Richard Barnes

I solve problems on the web and in science and engineering using novel approaches from my background in computation, physics, and sensors.
Interested in collaborating? Drop me an email.

Education

Physics, B.S., 2011
Magna cum Laude
University of Minnesota

Philosophy, B.A., 2010
Magna cum Laude
University of Minnesota

Computer Science Minor

Mathematics Minor

Certifications

Wilderness First Responder
2010, 2013
Wilderness Medicine Institute

HAM Extra Class License
2006
American Radio Relay League

What's Up?

Invited Speaker
New Roots For Ecological Intensification Conference
October 02014, Estes Park

MyFutureClimate featured in Tech.MN
October 02014, Minneapolis

More…

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.

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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:

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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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Grid Drafter

This Python program is used to draw and manage two-dimensional integer elevation grids.

It can handle both square and hexagonal grids.

When the program is first run, it will display a blank screen with a grid on it.

Pressing keys 0-8 will then allow you to fill the grid cells in with a colour which corresponds to that key.

Pressing “S” will save the grid file in a format which can be read back in by the program for further editing. The colours drawn previously will be saved as integer numbers.

I use this program for creating and editing small digital elevation models for testing with hydrologic algorithms.

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Simple Integrator

There are many integrators in the world. Many of the emphasise accuracy and use high-order methods to estimate and minimize error. This kind of accuracy is expensive. For systems that are generally well-behaved where the goal is understanding of dynamics, rather than exact predictions, accuracy is no longer paramount.

This C++11 library implements a simple adaptive step-size integrator based on Euler's method. The method is both fast and simple, allowing for the quick simulation of many-dimensional systems.

Additionally, a special class is provided which allows for discrete-time events which instantaneously alter the state of a system. The integrator approaches such events cautiously, using an exponentially-decreasing step-size. It withdraws with equal caution.

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SDR33 Triangulator

The Sokkia SDR33 data logger is used in surveying to record data from, and to control, certain total stations. Situations arise where a point to be surveyed cannot be directly accessed for surveying in the field; however, the location of such a point can be triangulated by moving the total station to two different locations and measuring the angles from each of these locations to the unknown point.

Since the SDR33 data logger does not have a triangulation option built in, an external program must be used to post-process the data. This program performs this processing. The program reads an unreduced SDR33 data file produced with Sokkia's ProLink software and returns the triangulated position of one or more points.

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Journal Articles

Expand abstractThe Reflective Plant Breeding Paradigm: A Robust System of Germplasm Development to Support Strategic Diversification of Agroecosystems BC Runck, MB Kantar, NR Jordan, JA Anderson, DL Wyse, JO Eckberg, R Barnes, CL Lehman, LR DeHaan, RM Stupar, CC Sheaffer, PM Porter Crop Science (Volume 54, Sep–Oct 2014, Pages 1939–1948) PDFPDF Web Linkdoi: 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.

Expand abstractModeling of Bovine Spongiform Encephalopathy in a Two-Species Feedback Loop R. Barnes, C. Lehman Epidemics (Volume 5, Issue 2, June 2013, Pages 85–91) PDFPDF Web Linkdoi: 10.1016/j.epidem.2013.04.001 Web LinkCode

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.

Expand abstractAn Efficient Assignment of Drainage Direction Over Flat Surfaces in Raster Digital Elevation Models R. Barnes, C. Lehman, D. Mulla Computers & Geosciences. Vol 62, Jan 2014, pp 128-135, ISSN 0098-3004. PDFPDF Web Linkdoi: 10.1016/j.cageo.2013.01.009 Web LinkCode

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.

Expand abstractPriority-Flood: An Optimal Depression-Filling and Watershed-Labeling Algorithm for Digital Elevation Models R. Barnes, C. Lehman, D. Mulla Computers & Geosciences. Vol 62, Jan 2014, pp 117-127, ISSN 0098-3004. PDFPDF Web Linkdoi: 10.1016/j.cageo.2013.04.024 Web LinkCode

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.

Expand abstractE-tracers: Development of a low cost wireless technique for exploring sub-surface hydrological systems E. Bagshaw, S. Burrow, J.L. Wadham, J. Bowden, B. Lishman, M. Salter, R. Barnes, P. Nienow Hydrological Processes 26, 3157–3160 (2012) PDFPDF Web Linkdoi: 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.

Conference Presentations

Expand abstractPerennial possibilities: a theory for yield differences between annual and perennial grains R. Barnes, M. Kantar, C. Lehman, L. DeHaan, D. Wyse 98th Annual Meeting of the Ecological Society of America, Minneapolis, 2013 (8/4–8/9) PDFSlides

Background/Question/Methods

Agricultural production has increased greatly over the past century, but gains have often come at the cost of long-term sustainability. Crop systems often require fossil fuel-based fertilizers, strain sources of fresh water, contribute to soil loss, and may ultimately reduce arable land. Addressing these shortfalls is essential for future food production, especially in the face of an increasing global population. Perennial crops offer a possible alternative to the annuals upon which current agriculture systems are based. They sequester nutrients and may reduce both soil erosion and the need for tilling. Additionally, because perennial grains have reduced input costs, they may equal the profitability of an annual grain even while producing lower yields.

However, despite their potential, relatively little theoretical research has been done on high-yielding perennial grains. This may be partly because they have not been found in nature. But it may also be a consequence of theories which predict mutually exclusive trade-offs between longevity and seed production. Whatever the case, the controlled conditions of an agriculture system present a novel selective regime which can be studied in its own right and exploited to develop life cycle strategies not possible elsewhere.

Results/Conclusions

Accordingly, we have developed a physiological model of resource allocation within a grain species. The allocation functions themselves are mutable. This permits virtual breeding of modeled grains in order to explore the model's "gene space" and to locate optimal plants for a given set of harvest conditions.

The model is observed to rapidly produce both annual and perennial solutions following a random initialization. Both annuals and perennials may be bred to produce a perennial or annual, respectively. Perennial seed production in the model has been observed to equal or surpass that of annuals under some conditions. Insofar as the model is representative of reality, the implication is that high-yielding perennial grains may be bred in the real world, and that they may offer a competitive alternative to annuals.

Expand abstractDecoupling our natural and artificial watersheds—an example of whole ecosystem complementarity C. Lehman, R. Barnes, D. Mulla, J. Nelson, J. Galzki, H. Wan 98th Annual Meeting of the Ecological Society of America, Minneapolis, 2013 (8/4–8/9) PDFSlides

Agricultural regions of the world have vast natural watersheds of lakes, ponds, rivers, and streams. Interwoven are large artificial watersheds of drain tiles and ditches. Just as household plants benefit from drains in their pots, so agricultural crops benefit from drain tiles in their fields. In today's world the drain tiles carry not only water but also fertilizers, antibiotics, pesticides, hormones, and other chemicals into the natural watershed. We analyzed where wetlands and buffers for bioenergy and other applications could be placed on the Minnesota landscape to intercept drain waters and help purify them before they reach the natural watershed.

Expand abstractSimultaneous measurement of active potentials and bioimpedance during muscle movement R. Barnes, U. Pliquett, A Barthel 15th Intn'l Conf. on Electrical Bio-Impedance, 2013 (4/22–4/25) PDFPDF

Numerous studies have shown electromyographic signals (EMGs) as useful for controlling prostheses and ortheses. Their great potential stems from the degree of voluntary control we wield over these signals, even if limbs are missing, especially in the EMGs of skeletal muscles. However, despite several decades of exploration, the potential of electrical myoimpedance (EMI) as a separate control signal has been largely ignored. The greatest barrier to utilizing this signal is that skin-based measurements suffer from low-sensitivity with the only alternative being invasive methods, such as needles.

Since the EMI signal is known to correlate with the passive properties of materials under test, specifically their geometry, it is expected to be highly sensitive to the morphologic changes which occur during concentric contractions. In contrast, EMG signals occur any time a muscle is contracted, whether or not this results in morphologic changes. Therefore, the EMI and EMG signals should not be highly-correlated, suggesting an additional control channel.

To test this, we developed a non-invasive procedure for making simultaneous skin-based measurements of EMG and EMI signals during both concentric and isometric contractions. A video camera was synchronized with the measurement system to facilitate the correlation of signal features with muscle actions. We conclude that the two signals can be distinguished.

Expand abstractPerennial possibilities R. Barnes, C. Lehman, M. Kantar, L. DeHaan, D. Wyse 2013 U of MN Student Sustainability Symposium Lightning Talks (4/5) PDFSlides

Agricultural production has increased greatly over the past century, but gains have often come at the cost of long-term sustainability. Crop systems often require fossil fuel-based fertilizers, strain or deplete sources of fresh water, contribute to soil loss, and may ultimately reduce arable land. Addressing these shortfalls is essential for future food production, especially in the face of an increasing global population. Perennial crops offer an attractive alternative to the annuals upon which current agriculture systems are based. They sequester nutrients and may reduce both soil erosion and the need for tilling. Additionally, because perennial grains have reduced input costs, they may equal the profitability of an annual grain even if they ultimately yield less seed.

However, despite their potential, relatively little research has been done on high-yielding perennial grains. This may be partly because they have not been found in nature. But it may also be a consequence of theories which predict mutually exclusive trade-offs between longevity and seed production. Whatever the case, the controlled conditions of an agriculture system present a novel selective regime which can be studied in its own right and exploited to develop life cycle strategies not possible elsewhere in nature.

Accordingly, we have developed a physiologic model of resource allocation within a grain and parameterized this model based on actual environmental data and crop mass ratios. The allocation functions themselves are mutable. This permits the breeding of modeled grains in order to explore the model's "gene space" and to locate optimal plants for a given set of harvest conditions. My talk will discuss our model as well as some promising preliminary findings indicating that perennial grains may yet be a possibility.

Expand abstractAutomated Identification of Remediable Wetlands for Water Filtration and Biofuel R. Barnes, C. Lehman, D. Mulla, J. Jungers, J. Galzki, H. Wan, J. Nelson 5th Annual Intn'l Ecosystem Services Partnership Conference, Portland, 2012 (7/30–8/4)

Interwoven with the natural watersheds of the United States—made up of lakes, ponds, and rivers—are large artificial watersheds of drain tiles and ditches which prevent fields from becoming too damp by draining them of excess water. The drained water carries fertilizers, antibiotics, pesticides, hormones, and other chemicals into natural watersheds. Fortunately, wetlands and vegetative buffers can provide ecosystem services to filter and absorb such chemicals, leaving natural waterways clean. Additionally, the filtering vegetation can be used as a biofuel source. This project has used public databases, coupled with efficient new GIS algorithms which reduce processing times from days to minutes, to analyse the landscape and automatically determine wetlands suitable for rehabilitation. As a result, it is possible to make policy recommendations on state-wide scales, while the ever-evolving nature of these artificial watersheds reduces the cost of interventions. This talk explains the project, presenting the algorithms, processes, and data sources used, and discussing the data we have available for understanding the practicalities of resulting solutions.

Expand abstractTracting the Intractable: Efficient Methods for Modeling Ecosystems at the Level of Individuals R. Barnes, A. Keen, C. Lehman 5th Annual Intn'l Ecosystem Services Partnership Conference, Portland, 2012 (7/30–8/4)

Intractable problems in modeling ecosystems and their services can often be solved through the application of appropriate algorithms: reconceptualization of a problem may reduce computation times from days to minutes. Despite this, many popular analysis packages—and many modelers—use inefficient algorithms. For example, statewide DEMs have reached 1m resolutions, resulting in datasets on the terabyte level. Appropriately used, such data has a tremendous capacity to inform and impact ecosystem management and policy, yet processing single watersheds is still considered onerous by those using traditional GIS algorithms. We overview efficient algorithms which have allowed us to automatically identify remediable wetlands across thousands of square miles of Minnesota. The same techniques which permit such processing have analogues in the realm of disease modeling, enabling us to track the fates of each individual in a population of millions. Tuberculosis, mad cow disease, competition among grains, the flow in a watershed, and the decline of insect pollinators all have the same computational requirements which can be addressed through the judicious use of old, new, and under-utilized algorithms. As above, this talk addresses our experience approaching a range of problems and problem domains with an eye towards the commonalities and practical take-aways for attendees.

Expand abstractTrading Space for Time: Constant-Speed Algorithms for Managing Future Events in Scientific Simulations C. Lehman, A. Keen, R. Barnes 2012 Int'l Conf. Scientific Computing PDFPDF

Given vast increases in computing capacity, applications in science and engineering that were formerly interpreted with ordinary or partial differential equations, or by integro-partial differential equations, can now be understood through microscale modeling. Interactions among individual particles—be they molecules, viruses, or individual humans—are modeled directly, rather than first abstracting the interactions into mathematical equations and then simulating the equations. One approach to microscale modeling involves scheduling all events into the future, wherever that is possible. With sufficient space-for-time tradeoffs, this considerably improves the speed of the simulation, but requires scheduling algorithms of high efficiency. In this paper we describe our variation on calendar queues and their usage, presenting detailed algorithms, intuitive explanations of the methods, and notes from our experiences applying them in large-scale simulations. Results can be useful to scientists in ecology, epidemiology, economics, and other disciplines that employ microscale modeling.

Expand abstractDistributed Parallel D8 Up-Slope Area Calculation in Digital Elevation Models R. Barnes, C. Lehman, D. Mulla 2011 Intn'l Conf. on Parallel & Distributed Processing Techniques & Applications PDFPDF

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.

Expand abstractE-tracers: A New Technique for Wireless Sensing Under Ice Sheets S. Burrow, J.L. Wadham, M. Salter, R. Barnes 2009 AGU Fall Meeting Web Linklink: http://adsabs.harvard.edu/abs/2009AGUFM.C43B0506B

A significant hurdle to the understanding of ice sheet basal hydrology and its coupling with ice motion is the difficulty in making in-situ measurements along a flow path. While dye tracing techniques may be used in small glaciers to determine transit times of surface melt water through the sub-glacial system, they provide no information on in situ conditions (e.g. pressure) and are ineffective at ice-sheet scale where dilution is high. The use of tethered sensor packages is complicated by the long lengths (~100’s m) and torturous path of the moulins and conduits within ice sheets. Recent attempts to pass solid objects (rubber ducks) and other sensor packages through glacial moulins have confirmed the difficultly in deploying sensors into the sub glacial environment. Here, we report the first successful deployment and recovery of compact, electronic units to moulins up to 7 km from the margin of a large land-terminating Greenland outlet. The technique uses RF (Radio Frequency) location to create an electronic tracer (an ‘e-tracer’) enabling a data-logging sensor package to be located in the pro-glacial flood plain once it has passed through the ice sheet. A number of individual packages are used in each deployment mitigating for the risk that some may become stuck within the moulin or lodge in an inaccessible part of the floodplain. In preliminary tests on the Leverett glacier in West Greenland during August 2009 we have demonstrated that this technique can be used to locate and retrieve dummy sensor packages: 50% and 20% of the dummy sensor packages introduced to moulins at 1 and 7 km from the ice sheet terminus respectively, emerged in the sub-glacial stream. It was possible to effectively detect the e-tracer units (which broadcast on 151MHz with 10mW of power) over a horizontal range of up to 5km across the pro-glacial floodplain and locate them to a high accuracy, allowing visual recognition and manual recovery. These performance statistics give this technique strong potential for investigating in-situ conditions along a flow path at ice sheet scale.

Expand abstractAn Integrated Sanitation System in Cap-Haïtien, Haiti R. Barnes, J. Konen, L. Kucek 2009 Engineers Without Borders—USA Intn'l Conf., Milwaukee
Abstract unavailable
Expand abstractMonitoring Lemon Creek and Mendenhall Watersheds Using a Wireless Sensor Web in Juneau, Alaska: SEAMONSTER Heavner, Fatland, E. Hood, Connor, Habermann, Berner, Jones, Barnes Northwest Glaciologists, Seattle, October 18, 2008 Web LinkLink
Abstract unavailable.
Expand abstractDeveloping a Text-Based MMORPG to Motivate Students in CS1 R. Barnes and M. Gini Association for the Advancement of Artificial Intelligence Conference, Chicago, 2008
Education Colloqium.
PDFPDF PDFSlides Web Linklink: http://www.cs.hmc.edu/aieducation/

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 CS1 course, 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.

Posters

Expand abstractEfficient Algorithms for Geographic Watershed Analysis R. Barnes, C. Lehman, D. Mulla, J. Galzki, H. Wan, J. Nelson 2012 Minnesota Supercomputing Institute Research Exhibition Web Linklink: http://purl.umn.edu/126871
Thumbnail of poster entitled 'Efficient Algorithms for Geographic Watershed Analysis'

This project is to analyze where wetlands and other vegetated buffers can be placed on the landscape to intercept drain waters and help purify them before they reach the natural watershed. The computational problem comes because new LIDAR images have expanded the resolution of geographic digital elevation models (DEMs) up to a thousandfold or more. This in turn has taxed the ability of existing algorithms to process the expanded datasets. Here we explain the project and present new efficient algorithms for parallel and scalar processing that reduce run-times from days on ordinary computers to minutes or second using the new algorithms in a parallel supercomputing environment.

Expand abstractEcology of Open Star Clusters C. Lehman, F. Lehman, R. Barnes 2012 Minnesota Supercomputing Institute Research Exhibition Web Linklink: http://purl.umn.edu/125315

“Ecology of star clusters” examines the interactions of stars, and what can be gleaned from those interactions about the evolution and ultimate fate of star clusters large and small. Questions like: 1) What is the force that causes small star clusters to expand? 2) Why do the ancient globular clusters have many binary stars? 3) Why are close triple stars so rare?

Thumbnail of poster entitled 'Ecology of Open Star Clusters'
Expand abstractThe evolutionary commonality of sexually transmitted and vector-borne disease C. Lehman, R. Barnes, B. Kerr, F. Denison, G. Shirreff, A. Keen 11th Intn'l Conf. on Molecular Epidemiology & Evolutionary Genetics of Infectious Disease (MEEGID XI, 2012)

Typical pathogens are minuscule and immobile and therefore need external means of transferring from host to host. Many manifestations of disease are merely mechanisms to effect such transfer, with some of the more elaborate mechanisms appearing in vector-borne diseases. In the simplest case, the disease infects two hosts alternately, one being small and mobile, the other larger. In vector-borne diseases such as malaria, the pathogen is relatively non-virulent in one host (the mosquito vector) and more virulent in the other (the vertebrate host). Non-virulence in the vector clearly favors transmission of the pathogen, as the vector remains relatively healthy to move about and propagate the pathogen. But how did such systems evolve? Here we show that their evolution is a natural consequence of the dynamics of diseases which alternate between hosts, where selection pressures on the pathogen tend to decrease the difference in infectivity between the hosts but increase the difference in virulence. The maximal difference in virulence occurs when a disease becomes effectively non-virulent in one of the hosts. When this occurs in the smaller of the two hosts, it is simply referred to as a vector-borne disease. The selection pressures remain consistent from emergence near the disease-free equilibrium through high-prevalence at interior equilibria, as indicated by terms in the eigenvalues of broad macroscale models and by detailed microscale simulations. Curiously, similar dynamics appear in sexually transmitted diseases when they alternate between male and female, where such diseases can become comparatively non-virulent in one of the two sexes. The theory we present can shed light on the natural history of vector-borne and sexually transmitted diseases, and can provide information for their treatment and amelioration.

Expand abstractClimate Tracking: Applications of a Novel Technique to Sustainability R. Barnes, C. Lehman, S. Williams, L. Frelich 2011 U of MN Student Sustainability Symposium Web Linklink: http://purl.umn.edu/128894
Thumbnail of poster entitled 'Climate Tracking: Applications of a Novel Technique to Sustainability'

Climate change has profound implications for the sustainability of society and the environment, yet estimates of climate change cover times scales which make results difficult to verify, are often computationally expensive to make, and have uncertainties which are not easily communicated, especially outside the area of computational meteorology and mathematics. We present a method of quantifying climate change over the past century and into the near‐future which bypasses many of these problems. Using historical weather data and a surface‐fitting algorithm, we are able to extract "climate velocities", representing the surface speed and direction of the climate for any location. Projections from these velocities can be used to extract possible future locations and direction‐of‐movement of biomes, biofuel hotspots, and agricultural productivity, with implications for conservation parkways, preemptive revegetation, agricultural policy.

Expand abstractSatellite observations of banded VLF emissions in conjunction with energy-banded ions during very large geomagnetic storms C. Colpitts, C. Cattell, J. Kozyra, M. Parrot, R. Barnes 2010 American Geophysical Union, Fall Meeting PDFPoster

Electromagnetic VLF emissions banded in frequency, coincident with warm energy-banded ions in the low latitude auroral zone, and associated with very strong geomagnetic storms, are observed separately on two low-earth polar orbiting satellites, FAST and DEMETER. Both satellites carry a full complement of field and particle detectors. The FAST satellite, launched August 21, 1996 into an elliptical polar orbit with perigee 350 km and apogee 4175 km, traversed the auroral zone four times per orbit across a wide range of altitudes and local times. The DEMETER satellite was launched on June 29, 2004 into a circular sun-synchronous polar orbit at altitude 710 km, with data recorded at all invariant latitudes less than ~65 degrees. The ion bands were first reported in association with the Halloween storms [Cattell et al., 2004; Kozyra et al., 2004, Yao et al., 2008]. Banded ions are observed on FAST during every large magnetic storm in discrete energy bands at energies ~10 eV – 10 keV and lasting up to 12 hrs. The energy flux peaks in the trapped population but is also evident in the precipitating ions, and in certain cases a significant upgoing ion component appears at low invariant latitudes. These bands were observed over several orbits at similar latitudes in both dawn and evening sectors, with the signature typically more pronounced in the dawn sector. In this study we focus on the coincidence of the energy-banded ions with observations of frequency-banded VLF electromagnetic emissions. During all of these very large storms, banded VLF emissions are evident in both the electric and magnetic field, appearing as discrete frequency bands between ~100 and ~1500 Hz separated by 75–150 Hz. These banded emissions persist for several FAST or DEMETER orbits, lasting up to 10 hrs, in both the northern and southern hemispheres. There appears to be a correlation between the banded wave observations and ion and electron density enhancements. Possible generation mechanisms for the banded emissions include EMIC waves generated in the equatorial ring current region which bounce to higher L-shells and propagate down auroral field lines to the spacecraft location.

Thumbnail of poster entitled 'Satellite observations of banded VLF emissions in conjunction with energy-banded ions during very large geomagnetic storms'

Invited Talks

Expand abstractModeling physiological tradeoffs in perennial vs. annual crops R. Barnes New Roots For Ecological Intensification Conference, Estes Park (2014-10-28)
Not yet available.
Expand abstractConsidering grain yield through physioevolutionary simulation R. Barnes, M. Kantar, C. Lehman, L. DeHaan, D. Wyse University of Minnesota Applied Plant Sciences Seminar (2013-09-09) PDFSlides

Agricultural production has increased greatly over the past century, but gains have often come at the cost of long-term sustainability. Crop systems often require fossil fuel-based fertilizers, strain sources of fresh water, contribute to soil loss, and may ultimately reduce arable land. Addressing these shortfalls is essential for future food production, especially in the face of an increasing global population. Perennial crops offer a possible alternative to the annuals upon which current agriculture systems are based. They sequester nutrients and may reduce both soil erosion and the need for tilling. Additionally, because perennial grains have reduced input costs, they may equal the profitability of an annual grain even while producing lower yields.

However, despite their potential, high-yielding perennial grains remain contentious: it is unclear whether their production potential can be increased to levels comparable to annual grains. Here, that high-yielding grains, if present in nature, would exist in an unstable region of the evolutionary state space and be replaced by the low-yielding, long-lived and high-yielding, short-lived species we see today. I propose that, despite this, the controlled conditions of an agricultural system present a novel selective regime which can be studied in its own right and exploited to develop life cycle strategies not possible elsewhere.

Accordingly, we have developed a physiological model of resource allocation within a grain species. The allocation functions themselves are mutable. This permits virtual breeding of modeled grains in order to explore the model's "gene space" and to locate optimal plants for a given set of harvest conditions.

The model is observed to rapidly produce both annual and perennial solutions following a random initialization. Both annuals and perennials may be bred to produce a perennial or annual, respectively. Perennial seed production in the model has been observed to equal or surpass that of annuals under some conditions. Insofar as the model is representative of reality, the implication is that high-yielding perennial grains may be bred in the real world, and that they may offer a competitive alternative to annuals.

White Papers

Expand abstractDevelopment of Continuous Living Cover Breeding Programs to Enhance Agriculture's Contribution to Ecosystem Services Runck, Kantar, Eckberg, Barnes, Lehman, DeHaan, Jordan, Sheaffer, Porter, Wyse Perennial Crops for Food Security: Proceedings of the FAO Expert Workshop. Rome, 2013. p. 229. PDFPDF

No abstract available.

Reviews

I have reviewed articles for the following journals:

omgTransit.com

omgTransit.com presents a minimalistic interface for a user to explore public transit options near them while providing real-time information about these options. It merges information from a variety of databases and APIs providing a cohesive view on what would otherwise be a disparate dig. The app runs on Rails and Node.js with ElasticSearch, Redis, and PostgreSQL handling data. On the client-side Bootstrap, Backbone, jQuery, UnderScore, and Google Maps v3 work together.

mspbus.org screenshot

omgTransit.org

Getting you from A to B without your C

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omgTransit.com won an ESRI National Day of Civic Hacking Innovation Award, a Champions of Change commendation from the White House, and won the January 2014 Beta.MN Start-up Competition. The project has been accepted to Intel Labs' Data Services Accelerator.

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. The tracks Climate Tracker produces can be used to calculate climate velocities, providing a simple means of understanding climate, its changes, and its interactions with the landcsape. It runs on a LAMP stack with C++, Python, and NumPy providing analysis. The client side uses jQuery and OpenLayers.

Climate Tracker screenshot

Climate Tracker

A velocity visualization of historic climate trends in the U.S. and Canada, with hints at what the near future may bring

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EWB-USA Logo Generator

The Logo Designer is an application for Engineers Without Borders—USA. EWB-USA is an international development organization with over 300 chapters in the U.S. Each chapter needs a unique logo that can serve on their web site, stationary, banners, and other displays. The Logo Designer provides chapters access to their logo in an array of different sizes and file types.

EWB-USA Logo Designer screenshot

EWB-USA Logo Designer

Automatic generator of chapter logos for a national umbrella organization

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The Open Harp

TheOpenHarp.com is an app for easily viewing and browsing public domain tunebooks and hymnals online. It's still a work-in-progress.

TheOpenHarp screenshot

TheOpenHarp.com

Easily browse old tunebooks and hymnals

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NiceUnits

NiceUnits.com finds quantities of comparable magnitude by referencing a large database of areas, lengths, volumes, and other measurements of the world. Given a quantity such as “8000 sq miles”, NiceUnits can tell you that this is about the area of both Israel and the drainage basin of South Dakota's White River.

EWB-USA Logo Designer screenshot

NiceUnits.com

Converts obtuse numbers into nice, familiar quantities

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Intraglacial Flow Sensors

Role: Research Collaborator, Sensor Payload Designer
University of Bristol, 2009

During the summer, meltwater on the surface of glaciers forms pools and rivers. Many of these eventually drain to the base of the ice sheet through moulins. Basal meltwater is believed to play a significant role in the movement of glaciers and the evolution of ice sheets by lubricating the base of the glacier or, in high-pressure situations, actually lifting it.

Diagram of a moulin
Diagram of a moulin

Unfortunately, extracting measurements from the extreme environments of subglacial hydrologic systems poses severe logistic and technical challenges for scientists. First, you have to get to the moulin without sliding in, then you have to get your equipment through more than a half-kilometer of ice… and get it back again.

The entrance of a moulin
The entrance of a moulin

Dye tracing has been used to limit transit times and dispersion properties of these systems, but it cannot provide information about the temperature, pressure, and distribution of turbulence of basal flows. Tethered sensors provide a partial solution and have yielded pressure information on small valley glaciers. However, there are challenges associated with first passing tethered sensors through thicker ice sheets and, second, finding flow channels of interest amid highly turbulent environments and tortuous flow paths. Additionally, the data gathered by a tethered sensor is limited to a single or limited number of points. Consequently, a device is required that can measure water pressure, temperature, and turbulence at a range of locations near the ice bed without requiring a constant physical connection with the surface.

Prototype E-tracer
A prototype e-Tracer

Our solution to this problem was to develop an electronic tracer (E-tracer) capable of travelling through the subglacial drainage system, measuring and recording in situ information as it transits. The device is equipped with a radio direction finding (RDF) transmitter, which allows it to be located once it has emerged from beneath the ice sheet for collection of data stored on the internal, non-volatile memory. This provides a new way of accessing the ice sheet bed and making in situ measurements, which is potentially transferable to other sub-surface environments where access problems prevent the deployment of conventional sensing technologies.

Early E-tracer prototype
An early E-tracer sensor payload prototype

The E-tracers are composed of a microcontroller, with radiofrequency (RF) beacon, data storage, and sensors contained within a spherical housing. The density of the device is adjusted for neutral bouyancy, meaning that the tracers float just below the water surface. The E-tracers consume 0.9mW average power giving them a 3 month lifespan with one half AA lithium battery. The recovery beacon has a line-of-sight detection range of 3–5 km.

This project represents the first successful deployment and recovery of wireless sensors through the subglacial drainage system beneath the Greenland ice sheet.

BBC News link.


Myoimpedance Prosthetic Sensors

Role: DAAD Professional Research Intern Fellow
Institut für Bioprozess- und Analysenmesstechnik, Heiligenstadt, Germany, 2012

Numerous studies and applications have shown electromyographic signals (EMGs) as useful for controlling prostheses and ortheses. Their great utility stems from the degree of voluntary control a user can wield over these signals, even if limbs are missing, especially in the EMGs of skeletal muscles. Despite the success and utility of EMGs, a related signal---the electrical myoimpedance (EMI)---has been largely ignored. Previously this was due to the low-sensitivity of skin-based measurements and the undesirability of invasive methods, such as needles. But these are problems which can be overcome. In this project, I demonstrated that non-invasive skin-based EMI measurements are possible and that they provide additional information which is not present in the EMG signal.

The EMG signal is a measurement of the voltage drop between two or more points. Since muscle contractions are caused by neuroeletric signals and produce voltage changes, EMG signals occur any time a muscle is contracted. In contrast, the EMI signal is a measurement of a muscle's resistance to an injected current flow at a particular frequency or set of frequencies. Since resistance is directly proportional to the current's path length and inversely proportional to its cross-sectional area, the EMI signal correlates to the geometry of the muscle. Therefore, it is expected to be sensitive to morphologic changes which occur during concentric contractions.


Schematic representation of measurement setup

To test this, I developed a non-invasive procedure for making simultaneous skin-based measurements of EMG and EMI signals during both concentric and isometric contractions. A 1V square-wave signal was passed through a 100kΩ resistor to produce a small injection current for measuring the EMI. This signal, along with the EMG, was sampled using a two-electrode sensor. A Fourier transform was used to separate the EMI and EMG signals. To facilitate the correlation of signal features with muscle actions, a video camera was synchronized with the measurement system.


Example of a measurement: blue is the active (EMG) signal and green is the passive (EMI) signal

Fifty isometric and fifty concentric contractions were recorded, normalized, and co-registered resulting in the aggregated signal views shown below, where red indicates high-densities of measured points and light-blue indicates low-densities. The EMI signal shows stark differences depending on the contraction whereas the EMG signal does not. Low-density regions in both signals are caused by high-amplitude signals, but such regions cannot be used to differentiate between types of contractions using the EMG signal because they are wholly dependent on the length of a contraction, be it concentric or isometric.


Aggregated muscle response signals

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