News
Teacher
ESA Short Course on Mathematical Programming in Ecology
Virtual
Mentor
MIT Summer Geometry Initiative
Virtual
Panelist
Workshop on the Science of Scientific-Software Development and Use
Virtual
Finding Antarctica's Pole of Inaccessibility
Published at Polar Record
Invited Talk
Lawrence Berkeley National Lab
Berkeley, CA
Invited Talk
CMU Electrical and Computer Engineering
Pittsburgh, PN
Invited Talk
Flatiron Institute
New York, NY
2nd Place
SC20 ACM Research Competition
Global
PhD Computational Science
UC Berkeley
MS Computer Science
UC Berkeley
Invited Lecturer
OpenGeoHub Summer School
Wageningen, Netherlands
Depression Hierarchies
Published at Earth Surface Dynamics
Fill-Spill-Merge
Preprint at Earth Surface Dynamics
Invited Talk
Santa Fe Institute
Santa Fe, NM
Outstanding Presentation Award
AGU
Cryosphere Innovation Award
AGU
Invited Talk
U. Minnesota Department of Geography, Environment, and Society.
Minneapolis, MN
Depression Hierarchies
Preprint at Earth Surface Dynamics
Keynote Speaker
JRC Workshop on Benchmarking Global Digital Elevation Models
Ispra, Italy
1st Prize
MCED Award for Innovative Contributions to Ecological Modelling
Global
Presenter
Geomorphometry 2018
Boulder, CO
Best Student Paper
Geomorphometry 2018
Boulder, CO
Fellow
Berkeley Institute for Data Science
Berkeley, CA
Participant
Second Workshop on Conceptualizing a Geospatial Software Institute
Chicago, IL
Software Carpentry Instructor
Berkeley Institute for Data Science
Berkeley, CA
Mentor
CU Boulder GPU Hackathon
Boulder, CO
Invited Talk
Pacific Northwest National Lab’s “Computing at PNNL” Seminar
Richland, WA
Mentor
BNL KNL Hackathon
Upton, NY
Mentor
ORNL OpenACC Hackathon
Knoxville, TN
Invited Talk
LBNL Terrestrial Biogeochemistry Group
Berkeley, CA
Presenter
FOSS4G
Boston, MA
Most Innovative Project
TOM Berkeley Makeathon
Berkeley, CA
A Pipeline Strategy For Crop Domestication
Published at Crop Science
MS Evolutionary Ecology
U Minnesota
Virtual Division Winner
NASA Space Apps Challenge
Global
Invited Speaker
New Roots For Ecological Intensification Conference
Estes Park, CO
Invited Speaker
Twin Cities Climate Hack
Minneapolis, MN
Invited Speaker
Twin Cities Climate Hack
Minneapolis, MN
First Place
Hack4Good Global Climate Challenge
Global
3rd Place High Tech Division (for OMG Transit)
Minnesota Cup
Minneapolis, MN
Finalist
Knight Green Line Challenge
St. Paul, MN
Best Use of Public Data
National Day of Civic Hacking
Minneapolis, MN
Code for Good Prize
National Day of Civic Hacking
Seattle, WA
Presenter
Data Services Accelerator Demo Day
Santa Clara, CA
Fellow
NSF Graduate Research Fellowship
USA
Winner
Beta.MN Start-Up Competition
Minneapolis, MN
Selected for the
Intel Labs' Innovation Pipeline
Portland, OR
Invited Speaker
Seminar
St. Paul, MN
Ignite Presenter
ESA 2013
Minneapolis, MN
Presenter
ESA 2013
Minneapolis, MN
Panelist
House of Genius
Minneapolis, MN
Presenter
MinneDemo
Minneapolis, MN
Invitee
Champions of Change
The White House
ESRI Innovation Award
National Day of Civic Hacking
Minneapolis, MN
Publications
2022
Advances in hexagon mesh-based flow direction modeling
Chang Liao, Tian Zhou, Donghui Xu, Barnes, Gautam Bisht, Hong-Yi Li, Zeli Tan, Teklu Tesfa, Zhuoran Duan, Darren Engwirda, L. Ruby Leung
Advances in Water Resources
Abstract 10.1016/j.advwatres.2021.104099
Watershed delineation and flow direction representation are the foundations of streamflow routing in spatially distributed hydrologic modeling. A recent study showed that hexagon-based watershed discretization has several advantages compared to the traditional Cartesian (latitude-longitude) discretization, such as uniform connectivity and compatibility with other Earth system model components based on unstructured mesh systems (e.g., oceanic models). Despite these advantages, hexagon-based discretization has not been widely adopted by the current generation of hydrologic models. One major reason is that there is no existing model that can delineate hexagon-based watersheds while maintaining accurate representations of flow direction across various spatial resolutions. In this study, we explored approaches such as spatial resampling and hybrid breaching-filling stream burning techniques to improve watershed delineation and flow direction representation using a newly developed hexagonal mesh watershed delineation model (HexWatershed). We applied these improvements to the Columbia River basin and performed 16 simulations with different configurations. The results show that (1) spatial resampling modulates flow direction around headwaters and provides an opportunity to extract subgrid information; and (2) stream burning corrects the flow directions in mountainous areas with complex terrain features.
2021
Ten simple rules on writing clean and reliable open-source scientific software
Hunter-Zinck, Fioravante de Siqueira, Vásquez, Barnes, Martinez
PLOS Computational Biology
Abstract 10.1371/journal.pcbi.1009481
Functional, usable, and maintainable open-source software is increasingly essential to scientific research, but there is a large variation in formal training for software development and maintainability. Here, we propose 10 “rules” centered on 2 best practice components: clean code and testing. These 2 areas are relatively straightforward and provide substantial utility relative to the learning investment. Adopting clean code practices helps to standardize and organize software code in order to enhance readability and reduce cognitive load for both the initial developer and subsequent contributors; this allows developers to concentrate on core functionality and reduce errors. Clean coding styles make software code more amenable to testing, including unit tests that work best with modular and consistent software code. Unit tests interrogate specific and isolated coding behavior to reduce coding errors and ensure intended functionality, especially as code increases in complexity; unit tests also implicitly provide example usages of code. Other forms of testing are geared to discover erroneous behavior arising from unexpected inputs or emerging from the interaction of complex codebases. Although conforming to coding styles and designing tests can add time to the software development project in the short term, these foundational tools can help to improve the correctness, quality, usability, and maintainability of open-source scientific software code. They also advance the principal point of scientific research: producing accurate results in a reproducible way. In addition to suggesting several tips for getting started with clean code and testing practices, we recommend numerous tools for the popular open-source scientific software languages Python, R, and Julia.
Finding Antarctica's Pole of Inaccessibility
Rees, Gerrish, Fox, Barnes
Polar Record
Abstract Code 10.1017/S0032247421000620
Antarctica’s Pole of Inaccessibility (Southern Pole of Inaccessibility: SPI) is the point on the Antarctic continent farthest from its edge. Existing literature exhibits disagreement over its location. Using two revisions of the Scientific Committee on Antarctic Research’s Antarctic Digital Database, we calculate modern-day positions for the SPI around 10 years apart, based on the position of the ‘outer’ Antarctic coastline i.e. its boundary with the ocean. These show that the position of the SPI in the year 2010 was around 83˚ 54’ S, 64˚ 53’ E, shifting on the order of 1 km per year as a result of changes of a similar magnitude in the Amery, Ronne-Filchner and Ross Ice Shelves. Excepting a position of the SPI calculated by British Antarctic Survey in 2005, to which it is very close, our newly calculated position differs by 150 to 900 km from others reported in the literature. We also consider the ‘inner’ SPI, defined by the coastline with floating ice removed. The position of this SPI in 2010 is estimated as 83˚37’ S, 53˚ 43’ E, differing significantly from other reported positions. Earlier cartographic data are probably not sufficiently accurate to allow its rate of change to be calculated meaningfully.
Fill-Spill-Merge: Flow routing in depression hierarchies
Barnes, Callaghan, Wickert
Earth Surface Dynamics
Abstract Code 10.5194/esurf-9-105-2021
Depressions—inwardly-draining regions—are common to many landscapes. When there is sufficient moisture, depressions take the form of lakes and wetlands; otherwise, they may be dry. Hydrological flow models used in geomorphology, hydrology, planetary science, soil and water conservation, and other fields often eliminate depressions through filling or breaching; however, this can produce unrealistic results. Models that retain depressions, on the other hand, are often undesirably expensive to run. In previous work we began to address this by developing a depression hierarchy data structure to capture the full topographic complexity of depressions in a region. Here, we extend this work by presenting a Fill-Spill-Merge algorithm that utilizes our depression hierarchy data structure to rapidly process and distribute runoff. Runoff fills depressions, which then overflow and spill into their neighbors. If both a depression and its neighbor fill, they merge. We provide a detailed explanation of the algorithm as well as results from two sample study areas. In these case studies, the algorithm runs 90–2,600× faster (with a 2,000–63,000× reduction in compute time) than the commonly-used Jacobi iteration and produces a more accurate output. Complete, well-commented, open-source code with 97% test coverage is available on Github and Zenodo.
2020
Gerrymandering and Compactness: Implementation Flexibility and Abuse
Barnes and Solomon
Political Analysis
Abstract Code 10.1017/pan.2020.36 arXiv: 1803.02857
Political districts may be drawn to favor one group or political party over another, or gerrymandered. A number of measurements have been suggested as ways to detect and prevent such behavior. These measures give concrete axes along which districts and districting plans can be compared. However, measurement values are affected by both noise and the compounding effects of seemingly innocuous implementation decisions. Such issues will arise for any measure. As a case study demonstrating the effect, we show that commonly-used measures of geometric compactness for district boundaries are affected by several factors irrelevant to fairness or compliance with civil rights law. We further show that an adversary could manipulate measurements to affect the assessment of a given plan. This instability complicates using these measurements as legislative or judicial standards to counteract unfair redistricting practices. This paper accompanies the release of packages in C++, Python, and R that correctly, efficiently, and reproducibly calculate a variety of compactness scores.
BusTr: predicting bus travel times from real-time traffic
Barnes, Buthpitiya, Cook, Fabrikant, Tomkins, Xu
ACM SIGKDD
Abstract 10.1145/3394486.3403376 arXiv: 2007.00882
We present BusTr, a machine-learned model for translating road traffic forecasts into predictions of bus delays, used by Google Maps to serve the majority of the world’s public transit systems where no official real-time bus tracking is provided. We demonstrate that our neural sequence model improves over DeepTTE, the state-of-the-art baseline, both in performance (−30% MAPE) and training stability. We also demonstrate significant generalization gains over simpler models, evaluated on longitudinal data to cope with a constantly evolving world.
Finding hierarchies in depressions and morphological segmentations
Barnes, Callaghan, Wickert
Earth Surface Dynamics
Abstract Code 10.5194/esurf-8-431-2020
Depressions – inwardly draining regions of digital elevation models – present difficulties for terrain analysis and hydrological modeling. Analogous “depressions” also arise in image processing and morphological segmentation, where they may represent noise, features of interest, or both. Here we provide a new data structure – the depression hierarchy – that captures the full topologic and topographic complexity of depressions in a region. We treat depressions as networks in a way that is analogous to surface-water flow paths, in which individual sub-depressions merge together to form meta-depressions in a process that continues until they begin to drain externally. This hierarchy can be used to selectively fill or breach depressions or to accelerate dynamic models of hydrological flow. Complete, well-commented, open-source code and correctness tests are available on GitHub and Zenodo.
2019
Rescal-snow: Simulating snow dunes with cellular automata
Kochanski, Defazio, Green, Barnes, Downie, Rubin, and Rountree
Journal of Open Source Software
Abstract PDF Code 21105/joss.01699
When wind blows over dry snow, it creates shapes known as snow bedforms. These features, which include snow dunes, waves, snow-steps and sastrugi, ornament Antarctica, Arctic sea ice, tundra, and mountain ridges. They change the reflectivity and average thermal conductivity of snow, and may change the patterns of snow accumulation and transport. Despite these effects, however, snow bedforms are poorly understood and not yet included in major snow or climate models. Here, we present a model which generates snow bedforms.
Optimal orientations of discrete global grids and the Poles of Inaccessibility
Barnes
International Journal of Digital Earth
Abstract PDF Code 10.1080/17538947.2019.1576786
Spatial analyses involving binning often require that every bin have the same area, but this is impossible using a rectangular grid laid over the Earth or over any projection of the Earth. Discrete global grids use hexagons, triangles, and diamonds to overcome this issue, overlaying the Earth with equally-sized bins. Such discrete global grids are formed by tiling the faces of a polyhedron. Previously, the orientations of these polyhedra have been chosen to satisfy only simple criteria such as equatorial symmetry or minimizing the number of vertices intersecting landmasses. However, projection distortion and singularities in discrete global grids mean that such simple orientations may not be sufficient for all use cases. Here, I present an algorithm for finding suitable orientations; this involves solving a nonconvex optimization problem. As a side-effect of this study I show that Fuller’s Dymaxion map corresponds closely to one of the optimal orientations I find. I also give new high-accuracy calculations of the Poles of Inaccessibility, which show that Point Nemo, the Oceanic Pole of Inaccessibility, is 15 km farther from land than previously recognized.
Accelerating a fluvial incision and landscape evolution model with parallelism
Barnes
Geomorphology 330
Abstract PDF Code 10.1016/j.geomorph.2019.01.002 arXiv: 1803.02977
Solving inverse problems, performing sensitivity analyses, and achieving statistical rigour in landscape evolution models requires running many model realizations. Parallel computation is necessary to achieve this in a reasonable time. However, no previous landscape evolution algorithm is able to leverage modern parallelism. Here, I describe an algorithm that can utilize the parallel potential of GPUs and many-core processors, in addition to working well in serial. The new algorithm runs 43x faster (70s vs. 3000s on a 10,000x10,000 input) than the previous state of the art and exhibits sublinear scaling with input size. I also identify key techniques for multiple flow direction routing and quickly eliminating landscape depressions and local minima. Complete, well-commented, easily adaptable source code for all versions of the algorithm is available on Github and Zenodo.
2017
Parallel Non-divergent Flow Accumulation For Trillion Cell Digital Elevation Models On Desktops Or Clusters
Barnes
Environmental Modelling & Software 92: 202–212
Abstract PDF Code 10.1016/j.envsoft.2017.02.022
Continent-scale datasets challenge hydrological algorithms for processing digital elevation models. Flow accumulation is an important input for many such algorithms; here, I parallelize its calculation. The new algorithm works on one or many cores, or multiple machines, and can take advantage of large memories or cope with small ones. Unlike previous algorithms, the new algorithm guarantees a fixed number of memory access and communication events per raster cell. In testing, the new algorithm ran faster and used fewer resources than previous algorithms exhibiting ~30% strong and weak scaling efficiencies up to 48 cores and linear scaling across datasets ranging over three orders of magnitude. The largest dataset tested has two trillion (2*10^12) cells. With 48 cores, processing required 24 minutes wall-time (14.5 compute-hours). This test is three orders of magnitude larger than any previously performed in the literature. Complete, well-commented source code and correctness tests are available for download from Github.
65 Million Years of Change in Temperature and Topography Explain Evolutionary History in Eastern North American Plethodontid Salamanders
Barnes and Clark
American Naturalist 190(1)
Abstract PDF Code 10.1086/691796
For many taxa and systems, species richness peaks at mid-elevations. One potential explanation for this pattern is that large-scale changes in climate and geography have, over evolutionary time, selected for traits that are favored under conditions found in contemporary mid-elevation regions. To test this hypothesis, we used records of historical temperature and topographic changes over the past 65 Myr to construct a general simulation model of Plethodontid salamander evolution in eastern North America. We then explore possible mechanisms constraining species to mid-elevation bands by using the model to predict Plethodontid evolutionary history and contemporary geographic distributions. Our results show that models which incorporate both temperature and topographic changes are better able to predict these patterns, suggesting that both processes may have played an important role in driving Plethodontid evolution in the region. Additionally, our model (whose annotated source code is included as a supplement) represents a proof of concept to encourage future work that takes advantage of recent advances in computing power to combine models of ecology, evolution, and earth history to better explain the abundance and distribution of species over time.
2016
Parallel Priority-Flood Depression Filling For Trillion Cell Digital Elevation Models On Desktops Or Clusters
Barnes
Computers & Geosciences (Volume 96, Nov 2016, pp. 56–68)
Abstract PDF Code 10.1016/j.cageo.2016.07.001
Algorithms for extracting hydrologic features and properties from digital elevation models (DEMs) are challenged by large datasets, which often cannot fit within a computer's RAM. Depression filling is an important preconditioning step to many of these algorithms. Here, I present a new, linearly-scaling algorithm which parallelizes the Priority-Flood depression-filling algorithm by subdividing a DEM into tiles. Using a single-producer, multi-consumer design, the new algorithm works equally well on one core, multiple cores, or multiple machines and can take advantage of large memories or cope with small ones. Unlike previous algorithms, the new algorithm guarantees a fixed number of memory access and communication events per subdivision of the DEM. In comparison testing, this results in the new algorithm running generally faster while using fewer resources than previous algorithms. For moderately sized tiles, the algorithm exhibits ~60% strong and weak scaling efficiencies up to 48 cores, and linear time scaling across datasets ranging over three orders of magnitude. The largest dataset on which I run the algorithm has 2 trillion (2*1012) cells. With 48 cores, processing required 4.8 hours wall-time (9.3 compute-days). This test is three orders of magnitude larger than any previously performed in the literature. Complete, well-commented source code and correctness tests are available for download from a repository.
A Pipeline Strategy For Crop Domestication
DeHaan, VanTassel, Anderson, Asselin, Barnes, Baute, Cattani, Culman, Dorn, Hulke, Kantar, Larson, Marks, Miller, Poland, Ravetta, Rude, Ryan, Wyse, Zhang
Crop Science (Volume 56, May–Jun 2016, Pages 1–14)
Abstract PDF 10.2135/cropsci2015.06.0356
In the interest of diversifying the global food system, improving human nutrition, and making agriculture more sustainable, there have been many proposals to domesticate wild plants or complete the domestication of semi-domesticated “orphan” crops. However, very few new crops have recently been fully domesticated. Many wild plants have traits limiting their production or consumption that could be costly and slow to change. Others may have fortuitous pre-adaptations that make them easier to develop or feasible as high-value, albeit low-yielding, crops. To increase success in contemporary domestication of new crops, we propose a “pipeline” approach, with attrition expected as species advance through the pipeline. We list criteria for ranking domestication candidates to help enrich the starting pool with more pre-adapted, promising species. We also discuss strategies for prioritizing initial research efforts once the candidates have been selected: developing higher value products and services from the crop, increasing yield potential, and focusing on overcoming undesirable traits. Finally, we present new-crop case studies which demonstrate that wild species' limitations and potential (in agronomic culture, shattering, seed size, harvest, cleaning, hybridization, etc.) are often only revealed during the early phases of domestication. When nearly insurmountable barriers were reached in some species, they have been (at least temporarily) eliminated from the pipeline. Conversely, a few species have moved quickly through the pipeline as hurdles such as low seed weight or low seed number per head were rapidly overcome, leading to increased confidence, farmer collaboration, and program expansion.
2014
The Reflective Plant Breeding Paradigm: A Robust System of Germplasm Development to Support Strategic Diversification of Agroecosystems
Runck, Kantar, Jordan, Anderson, Wyse, Eckberg, Barnes, Lehman, DeHaan, Stupar, Sheaffer, Porter
Crop Science (Volume 54, Sep–Oct 2014, Pages 1939–1948)
Abstract PDF 10.2135/cropsci2014.03.0195
Over the last half-century, crop breeding and agronomic advances have dramatically enhanced yields in temperate summer-annual cropping systems. Now, diversification of these cropping systems is emerging as a strategy for sustainable intensification, potentially increasing both crop production and resource conservation. In temperate zones, diversification is largely based on the introduction of winter-annual and perennial crops at spatial and temporal locations in annual-crop production systems that efficiently increase production and resource conservation. Germplasm development will be critical to this strategy, but we contend that to be feasible and efficient, germplasm improvement must be closely integrated with commercialization of these crops. To accomplish this integration, we propose a novel approach to germplasm development: the reflective plant breeding paradigm (RPBP). Our approach is enabled by developments in genomics, agroecosystem management, and innovation theory and practice. These developments and new plant-breeding technologies (e.g., low-cost sequencing, phenotyping, and spatial modeling of agroecosystems) now enable germplasm development to proceed on a time scale that enables close coordination of breeding and commercialization (i.e, development of cost-effective production systems and supply–value chains for end-use markets). The RPBP approach is based on close coordination of germplasm development with enterprise development. In addition to supporting strategic diversification of current annual-cropping systems, the RPBP may be useful in rapid adaptation of agriculture to climate change. Finally, the RPBP may offer a novel and distinctive pathway for future development of the public plant-breeding programs of land-grant universities with implications for graduate education for public- and private-sector plant breeders.
An Efficient Assignment of Drainage Direction Over Flat Surfaces in Raster Digital Elevation Models
Barnes, Lehman, Mulla
Computers & Geosciences. Vol 62, Jan 2014, pp 128-135, ISSN 0098-3004.
Abstract PDF Code 10.1016/j.cageo.2013.01.009
In processing raster digital elevation models (DEMs) it is often necessary to assign drainage directions over flats—that is, over regions with no local elevation gradient. This paper presents an approach to drainage direction assignment which is not restricted by a flat's shape, number of outlets, or surrounding topography. Flow is modeled by superimposing a gradient away from higher terrain with a gradient towards lower terrain resulting in a drainage field exhibiting flow convergence, an improvement over methods which produce regions of parallel flow. This approach builds on previous work by Garbrecht and Martz (1997), but presents several important improvements. The improved algorithm guarantees that flats are only resolved if they have outlets. The algorithm does not require iterative application; a single pass is sufficient to resolve all flats. The algorithm presents a clear strategy for identifying flats and their boundaries. The algorithm is not susceptible to loss of floating-point precision. Furthermore, the algorithm is efficient, operating in O(N) time whereas the older algorithm operates in O(N3/2) time. In testing, the improved algorithm ran 6.5 times faster than the old for a 100x100 cell flat and 69 times faster for a 700x700 cell flat. In tests on actual DEMs, the improved algorithm finished its processing 38–110 times sooner while running on a single processor than a parallel implementation of the old algorithm did while running on 16 processors. The improved algorithm is an optimal, accurate, easy-to-implement drop-in replacement for the original. Pseudocode is provided in the paper and working source code is provided in the Supplemental Materials.
Priority-Flood: An Optimal Depression-Filling and Watershed-Labeling Algorithm for Digital Elevation Models
Barnes, Lehman, Mulla
Computers & Geosciences. Vol 62, Jan 2014, pp 117-127, ISSN 0098-3004.
Abstract PDF Code 10.1016/j.cageo.2013.04.024
Depressions (or pits) are low areas within a digital elevation model that are surrounded by higher terrain, with no outlet to lower areas. Filling them so they are level, as fluid would fill them if the terrain were impermeable, is often necessary in preprocessing DEMs. The depression-filling algorithm presented here—called Priority-Flood—unifies and improves on the work of a number of previous authors who have published similar algorithms. The algorithm operates by flooding DEMs inwards from their edges using a priority queue to determine the next cell to be flooded. The resultant DEM has no depressions or digital dams: every cell is guaranteed to drain. The algorithm is optimal for both integer and floating-point data, working in O(n) and O(n log2 n) time, respectively. It is shown that by using a plain queue to fill depressions once they have been found, an O(m log2 m) time-complexity can be achieved, where m does not exceed the number of cells n. This is the lowest time complexity of any known floating-point depression-filling algorithm. In testing, this improved variation of the algorithm performed up to 37% faster than the original. Additionally, a parallel version of an older, but widely-used depression-filling algorithm required six parallel processors to achieve a run-time on par with what the newer algorithm's improved variation took on a single processor. The Priority-Flood Algorithm is simple to understand and implement: the included pseudocode is only 20 lines and the included C++ reference implementation is under a hundred lines. The algorithm can work on irregular meshes as well as 4-, 6-, 8-, and n-connected grids. It can also be adapted to label watersheds and determine flow directions through either incremental elevation changes or depression carving. In the case of incremental elevation changes, the algorithm includes safety checks not present in other algorithms.
2013
Modeling of Bovine Spongiform Encephalopathy in a Two-Species Feedback Loop
Barnes and Lehman
Epidemics (Volume 5, Issue 2, June 2013, Pages 85–91)
Abstract PDF Code 10.1016/j.epidem.2013.04.001
Bovine spongiform encephalopathy, otherwise known as mad cow disease, can spread when an individual cow consumes feed containing the infected tissues of another individual, forming a one-species feedback loop. Such feedback is the primary means of transmission for BSE during epidemic conditions. Following outbreaks in the European Union and elsewhere, many governments enacted legislation designed to limit the spread of such diseases via elimination or reduction of one-species feedback loops in agricultural systems. However, two-species feedback loops—those in which infectious material from one-species is consumed by a secondary species whose tissue is then consumed by the first species—were not universally prohibited and have not been studied before. Here we present a basic ecological disease model which examines the rôle feedback loops may play in the spread of BSE and related diseases. Our model shows that there are critical thresholds between the infection's expansion and decrease related to the lifespan of the hosts, the growth rate of the prions, and the amount of prions circulating between hosts. The ecological disease dynamics can be intrinsically oscillatory, having outbreaks as well as refractory periods which can make it appear that the disease is under control while it is still increasing. We show that non-susceptible species that have been intentionally inserted into a feedback loop to stop the spread of disease do not, strictly by themselves, guarantee its control, though they may give that appearance by increasing the refractory period of an epidemic's oscillations. We suggest ways in which age-related dynamics and cross-species coupling should be considered in continuing evaluations aimed at maintaining a safe food supply.
2012
E-tracers: Development of a low cost wireless technique for exploring sub-surface hydrological systems
Bagshaw, Burrow, Wadham, Bowden, Lishman, Salter, Barnes, Nienow
Hydrological Processes. Vol 26, Issue 20, Jul 2012, Pages 3157–3160.
Abstract PDF 10.1002/hyp.9451
This briefing describes the first deployment of a new electronic tracer (E-tracer) for obtaining along-flowpath measurements in subsurface hydrological systems. These low-cost, wireless sensor platforms were deployed into moulins on the Greenland Ice Sheet. After descending into the moulin, the tracers travelled through the subglacial drainage system before emerging at the glacier portal. They are capable of collecting along-flowpath data from the point of injection until detection. The E-tracers emit a radio frequency signal, which enables sensor identification, location and recovery from the proglacial plain. The second generation of prototype E-tracers recorded water pressure, but the robust sensor design provides a versatile platform for measuring a range of parameters, including temperature and electrical conductivity, in hydrological environments that are challenging to monitor using tethered sensors.
Trading Space for Time: Constant-Speed Algorithms for Managing Future Events in Scientific Simulations
Lehman, Keen, Barnes
CSC
Abstract PDF
This briefing describes the first deployment of a new electronic tracer (E-tracer) for obtaining along-flowpath measurements in subsurface hydrological systems. These low-cost, wireless sensor platforms were deployed into moulins on the Greenland Ice Sheet. After descending into the moulin, the tracers travelled through the subglacial drainage system before emerging at the glacier portal. They are capable of collecting along-flowpath data from the point of injection until detection. The E-tracers emit a radio frequency signal, which enables sensor identification, location and recovery from the proglacial plain. The second generation of prototype E-tracers recorded water pressure, but the robust sensor design provides a versatile platform for measuring a range of parameters, including temperature and electrical conductivity, in hydrological environments that are challenging to monitor using tethered sensors.
2011
Distributed Parallel D8 Up-Slope Area Calculation in Digital Elevation Models
Barnes, Lehman, Mulla
PDPTA
Abstract 10.5281/zenodo.1162392
This paper presents a parallel algorithm for calculating the eight-directional (D8) up-slope contributing area in digital elevation models (DEMs). In contrast with previous algorithms, which have potentially unbounded inter-node communications, the algorithm presented here realizes strict bounds on the number of inter-node communications. Those bounds in turn allow D8 attributes to be processed for arbitrarily large DEMs on hardware ranging from average desktops to supercomputers. The algorithm can use the OpenMP and MPI parallel computing models, either in combination or separately. It partitions the DEM between slave nodes, calculates an internal up-slope area by replacing information from other slaves with variables representing unknown quantities, passes the results on to a master node which combines all the slaves' data, and passes information back to each slave, which then computes its final result. In this way each slave's DEM partition is treated as a simple unit in the DEM as a whole and only two communications take place per node.
2008
Developing a Text-Based MMORPG to Motivate Students in CS1
Barnes and Gini
AAAI Conference – AI Education Workshop
Abstract 10.5281/zenodo.3780678
We present the outline of a class project in which entry-level students in our CS1 course spent a full day developing a text-based massively multi-player online role-playing game(MMORPG) using Scheme. We describe briefly our CS1course, the specifics of the game we asked students to implement, and the project organization. Comments from the students about their experience are also presented. Most students felt that the project was a beneficial learning experience. The project was organized as part of a larger multi-year effort to increase student learning and student participation.Class performance shows that more students have completed the course and have obtained higher grades than in the past,providing support to the educational value of this project and the other active learning opportunities we have used during the semester.
Software
dggridR
Spatial analyses involving binning requires that every bin have the same area, but this is impossible using a rectangular grid laid over the Earth or over any projection of the Earth. Discrete global grids use hexagons, triangles, and diamonds to overcome this issue, overlaying the Earth with equally-sized bins. This package provides utilities for working with discrete global grids, along with utilities to aid in plotting such data.
Webglobe
You want to understand your data, but it's spatially distributed and you're afraid that trying to make sense of it on something gross, like a Mercator projection, is going to lead you to bad intuitions. Webglobe can help you fix this! It allows you to interactively visualize your data on either a three-dimensional globe or a flat map.
RichDEM
RichDEM is a set of hydrologic analysis tools for use on digital elevation models (DEMs). RichDEM uses parallel processing and state of the art algorithms to quickly process even very large DEMs.
RichDEM can use both the D8 and D∞ (Tarboton) flow metrics. It can resolve terrain depressions (or pits) either by filling or by channel carving. It can calculate contributing/up-slope areas, slopes, curvatures, and aspects.
The present version is built in C++ for speed and uses OpenMP to achieve parallelism; future versions may use Intel's Thread Building Blocks to achieve additional increases in speed.
RichDEM has resulted in the following publications:
- Parallel Non-divergent Flow Accumulation For Trillion Cell Digital Elevation Models On Desktops Or Clusters (Link)
- Parallel Priority-Flood Depression Filling For Trillion Cell Digital Elevation Models On Desktops Or Clusters (Link)
- An Efficient Assignment of Drainage Direction Over Flat Surfaces in Raster Digital Elevation Models (Link)
- Priority-Flood: An Optimal Depression-Filling and Watershed-Labeling Algorithm for Digital Elevation Models (Link)
- Distributed Parallel D8 Up-Slope Area Calculation in Digital Elevation Models (Link)
ArcRasterRescue
ArcRasterRescue is a C++ utility for quickly extracting raster data from ESRI's ArcGeodatabase format. It is the only available open source software which performs this operation and an important resource to folks seeking to extract valuable data that might otherwise be lost.
Grid Engine
grid_engine is a C++ class for flexibily working with different kinds of two-dimensional grids.
It can handle hexagonal, 4-connected, and 8-connected grids.
Any of these grids can be used as a toroid, such that the edges of the grid wrap around.
The same grid may be treated as a toroid, non-toroid, 4-, 8-, or hex-connected without needing to perform any modifications to the data structure. Toroidness and connectivity are not treated as fundamental aspects of a grid, but, rather, as artefacts of the way a grid is traversed.
Adjaceny neighbourhoods and visuals are generated with Python.
Climate Tracker
Climate Tracker is a simple model for visualizing historic climate data from the United States and Canada as tracks running across the landscape and through time.
Climate Tracker uses OpenLayers to display climate maps, aggregates data with C++, and uses Python and NumPy to fit the models. PHP routes respones from the client to the server.
The tracks Climate Tracker produces can be used to calculate climate velocities producing a simple means of understanding climate, its changes, and its interactions with the landcsape.
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