virginia Main Campus

Baoxing Xu

[email protected]

Dynamic impacts can cause stress waves within solid materials, resulting in damage to infrastructure, personnel, or devices. However, current approaches to mitigate stress waves are inadequate in that they rely on energy absorption associated with unrecoverable buckling and/or plastic deformation of materials and structures. Moreover, the time required to deform these materials is typically much longer than the time needed for dynamic impacts and stress waves to propagate through these protection materials. Nanofluidics, in which the liquid is forced into nanoscale channels by an external pressure or stress, is expected to attenuate stress waves and offers a entirely new paradigm for the design of protection materials and structures. The overarching goal of this project is to investigate and understand nanofluidics-enabled mitigation of dynamic impacts and stress waves with particular focus on nanofluidics in three-dimensional nanoporous networks. This collaborative project will also provide a broad impact on education including professional trainings to both graduate and undergraduate students, and on outreach including inspiring interactions with local high schools.<br/><br/>The objective of this collaborative project is to systematically investigate the science of nanofluidics in non-wetting liquid-solid nanoporous composite materials, and to explore its underlying protection mechanism for mitigating dynamic impacts and stress waves. To this end, the proposed research will focus on three tasks: (i) to investigate and unveil the science of nanofluidics in non-wetting liquid-solid nanoporous structures under a high speed loading using atomistic simulations, (ii) to develop a theoretical model of nanofluidic energy capture mechanism to quantify nanofluidic responses to dynamic impacts and stress waves, and (iii) to design and carry out verification experiments at high strain rates by employing non-wetting liquid-solid nanoporous materials platforms. The nanofluidic energy capture mechanism will refresh existing design strategies of protection materials and structures subjected to stress waves, thereby revolutionizing both fundamental nanofluidics and application technologies.<br/><br/>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

Virtual Reality Research

Intrinsic Alignment Models for Precision Cosmology: Carnegie-Mellon University

Rachel Mandelbaum

[email protected]

One of the key mysteries in modern cosmology is the nature of the dark energy that is responsible for the accelerated expansion rate of our Universe. Weak gravitational lensing, the coherent distortion of galaxy shapes due to deflection of light by mass, is the most promising observational method for uncovering the nature of dark energy. As a result, large upcoming surveys such as the Large Synoptic Survey Telescope (LSST) have been planned to measure weak lensing very precisely. The objective of this project is to provide accurate theoretical predictions that will eliminate a key source of uncertainty in weak lensing measurements and test their use in analysis of data from an ongoing sky survey. Work such as this, that will contribute to the solution of the biggest mystery in modern cosmology, will clearly promote the progress of science. As an additional benefit, the investigators will extend an existing, highly successful educational outreach program ("Space Public Outreach Team" or SPOT) to the Pittsburgh area, focusing on schools with a significant fraction of under-represented minorities. This project will have an impact both on K-12 education and undergraduate and graduate education.<br/><br/>Weak gravitational lensing has great potential to solve some of the major outstanding issues in cosmology, such as the nature of dark energy. However, a major source of uncertainty is that these measurements are typically interpreted assuming that all coherent galaxy shape alignments are due to weak lensing, but unfortunately, galaxies do exhibit coherent "intrinsic alignments" with large-scale density fields. The alignments contaminate weak lensing measurements at a level that will significantly exceed the statistical error bars on weak lensing measurements with the LSST. This project has three main objectives. The first objective is to use large volume, extremely high resolution hydrodynamic simulations to further our understanding of the physics behind intrinsic alignments and build improved intrinsic alignments models. The second objective is to produce mock galaxy catalogs with intrinsic alignments for use in testing intrinsic alignments mitigation schemes. The final objective is to carry out cosmological weak lensing analysis including strategies to marginalize over intrinsic alignments using improved intrinsic alignment models that are motivated by state-of-the-art simulations, analytic theory, and observations.

Virtual Reality Research

Growing Pathways to STEM (Project GPS): Central Community College

Steven Heinisch

[email protected]

Project Growing Pathways to Science, Technology, Engineering, and Mathematics (Project GPS) will provide scholarships for 25 academically talented, low-income students pursuing Associate of Science degrees in STEM fields. The project will focus on rural students in the State of Nebraska, and will work with local high schools that offer both dual credit and career pathways, to assist in early identification and recruitment of academically talented scholars. Students will benefit from mentorship through networking, team-building, and practical career experience, that includes unique, collaborative college-industry partnerships. Support services will address financial and academic support barriers specific to rural student success. <br/><br/>Project GPS will investigate an interventionist model of the relationships between mentors, cohorts, students, and industry. This potentially transformative model is possible through college-industry-community partnerships. These partnerships will bridge established gaps that inhibit student success, and help students develop critical thinking skills needed for life beyond the community college. An Immersive Service Learning Experience (ISLE) will provide an intensive orientation experience and include a summer component with student participation in independent/collaborative research, a cooperative education program, or industry internship/job shadow experiences influenced by cohort composition and local business/industry input. All ISLE projects will incorporate global sustainability concepts on a local scale, with intended measurable benefits in and beyond the local community. The project will generate new knowledge regarding the engagement and support of rural, community college students, and effective practices for supporting their degree completion and transfer to baccalaureate degree programs or entry into the STEM workforce.

Virtual Reality Research

Digitization TCN: Collaborative Research: Capturing California's Flowers: using digital images to investigate phenological change in a biodiversity hotspot: Santa Barbara Botanic Garden

Christopher Guilliams

[email protected]

Flowering time is an important biological phenomenon, affecting human societies through its effects on agricultural crops, pollinators, pests, and biodiversity. Given the sensitivity of flowering times to climatic conditions, a thorough understanding of how plants respond to changing environments is necessary for predicting the consequences for pollinators, herbivores, parasites, and plant populations. A record of historical flowering times is found within the nation's herbaria. This award establishes a thematic collection network (TCN) dedicated to understanding flowering time shifts in the California flora. California has the most diverse native flora of any state in the U.S., containing more than one-third of all U.S. plant species. The state is a biodiversity hotspot due to the high number of endemic species that are also threatened. The Capturing California's Flowers (CCF) TCN will record flowering times from and create images of over 900,000 herbarium specimens from the oldest records, the most diverse families, and most threatened families in California. Twenty-two institutions spanning the state, including public universities, state agencies, museums, and botanic gardens, will participate in these efforts. This project will generate data that will increase our understanding of flowering time shifts – a critical need for agriculturalists, conservation biologists, plant taxonomists, land managers, and wildlife biologists.<br/><br/>Digitization of each specimen in the CCF TCN will result in a high-resolution image, a databased record of collection metadata, a georeferenced point, and the reproductive status of the specimen. New tools will be developed for the public to search and display phenological data through a Symbiota portal interface. The CCF TCN will develop novel data standards for capturing and sharing trait data from specimens. Building on already successful national and regional programs, the CCF TCN will partner with schools, universities, botanical clubs, and the general public to crowd source phenological measurements through online expeditions, workshops, new college courses, and K-12 educational programs. The CCF TCN will provide a historical record of plants currently being monitored through the National Phenology Network and other regional programs. Finally, this award will expand efforts to train the "next generation" of museum curators, collectors, and researchers. This award is made as part of the National Resource for Digitization of Biological Collections through the Advancing Digitization of Biological Collections program, and all data resulting from this award will be available through the national resource (iDigBio.org).<br/><br/>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

Virtual Reality Research

Digitization TCN: Collaborative Research: Capturing California's Flowers: using digital images to investigate phenological change in a biodiversity hotspot: San Diego State University Foundation

Michael Simpson

[email protected]

Flowering time is an important biological phenomenon, affecting human societies through its effects on agricultural crops, pollinators, pests, and biodiversity. Given the sensitivity of flowering times to climatic conditions, a thorough understanding of how plants respond to changing environments is necessary for predicting the consequences for pollinators, herbivores, parasites, and plant populations. A record of historical flowering times is found within the nation's herbaria. This award establishes a thematic collection network (TCN) dedicated to understanding flowering time shifts in the California flora. California has the most diverse native flora of any state in the U.S., containing more than one-third of all U.S. plant species. The state is a biodiversity hotspot due to the high number of endemic species that are also threatened. The Capturing California's Flowers (CCF) TCN will record flowering times from and create images of over 900,000 herbarium specimens from the oldest records, the most diverse families, and most threatened families in California. Twenty-two institutions spanning the state, including public universities, state agencies, museums, and botanic gardens, will participate in these efforts. This project will generate data that will increase our understanding of flowering time shifts – a critical need for agriculturalists, conservation biologists, plant taxonomists, land managers, and wildlife biologists.<br/><br/>Digitization of each specimen in the CCF TCN will result in a high-resolution image, a databased record of collection metadata, a georeferenced point, and the reproductive status of the specimen. New tools will be developed for the public to search and display phenological data through a Symbiota portal interface. The CCF TCN will develop novel data standards for capturing and sharing trait data from specimens. Building on already successful national and regional programs, the CCF TCN will partner with schools, universities, botanical clubs, and the general public to crowd source phenological measurements through online expeditions, workshops, new college courses, and K-12 educational programs. The CCF TCN will provide a historical record of plants currently being monitored through the National Phenology Network and other regional programs. Finally, this award will expand efforts to train the "next generation" of museum curators, collectors, and researchers. This award is made as part of the National Resource for Digitization of Biological Collections through the Advancing Digitization of Biological Collections program, and all data resulting from this award will be available through the national resource (iDigBio.org).<br/><br/>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

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