SpectraFox: A free open-source data management and analysis tool for scanning probe microscopy and spectroscopy

NASA Astrophysics Data System (ADS)

Ruby, Michael

In the last decades scanning probe microscopy and spectroscopy have become well-established tools in nanotechnology and surface science. This opened the market for many commercial manufacturers, each with different hardware and software standards. Besides the advantage of a wide variety of available hardware, the diversity may software-wise complicate the data exchange between scientists, and the data analysis for groups working with hardware developed by different manufacturers. Not only the file format differs between manufacturers, but also the data often requires further numerical treatment before publication. SpectraFox is an open-source and independent tool which manages, processes, and evaluates scanning probe spectroscopy and microscopy data. It aims at simplifying the documentation in parallel to measurement, and it provides solid evaluation tools for a large number of data.

Open source software to control Bioflo bioreactors.

PubMed

Burdge, David A; Libourel, Igor G L

2014-01-01

Bioreactors are designed to support highly controlled environments for growth of tissues, cell cultures or microbial cultures. A variety of bioreactors are commercially available, often including sophisticated software to enhance the functionality of the bioreactor. However, experiments that the bioreactor hardware can support, but that were not envisioned during the software design cannot be performed without developing custom software. In addition, support for third party or custom designed auxiliary hardware is often sparse or absent. This work presents flexible open source freeware for the control of bioreactors of the Bioflo product family. The functionality of the software includes setpoint control, data logging, and protocol execution. Auxiliary hardware can be easily integrated and controlled through an integrated plugin interface without altering existing software. Simple experimental protocols can be entered as a CSV scripting file, and a Python-based protocol execution model is included for more demanding conditional experimental control. The software was designed to be a more flexible and free open source alternative to the commercially available solution. The source code and various auxiliary hardware plugins are publicly available for download from https://github.com/LibourelLab/BiofloSoftware. In addition to the source code, the software was compiled and packaged as a self-installing file for 32 and 64 bit windows operating systems. The compiled software will be able to control a Bioflo system, and will not require the installation of LabVIEW.

Open Source Software to Control Bioflo Bioreactors

PubMed Central

Burdge, David A.; Libourel, Igor G. L.

2014-01-01

Bioreactors are designed to support highly controlled environments for growth of tissues, cell cultures or microbial cultures. A variety of bioreactors are commercially available, often including sophisticated software to enhance the functionality of the bioreactor. However, experiments that the bioreactor hardware can support, but that were not envisioned during the software design cannot be performed without developing custom software. In addition, support for third party or custom designed auxiliary hardware is often sparse or absent. This work presents flexible open source freeware for the control of bioreactors of the Bioflo product family. The functionality of the software includes setpoint control, data logging, and protocol execution. Auxiliary hardware can be easily integrated and controlled through an integrated plugin interface without altering existing software. Simple experimental protocols can be entered as a CSV scripting file, and a Python-based protocol execution model is included for more demanding conditional experimental control. The software was designed to be a more flexible and free open source alternative to the commercially available solution. The source code and various auxiliary hardware plugins are publicly available for download from https://github.com/LibourelLab/BiofloSoftware. In addition to the source code, the software was compiled and packaged as a self-installing file for 32 and 64 bit windows operating systems. The compiled software will be able to control a Bioflo system, and will not require the installation of LabVIEW. PMID:24667828

Neural ensemble communities: open-source approaches to hardware for large-scale electrophysiology.

PubMed

Siegle, Joshua H; Hale, Gregory J; Newman, Jonathan P; Voigts, Jakob

2015-06-01

One often-overlooked factor when selecting a platform for large-scale electrophysiology is whether or not a particular data acquisition system is 'open' or 'closed': that is, whether or not the system's schematics and source code are available to end users. Open systems have a reputation for being difficult to acquire, poorly documented, and hard to maintain. With the arrival of more powerful and compact integrated circuits, rapid prototyping services, and web-based tools for collaborative development, these stereotypes must be reconsidered. We discuss some of the reasons why multichannel extracellular electrophysiology could benefit from open-source approaches and describe examples of successful community-driven tool development within this field. In order to promote the adoption of open-source hardware and to reduce the need for redundant development efforts, we advocate a move toward standardized interfaces that connect each element of the data processing pipeline. This will give researchers the flexibility to modify their tools when necessary, while allowing them to continue to benefit from the high-quality products and expertise provided by commercial vendors. Copyright © 2014 Elsevier Ltd. All rights reserved.

Oculomatic: High speed, reliable, and accurate open-source eye tracking for humans and non-human primates.

PubMed

Zimmermann, Jan; Vazquez, Yuriria; Glimcher, Paul W; Pesaran, Bijan; Louie, Kenway

2016-09-01

Video-based noninvasive eye trackers are an extremely useful tool for many areas of research. Many open-source eye trackers are available but current open-source systems are not designed to track eye movements with the temporal resolution required to investigate the mechanisms of oculomotor behavior. Commercial systems are available but employ closed source hardware and software and are relatively expensive, limiting wide-spread use. Here we present Oculomatic, an open-source software and modular hardware solution to eye tracking for use in humans and non-human primates. Oculomatic features high temporal resolution (up to 600Hz), real-time eye tracking with high spatial accuracy (<0.5°), and low system latency (∼1.8ms, 0.32ms STD) at a relatively low-cost. Oculomatic compares favorably to our existing scleral search-coil system while being fully non invasive. We propose that Oculomatic can support a wide range of research into the properties and neural mechanisms of oculomotor behavior. Copyright © 2016 Elsevier B.V. All rights reserved.

Open Source Hardware for DIY Environmental Sensing

NASA Astrophysics Data System (ADS)

Aufdenkampe, A. K.; Hicks, S. D.; Damiano, S. G.; Montgomery, D. S.

2014-12-01

The Arduino open source electronics platform has been very popular within the DIY (Do It Yourself) community for several years, and it is now providing environmental science researchers with an inexpensive alternative to commercial data logging and transmission hardware. Here we present the designs for our latest series of custom Arduino-based dataloggers, which include wireless communication options like self-meshing radio networks and cellular phone modules. The main Arduino board uses a custom interface board to connect to various research-grade sensors to take readings of turbidity, dissolved oxygen, water depth and conductivity, soil moisture, solar radiation, and other parameters. Sensors with SDI-12 communications can be directly interfaced to the logger using our open Arduino-SDI-12 software library (https://github.com/StroudCenter/Arduino-SDI-12). Different deployment options are shown, like rugged enclosures to house the loggers and rigs for mounting the sensors in both fresh water and marine environments. After the data has been collected and transmitted by the logger, the data is received by a mySQL-PHP stack running on a web server that can be accessed from anywhere in the world. Once there, the data can be visualized on web pages or served though REST requests and Water One Flow (WOF) services. Since one of the main benefits of using open source hardware is the easy collaboration between users, we are introducing a new web platform for discussion and sharing of ideas and plans for hardware and software designs used with DIY environmental sensors and data loggers.

NASA Operational Simulator for Small Satellites: Tools for Software Based Validation and Verification of Small Satellites

NASA Technical Reports Server (NTRS)

Grubb, Matt

2016-01-01

The NASA Operational Simulator for Small Satellites (NOS3) is a suite of tools to aid in areas such as software development, integration test (IT), mission operations training, verification and validation (VV), and software systems check-out. NOS3 provides a software development environment, a multi-target build system, an operator interface-ground station, dynamics and environment simulations, and software-based hardware models. NOS3 enables the development of flight software (FSW) early in the project life cycle, when access to hardware is typically not available. For small satellites there are extensive lead times on many of the commercial-off-the-shelf (COTS) components as well as limited funding for engineering test units (ETU). Considering the difficulty of providing a hardware test-bed to each developer tester, hardware models are modeled based upon characteristic data or manufacturers data sheets for each individual component. The fidelity of each hardware models is such that FSW executes unaware that physical hardware is not present. This allows binaries to be compiled for both the simulation environment, and the flight computer, without changing the FSW source code. For hardware models that provide data dependent on the environment, such as a GPS receiver or magnetometer, an open-source tool from NASA GSFC (42 Spacecraft Simulation) is used to provide the necessary data. The underlying infrastructure used to transfer messages between FSW and the hardware models can also be used to monitor, intercept, and inject messages, which has proven to be beneficial for VV of larger missions such as James Webb Space Telescope (JWST). As hardware is procured, drivers can be added to the environment to enable hardware-in-the-loop (HWIL) testing. When strict time synchronization is not vital, any number of combinations of hardware components and software-based models can be tested. The open-source operator interface used in NOS3 is COSMOS from Ball Aerospace. For testing, plug-ins are implemented in COSMOS to control the NOS3 simulations, while the command and telemetry tools available in COSMOS are used to communicate with FSW. NOS3 is actively being used for FSW development and component testing of the Simulation-to-Flight 1 (STF-1) CubeSat. As NOS3 matures, hardware models have been added for common CubeSat components such as Novatel GPS receivers, ClydeSpace electrical power systems and batteries, ISISpace antenna systems, etc. In the future, NASA IVV plans to distribute NOS3 to other CubeSat developers and release the suite to the open-source community.

Neural ensemble communities: Open-source approaches to hardware for large-scale electrophysiology

PubMed Central

Siegle, Joshua H.; Hale, Gregory J.; Newman, Jonathan P.; Voigts, Jakob

2014-01-01

One often-overlooked factor when selecting a platform for large-scale electrophysiology is whether or not a particular data acquisition system is “open” or “closed”: that is, whether or not the system’s schematics and source code are available to end users. Open systems have a reputation for being difficult to acquire, poorly documented, and hard to maintain. With the arrival of more powerful and compact integrated circuits, rapid prototyping services, and web-based tools for collaborative development, these stereotypes must be reconsidered. We discuss some of the reasons why multichannel extracellular electrophysiology could benefit from open-source approaches and describe examples of successful community-driven tool development within this field. In order to promote the adoption of open-source hardware and to reduce the need for redundant development efforts, we advocate a move toward standardized interfaces that connect each element of the data processing pipeline. This will give researchers the flexibility to modify their tools when necessary, while allowing them to continue to benefit from the high-quality products and expertise provided by commercial vendors. PMID:25528614

Open source and DIY hardware for DNA nanotechnology labs.

PubMed

Damase, Tulsi R; Stephens, Daniel; Spencer, Adam; Allen, Peter B

A set of instruments and specialized equipment is necessary to equip a laboratory to work with DNA. Reducing the barrier to entry for DNA manipulation should enable and encourage new labs to enter the field. We present three examples of open source/DIY technology with significantly reduced costs relative to commercial equipment. This includes a gel scanner, a horizontal PAGE gel mold, and a homogenizer for generating DNA-coated particles. The overall cost savings obtained by using open source/DIY equipment was between 50 and 90%.

OSIRIX: open source multimodality image navigation software

NASA Astrophysics Data System (ADS)

Rosset, Antoine; Pysher, Lance; Spadola, Luca; Ratib, Osman

2005-04-01

The goal of our project is to develop a completely new software platform that will allow users to efficiently and conveniently navigate through large sets of multidimensional data without the need of high-end expensive hardware or software. We also elected to develop our system on new open source software libraries allowing other institutions and developers to contribute to this project. OsiriX is a free and open-source imaging software designed manipulate and visualize large sets of medical images: http://homepage.mac.com/rossetantoine/osirix/

Open Source Platform Application to Groundwater Characterization and Monitoring

NASA Astrophysics Data System (ADS)

Ntarlagiannis, D.; Day-Lewis, F. D.; Falzone, S.; Lane, J. W., Jr.; Slater, L. D.; Robinson, J.; Hammett, S.

2017-12-01

Groundwater characterization and monitoring commonly rely on the use of multiple point sensors and human labor. Due to the number of sensors, labor, and other resources needed, establishing and maintaining an adequate groundwater monitoring network can be both labor intensive and expensive. To improve and optimize the monitoring network design, open source software and hardware components could potentially provide the platform to control robust and efficient sensors thereby reducing costs and labor. This work presents early attempts to create a groundwater monitoring system incorporating open-source software and hardware that will control the remote operation of multiple sensors along with data management and file transfer functions. The system is built around a Raspberry PI 3, that controls multiple sensors in order to perform on-demand, continuous or `smart decision' measurements while providing flexibility to incorporate additional sensors to meet the demands of different projects. The current objective of our technology is to monitor exchange of ionic tracers between mobile and immobile porosity using a combination of fluid and bulk electrical-conductivity measurements. To meet this objective, our configuration uses four sensors (pH, specific conductance, pressure, temperature) that can monitor the fluid electrical properties of interest and guide the bulk electrical measurement. This system highlights the potential of using open source software and hardware components for earth sciences applications. The versatility of the system makes it ideal for use in a large number of applications, and the low cost allows for high resolution (spatially and temporally) monitoring.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Seyong; Kim, Jungwon; Vetter, Jeffrey S

This paper presents a directive-based, high-level programming framework for high-performance reconfigurable computing. It takes a standard, portable OpenACC C program as input and generates a hardware configuration file for execution on FPGAs. We implemented this prototype system using our open-source OpenARC compiler; it performs source-to-source translation and optimization of the input OpenACC program into an OpenCL code, which is further compiled into a FPGA program by the backend Altera Offline OpenCL compiler. Internally, the design of OpenARC uses a high- level intermediate representation that separates concerns of program representation from underlying architectures, which facilitates portability of OpenARC. In fact, thismore » design allowed us to create the OpenACC-to-FPGA translation framework with minimal extensions to our existing system. In addition, we show that our proposed FPGA-specific compiler optimizations and novel OpenACC pragma extensions assist the compiler in generating more efficient FPGA hardware configuration files. Our empirical evaluation on an Altera Stratix V FPGA with eight OpenACC benchmarks demonstrate the benefits of our strategy. To demonstrate the portability of OpenARC, we show results for the same benchmarks executing on other heterogeneous platforms, including NVIDIA GPUs, AMD GPUs, and Intel Xeon Phis. This initial evidence helps support the goal of using a directive-based, high-level programming strategy for performance portability across heterogeneous HPC architectures.« less

Launching GUPPI: the Green Bank Ultimate Pulsar Processing Instrument

NASA Astrophysics Data System (ADS)

DuPlain, Ron; Ransom, Scott; Demorest, Paul; Brandt, Patrick; Ford, John; Shelton, Amy L.

2008-08-01

The National Radio Astronomy Observatory (NRAO) is launching the Green Bank Ultimate Pulsar Processing Instrument (GUPPI), a prototype flexible digital signal processor designed for pulsar observations with the Robert C. Byrd Green Bank Telescope (GBT). GUPPI uses field programmable gate array (FPGA) hardware and design tools developed by the Center for Astronomy Signal Processing and Electronics Research (CASPER) at the University of California, Berkeley. The NRAO has been concurrently developing GUPPI software and hardware using minimal software resources. The software handles instrument monitor and control, data acquisition, and hardware interfacing. GUPPI is currently an expert-only spectrometer, but supports future integration with the full GBT production system. The NRAO was able to take advantage of the unique flexibility of the CASPER FPGA hardware platform, develop hardware and software in parallel, and build a suite of software tools for monitoring, controlling, and acquiring data with a new instrument over a short timeline of just a few months. The NRAO interacts regularly with CASPER and its users, and GUPPI stands as an example of what reconfigurable computing and open-source development can do for radio astronomy. GUPPI is modular for portability, and the NRAO provides the results of development as an open-source resource.

Development of AN Open-Source Automatic Deformation Monitoring System for Geodetical and Geotechnical Measurements

NASA Astrophysics Data System (ADS)

Engel, P.; Schweimler, B.

2016-04-01

The deformation monitoring of structures and buildings is an important task field of modern engineering surveying, ensuring the standing and reliability of supervised objects over a long period. Several commercial hardware and software solutions for the realization of such monitoring measurements are available on the market. In addition to them, a research team at the Neubrandenburg University of Applied Sciences (NUAS) is actively developing a software package for monitoring purposes in geodesy and geotechnics, which is distributed under an open source licence and free of charge. The task of managing an open source project is well-known in computer science, but it is fairly new in a geodetic context. This paper contributes to that issue by detailing applications, frameworks, and interfaces for the design and implementation of open hardware and software solutions for sensor control, sensor networks, and data management in automatic deformation monitoring. It will be discussed how the development effort of networked applications can be reduced by using free programming tools, cloud computing technologies, and rapid prototyping methods.

Open source and DIY hardware for DNA nanotechnology labs

PubMed Central

Damase, Tulsi R.; Stephens, Daniel; Spencer, Adam; Allen, Peter B.

2015-01-01

A set of instruments and specialized equipment is necessary to equip a laboratory to work with DNA. Reducing the barrier to entry for DNA manipulation should enable and encourage new labs to enter the field. We present three examples of open source/DIY technology with significantly reduced costs relative to commercial equipment. This includes a gel scanner, a horizontal PAGE gel mold, and a homogenizer for generating DNA-coated particles. The overall cost savings obtained by using open source/DIY equipment was between 50 and 90%. PMID:26457320

Instrumentino: An Open-Source Software for Scientific Instruments.

PubMed

Koenka, Israel Joel; Sáiz, Jorge; Hauser, Peter C

2015-01-01

Scientists often need to build dedicated computer-controlled experimental systems. For this purpose, it is becoming common to employ open-source microcontroller platforms, such as the Arduino. These boards and associated integrated software development environments provide affordable yet powerful solutions for the implementation of hardware control of transducers and acquisition of signals from detectors and sensors. It is, however, a challenge to write programs that allow interactive use of such arrangements from a personal computer. This task is particularly complex if some of the included hardware components are connected directly to the computer and not via the microcontroller. A graphical user interface framework, Instrumentino, was therefore developed to allow the creation of control programs for complex systems with minimal programming effort. By writing a single code file, a powerful custom user interface is generated, which enables the automatic running of elaborate operation sequences and observation of acquired experimental data in real time. The framework, which is written in Python, allows extension by users, and is made available as an open source project.

Swan: A tool for porting CUDA programs to OpenCL

NASA Astrophysics Data System (ADS)

Harvey, M. J.; De Fabritiis, G.

2011-04-01

The use of modern, high-performance graphical processing units (GPUs) for acceleration of scientific computation has been widely reported. The majority of this work has used the CUDA programming model supported exclusively by GPUs manufactured by NVIDIA. An industry standardisation effort has recently produced the OpenCL specification for GPU programming. This offers the benefits of hardware-independence and reduced dependence on proprietary tool-chains. Here we describe a source-to-source translation tool, "Swan" for facilitating the conversion of an existing CUDA code to use the OpenCL model, as a means to aid programmers experienced with CUDA in evaluating OpenCL and alternative hardware. While the performance of equivalent OpenCL and CUDA code on fixed hardware should be comparable, we find that a real-world CUDA application ported to OpenCL exhibits an overall 50% increase in runtime, a reduction in performance attributable to the immaturity of contemporary compilers. The ported application is shown to have platform independence, running on both NVIDIA and AMD GPUs without modification. We conclude that OpenCL is a viable platform for developing portable GPU applications but that the more mature CUDA tools continue to provide best performance. Program summaryProgram title: Swan Catalogue identifier: AEIH_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIH_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU Public License version 2 No. of lines in distributed program, including test data, etc.: 17 736 No. of bytes in distributed program, including test data, etc.: 131 177 Distribution format: tar.gz Programming language: C Computer: PC Operating system: Linux RAM: 256 Mbytes Classification: 6.5 External routines: NVIDIA CUDA, OpenCL Nature of problem: Graphical Processing Units (GPUs) from NVIDIA are preferentially programed with the proprietary CUDA programming toolkit. An alternative programming model promoted as an industry standard, OpenCL, provides similar capabilities to CUDA and is also supported on non-NVIDIA hardware (including multicore ×86 CPUs, AMD GPUs and IBM Cell processors). The adaptation of a program from CUDA to OpenCL is relatively straightforward but laborious. The Swan tool facilitates this conversion. Solution method:Swan performs a translation of CUDA kernel source code into an OpenCL equivalent. It also generates the C source code for entry point functions, simplifying kernel invocation from the host program. A concise host-side API abstracts the CUDA and OpenCL APIs. A program adapted to use Swan has no dependency on the CUDA compiler for the host-side program. The converted program may be built for either CUDA or OpenCL, with the selection made at compile time. Restrictions: No support for CUDA C++ features Running time: Nominal

Implementation, reliability, and feasibility test of an Open-Source PACS.

PubMed

Valeri, Gianluca; Zuccaccia, Matteo; Badaloni, Andrea; Ciriaci, Damiano; La Riccia, Luigi; Mazzoni, Giovanni; Maggi, Stefania; Giovagnoni, Andrea

2015-12-01

To implement a hardware and software system able to perform the major functions of an Open-Source PACS, and to analyze it in a simulated real-world environment. A small home network was implemented, and the Open-Source operating system Ubuntu 11.10 was installed in a laptop containing the Dcm4chee suite with the software devices needed. The Open-Source PACS implemented is compatible with Linux OS, Microsoft OS, and Mac OS X; furthermore, it was used with operating systems that guarantee the operation in portable devices (smartphone, tablet) Android and iOS. An OSS PACS is useful for making tutorials and workshops on post-processing techniques for educational and training purposes.

"Do-It-Yourself" reliable pH-stat device by using open-source software, inexpensive hardware and available laboratory equipment

PubMed Central

Kragic, Rastislav; Kostic, Mirjana

2018-01-01

In this paper, we present the construction of a reliable and inexpensive pH stat device, by using open-source “OpenPhControl” software, inexpensive hardware (a peristaltic and a syringe pump, Arduino, a step motor…), readily available laboratory devices: a pH meter, a computer, a webcam, and some 3D printed parts. We provide a methodology for the design, development and test results of each part of the device, as well as of the entire system. In addition to dosing reagents by means of a low-cost peristaltic pump, we also present carefully controlled dosing of reagents by an open-source syringe pump. The upgrading of the basic open-source syringe pump is given in terms of pump control and application of a larger syringe. In addition to the basic functions of pH stat, i.e. pH value measurement and maintenance, an improvement allowing the device to be used for potentiometric titration has been made as well. We have demonstrated the device’s utility when applied for cellulose fibers oxidation with 2,2,6,6-tetramethylpiperidine-1-oxyl radical, i.e. for TEMPO-mediated oxidation. In support of this, we present the results obtained for the oxidation kinetics, the consumption of added reagent and experimental repeatability. Considering that the open-source scientific tools are available to everyone, and that researchers can construct and adjust the device according to their needs, as well as, that the total cost of the open-source pH stat device, excluding the existing laboratory equipment (pH meter, computer and glossary) was less than 150 EUR, we believe that, at a small fraction of the cost of available commercial offers, our open-source pH stat can significantly improve experimental work where the use of pH stat is necessary. PMID:29509793

"Do-It-Yourself" reliable pH-stat device by using open-source software, inexpensive hardware and available laboratory equipment.

PubMed

Milanovic, Jovana Z; Milanovic, Predrag; Kragic, Rastislav; Kostic, Mirjana

2018-01-01

In this paper, we present the construction of a reliable and inexpensive pH stat device, by using open-source "OpenPhControl" software, inexpensive hardware (a peristaltic and a syringe pump, Arduino, a step motor…), readily available laboratory devices: a pH meter, a computer, a webcam, and some 3D printed parts. We provide a methodology for the design, development and test results of each part of the device, as well as of the entire system. In addition to dosing reagents by means of a low-cost peristaltic pump, we also present carefully controlled dosing of reagents by an open-source syringe pump. The upgrading of the basic open-source syringe pump is given in terms of pump control and application of a larger syringe. In addition to the basic functions of pH stat, i.e. pH value measurement and maintenance, an improvement allowing the device to be used for potentiometric titration has been made as well. We have demonstrated the device's utility when applied for cellulose fibers oxidation with 2,2,6,6-tetramethylpiperidine-1-oxyl radical, i.e. for TEMPO-mediated oxidation. In support of this, we present the results obtained for the oxidation kinetics, the consumption of added reagent and experimental repeatability. Considering that the open-source scientific tools are available to everyone, and that researchers can construct and adjust the device according to their needs, as well as, that the total cost of the open-source pH stat device, excluding the existing laboratory equipment (pH meter, computer and glossary) was less than 150 EUR, we believe that, at a small fraction of the cost of available commercial offers, our open-source pH stat can significantly improve experimental work where the use of pH stat is necessary.

Monitoring Heritage Buildings with Open Source Hardware Sensors: A Case Study of the Mosque-Cathedral of Córdoba

PubMed Central

Mesas-Carrascosa, Francisco Javier; Verdú Santano, Daniel; Meroño de Larriva, Jose Emilio; Ortíz Cordero, Rafael; Hidalgo Fernández, Rafael Enrique; García-Ferrer, Alfonso

2016-01-01

A number of physical factors can adversely affect cultural heritage. Therefore, monitoring parameters involved in the deterioration process, principally temperature and relative humidity, is useful for preventive conservation. In this study, a total of 15 microclimate stations using open source hardware were developed and stationed at the Mosque-Cathedral of Córdoba, which is registered with UNESCO for its outstanding universal value, to assess the behavior of interior temperature and relative humidity in relation to exterior weather conditions, public hours and interior design. Long-term monitoring of these parameters is of interest in terms of preservation and reducing the costs of future conservation strategies. Results from monitoring are presented to demonstrate the usefulness of this system. PMID:27690056

Open source IPSEC software in manned and unmanned space missions

NASA Astrophysics Data System (ADS)

Edwards, Jacob

Network security is a major topic of research because cyber attackers pose a threat to national security. Securing ground-space communications for NASA missions is important because attackers could endanger mission success and human lives. This thesis describes how an open source IPsec software package was used to create a secure and reliable channel for ground-space communications. A cost efficient, reproducible hardware testbed was also created to simulate ground-space communications. The testbed enables simulation of low-bandwidth and high latency communications links to experiment how the open source IPsec software reacts to these network constraints. Test cases were built that allowed for validation of the testbed and the open source IPsec software. The test cases also simulate using an IPsec connection from mission control ground routers to points of interest in outer space. Tested open source IPsec software did not meet all the requirements. Software changes were suggested to meet requirements.

Upon the Shoulders of Giants: Open-Source Hardware and Software in Analytical Chemistry.

PubMed

Dryden, Michael D M; Fobel, Ryan; Fobel, Christian; Wheeler, Aaron R

2017-04-18

Isaac Newton famously observed that "if I have seen further it is by standing on the shoulders of giants." We propose that this sentiment is a powerful motivation for the "open-source" movement in scientific research, in which creators provide everything needed to replicate a given project online, as well as providing explicit permission for users to use, improve, and share it with others. Here, we write to introduce analytical chemists who are new to the open-source movement to best practices and concepts in this area and to survey the state of open-source research in analytical chemistry. We conclude by considering two examples of open-source projects from our own research group, with the hope that a description of the process, motivations, and results will provide a convincing argument about the benefits that this movement brings to both creators and users.

PC Scene Generation

NASA Astrophysics Data System (ADS)

Buford, James A., Jr.; Cosby, David; Bunfield, Dennis H.; Mayhall, Anthony J.; Trimble, Darian E.

2007-04-01

AMRDEC has successfully tested hardware and software for Real-Time Scene Generation for IR and SAL Sensors on COTS PC based hardware and video cards. AMRDEC personnel worked with nVidia and Concurrent Computer Corporation to develop a Scene Generation system capable of frame rates of at least 120Hz while frame locked to an external source (such as a missile seeker) with no dropped frames. Latency measurements and image validation were performed using COTS and in-house developed hardware and software. Software for the Scene Generation system was developed using OpenSceneGraph.

Design and Implementation of a Modern Automatic Deformation Monitoring System

NASA Astrophysics Data System (ADS)

Engel, Philipp; Schweimler, Björn

2016-03-01

The deformation monitoring of structures and buildings is an important task field of modern engineering surveying, ensuring the standing and reliability of supervised objects over a long period. Several commercial hardware and software solutions for the realization of such monitoring measurements are available on the market. In addition to them, a research team at the University of Applied Sciences in Neubrandenburg (NUAS) is actively developing a software package for monitoring purposes in geodesy and geotechnics, which is distributed under an open source licence and free of charge. The task of managing an open source project is well-known in computer science, but it is fairly new in a geodetic context. This paper contributes to that issue by detailing applications, frameworks, and interfaces for the design and implementation of open hardware and software solutions for sensor control, sensor networks, and data management in automatic deformation monitoring. It will be discussed how the development effort of networked applications can be reduced by using free programming tools, cloud computing technologies, and rapid prototyping methods.

Towards open-source, low-cost haptics for surgery simulation.

PubMed

Suwelack, Stefan; Sander, Christian; Schill, Julian; Serf, Manuel; Danz, Marcel; Asfour, Tamim; Burger, Wolfgang; Dillmann, Rüdiger; Speidel, Stefanie

2014-01-01

In minimally invasive surgery (MIS), virtual reality (VR) training systems have become a promising education tool. However, the adoption of these systems in research and clinical settings is still limited by the high costs of dedicated haptics hardware for MIS. In this paper, we present ongoing research towards an open-source, low-cost haptic interface for MIS simulation. We demonstrate the basic mechanical design of the device, the sensor setup as well as its software integration.

Easy Handling of Sensors and Actuators over TCP/IP Networks by Open Source Hardware/Software

PubMed Central

Mejías, Andrés; Herrera, Reyes S.; Márquez, Marco A.; Calderón, Antonio José; González, Isaías; Andújar, José Manuel

2017-01-01

There are several specific solutions for accessing sensors and actuators present in any process or system through a TCP/IP network, either local or a wide area type like the Internet. The usage of sensors and actuators of different nature and diverse interfaces (SPI, I2C, analogue, etc.) makes access to them from a network in a homogeneous and secure way more complex. A framework, including both software and hardware resources, is necessary to simplify and unify networked access to these devices. In this paper, a set of open-source software tools, specifically designed to cover the different issues concerning the access to sensors and actuators, and two proposed low-cost hardware architectures to operate with the abovementioned software tools are presented. They allow integrated and easy access to local or remote sensors and actuators. The software tools, integrated in the free authoring tool Easy Java and Javascript Simulations (EJS) solve the interaction issues between the subsystem that integrates sensors and actuators into the network, called convergence subsystem in this paper, and the Human Machine Interface (HMI)—this one designed using the intuitive graphical system of EJS—located on the user’s computer. The proposed hardware architectures and software tools are described and experimental implementations with the proposed tools are presented. PMID:28067801

Easy Handling of Sensors and Actuators over TCP/IP Networks by Open Source Hardware/Software.

PubMed

Mejías, Andrés; Herrera, Reyes S; Márquez, Marco A; Calderón, Antonio José; González, Isaías; Andújar, José Manuel

2017-01-05

There are several specific solutions for accessing sensors and actuators present in any process or system through a TCP/IP network, either local or a wide area type like the Internet. The usage of sensors and actuators of different nature and diverse interfaces (SPI, I2C, analogue, etc.) makes access to them from a network in a homogeneous and secure way more complex. A framework, including both software and hardware resources, is necessary to simplify and unify networked access to these devices. In this paper, a set of open-source software tools, specifically designed to cover the different issues concerning the access to sensors and actuators, and two proposed low-cost hardware architectures to operate with the abovementioned software tools are presented. They allow integrated and easy access to local or remote sensors and actuators. The software tools, integrated in the free authoring tool Easy Java and Javascript Simulations (EJS) solve the interaction issues between the subsystem that integrates sensors and actuators into the network, called convergence subsystem in this paper, and the Human Machine Interface (HMI)-this one designed using the intuitive graphical system of EJS-located on the user's computer. The proposed hardware architectures and software tools are described and experimental implementations with the proposed tools are presented.

Experience of public procurement of Open Compute servers

NASA Astrophysics Data System (ADS)

Bärring, Olof; Guerri, Marco; Bonfillou, Eric; Valsan, Liviu; Grigore, Alexandru; Dore, Vincent; Gentit, Alain; Clement, Benoît; Grossir, Anthony

2015-12-01

The Open Compute Project. OCP (http://www.opencompute.org/). was launched by Facebook in 2011 with the objective of building efficient computing infrastructures at the lowest possible cost. The technologies are released as open hardware. with the goal to develop servers and data centres following the model traditionally associated with open source software projects. In 2013 CERN acquired a few OCP servers in order to compare performance and power consumption with standard hardware. The conclusions were that there are sufficient savings to motivate an attempt to procure a large scale installation. One objective is to evaluate if the OCP market is sufficiently mature and broad enough to meet the constraints of a public procurement. This paper summarizes this procurement. which started in September 2014 and involved the Request for information (RFI) to qualify bidders and Request for Tender (RFT).

Falcon: a highly flexible open-source software for closed-loop neuroscience.

PubMed

Ciliberti, Davide; Kloosterman, Fabian

2017-08-01

Closed-loop experiments provide unique insights into brain dynamics and function. To facilitate a wide range of closed-loop experiments, we created an open-source software platform that enables high-performance real-time processing of streaming experimental data. We wrote Falcon, a C++ multi-threaded software in which the user can load and execute an arbitrary processing graph. Each node of a Falcon graph is mapped to a single thread and nodes communicate with each other through thread-safe buffers. The framework allows for easy implementation of new processing nodes and data types. Falcon was tested both on a 32-core and a 4-core workstation. Streaming data was read from either a commercial acquisition system (Neuralynx) or the open-source Open Ephys hardware, while closed-loop TTL pulses were generated with a USB module for digital output. We characterized the round-trip latency of our Falcon-based closed-loop system, as well as the specific latency contribution of the software architecture, by testing processing graphs with up to 32 parallel pipelines and eight serial stages. We finally deployed Falcon in a task of real-time detection of population bursts recorded live from the hippocampus of a freely moving rat. On Neuralynx hardware, round-trip latency was well below 1 ms and stable for at least 1 h, while on Open Ephys hardware latencies were below 15 ms. The latency contribution of the software was below 0.5 ms. Round-trip and software latencies were similar on both 32- and 4-core workstations. Falcon was used successfully to detect population bursts online with ~40 ms average latency. Falcon is a novel open-source software for closed-loop neuroscience. It has sub-millisecond intrinsic latency and gives the experimenter direct control of CPU resources. We envisage Falcon to be a useful tool to the neuroscientific community for implementing a wide variety of closed-loop experiments, including those requiring use of complex data structures and real-time execution of computationally intensive algorithms, such as population neural decoding/encoding from large cell assemblies.

Falcon: a highly flexible open-source software for closed-loop neuroscience

NASA Astrophysics Data System (ADS)

Ciliberti, Davide; Kloosterman, Fabian

2017-08-01

Objective. Closed-loop experiments provide unique insights into brain dynamics and function. To facilitate a wide range of closed-loop experiments, we created an open-source software platform that enables high-performance real-time processing of streaming experimental data. Approach. We wrote Falcon, a C++ multi-threaded software in which the user can load and execute an arbitrary processing graph. Each node of a Falcon graph is mapped to a single thread and nodes communicate with each other through thread-safe buffers. The framework allows for easy implementation of new processing nodes and data types. Falcon was tested both on a 32-core and a 4-core workstation. Streaming data was read from either a commercial acquisition system (Neuralynx) or the open-source Open Ephys hardware, while closed-loop TTL pulses were generated with a USB module for digital output. We characterized the round-trip latency of our Falcon-based closed-loop system, as well as the specific latency contribution of the software architecture, by testing processing graphs with up to 32 parallel pipelines and eight serial stages. We finally deployed Falcon in a task of real-time detection of population bursts recorded live from the hippocampus of a freely moving rat. Main results. On Neuralynx hardware, round-trip latency was well below 1 ms and stable for at least 1 h, while on Open Ephys hardware latencies were below 15 ms. The latency contribution of the software was below 0.5 ms. Round-trip and software latencies were similar on both 32- and 4-core workstations. Falcon was used successfully to detect population bursts online with ~40 ms average latency. Significance. Falcon is a novel open-source software for closed-loop neuroscience. It has sub-millisecond intrinsic latency and gives the experimenter direct control of CPU resources. We envisage Falcon to be a useful tool to the neuroscientific community for implementing a wide variety of closed-loop experiments, including those requiring use of complex data structures and real-time execution of computationally intensive algorithms, such as population neural decoding/encoding from large cell assemblies.

Evaluation of the OpenCL AES Kernel using the Intel FPGA SDK for OpenCL

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jin, Zheming; Yoshii, Kazutomo; Finkel, Hal

The OpenCL standard is an open programming model for accelerating algorithms on heterogeneous computing system. OpenCL extends the C-based programming language for developing portable codes on different platforms such as CPU, Graphics processing units (GPUs), Digital Signal Processors (DSPs) and Field Programmable Gate Arrays (FPGAs). The Intel FPGA SDK for OpenCL is a suite of tools that allows developers to abstract away the complex FPGA-based development flow for a high-level software development flow. Users can focus on the design of hardware-accelerated kernel functions in OpenCL and then direct the tools to generate the low-level FPGA implementations. The approach makes themore » FPGA-based development more accessible to software users as the needs for hybrid computing using CPUs and FPGAs are increasing. It can also significantly reduce the hardware development time as users can evaluate different ideas with high-level language without deep FPGA domain knowledge. In this report, we evaluate the performance of the kernel using the Intel FPGA SDK for OpenCL and Nallatech 385A FPGA board. Compared to the M506 module, the board provides more hardware resources for a larger design exploration space. The kernel performance is measured with the compute kernel throughput, an upper bound to the FPGA throughput. The report presents the experimental results in details. The Appendix lists the kernel source code.« less

Ethoscopes: An open platform for high-throughput ethomics.

PubMed

Geissmann, Quentin; Garcia Rodriguez, Luis; Beckwith, Esteban J; French, Alice S; Jamasb, Arian R; Gilestro, Giorgio F

2017-10-01

Here, we present the use of ethoscopes, which are machines for high-throughput analysis of behavior in Drosophila and other animals. Ethoscopes provide a software and hardware solution that is reproducible and easily scalable. They perform, in real-time, tracking and profiling of behavior by using a supervised machine learning algorithm, are able to deliver behaviorally triggered stimuli to flies in a feedback-loop mode, and are highly customizable and open source. Ethoscopes can be built easily by using 3D printing technology and rely on Raspberry Pi microcomputers and Arduino boards to provide affordable and flexible hardware. All software and construction specifications are available at http://lab.gilest.ro/ethoscope.

OPTiM: Optical projection tomography integrated microscope using open-source hardware and software

PubMed Central

Andrews, Natalie; Davis, Samuel; Bugeon, Laurence; Dallman, Margaret D.; McGinty, James

2017-01-01

We describe the implementation of an OPT plate to perform optical projection tomography (OPT) on a commercial wide-field inverted microscope, using our open-source hardware and software. The OPT plate includes a tilt adjustment for alignment and a stepper motor for sample rotation as required by standard projection tomography. Depending on magnification requirements, three methods of performing OPT are detailed using this adaptor plate: a conventional direct OPT method requiring only the addition of a limiting aperture behind the objective lens; an external optical-relay method allowing conventional OPT to be performed at magnifications >4x; a remote focal scanning and region-of-interest method for improved spatial resolution OPT (up to ~1.6 μm). All three methods use the microscope’s existing incoherent light source (i.e. arc-lamp) and all of its inherent functionality is maintained for day-to-day use. OPT acquisitions are performed on in vivo zebrafish embryos to demonstrate the implementations’ viability. PMID:28700724

Project-based physics labs using low-cost open-source hardware

NASA Astrophysics Data System (ADS)

Bouquet, F.; Bobroff, J.; Fuchs-Gallezot, M.; Maurines, L.

2017-03-01

We describe a project-based physics lab, which we proposed to third-year university students. These labs are based on new open-source low-cost equipment (Arduino microcontrollers and compatible sensors). Students are given complete autonomy: they develop their own experimental setup and study the physics topic of their choice. The goal of these projects is to let students to discover the reality of experimental physics. Technical specifications of the acquisition material and case studies are presented for practical implementation in other universities.

An automatic speech recognition system with speaker-independent identification support

NASA Astrophysics Data System (ADS)

Caranica, Alexandru; Burileanu, Corneliu

2015-02-01

The novelty of this work relies on the application of an open source research software toolkit (CMU Sphinx) to train, build and evaluate a speech recognition system, with speaker-independent support, for voice-controlled hardware applications. Moreover, we propose to use the trained acoustic model to successfully decode offline voice commands on embedded hardware, such as an ARMv6 low-cost SoC, Raspberry PI. This type of single-board computer, mainly used for educational and research activities, can serve as a proof-of-concept software and hardware stack for low cost voice automation systems.

Open-source colorimeter.

PubMed

Anzalone, Gerald C; Glover, Alexandra G; Pearce, Joshua M

2013-04-19

The high cost of what have historically been sophisticated research-related sensors and tools has limited their adoption to a relatively small group of well-funded researchers. This paper provides a methodology for applying an open-source approach to design and development of a colorimeter. A 3-D printable, open-source colorimeter utilizing only open-source hardware and software solutions and readily available discrete components is discussed and its performance compared to a commercial portable colorimeter. Performance is evaluated with commercial vials prepared for the closed reflux chemical oxygen demand (COD) method. This approach reduced the cost of reliable closed reflux COD by two orders of magnitude making it an economic alternative for the vast majority of potential users. The open-source colorimeter demonstrated good reproducibility and serves as a platform for further development and derivation of the design for other, similar purposes such as nephelometry. This approach promises unprecedented access to sophisticated instrumentation based on low-cost sensors by those most in need of it, under-developed and developing world laboratories.

Open-Source Colorimeter

PubMed Central

Anzalone, Gerald C.; Glover, Alexandra G.; Pearce, Joshua M.

2013-01-01

The high cost of what have historically been sophisticated research-related sensors and tools has limited their adoption to a relatively small group of well-funded researchers. This paper provides a methodology for applying an open-source approach to design and development of a colorimeter. A 3-D printable, open-source colorimeter utilizing only open-source hardware and software solutions and readily available discrete components is discussed and its performance compared to a commercial portable colorimeter. Performance is evaluated with commercial vials prepared for the closed reflux chemical oxygen demand (COD) method. This approach reduced the cost of reliable closed reflux COD by two orders of magnitude making it an economic alternative for the vast majority of potential users. The open-source colorimeter demonstrated good reproducibility and serves as a platform for further development and derivation of the design for other, similar purposes such as nephelometry. This approach promises unprecedented access to sophisticated instrumentation based on low-cost sensors by those most in need of it, under-developed and developing world laboratories. PMID:23604032

Understanding How the "Open" of Open Source Software (OSS) Will Improve Global Health Security.

PubMed

Hahn, Erin; Blazes, David; Lewis, Sheri

2016-01-01

Improving global health security will require bold action in all corners of the world, particularly in developing settings, where poverty often contributes to an increase in emerging infectious diseases. In order to mitigate the impact of emerging pandemic threats, enhanced disease surveillance is needed to improve early detection and rapid response to outbreaks. However, the technology to facilitate this surveillance is often unattainable because of high costs, software and hardware maintenance needs, limited technical competence among public health officials, and internet connectivity challenges experienced in the field. One potential solution is to leverage open source software, a concept that is unfortunately often misunderstood. This article describes the principles and characteristics of open source software and how it may be applied to solve global health security challenges.

PyNCS: a microkernel for high-level definition and configuration of neuromorphic electronic systems

PubMed Central

Stefanini, Fabio; Neftci, Emre O.; Sheik, Sadique; Indiveri, Giacomo

2014-01-01

Neuromorphic hardware offers an electronic substrate for the realization of asynchronous event-based sensory-motor systems and large-scale spiking neural network architectures. In order to characterize these systems, configure them, and carry out modeling experiments, it is often necessary to interface them to workstations. The software used for this purpose typically consists of a large monolithic block of code which is highly specific to the hardware setup used. While this approach can lead to highly integrated hardware/software systems, it hampers the development of modular and reconfigurable infrastructures thus preventing a rapid evolution of such systems. To alleviate this problem, we propose PyNCS, an open-source front-end for the definition of neural network models that is interfaced to the hardware through a set of Python Application Programming Interfaces (APIs). The design of PyNCS promotes modularity, portability and expandability and separates implementation from hardware description. The high-level front-end that comes with PyNCS includes tools to define neural network models as well as to create, monitor and analyze spiking data. Here we report the design philosophy behind the PyNCS framework and describe its implementation. We demonstrate its functionality with two representative case studies, one using an event-based neuromorphic vision sensor, and one using a set of multi-neuron devices for carrying out a cognitive decision-making task involving state-dependent computation. PyNCS, already applicable to a wide range of existing spike-based neuromorphic setups, will accelerate the development of hybrid software/hardware neuromorphic systems, thanks to its code flexibility. The code is open-source and available online at https://github.com/inincs/pyNCS. PMID:25232314

PyNCS: a microkernel for high-level definition and configuration of neuromorphic electronic systems.

PubMed

Stefanini, Fabio; Neftci, Emre O; Sheik, Sadique; Indiveri, Giacomo

2014-01-01

Neuromorphic hardware offers an electronic substrate for the realization of asynchronous event-based sensory-motor systems and large-scale spiking neural network architectures. In order to characterize these systems, configure them, and carry out modeling experiments, it is often necessary to interface them to workstations. The software used for this purpose typically consists of a large monolithic block of code which is highly specific to the hardware setup used. While this approach can lead to highly integrated hardware/software systems, it hampers the development of modular and reconfigurable infrastructures thus preventing a rapid evolution of such systems. To alleviate this problem, we propose PyNCS, an open-source front-end for the definition of neural network models that is interfaced to the hardware through a set of Python Application Programming Interfaces (APIs). The design of PyNCS promotes modularity, portability and expandability and separates implementation from hardware description. The high-level front-end that comes with PyNCS includes tools to define neural network models as well as to create, monitor and analyze spiking data. Here we report the design philosophy behind the PyNCS framework and describe its implementation. We demonstrate its functionality with two representative case studies, one using an event-based neuromorphic vision sensor, and one using a set of multi-neuron devices for carrying out a cognitive decision-making task involving state-dependent computation. PyNCS, already applicable to a wide range of existing spike-based neuromorphic setups, will accelerate the development of hybrid software/hardware neuromorphic systems, thanks to its code flexibility. The code is open-source and available online at https://github.com/inincs/pyNCS.

Real-Time Processing Library for Open-Source Hardware Biomedical Sensors

PubMed Central

Castro-García, Juan A.; Lebrato-Vázquez, Clara

2018-01-01

Applications involving data acquisition from sensors need samples at a preset frequency rate, the filtering out of noise and/or analysis of certain frequency components. We propose a novel software architecture based on open-software hardware platforms which allows programmers to create data streams from input channels and easily implement filters and frequency analysis objects. The performances of the different classes given in the size of memory allocated and execution time (number of clock cycles) were analyzed in the low-cost platform Arduino Genuino. In addition, 11 people took part in an experiment in which they had to implement several exercises and complete a usability test. Sampling rates under 250 Hz (typical for many biomedical applications) makes it feasible to implement filters, sliding windows and Fourier analysis, operating in real time. Participants rated software usability at 70.2 out of 100 and the ease of use when implementing several signal processing applications was rated at just over 4.4 out of 5. Participants showed their intention of using this software because it was percieved as useful and very easy to use. The performances of the library showed that it may be appropriate for implementing small biomedical real-time applications or for human movement monitoring, even in a simple open-source hardware device like Arduino Genuino. The general perception about this library is that it is easy to use and intuitive. PMID:29596394

Real-Time Processing Library for Open-Source Hardware Biomedical Sensors.

PubMed

Molina-Cantero, Alberto J; Castro-García, Juan A; Lebrato-Vázquez, Clara; Gómez-González, Isabel M; Merino-Monge, Manuel

2018-03-29

Applications involving data acquisition from sensors need samples at a preset frequency rate, the filtering out of noise and/or analysis of certain frequency components. We propose a novel software architecture based on open-software hardware platforms which allows programmers to create data streams from input channels and easily implement filters and frequency analysis objects. The performances of the different classes given in the size of memory allocated and execution time (number of clock cycles) were analyzed in the low-cost platform Arduino Genuino. In addition, 11 people took part in an experiment in which they had to implement several exercises and complete a usability test. Sampling rates under 250 Hz (typical for many biomedical applications) makes it feasible to implement filters, sliding windows and Fourier analysis, operating in real time. Participants rated software usability at 70.2 out of 100 and the ease of use when implementing several signal processing applications was rated at just over 4.4 out of 5. Participants showed their intention of using this software because it was percieved as useful and very easy to use. The performances of the library showed that it may be appropriate for implementing small biomedical real-time applications or for human movement monitoring, even in a simple open-source hardware device like Arduino Genuino. The general perception about this library is that it is easy to use and intuitive.

SensoTube: A Scalable Hardware Design Architecture for Wireless Sensors and Actuators Networks Nodes in the Agricultural Domain.

PubMed

Piromalis, Dimitrios; Arvanitis, Konstantinos

2016-08-04

Wireless Sensor and Actuators Networks (WSANs) constitute one of the most challenging technologies with tremendous socio-economic impact for the next decade. Functionally and energy optimized hardware systems and development tools maybe is the most critical facet of this technology for the achievement of such prospects. Especially, in the area of agriculture, where the hostile operating environment comes to add to the general technological and technical issues, reliable and robust WSAN systems are mandatory. This paper focuses on the hardware design architectures of the WSANs for real-world agricultural applications. It presents the available alternatives in hardware design and identifies their difficulties and problems for real-life implementations. The paper introduces SensoTube, a new WSAN hardware architecture, which is proposed as a solution to the various existing design constraints of WSANs. The establishment of the proposed architecture is based, firstly on an abstraction approach in the functional requirements context, and secondly, on the standardization of the subsystems connectivity, in order to allow for an open, expandable, flexible, reconfigurable, energy optimized, reliable and robust hardware system. The SensoTube implementation reference model together with its encapsulation design and installation are analyzed and presented in details. Furthermore, as a proof of concept, certain use cases have been studied in order to demonstrate the benefits of migrating existing designs based on the available open-source hardware platforms to SensoTube architecture.

Frame Decoder for Consultative Committee for Space Data Systems (CCSDS)

NASA Technical Reports Server (NTRS)

Reyes, Miguel A. De Jesus

2014-01-01

GNU Radio is a free and open source development toolkit that provides signal processing to implement software radios. It can be used with low-cost external RF hardware to create software defined radios, or without hardware in a simulation-like environment. GNU Radio applications are primarily written in Python and C++. The Universal Software Radio Peripheral (USRP) is a computer-hosted software radio designed by Ettus Research. The USRP connects to a host computer via high-speed Gigabit Ethernet. Using the open source Universal Hardware Driver (UHD), we can run GNU Radio applications using the USRP. An SDR is a "radio in which some or all physical layer functions are software defined"(IEEE Definition). A radio is any kind of device that wirelessly transmits or receives radio frequency (RF) signals in the radio frequency. An SDR is a radio communication system where components that have been typically implemented in hardware are implemented in software. GNU Radio has a generic packet decoder block that is not optimized for CCSDS frames. Using this generic packet decoder will add bytes to the CCSDS frames and will not permit for bit error correction using Reed-Solomon. The CCSDS frames consist of 256 bytes, including a 32-bit sync marker (0x1ACFFC1D). This frames are generated by the Space Data Processor and GNU Radio will perform the modulation and framing operations, including frame synchronization.

Ethoscopes: An open platform for high-throughput ethomics

PubMed Central

Geissmann, Quentin; Garcia Rodriguez, Luis; Beckwith, Esteban J.; French, Alice S.; Jamasb, Arian R.

2017-01-01

Here, we present the use of ethoscopes, which are machines for high-throughput analysis of behavior in Drosophila and other animals. Ethoscopes provide a software and hardware solution that is reproducible and easily scalable. They perform, in real-time, tracking and profiling of behavior by using a supervised machine learning algorithm, are able to deliver behaviorally triggered stimuli to flies in a feedback-loop mode, and are highly customizable and open source. Ethoscopes can be built easily by using 3D printing technology and rely on Raspberry Pi microcomputers and Arduino boards to provide affordable and flexible hardware. All software and construction specifications are available at http://lab.gilest.ro/ethoscope. PMID:29049280

Inexpensive, Low Power, Open-Source Data Logging in the Field

NASA Astrophysics Data System (ADS)

Sandell, C. T.; Wickert, A. D.

2016-12-01

Collecting a robust data set of environmental conditions with commercial equipment is often cost prohibitive. I present the ALog, a general-purpose, inexpensive, low-power, open-source data logger that has proven its durability on long-term deployments in the harsh conditions of high altitude glaciers and humid river deltas. The ALog was developed to fill the need for a capable, rugged, easy-to-use, inexpensive, open-source hardware targeted at long-term remote deployment in nearly any environment. Building on the popular Arduino platform, the hardware features a high-precision clock, full size SD card slot for high-volume data storage, screw terminals, six analog inputs, two digital inputs, one digital interrupt, 3.3V and 5V power outputs, and SPI and I2C communication capability. The design is focused on extremely low power consumption allowing the Alog to be deployed for years on a single set of common alkaline batteries. The power efficiency of the Alog eliminates the difficulties associated with field power collection including additional hardware and installation costs, dependence on weather conditions, possible equipment failure, and the transport of bulky/heavy equipment to a remote site. Battery power increases suitable data collection sites (too shaded for photovoltaics) and allows for low profile installation options (including underground). The ALog has gone through continuous development with over four years of successful data collection in hydrologic field research. Over this time, software support for a wide range of sensors has been made available such as ultrasonic rangefinders (for water level, snow accumulation and glacial melt), temperature sensors (air and groundwater), humidity sensors, pyranometers, inclinometers, rain gauges, soil moisture and water potential sensors, resistance-based tools to measure frost heave, and cameras that trigger on events. The software developed for use with the ALog allows simple integration of established commercial sensors, including example implementation code so users with limited programming knowledge can get up and running with ease. All development files including design schematics, circuit board layouts, and source code files are open-source to further eliminate barriers to its use and allow community development contribution.

SensoTube: A Scalable Hardware Design Architecture for Wireless Sensors and Actuators Networks Nodes in the Agricultural Domain

PubMed Central

Piromalis, Dimitrios; Arvanitis, Konstantinos

2016-01-01

Wireless Sensor and Actuators Networks (WSANs) constitute one of the most challenging technologies with tremendous socio-economic impact for the next decade. Functionally and energy optimized hardware systems and development tools maybe is the most critical facet of this technology for the achievement of such prospects. Especially, in the area of agriculture, where the hostile operating environment comes to add to the general technological and technical issues, reliable and robust WSAN systems are mandatory. This paper focuses on the hardware design architectures of the WSANs for real-world agricultural applications. It presents the available alternatives in hardware design and identifies their difficulties and problems for real-life implementations. The paper introduces SensoTube, a new WSAN hardware architecture, which is proposed as a solution to the various existing design constraints of WSANs. The establishment of the proposed architecture is based, firstly on an abstraction approach in the functional requirements context, and secondly, on the standardization of the subsystems connectivity, in order to allow for an open, expandable, flexible, reconfigurable, energy optimized, reliable and robust hardware system. The SensoTube implementation reference model together with its encapsulation design and installation are analyzed and presented in details. Furthermore, as a proof of concept, certain use cases have been studied in order to demonstrate the benefits of migrating existing designs based on the available open-source hardware platforms to SensoTube architecture. PMID:27527180

The TJO-OAdM robotic observatory: OpenROCS and dome control

NASA Astrophysics Data System (ADS)

Colomé, Josep; Francisco, Xavier; Ribas, Ignasi; Casteels, Kevin; Martín, Jonatan

2010-07-01

The Telescope Joan Oró at the Montsec Astronomical Observatory (TJO - OAdM) is a small-class observatory working in completely unattended control. There are key problems to solve when a robotic control is envisaged, both on hardware and software issues. We present the OpenROCS (ROCS stands for Robotic Observatory Control System), an open source platform developed for the robotic control of the TJO - OAdM and similar astronomical observatories. It is a complex software architecture, composed of several applications for hardware control, event handling, environment monitoring, target scheduling, image reduction pipeline, etc. The code is developed in Java, C++, Python and Perl. The software infrastructure used is based on the Internet Communications Engine (Ice), an object-oriented middleware that provides object-oriented remote procedure call, grid computing, and publish/subscribe functionality. We also describe the subsystem in charge of the dome control: several hardware and software elements developed to specially protect the system at this identified single point of failure. It integrates a redundant control and a rain detector signal for alarm triggering and it responds autonomously in case communication with any of the control elements is lost (watchdog functionality). The self-developed control software suite (OpenROCS) and dome control system have proven to be highly reliable.

Managing a Real-Time Embedded Linux Platform with Buildroot

DOE Office of Scientific and Technical Information (OSTI.GOV)

Diamond, J.; Martin, K.

2015-01-01

Developers of real-time embedded software often need to build the operating system, kernel, tools and supporting applications from source to work with the differences in their hardware configuration. The first attempts to introduce Linux-based real-time embedded systems into the Fermilab accelerator controls system used this approach but it was found to be time-consuming, difficult to maintain and difficult to adapt to different hardware configurations. Buildroot is an open source build system with a menu-driven configuration tool (similar to the Linux kernel build system) that automates this process. A customized Buildroot [1] system has been developed for use in the Fermilabmore » accelerator controls system that includes several hardware configuration profiles (including Intel, ARM and PowerPC) and packages for Fermilab support software. A bootable image file is produced containing the Linux kernel, shell and supporting software suite that varies from 3 to 20 megabytes large – ideal for network booting. The result is a platform that is easier to maintain and deploy in diverse hardware configurations« less

Forward and adjoint spectral-element simulations of seismic wave propagation using hardware accelerators

NASA Astrophysics Data System (ADS)

Peter, Daniel; Videau, Brice; Pouget, Kevin; Komatitsch, Dimitri

2015-04-01

Improving the resolution of tomographic images is crucial to answer important questions on the nature of Earth's subsurface structure and internal processes. Seismic tomography is the most prominent approach where seismic signals from ground-motion records are used to infer physical properties of internal structures such as compressional- and shear-wave speeds, anisotropy and attenuation. Recent advances in regional- and global-scale seismic inversions move towards full-waveform inversions which require accurate simulations of seismic wave propagation in complex 3D media, providing access to the full 3D seismic wavefields. However, these numerical simulations are computationally very expensive and need high-performance computing (HPC) facilities for further improving the current state of knowledge. During recent years, many-core architectures such as graphics processing units (GPUs) have been added to available large HPC systems. Such GPU-accelerated computing together with advances in multi-core central processing units (CPUs) can greatly accelerate scientific applications. There are mainly two possible choices of language support for GPU cards, the CUDA programming environment and OpenCL language standard. CUDA software development targets NVIDIA graphic cards while OpenCL was adopted mainly by AMD graphic cards. In order to employ such hardware accelerators for seismic wave propagation simulations, we incorporated a code generation tool BOAST into an existing spectral-element code package SPECFEM3D_GLOBE. This allows us to use meta-programming of computational kernels and generate optimized source code for both CUDA and OpenCL languages, running simulations on either CUDA or OpenCL hardware accelerators. We show here applications of forward and adjoint seismic wave propagation on CUDA/OpenCL GPUs, validating results and comparing performances for different simulations and hardware usages.

CheapStat: an open-source, "do-it-yourself" potentiostat for analytical and educational applications.

PubMed

Rowe, Aaron A; Bonham, Andrew J; White, Ryan J; Zimmer, Michael P; Yadgar, Ramsin J; Hobza, Tony M; Honea, Jim W; Ben-Yaacov, Ilan; Plaxco, Kevin W

2011-01-01

Although potentiostats are the foundation of modern electrochemical research, they have seen relatively little application in resource poor settings, such as undergraduate laboratory courses and the developing world. One reason for the low penetration of potentiostats is their cost, as even the least expensive commercially available laboratory potentiostats sell for more than one thousand dollars. An inexpensive electrochemical workstation could thus prove useful in educational labs, and increase access to electrochemistry-based analytical techniques for food, drug and environmental monitoring. With these motivations in mind, we describe here the CheapStat, an inexpensive (<$80), open-source (software and hardware), hand-held potentiostat that can be constructed by anyone who is proficient at assembling circuits. This device supports a number of potential waveforms necessary to perform cyclic, square wave, linear sweep and anodic stripping voltammetry. As we demonstrate, it is suitable for a wide range of applications ranging from food- and drug-quality testing to environmental monitoring, rapid DNA detection, and educational exercises. The device's schematics, parts lists, circuit board layout files, sample experiments, and detailed assembly instructions are available in the supporting information and are released under an open hardware license.

CheapStat: An Open-Source, “Do-It-Yourself” Potentiostat for Analytical and Educational Applications

PubMed Central

Rowe, Aaron A.; Bonham, Andrew J.; White, Ryan J.; Zimmer, Michael P.; Yadgar, Ramsin J.; Hobza, Tony M.; Honea, Jim W.; Ben-Yaacov, Ilan; Plaxco, Kevin W.

2011-01-01

Although potentiostats are the foundation of modern electrochemical research, they have seen relatively little application in resource poor settings, such as undergraduate laboratory courses and the developing world. One reason for the low penetration of potentiostats is their cost, as even the least expensive commercially available laboratory potentiostats sell for more than one thousand dollars. An inexpensive electrochemical workstation could thus prove useful in educational labs, and increase access to electrochemistry-based analytical techniques for food, drug and environmental monitoring. With these motivations in mind, we describe here the CheapStat, an inexpensive (<$80), open-source (software and hardware), hand-held potentiostat that can be constructed by anyone who is proficient at assembling circuits. This device supports a number of potential waveforms necessary to perform cyclic, square wave, linear sweep and anodic stripping voltammetry. As we demonstrate, it is suitable for a wide range of applications ranging from food- and drug-quality testing to environmental monitoring, rapid DNA detection, and educational exercises. The device's schematics, parts lists, circuit board layout files, sample experiments, and detailed assembly instructions are available in the supporting information and are released under an open hardware license. PMID:21931613

Aerodynamics and Control of Quadrotors

NASA Astrophysics Data System (ADS)

Bangura, Moses

Quadrotors are aerial vehicles with a four motor-rotor assembly for generating lift and controllability. Their light weight, ease of design and simple dynamics have increased their use in aerial robotics research. There are many quadrotors that are commercially available or under development. Commercial off-the-shelf quadrotors usually lack the ability to be reprogrammed and are unsuitable for use as research platforms. The open-source code developed in this thesis differs from other open-source systems by focusing on the key performance road blocks in implementing high performance experimental quadrotor platforms for research: motor-rotor control for thrust regulation, velocity and attitude estimation, and control for position regulation and trajectory tracking. In all three of these fundamental subsystems, code sub modules for implementation on commonly available hardware are provided. In addition, the thesis provides guidance on scoping and commissioning open-source hardware components to build a custom quadrotor. A key contribution of the thesis is then a design methodology for the development of experimental quadrotor platforms from open-source or commercial off-the-shelf software and hardware components that have active community support. Quadrotors built following the methodology allows the user access to the operation of the subsystems and, in particular, the user can tune the gains of the observers and controllers in order to push the overall system to its performance limits. This enables the quadrotor framework to be used for a variety of applications such as heavy lifting and high performance aggressive manoeuvres by both the hobby and academic communities. To address the question of thrust control, momentum and blade element theories are used to develop aerodynamic models for rotor blades specific to quadrotors. With the aerodynamic models, a novel thrust estimation and control scheme that improves on existing RPM (revolutions per minute) control of rotors is proposed. The approach taken uses the measured electrical power into the rotors compensating for electrical loses, to estimate changing aerodynamic conditions around a rotor as well as the aerodynamic thrust force. The resulting control algorithms are implemented in real-time on the embedded electronic speed controller (ESC) hardware. Using the estimates of the aerodynamic conditions around the rotor at this level improves the dynamic response to gust as the low-level thrust control is the fastest dynamic level on the vehicle. The aerodynamic estimation scheme enables the vehicle to react almost instantaneously to aerodynamic changes in the environment without affecting the overall dynamic performance of the vehicle. (Abstract shortened by ProQuest.).

The Development of an Open Hardware and Software System Onboard Unmanned Aerial Vehicles to Monitor Concentrated Solar Power Plants

PubMed Central

Mesas-Carrascosa, Francisco Javier; Verdú Santano, Daniel; Pérez Porras, Fernando; Meroño-Larriva, José Emilio; García-Ferrer, Alfonso

2017-01-01

Concentrated solar power (CSP) plants are increasingly gaining interest as a source of renewable energy. These plants face several technical problems and the inspection of components such as absorber tubes in parabolic trough concentrators (PTC), which are widely deployed, is necessary to guarantee plant efficiency. This article presents a system for real-time industrial inspection of CSP plants using low-cost, open-source components in conjunction with a thermographic sensor and an unmanned aerial vehicle (UAV). The system, available in open-source hardware and software, is designed to be employed independently of the type of device used for inspection (laptop, smartphone, tablet or smartglasses) and its operating system. Several UAV flight missions were programmed as follows: flight altitudes at 20, 40, 60, 80, 100 and 120 m above ground level; and three cruising speeds: 5, 7 and 10 m/s. These settings were chosen and analyzed in order to optimize inspection time. The results indicate that it is possible to perform inspections by an UAV in real time at CSP plants as a means of detecting anomalous absorber tubes and improving the effectiveness of methodologies currently being utilized. Moreover, aside from thermographic sensors, this contribution can be applied to other sensors and can be used in a broad range of applications where real-time georeferenced data visualization is necessary. PMID:28594353

The Development of an Open Hardware and Software System Onboard Unmanned Aerial Vehicles to Monitor Concentrated Solar Power Plants.

PubMed

Mesas-Carrascosa, Francisco Javier; Verdú Santano, Daniel; Pérez Porras, Fernando; Meroño-Larriva, José Emilio; García-Ferrer, Alfonso

2017-06-08

Concentrated solar power (CSP) plants are increasingly gaining interest as a source of renewable energy. These plants face several technical problems and the inspection of components such as absorber tubes in parabolic trough concentrators (PTC), which are widely deployed, is necessary to guarantee plant efficiency. This article presents a system for real-time industrial inspection of CSP plants using low-cost, open-source components in conjunction with a thermographic sensor and an unmanned aerial vehicle (UAV). The system, available in open-source hardware and software, is designed to be employed independently of the type of device used for inspection (laptop, smartphone, tablet or smartglasses) and its operating system. Several UAV flight missions were programmed as follows: flight altitudes at 20, 40, 60, 80, 100 and 120 m above ground level; and three cruising speeds: 5, 7 and 10 m/s. These settings were chosen and analyzed in order to optimize inspection time. The results indicate that it is possible to perform inspections by an UAV in real time at CSP plants as a means of detecting anomalous absorber tubes and improving the effectiveness of methodologies currently being utilized. Moreover, aside from thermographic sensors, this contribution can be applied to other sensors and can be used in a broad range of applications where real-time georeferenced data visualization is necessary.

Performance evaluation of OpenFOAM on many-core architectures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brzobohatý, Tomáš; Říha, Lubomír; Karásek, Tomáš, E-mail: tomas.karasek@vsb.cz

In this article application of Open Source Field Operation and Manipulation (OpenFOAM) C++ libraries for solving engineering problems on many-core architectures is presented. Objective of this article is to present scalability of OpenFOAM on parallel platforms solving real engineering problems of fluid dynamics. Scalability test of OpenFOAM is performed using various hardware and different implementation of standard PCG and PBiCG Krylov iterative methods. Speed up of various implementations of linear solvers using GPU and MIC accelerators are presented in this paper. Numerical experiments of 3D lid-driven cavity flow for several cases with various number of cells are presented.

Design and Deployment of a General Purpose, Open Source LoRa to Wi-Fi Hub and Data Logger

NASA Astrophysics Data System (ADS)

DeBell, T. C.; Udell, C.; Kwon, M.; Selker, J. S.; Lopez Alcala, J. M.

2017-12-01

Methods and technologies facilitating internet connectivity and near-real-time status updates for in site environmental sensor data are of increasing interest in Earth Science. However, Open Source, Do-It-Yourself technologies that enable plug and play functionality for web-connected sensors and devices remain largely inaccessible for typical researchers in our community. The Openly Published Environmental Sensing Lab at Oregon State University (OPEnS Lab) constructed an Open Source 900 MHz Long Range Radio (LoRa) receiver hub with SD card data logger, Ethernet and Wi-Fi shield, and 3D printed enclosure that dynamically uploads transmissions from multiple wirelessly-connected environmental sensing devices. Data transmissions may be received from devices up to 20km away. The hub time-stamps, saves to SD card, and uploads all transmissions to a Google Drive spreadsheet to be accessed in near-real-time by researchers and GeoVisualization applications (such as Arc GIS) for access, visualization, and analysis. This research expands the possibilities of scientific observation of our Earth, transforming the technology, methods, and culture by combining open-source development and cutting edge technology. This poster details our methods and evaluates the application of using 3D printing, Arduino Integrated Development Environment (IDE), Adafruit's Open-Hardware Feather development boards, and the WIZNET5500 Ethernet shield for designing this open-source, general purpose LoRa to Wi-Fi data logger.

Open-source hardware is a low-cost alternative for scientific instrumentation and research

USDA-ARS?s Scientific Manuscript database

Scientific research requires the collection of data in order to study, monitor, analyze, describe, or understand a particular process or event. Data collection efforts are often a compromise: manual measurements can be time-consuming and labor-intensive, resulting in data being collected at a low f...

Targeting multiple heterogeneous hardware platforms with OpenCL

NASA Astrophysics Data System (ADS)

Fox, Paul A.; Kozacik, Stephen T.; Humphrey, John R.; Paolini, Aaron; Kuller, Aryeh; Kelmelis, Eric J.

2014-06-01

The OpenCL API allows for the abstract expression of parallel, heterogeneous computing, but hardware implementations have substantial implementation differences. The abstractions provided by the OpenCL API are often insufficiently high-level to conceal differences in hardware architecture. Additionally, implementations often do not take advantage of potential performance gains from certain features due to hardware limitations and other factors. These factors make it challenging to produce code that is portable in practice, resulting in much OpenCL code being duplicated for each hardware platform being targeted. This duplication of effort offsets the principal advantage of OpenCL: portability. The use of certain coding practices can mitigate this problem, allowing a common code base to be adapted to perform well across a wide range of hardware platforms. To this end, we explore some general practices for producing performant code that are effective across platforms. Additionally, we explore some ways of modularizing code to enable optional optimizations that take advantage of hardware-specific characteristics. The minimum requirement for portability implies avoiding the use of OpenCL features that are optional, not widely implemented, poorly implemented, or missing in major implementations. Exposing multiple levels of parallelism allows hardware to take advantage of the types of parallelism it supports, from the task level down to explicit vector operations. Static optimizations and branch elimination in device code help the platform compiler to effectively optimize programs. Modularization of some code is important to allow operations to be chosen for performance on target hardware. Optional subroutines exploiting explicit memory locality allow for different memory hierarchies to be exploited for maximum performance. The C preprocessor and JIT compilation using the OpenCL runtime can be used to enable some of these techniques, as well as to factor in hardware-specific optimizations as necessary.

Toward a Wireless Open Source Instrument: Functional Near-infrared Spectroscopy in Mobile Neuroergonomics and BCI Applications

PubMed Central

von Lühmann, Alexander; Herff, Christian; Heger, Dominic; Schultz, Tanja

2015-01-01

Brain-Computer Interfaces (BCIs) and neuroergonomics research have high requirements regarding robustness and mobility. Additionally, fast applicability and customization are desired. Functional Near-Infrared Spectroscopy (fNIRS) is an increasingly established technology with a potential to satisfy these conditions. EEG acquisition technology, currently one of the main modalities used for mobile brain activity assessment, is widely spread and open for access and thus easily customizable. fNIRS technology on the other hand has either to be bought as a predefined commercial solution or developed from scratch using published literature. To help reducing time and effort of future custom designs for research purposes, we present our approach toward an open source multichannel stand-alone fNIRS instrument for mobile NIRS-based neuroimaging, neuroergonomics and BCI/BMI applications. The instrument is low-cost, miniaturized, wireless and modular and openly documented on www.opennirs.org. It provides features such as scalable channel number, configurable regulated light intensities, programmable gain and lock-in amplification. In this paper, the system concept, hardware, software and mechanical implementation of the lightweight stand-alone instrument are presented and the evaluation and verification results of the instrument's hardware and physiological fNIRS functionality are described. Its capability to measure brain activity is demonstrated by qualitative signal assessments and a quantitative mental arithmetic based BCI study with 12 subjects. PMID:26617510

A reliable, low-cost picture archiving and communications system for small and medium veterinary practices built using open-source technology.

PubMed

Iotti, Bryan; Valazza, Alberto

2014-10-01

Picture Archiving and Communications Systems (PACS) are the most needed system in a modern hospital. As an integral part of the Digital Imaging and Communications in Medicine (DICOM) standard, they are charged with the responsibility for secure storage and accessibility of the diagnostic imaging data. These machines need to offer high performance, stability, and security while proving reliable and ergonomic in the day-to-day and long-term storage and retrieval of the data they safeguard. This paper reports the experience of the authors in developing and installing a compact and low-cost solution based on open-source technologies in the Veterinary Teaching Hospital for the University of Torino, Italy, during the course of the summer of 2012. The PACS server was built on low-cost x86-based hardware and uses an open source operating system derived from Oracle OpenSolaris (Oracle Corporation, Redwood City, CA, USA) to host the DCM4CHEE PACS DICOM server (DCM4CHEE, http://www.dcm4che.org ). This solution features very high data security and an ergonomic interface to provide easy access to a large amount of imaging data. The system has been in active use for almost 2 years now and has proven to be a scalable, cost-effective solution for practices ranging from small to very large, where the use of different hardware combinations allows scaling to the different deployments, while the use of paravirtualization allows increased security and easy migrations and upgrades.

Teaching Robotics Software with the Open Hardware Mobile Manipulator

ERIC Educational Resources Information Center

Vona, M.; Shekar, N. H.

2013-01-01

The "open hardware mobile manipulator" (OHMM) is a new open platform with a unique combination of features for teaching robotics software and algorithms. On-board low- and high-level processors support real-time embedded programming and motor control, as well as higher-level coding with contemporary libraries. Full hardware designs and…

Implementation and performance evaluation open-source controller for precision control of gripper

NASA Astrophysics Data System (ADS)

Lee, Seung-Yong; Ham, Un-Hyeong; Park, Young-Woo; Jung, Hak-Sang; Jung, Il-Kyun; Lim, Sun

2017-12-01

This paper proposes integrating gripper embedded operating system, which consist of external interface structure for sophisticated gripper control. This system has multiple functions that control the gripping module and measure the pose of the gripper body with respect to contact environment. A controller based on open source only for the gripper is developed and an external communication interface between robot controller and gripper controller is designed. An experimental environment for the fixed-cycle test consists of integrating magic gripper software system and hardware on commercial business. As a result, a deviation is measured approximately 2% and the system were verified for gripper control.

The Open AUC Project.

PubMed

Cölfen, Helmut; Laue, Thomas M; Wohlleben, Wendel; Schilling, Kristian; Karabudak, Engin; Langhorst, Bradley W; Brookes, Emre; Dubbs, Bruce; Zollars, Dan; Rocco, Mattia; Demeler, Borries

2010-02-01

Progress in analytical ultracentrifugation (AUC) has been hindered by obstructions to hardware innovation and by software incompatibility. In this paper, we announce and outline the Open AUC Project. The goals of the Open AUC Project are to stimulate AUC innovation by improving instrumentation, detectors, acquisition and analysis software, and collaborative tools. These improvements are needed for the next generation of AUC-based research. The Open AUC Project combines on-going work from several different groups. A new base instrument is described, one that is designed from the ground up to be an analytical ultracentrifuge. This machine offers an open architecture, hardware standards, and application programming interfaces for detector developers. All software will use the GNU Public License to assure that intellectual property is available in open source format. The Open AUC strategy facilitates collaborations, encourages sharing, and eliminates the chronic impediments that have plagued AUC innovation for the last 20 years. This ultracentrifuge will be equipped with multiple and interchangeable optical tracks so that state-of-the-art electronics and improved detectors will be available for a variety of optical systems. The instrument will be complemented by a new rotor, enhanced data acquisition and analysis software, as well as collaboration software. Described here are the instrument, the modular software components, and a standardized database that will encourage and ease integration of data analysis and interpretation software.

ROSE::FTTransform - A Source-to-Source Translation Framework for Exascale Fault-Tolerance Research

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lidman, J; Quinlan, D; Liao, C

2012-03-26

Exascale computing systems will require sufficient resilience to tolerate numerous types of hardware faults while still assuring correct program execution. Such extreme-scale machines are expected to be dominated by processors driven at lower voltages (near the minimum 0.5 volts for current transistors). At these voltage levels, the rate of transient errors increases dramatically due to the sensitivity to transient and geographically localized voltage drops on parts of the processor chip. To achieve power efficiency, these processors are likely to be streamlined and minimal, and thus they cannot be expected to handle transient errors entirely in hardware. Here we present anmore » open, compiler-based framework to automate the armoring of High Performance Computing (HPC) software to protect it from these types of transient processor errors. We develop an open infrastructure to support research work in this area, and we define tools that, in the future, may provide more complete automated and/or semi-automated solutions to support software resiliency on future exascale architectures. Results demonstrate that our approach is feasible, pragmatic in how it can be separated from the software development process, and reasonably efficient (0% to 30% overhead for the Jacobi iteration on common hardware; and 20%, 40%, 26%, and 2% overhead for a randomly selected subset of benchmarks from the Livermore Loops [1]).« less

Open source 3D printers: an appropriate technology for building low cost optics labs for the developing communities

NASA Astrophysics Data System (ADS)

Gwamuri, J.; Pearce, Joshua M.

2017-08-01

The recent introduction of RepRap (self-replicating rapid prototyper) 3-D printers and the resultant open source technological improvements have resulted in affordable 3-D printing, enabling low-cost distributed manufacturing for individuals. This development and others such as the rise of open source-appropriate technology (OSAT) and solar powered 3-D printing are moving 3-D printing from an industry based technology to one that could be used in the developing world for sustainable development. In this paper, we explore some specific technological improvements and how distributed manufacturing with open-source 3-D printing can be used to provide open-source 3-D printable optics components for developing world communities through the ability to print less expensive and customized products. This paper presents an open-source low cost optical equipment library which enables relatively easily adapted customizable designs with the potential of changing the way optics is taught in resource constraint communities. The study shows that this method of scientific hardware development has a potential to enables a much broader audience to participate in optical experimentation both as research and teaching platforms. Conclusions on the technical viability of 3-D printing to assist in development and recommendations on how developing communities can fully exploit this technology to improve the learning of optics through hands-on methods have been outlined.

Getting started with Open-Hardware: Development and Control of Microfluidic Devices

PubMed Central

da Costa, Eric Tavares; Mora, Maria F.; Willis, Peter A.; do Lago, Claudimir L.; Jiao, Hong; Garcia, Carlos D.

2014-01-01

Understanding basic concepts of electronics and computer programming allows researchers to get the most out of the equipment found in their laboratories. Although a number of platforms have been specifically designed for the general public and are supported by a vast array of on-line tutorials, this subject is not normally included in university chemistry curricula. Aiming to provide the basic concepts of hardware and software, this article is focused on the design and use of a simple module to control a series of PDMS-based valves. The module is based on a low-cost microprocessor (Teensy) and open-source software (Arduino). The microvalves were fabricated using thin sheets of PDMS and patterned using CO2 laser engraving, providing a simple and efficient way to fabricate devices without the traditional photolithographic process or facilities. Synchronization of valve control enabled the development of two simple devices to perform injection (1.6 ± 0.4 μL/stroke) and mixing of different solutions. Furthermore, a practical demonstration of the utility of this system for microscale chemical sample handling and analysis was achieved performing an on-chip acid-base titration, followed by conductivity detection with an open-source low-cost detection system. Overall, the system provided a very reproducible (98%) platform to perform fluid delivery at the microfluidic scale. PMID:24823494

Acquiring Data by Mining the Past: Pairing Communities with Environmental Monitoring Methods through Open Online Collaborative Replication

NASA Astrophysics Data System (ADS)

Lippincott, M.; Lewis, E. S.; Gehrke, G. E.; Wise, A.; Pyle, S.; Sinatra, V.; Bland, G.; Bydlowski, D.; Henry, A.; Gilberts, P. A.

2016-12-01

Community groups are interested in low-cost sensors to monitor their environment. However, many new commercial sensors are unknown devices without peer-reviewed evaluations of data quality or pathways to regulatory acceptance, and the time to achieve these outcomes may be beyond a community's patience and attention. Rather than developing a device from scratch or validating a new commercial product, a workflow is presented whereby existing technologies, especially those that are out of patent, are replicated through open online collaboration between communities affected by environmental pollution, volunteers, academic institutions, and existing open hardware and open source software projects. Technology case studies will be presented, focusing primarily on a passive PM monitor based on the UNC Passive Monitor. Stages of the project will be detailed moving from identifying community needs, reviewing existing technology, partnership development, technology replication, IP review and licensing, data quality assurance (in process), and field evaluation with community partners (in process), with special attention to partnership development and technology review. We have leveraged open hardware and open source software to lower the cost and access barriers of existing technologies for PM10-2.5 and other atmospheric measures that have already been validated through peer review. Existing validation of and regulatory familiarity with a technology enables a rapid pathway towards collecting data, shortening the time it takes for communities to leverage data in environmental management decisions. Online collaboration requires rigorous documentation that aids in spreading research methods and promoting deep engagement by interested community researchers outside academia. At the same time, careful choice of technology and the use of small-scale fabrication through laser cutting, 3D printing, and open, shared repositories of plans and software enables educational engagement that broadens a project's reach.

Creating a Rackspace and NASA Nebula compatible cloud using the OpenStack project (Invited)

NASA Astrophysics Data System (ADS)

Clark, R.

2010-12-01

NASA and Rackspace have both provided technology to the OpenStack that allows anyone to create a private Infrastructure as a Service (IaaS) cloud using open source software and commodity hardware. OpenStack is designed and developed completely in the open and with an open governance process. NASA donated Nova, which powers the compute portion of NASA Nebula Cloud Computing Platform, and Rackspace donated Swift, which powers Rackspace Cloud Files. The project is now in continuous development by NASA, Rackspace, and hundreds of other participants. When you create a private cloud using Openstack, you will have the ability to easily interact with your private cloud, a government cloud, and an ecosystem of public cloud providers, using the same API.

EO/IR scene generation open source initiative for real-time hardware-in-the-loop and all-digital simulation

NASA Astrophysics Data System (ADS)

Morris, Joseph W.; Lowry, Mac; Boren, Brett; Towers, James B.; Trimble, Darian E.; Bunfield, Dennis H.

2011-06-01

The US Army Aviation and Missile Research, Development and Engineering Center (AMRDEC) and the Redstone Test Center (RTC) has formed the Scene Generation Development Center (SGDC) to support the Department of Defense (DoD) open source EO/IR Scene Generation initiative for real-time hardware-in-the-loop and all-digital simulation. Various branches of the DoD have invested significant resources in the development of advanced scene and target signature generation codes. The SGDC goal is to maintain unlimited government rights and controlled access to government open source scene generation and signature codes. In addition, the SGDC provides development support to a multi-service community of test and evaluation (T&E) users, developers, and integrators in a collaborative environment. The SGDC has leveraged the DoD Defense Information Systems Agency (DISA) ProjectForge (https://Project.Forge.mil) which provides a collaborative development and distribution environment for the DoD community. The SGDC will develop and maintain several codes for tactical and strategic simulation, such as the Joint Signature Image Generator (JSIG), the Multi-spectral Advanced Volumetric Real-time Imaging Compositor (MAVRIC), and Office of the Secretary of Defense (OSD) Test and Evaluation Science and Technology (T&E/S&T) thermal modeling and atmospherics packages, such as EOView, CHARM, and STAR. Other utility packages included are the ContinuumCore for real-time messaging and data management and IGStudio for run-time visualization and scenario generation.

Sensor Networks, Dataloggers, and Other Handy Gadgets Using Open-Source Electronics for the Christina River Basin CZO

NASA Astrophysics Data System (ADS)

Hicks, S. D.; Aufdenkampe, A. K.; Montgomery, D. S.

2011-12-01

The search for biogeochemical "hot spots" and "hot moments" that control ecosystem-level processes requires a rethinking of how we observe the environment. Extensive multi-sensor/measurement arrays are required to realize 2D, 3D, or 4D maps of environmental properties with sufficient spatial and temporal resolution to find and understand hot spots and hot moments. To date, the cost of the data logging and communication infrastructure has been a major limitation to large-scale sensor deployment, especially for near-real-time (NRT) wireless networks. A low-cost, user-friendly alternative is needed so that resources can be prioritized toward sensor hardware rather than data acquisition and communication hardware. A flexible development platform would also allow for easy creation of other useful devices in addition to the already apparent need for economical dataloggers. The recent proliferation of open-source electronics platforms offers an opportunity for environmental observatories to deploy sensors at large scales by reducing data logging and communications costs by more than an order of magnitude. Leading the open-source electronics revolution is the Arduino project, designed to make the process of using electronics in multidisciplinary projects more accessible to hobbyists and professionals alike. A large user community has developed and shared hundreds of practical applications for projects that interface with a variety of sensors and use embedded logic to control external hardware. Likewise, dozens of companies and individuals sell low-cost Arduino-compatible boards that can connect together in a modular framework, allowing the user to quickly create devices for a wide range of applications. Based on these open-source technologies and products, we are designing and building a variety of circuit devices for use in our research watersheds. One Arduino-based device is a multi-channel datalogger that can be used with a variety of analog and digital sensors, such as pressure transducers, conductivity sensors, soil moisture and temperature probes, and redox probes. Radio modules can be added to the loggers to create a self-meshing wireless network for streaming live sensor data. A variation of the logger circuit is a smaller handheld unit with a text display that can be used when testing sensors in the field. Another useful custom device is a remote streamwater sampling system, made up of an Arduino circuit and a prepaid cell phone, allowing a user to remotely control multiple pumps by following interactive voice menus and hearing live sensor value readouts. In the lab, an Arduino circuit is used in a multi-chamber CO2 respiration experiment where it is controlling dozens of solenoid valves and logging the data from the analytical instruments. One of the biggest benefits of open source hardware is the low cost of the components. Each of the devices we have built costs less than $100 and can be assembled in a few hours. These circuits could easily be adapted to other applications or interfaced with other sensors in a variety of configurations, making the Arduino platform an incredibly useful tool for researchers.

An Open-Source Hardware and Software System for Acquisition and Real-Time Processing of Electrophysiology during High Field MRI

PubMed Central

Purdon, Patrick L.; Millan, Hernan; Fuller, Peter L.; Bonmassar, Giorgio

2008-01-01

Simultaneous recording of electrophysiology and functional magnetic resonance imaging (fMRI) is a technique of growing importance in neuroscience. Rapidly evolving clinical and scientific requirements have created a need for hardware and software that can be customized for specific applications. Hardware may require customization to enable a variety of recording types (e.g., electroencephalogram, local field potentials, or multi-unit activity) while meeting the stringent and costly requirements of MRI safety and compatibility. Real-time signal processing tools are an enabling technology for studies of learning, attention, sleep, epilepsy, neurofeedback, and neuropharmacology, yet real-time signal processing tools are difficult to develop. We describe an open source system for simultaneous electrophysiology and fMRI featuring low-noise (< 0.6 uV p-p input noise), electromagnetic compatibility for MRI (tested up to 7 Tesla), and user-programmable real-time signal processing. The hardware distribution provides the complete specifications required to build an MRI-compatible electrophysiological data acquisition system, including circuit schematics, print circuit board (PCB) layouts, Gerber files for PCB fabrication and robotic assembly, a bill of materials with part numbers, data sheets, and vendor information, and test procedures. The software facilitates rapid implementation of real-time signal processing algorithms. This system has used in human EEG/fMRI studies at 3 and 7 Tesla examining the auditory system, visual system, sleep physiology, and anesthesia, as well as in intracranial electrophysiological studies of the non-human primate visual system during 3 Tesla fMRI, and in human hyperbaric physiology studies at depths of up to 300 feet below sea level. PMID:18761038

An open-source hardware and software system for acquisition and real-time processing of electrophysiology during high field MRI.

PubMed

Purdon, Patrick L; Millan, Hernan; Fuller, Peter L; Bonmassar, Giorgio

2008-11-15

Simultaneous recording of electrophysiology and functional magnetic resonance imaging (fMRI) is a technique of growing importance in neuroscience. Rapidly evolving clinical and scientific requirements have created a need for hardware and software that can be customized for specific applications. Hardware may require customization to enable a variety of recording types (e.g., electroencephalogram, local field potentials, or multi-unit activity) while meeting the stringent and costly requirements of MRI safety and compatibility. Real-time signal processing tools are an enabling technology for studies of learning, attention, sleep, epilepsy, neurofeedback, and neuropharmacology, yet real-time signal processing tools are difficult to develop. We describe an open-source system for simultaneous electrophysiology and fMRI featuring low-noise (<0.6microV p-p input noise), electromagnetic compatibility for MRI (tested up to 7T), and user-programmable real-time signal processing. The hardware distribution provides the complete specifications required to build an MRI-compatible electrophysiological data acquisition system, including circuit schematics, print circuit board (PCB) layouts, Gerber files for PCB fabrication and robotic assembly, a bill of materials with part numbers, data sheets, and vendor information, and test procedures. The software facilitates rapid implementation of real-time signal processing algorithms. This system has been used in human EEG/fMRI studies at 3 and 7T examining the auditory system, visual system, sleep physiology, and anesthesia, as well as in intracranial electrophysiological studies of the non-human primate visual system during 3T fMRI, and in human hyperbaric physiology studies at depths of up to 300 feet below sea level.

Open Ephys: an open-source, plugin-based platform for multichannel electrophysiology.

PubMed

Siegle, Joshua H; López, Aarón Cuevas; Patel, Yogi A; Abramov, Kirill; Ohayon, Shay; Voigts, Jakob

2017-08-01

Closed-loop experiments, in which causal interventions are conditioned on the state of the system under investigation, have become increasingly common in neuroscience. Such experiments can have a high degree of explanatory power, but they require a precise implementation that can be difficult to replicate across laboratories. We sought to overcome this limitation by building open-source software that makes it easier to develop and share algorithms for closed-loop control. We created the Open Ephys GUI, an open-source platform for multichannel electrophysiology experiments. In addition to the standard 'open-loop' visualization and recording functionality, the GUI also includes modules for delivering feedback in response to events detected in the incoming data stream. Importantly, these modules can be built and shared as plugins, which makes it possible for users to extend the functionality of the GUI through a simple API, without having to understand the inner workings of the entire application. In combination with low-cost, open-source hardware for amplifying and digitizing neural signals, the GUI has been used for closed-loop experiments that perturb the hippocampal theta rhythm in a phase-specific manner. The Open Ephys GUI is the first widely used application for multichannel electrophysiology that leverages a plugin-based workflow. We hope that it will lower the barrier to entry for electrophysiologists who wish to incorporate real-time feedback into their research.

Open Ephys: an open-source, plugin-based platform for multichannel electrophysiology

NASA Astrophysics Data System (ADS)

Siegle, Joshua H.; Cuevas López, Aarón; Patel, Yogi A.; Abramov, Kirill; Ohayon, Shay; Voigts, Jakob

2017-08-01

Objective. Closed-loop experiments, in which causal interventions are conditioned on the state of the system under investigation, have become increasingly common in neuroscience. Such experiments can have a high degree of explanatory power, but they require a precise implementation that can be difficult to replicate across laboratories. We sought to overcome this limitation by building open-source software that makes it easier to develop and share algorithms for closed-loop control. Approach. We created the Open Ephys GUI, an open-source platform for multichannel electrophysiology experiments. In addition to the standard ‘open-loop’ visualization and recording functionality, the GUI also includes modules for delivering feedback in response to events detected in the incoming data stream. Importantly, these modules can be built and shared as plugins, which makes it possible for users to extend the functionality of the GUI through a simple API, without having to understand the inner workings of the entire application. Main results. In combination with low-cost, open-source hardware for amplifying and digitizing neural signals, the GUI has been used for closed-loop experiments that perturb the hippocampal theta rhythm in a phase-specific manner. Significance. The Open Ephys GUI is the first widely used application for multichannel electrophysiology that leverages a plugin-based workflow. We hope that it will lower the barrier to entry for electrophysiologists who wish to incorporate real-time feedback into their research.

ExpertEyes: open-source, high-definition eyetracking.

PubMed

Parada, Francisco J; Wyatte, Dean; Yu, Chen; Akavipat, Ruj; Emerick, Brandi; Busey, Thomas

2015-03-01

ExpertEyes is a low-cost, open-source package of hardware and software that is designed to provide portable high-definition eyetracking. The project involves several technological innovations, including portability, high-definition video recording, and multiplatform software support. It was designed for challenging recording environments, and all processing is done offline to allow for optimization of parameter estimation. The pupil and corneal reflection are estimated using a novel forward eye model that simultaneously fits both the pupil and the corneal reflection with full ellipses, addressing a common situation in which the corneal reflection sits at the edge of the pupil and therefore breaks the contour of the ellipse. The accuracy and precision of the system are comparable to or better than what is available in commercial eyetracking systems, with a typical accuracy of less than 0.4° and best accuracy below 0.3°, and with a typical precision (SD method) around 0.3° and best precision below 0.2°. Part of the success of the system comes from a high-resolution eye image. The high image quality results from uncasing common digital camcorders and recording directly to SD cards, which avoids the limitations of the analog NTSC format. The software is freely downloadable, and complete hardware plans are available, along with sources for custom parts.

Looking Forward: Comment on Morgante, Zolfaghari, and Johnson

ERIC Educational Resources Information Center

Creel, Sarah C.

2012-01-01

Morgante et al. (in press) find inconsistencies in the time reporting of a Tobii T60XL eye tracker. Their study raises important questions about the use of the Tobii T-series in particular, and various software and hardware in general, in different infant eye tracking paradigms. It leaves open the question of the source of the inconsistencies.…

An IoT-Based Solution for Monitoring a Fleet of Educational Buildings Focusing on Energy Efficiency.

PubMed

Amaxilatis, Dimitrios; Akrivopoulos, Orestis; Mylonas, Georgios; Chatzigiannakis, Ioannis

2017-10-10

Raising awareness among young people and changing their behaviour and habits concerning energy usage is key to achieving sustained energy saving. Additionally, young people are very sensitive to environmental protection so raising awareness among children is much easier than with any other group of citizens. This work examines ways to create an innovative Information & Communication Technologies (ICT) ecosystem (including web-based, mobile, social and sensing elements) tailored specifically for school environments, taking into account both the users (faculty, staff, students, parents) and school buildings, thus motivating and supporting young citizens' behavioural change to achieve greater energy efficiency. A mixture of open-source IoT hardware and proprietary platforms on the infrastructure level, are currently being utilized for monitoring a fleet of 18 educational buildings across 3 countries, comprising over 700 IoT monitoring points. Hereon presented is the system's high-level architecture, as well as several aspects of its implementation, related to the application domain of educational building monitoring and energy efficiency. The system is developed based on open-source technologies and services in order to make it capable of providing open IT-infrastructure and support from different commercial hardware/sensor vendors as well as open-source solutions. The system presented can be used to develop and offer new app-based solutions that can be used either for educational purposes or for managing the energy efficiency of the building. The system is replicable and adaptable to settings that may be different than the scenarios envisioned here (e.g., targeting different climate zones), different IT infrastructures and can be easily extended to accommodate integration with other systems. The overall performance of the system is evaluated in real-world environment in terms of scalability, responsiveness and simplicity.

An IoT-Based Solution for Monitoring a Fleet of Educational Buildings Focusing on Energy Efficiency

PubMed Central

Akrivopoulos, Orestis

2017-01-01

Raising awareness among young people and changing their behaviour and habits concerning energy usage is key to achieving sustained energy saving. Additionally, young people are very sensitive to environmental protection so raising awareness among children is much easier than with any other group of citizens. This work examines ways to create an innovative Information & Communication Technologies (ICT) ecosystem (including web-based, mobile, social and sensing elements) tailored specifically for school environments, taking into account both the users (faculty, staff, students, parents) and school buildings, thus motivating and supporting young citizens’ behavioural change to achieve greater energy efficiency. A mixture of open-source IoT hardware and proprietary platforms on the infrastructure level, are currently being utilized for monitoring a fleet of 18 educational buildings across 3 countries, comprising over 700 IoT monitoring points. Hereon presented is the system’s high-level architecture, as well as several aspects of its implementation, related to the application domain of educational building monitoring and energy efficiency. The system is developed based on open-source technologies and services in order to make it capable of providing open IT-infrastructure and support from different commercial hardware/sensor vendors as well as open-source solutions. The system presented can be used to develop and offer new app-based solutions that can be used either for educational purposes or for managing the energy efficiency of the building. The system is replicable and adaptable to settings that may be different than the scenarios envisioned here (e.g., targeting different climate zones), different IT infrastructures and can be easily extended to accommodate integration with other systems. The overall performance of the system is evaluated in real-world environment in terms of scalability, responsiveness and simplicity. PMID:28994719

ProjectQ: Compiling quantum programs for various backends

NASA Astrophysics Data System (ADS)

Haener, Thomas; Steiger, Damian S.; Troyer, Matthias

In order to control quantum computers beyond the current generation, a high level quantum programming language and optimizing compilers will be essential. Therefore, we have developed ProjectQ - an open source software framework to facilitate implementing and running quantum algorithms both in software and on actual quantum hardware. Here, we introduce the backends available in ProjectQ. This includes a high-performance simulator and emulator to test and debug quantum algorithms, tools for resource estimation, and interfaces to several small-scale quantum devices. We demonstrate the workings of the framework and show how easily it can be further extended to control upcoming quantum hardware.

Digital beacon receiver for ionospheric TEC measurement developed with GNU Radio

NASA Astrophysics Data System (ADS)

Yamamoto, M.

2008-11-01

A simple digital receiver named GNU Radio Beacon Receiver (GRBR) was developed for the satellite-ground beacon experiment to measure the ionospheric total electron content (TEC). The open-source software toolkit for the software defined radio, GNU Radio, is utilized to realize the basic function of the receiver and perform fast signal processing. The software is written in Python for a LINUX PC. The open-source hardware called Universal Software Radio Peripheral (USRP), which best matches the GNU Radio, is used as a front-end to acquire the satellite beacon signals of 150 and 400 MHz. The first experiment was successful as results from GRBR showed very good agreement to those from the co-located analog beacon receiver. Detailed design information and software codes are open at the URL http://www.rish.kyoto-u.ac.jp/digitalbeacon/.

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation.

PubMed

Eastman, Peter; Friedrichs, Mark S; Chodera, John D; Radmer, Randall J; Bruns, Christopher M; Ku, Joy P; Beauchamp, Kyle A; Lane, Thomas J; Wang, Lee-Ping; Shukla, Diwakar; Tye, Tony; Houston, Mike; Stich, Timo; Klein, Christoph; Shirts, Michael R; Pande, Vijay S

2013-01-08

OpenMM is a software toolkit for performing molecular simulations on a range of high performance computing architectures. It is based on a layered architecture: the lower layers function as a reusable library that can be invoked by any application, while the upper layers form a complete environment for running molecular simulations. The library API hides all hardware-specific dependencies and optimizations from the users and developers of simulation programs: they can be run without modification on any hardware on which the API has been implemented. The current implementations of OpenMM include support for graphics processing units using the OpenCL and CUDA frameworks. In addition, OpenMM was designed to be extensible, so new hardware architectures can be accommodated and new functionality (e.g., energy terms and integrators) can be easily added.

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

PubMed Central

Eastman, Peter; Friedrichs, Mark S.; Chodera, John D.; Radmer, Randall J.; Bruns, Christopher M.; Ku, Joy P.; Beauchamp, Kyle A.; Lane, Thomas J.; Wang, Lee-Ping; Shukla, Diwakar; Tye, Tony; Houston, Mike; Stich, Timo; Klein, Christoph; Shirts, Michael R.; Pande, Vijay S.

2012-01-01

OpenMM is a software toolkit for performing molecular simulations on a range of high performance computing architectures. It is based on a layered architecture: the lower layers function as a reusable library that can be invoked by any application, while the upper layers form a complete environment for running molecular simulations. The library API hides all hardware-specific dependencies and optimizations from the users and developers of simulation programs: they can be run without modification on any hardware on which the API has been implemented. The current implementations of OpenMM include support for graphics processing units using the OpenCL and CUDA frameworks. In addition, OpenMM was designed to be extensible, so new hardware architectures can be accommodated and new functionality (e.g., energy terms and integrators) can be easily added. PMID:23316124

Integration of an open interface PC scene generator using COTS DVI converter hardware

NASA Astrophysics Data System (ADS)

Nordland, Todd; Lyles, Patrick; Schultz, Bret

2006-05-01

Commercial-Off-The-Shelf (COTS) personal computer (PC) hardware is increasingly capable of computing high dynamic range (HDR) scenes for military sensor testing at high frame rates. New electro-optical and infrared (EO/IR) scene projectors feature electrical interfaces that can accept the DVI output of these PC systems. However, military Hardware-in-the-loop (HWIL) facilities such as those at the US Army Aviation and Missile Research Development and Engineering Center (AMRDEC) utilize a sizeable inventory of existing projection systems that were designed to use the Silicon Graphics Incorporated (SGI) digital video port (DVP, also known as DVP2 or DD02) interface. To mate the new DVI-based scene generation systems to these legacy projection systems, CG2 Inc., a Quantum3D Company (CG2), has developed a DVI-to-DVP converter called Delta DVP. This device takes progressive scan DVI input, converts it to digital parallel data, and combines and routes color components to derive a 16-bit wide luminance channel replicated on a DVP output interface. The HWIL Functional Area of AMRDEC has developed a suite of modular software to perform deterministic real-time, wave band-specific rendering of sensor scenes, leveraging the features of commodity graphics hardware and open source software. Together, these technologies enable sensor simulation and test facilities to integrate scene generation and projection components with diverse pedigrees.

OpenROCS: a software tool to control robotic observatories

NASA Astrophysics Data System (ADS)

Colomé, Josep; Sanz, Josep; Vilardell, Francesc; Ribas, Ignasi; Gil, Pere

2012-09-01

We present the Open Robotic Observatory Control System (OpenROCS), an open source software platform developed for the robotic control of telescopes. It acts as a software infrastructure that executes all the necessary processes to implement responses to the system events that appear in the routine and non-routine operations associated to data-flow and housekeeping control. The OpenROCS software design and implementation provides a high flexibility to be adapted to different observatory configurations and event-action specifications. It is based on an abstract model that is independent of the specific hardware or software and is highly configurable. Interfaces to the system components are defined in a simple manner to achieve this goal. We give a detailed description of the version 2.0 of this software, based on a modular architecture developed in PHP and XML configuration files, and using standard communication protocols to interface with applications for hardware monitoring and control, environment monitoring, scheduling of tasks, image processing and data quality control. We provide two examples of how it is used as the core element of the control system in two robotic observatories: the Joan Oró Telescope at the Montsec Astronomical Observatory (Catalonia, Spain) and the SuperWASP Qatar Telescope at the Roque de los Muchachos Observatory (Canary Islands, Spain).

Proposed US Contributions to LOFT

NASA Technical Reports Server (NTRS)

Wilson-Hodge, Colleen

2013-01-01

Proposed US Enhancements include:Tantalum X -ray collimator, Additional ground station, Large Observatory for X-Ray Timing (LOFT) instrument team participation, US science support center & data archive, and Science enabled by US hardware. High-Z material with excellent stopping power. Fabricated using a combination of laser micromachining and chemical etching. Known technology capable of producing high-aspect ratio holes and large open fractions. Reduces LOFT LAD background by a factor of 3. Telemetry formats for LOFT based upon RXTE/EDS experience. Ground system software and strategies for WFM based upon RXTE/ASM automated pipeline software. MSFC engineering trade studies supporting the Ta collimator. Burst alert triggers based upon Fermi/GBM and HETE-2. Science Enhancements Enabled by US Hardware include: Tantalum collimator: Reduces background by factor of 3. Improves sensitivity to faint sources such as AGN. Eliminates contamination by bright/variable sources. outside the LAD field of view. US Ground Station: Enables continuous telemetry of all events from the WFM. Allows LAD to observe very bright >500 mCrab sources with full event resolution.

Design and Development of nEMoS, an All-in-One, Low-Cost, Web-Connected and 3D-Printed Device for Environmental Analysis

PubMed Central

Salamone, Francesco; Belussi, Lorenzo; Danza, Ludovico; Ghellere, Matteo; Meroni, Italo

2015-01-01

The Indoor Environmental Quality (IEQ) refers to the quality of the environment in relation to the health and well-being of the occupants. It is a holistic concept, which considers several categories, each related to a specific environmental parameter. This article describes a low-cost and open-source hardware architecture able to detect the indoor variables necessary for the IEQ calculation as an alternative to the traditional hardware used for this purpose. The system consists of some sensors and an Arduino board. One of the key strengths of Arduino is the possibility it affords of loading the script into the board’s memory and letting it run without interfacing with computers, thus granting complete independence, portability and accuracy. Recent works have demonstrated that the cost of scientific equipment can be reduced by applying open-source principles to their design using a combination of the Arduino platform and a 3D printer. The evolution of the 3D printer has provided a new means of open design capable of accelerating self-directed development. The proposed nano Environmental Monitoring System (nEMoS) instrument is shown to have good reliability and it provides the foundation for a more critical approach to the use of professional sensors as well as for conceiving new scenarios and potential applications. PMID:26053749

Getting started with open-hardware: development and control of microfluidic devices.

PubMed

da Costa, Eric Tavares; Mora, Maria F; Willis, Peter A; do Lago, Claudimir L; Jiao, Hong; Garcia, Carlos D

2014-08-01

Understanding basic concepts of electronics and computer programming allows researchers to get the most out of the equipment found in their laboratories. Although a number of platforms have been specifically designed for the general public and are supported by a vast array of on-line tutorials, this subject is not normally included in university chemistry curricula. Aiming to provide the basic concepts of hardware and software, this article is focused on the design and use of a simple module to control a series of PDMS-based valves. The module is based on a low-cost microprocessor (Teensy) and open-source software (Arduino). The microvalves were fabricated using thin sheets of PDMS and patterned using CO2 laser engraving, providing a simple and efficient way to fabricate devices without the traditional photolithographic process or facilities. Synchronization of valve control enabled the development of two simple devices to perform injection (1.6 ± 0.4 μL/stroke) and mixing of different solutions. Furthermore, a practical demonstration of the utility of this system for microscale chemical sample handling and analysis was achieved performing an on-chip acid-base titration, followed by conductivity detection with an open-source low-cost detection system. Overall, the system provided a very reproducible (98%) platform to perform fluid delivery at the microfluidic scale. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A low-cost, computer-controlled robotic flower system for behavioral experiments.

PubMed

Kuusela, Erno; Lämsä, Juho

2016-04-01

Human observations during behavioral studies are expensive, time-consuming, and error prone. For this reason, automatization of experiments is highly desirable, as it reduces the risk of human errors and workload. The robotic system we developed is simple and cheap to build and handles feeding and data collection automatically. The system was built using mostly off-the-shelf components and has a novel feeding mechanism that uses servos to perform refill operations. We used the robotic system in two separate behavioral studies with bumblebees (Bombus terrestris): The system was used both for training of the bees and for the experimental data collection. The robotic system was reliable, with no flight in our studies failing due to a technical malfunction. The data recorded were easy to apply for further analysis. The software and the hardware design are open source. The development of cheap open-source prototyping platforms during the recent years has opened up many possibilities in designing of experiments. Automatization not only reduces workload, but also potentially allows experimental designs never done before, such as dynamic experiments, where the system responds to, for example, learning of the animal. We present a complete system with hardware and software, and it can be used as such in various experiments requiring feeders and collection of visitation data. Use of the system is not limited to any particular experimental setup or even species.

Design and development of nEMoS, an all-in-one, low-cost, web-connected and 3D-printed device for environmental analysis.

PubMed

Salamone, Francesco; Belussi, Lorenzo; Danza, Ludovico; Ghellere, Matteo; Meroni, Italo

2015-06-04

The Indoor Environmental Quality (IEQ) refers to the quality of the environment in relation to the health and well-being of the occupants. It is a holistic concept, which considers several categories, each related to a specific environmental parameter. This article describes a low-cost and open-source hardware architecture able to detect the indoor variables necessary for the IEQ calculation as an alternative to the traditional hardware used for this purpose. The system consists of some sensors and an Arduino board. One of the key strengths of Arduino is the possibility it affords of loading the script into the board's memory and letting it run without interfacing with computers, thus granting complete independence, portability and accuracy. Recent works have demonstrated that the cost of scientific equipment can be reduced by applying open-source principles to their design using a combination of the Arduino platform and a 3D printer. The evolution of the 3D printer has provided a new means of open design capable of accelerating self-directed development. The proposed nano Environmental Monitoring System (nEMoS) instrument is shown to have good reliability and it provides the foundation for a more critical approach to the use of professional sensors as well as for conceiving new scenarios and potential applications.

SUPRA: open-source software-defined ultrasound processing for real-time applications : A 2D and 3D pipeline from beamforming to B-mode.

PubMed

Göbl, Rüdiger; Navab, Nassir; Hennersperger, Christoph

2018-06-01

Research in ultrasound imaging is limited in reproducibility by two factors: First, many existing ultrasound pipelines are protected by intellectual property, rendering exchange of code difficult. Second, most pipelines are implemented in special hardware, resulting in limited flexibility of implemented processing steps on such platforms. With SUPRA, we propose an open-source pipeline for fully software-defined ultrasound processing for real-time applications to alleviate these problems. Covering all steps from beamforming to output of B-mode images, SUPRA can help improve the reproducibility of results and make modifications to the image acquisition mode accessible to the research community. We evaluate the pipeline qualitatively, quantitatively, and regarding its run time. The pipeline shows image quality comparable to a clinical system and backed by point spread function measurements a comparable resolution. Including all processing stages of a usual ultrasound pipeline, the run-time analysis shows that it can be executed in 2D and 3D on consumer GPUs in real time. Our software ultrasound pipeline opens up the research in image acquisition. Given access to ultrasound data from early stages (raw channel data, radiofrequency data), it simplifies the development in imaging. Furthermore, it tackles the reproducibility of research results, as code can be shared easily and even be executed without dedicated ultrasound hardware.

Games for Traffic Education: An Experimental Study of a Game-Based Driving Simulator

ERIC Educational Resources Information Center

Backlund, Per; Engstrom, Henrik; Johannesson, Mikael; Lebram, Mikael

2010-01-01

In this article, the authors report on the construction and evaluation of a game-based driving simulator using a real car as a joystick. The simulator is constructed from off-the-shelf hardware and the simulation runs on open-source software. The feasibility of the simulator as a learning tool has been experimentally evaluated. Results are…

The design and construction of a cost-efficient confocal laser scanning microscope

NASA Astrophysics Data System (ADS)

Xi, Peng; Rajwa, Bartlomiej; Jones, James T.; Robinson, J. Paul

2007-03-01

The optical dissection ability of confocal microscopy makes it a powerful tool for biological materials. However, the cost and complexity of confocal scanning laser microscopy hinders its wide application in education. We describe the construction of a simplified confocal scanning laser microscope and demonstrate three-dimensional projection based on cost-efficient commercial hardware, together with available open source software.

PsyToolkit: a software package for programming psychological experiments using Linux.

PubMed

Stoet, Gijsbert

2010-11-01

PsyToolkit is a set of software tools for programming psychological experiments on Linux computers. Given that PsyToolkit is freely available under the Gnu Public License, open source, and designed such that it can easily be modified and extended for individual needs, it is suitable not only for technically oriented Linux users, but also for students, researchers on small budgets, and universities in developing countries. The software includes a high-level scripting language, a library for the programming language C, and a questionnaire presenter. The software easily integrates with other open source tools, such as the statistical software package R. PsyToolkit is designed to work with external hardware (including IoLab and Cedrus response keyboards and two common digital input/output boards) and to support millisecond timing precision. Four in-depth examples explain the basic functionality of PsyToolkit. Example 1 demonstrates a stimulus-response compatibility experiment. Example 2 demonstrates a novel mouse-controlled visual search experiment. Example 3 shows how to control light emitting diodes using PsyToolkit, and Example 4 shows how to build a light-detection sensor. The last two examples explain the electronic hardware setup such that they can even be used with other software packages.

Early Detection of Apathetic Phenotypes in Huntington's Disease Knock-in Mice Using Open Source Tools.

PubMed

Minnig, Shawn; Bragg, Robert M; Tiwana, Hardeep S; Solem, Wes T; Hovander, William S; Vik, Eva-Mari S; Hamilton, Madeline; Legg, Samuel R W; Shuttleworth, Dominic D; Coffey, Sydney R; Cantle, Jeffrey P; Carroll, Jeffrey B

2018-02-02

Apathy is one of the most prevalent and progressive psychiatric symptoms in Huntington's disease (HD) patients. However, preclinical work in HD mouse models tends to focus on molecular and motor, rather than affective, phenotypes. Measuring behavior in mice often produces noisy data and requires large cohorts to detect phenotypic rescue with appropriate power. The operant equipment necessary for measuring affective phenotypes is typically expensive, proprietary to commercial entities, and bulky which can render adequately sized mouse cohorts as cost-prohibitive. Thus, we describe here a home-built, open-source alternative to commercial hardware that is reliable, scalable, and reproducible. Using off-the-shelf hardware, we adapted and built several of the rodent operant buckets (ROBucket) to test Htt Q111/+ mice for attention deficits in fixed ratio (FR) and progressive ratio (PR) tasks. We find that, despite normal performance in reward attainment in the FR task, Htt Q111/+ mice exhibit reduced PR performance at 9-11 months of age, suggesting motivational deficits. We replicated this in two independent cohorts, demonstrating the reliability and utility of both the apathetic phenotype, and these ROBuckets, for preclinical HD studies.

Open-source micro-tensile testers via additive manufacturing for the mechanical characterization of thin films and papers

PubMed Central

Scheftic, Charlie M.; Brinson, L. Catherine

2018-01-01

The cost of specialized scientific equipment can be high and with limited funding resources, researchers and students are often unable to access or purchase the ideal equipment for their projects. In the fields of materials science and mechanical engineering, fundamental equipment such as tensile testing devices can cost tens to hundreds of thousands of dollars. While a research lab often has access to a large-scale testing machine suitable for conventional samples, loading devices for meso- and micro-scale samples for in-situ testing with the myriad of microscopy tools are often hard to source and cost prohibitive. Open-source software has allowed for great strides in the reduction of costs associated with software development and open-source hardware and additive manufacturing have the potential to similarly reduce the costs of scientific equipment and increase the accessibility of scientific research. To investigate the feasibility of open-source hardware, a micro-tensile tester was designed with a freely accessible computer-aided design package and manufactured with a desktop 3D-printer and off-the-shelf components. To our knowledge this is one of the first demonstrations of a tensile tester with additively manufactured components for scientific research. The capabilities of the tensile tester were demonstrated by investigating the mechanical properties of Graphene Oxide (GO) paper and thin films. A 3D printed tensile tester was successfully used in conjunction with an atomic force microscope to provide one of the first quantitative measurements of GO thin film buckling under compression. The tensile tester was also used in conjunction with an atomic force microscope to observe the change in surface topology of a GO paper in response to increasing tensile strain. No significant change in surface topology was observed in contrast to prior hypotheses from the literature. Based on this result obtained with the new open source tensile stage we propose an alternative hypothesis we term ‘superlamellae consolidation’ to explain the initial deformation of GO paper. The additively manufactured tensile tester tested represents cost savings of >99% compared to commercial solutions in its class and offers simple customization. However, continued development is needed for the tensile tester presented here to approach the technical specifications achievable with commercial solutions. PMID:29813103

Open-source micro-tensile testers via additive manufacturing for the mechanical characterization of thin films and papers.

PubMed

Nandy, Krishanu; Collinson, David W; Scheftic, Charlie M; Brinson, L Catherine

2018-01-01

The cost of specialized scientific equipment can be high and with limited funding resources, researchers and students are often unable to access or purchase the ideal equipment for their projects. In the fields of materials science and mechanical engineering, fundamental equipment such as tensile testing devices can cost tens to hundreds of thousands of dollars. While a research lab often has access to a large-scale testing machine suitable for conventional samples, loading devices for meso- and micro-scale samples for in-situ testing with the myriad of microscopy tools are often hard to source and cost prohibitive. Open-source software has allowed for great strides in the reduction of costs associated with software development and open-source hardware and additive manufacturing have the potential to similarly reduce the costs of scientific equipment and increase the accessibility of scientific research. To investigate the feasibility of open-source hardware, a micro-tensile tester was designed with a freely accessible computer-aided design package and manufactured with a desktop 3D-printer and off-the-shelf components. To our knowledge this is one of the first demonstrations of a tensile tester with additively manufactured components for scientific research. The capabilities of the tensile tester were demonstrated by investigating the mechanical properties of Graphene Oxide (GO) paper and thin films. A 3D printed tensile tester was successfully used in conjunction with an atomic force microscope to provide one of the first quantitative measurements of GO thin film buckling under compression. The tensile tester was also used in conjunction with an atomic force microscope to observe the change in surface topology of a GO paper in response to increasing tensile strain. No significant change in surface topology was observed in contrast to prior hypotheses from the literature. Based on this result obtained with the new open source tensile stage we propose an alternative hypothesis we term 'superlamellae consolidation' to explain the initial deformation of GO paper. The additively manufactured tensile tester tested represents cost savings of >99% compared to commercial solutions in its class and offers simple customization. However, continued development is needed for the tensile tester presented here to approach the technical specifications achievable with commercial solutions.

RMG An Open Source Electronic Structure Code for Multi-Petaflops Calculations

NASA Astrophysics Data System (ADS)

Briggs, Emil; Lu, Wenchang; Hodak, Miroslav; Bernholc, Jerzy

RMG (Real-space Multigrid) is an open source, density functional theory code for quantum simulations of materials. It solves the Kohn-Sham equations on real-space grids, which allows for natural parallelization via domain decomposition. Either subspace or Davidson diagonalization, coupled with multigrid methods, are used to accelerate convergence. RMG is a cross platform open source package which has been used in the study of a wide range of systems, including semiconductors, biomolecules, and nanoscale electronic devices. It can optionally use GPU accelerators to improve performance on systems where they are available. The recently released versions (>2.0) support multiple GPU's per compute node, have improved performance and scalability, enhanced accuracy and support for additional hardware platforms. New versions of the code are regularly released at http://www.rmgdft.org. The releases include binaries for Linux, Windows and MacIntosh systems, automated builds for clusters using cmake, as well as versions adapted to the major supercomputing installations and platforms. Several recent, large-scale applications of RMG will be discussed.

Open Biomedical Engineering education in Africa.

PubMed

Ahluwalia, Arti; Atwine, Daniel; De Maria, Carmelo; Ibingira, Charles; Kipkorir, Emmauel; Kiros, Fasil; Madete, June; Mazzei, Daniele; Molyneux, Elisabeth; Moonga, Kando; Moshi, Mainen; Nzomo, Martin; Oduol, Vitalice; Okuonzi, John

2015-08-01

Despite the virtual revolution, the mainstream academic community in most countries remains largely ignorant of the potential of web-based teaching resources and of the expansion of open source software, hardware and rapid prototyping. In the context of Biomedical Engineering (BME), where human safety and wellbeing is paramount, a high level of supervision and quality control is required before open source concepts can be embraced by universities and integrated into the curriculum. In the meantime, students, more than their teachers, have become attuned to continuous streams of digital information, and teaching methods need to adapt rapidly by giving them the skills to filter meaningful information and by supporting collaboration and co-construction of knowledge using open, cloud and crowd based technology. In this paper we present our experience in bringing these concepts to university education in Africa, as a way of enabling rapid development and self-sufficiency in health care. We describe the three summer schools held in sub-Saharan Africa where both students and teachers embraced the philosophy of open BME education with enthusiasm, and discuss the advantages and disadvantages of opening education in this way in the developing and developed world.

Creating a Clinical Video-Conferencing Facility in a Security-Constrained Environment Using Open-Source AccessGrid Software and Consumer Hardware

PubMed Central

Terrazas, Enrique; Hamill, Timothy R.; Wang, Ye; Channing Rodgers, R. P.

2007-01-01

The Department of Laboratory Medicine at the University of California, San Francisco (UCSF) has been split into widely separated facilities, leading to much time being spent traveling between facilities for meetings. We installed an open-source AccessGrid multi-media-conferencing system using (largely) consumer-grade equipment, connecting 6 sites at 5 separate facilities. The system was accepted rapidly and enthusiastically, and was inexpensive compared to alternative approaches. Security was addressed by aspects of the AG software and by local network administrative practices. The chief obstacles to deployment arose from security restrictions imposed by multiple independent network administration regimes, requiring a drastically reduced list of network ports employed by AG components. PMID:18693930

Three-dimensional printing physiology laboratory technology.

PubMed

Sulkin, Matthew S; Widder, Emily; Shao, Connie; Holzem, Katherine M; Gloschat, Christopher; Gutbrod, Sarah R; Efimov, Igor R

2013-12-01

Since its inception in 19th-century Germany, the physiology laboratory has been a complex and expensive research enterprise involving experts in various fields of science and engineering. Physiology research has been critically dependent on cutting-edge technological support of mechanical, electrical, optical, and more recently computer engineers. Evolution of modern experimental equipment is constrained by lack of direct communication between the physiological community and industry producing this equipment. Fortunately, recent advances in open source technologies, including three-dimensional printing, open source hardware and software, present an exciting opportunity to bring the design and development of research instrumentation to the end user, i.e., life scientists. Here we provide an overview on how to develop customized, cost-effective experimental equipment for physiology laboratories.

Creating a clinical video-conferencing facility in a security-constrained environment using open-source AccessGrid software and consumer hardware.

PubMed

Terrazas, Enrique; Hamill, Timothy R; Wang, Ye; Channing Rodgers, R P

2007-10-11

The Department of Laboratory Medicine at the University of California, San Francisco (UCSF) has been split into widely separated facilities, leading to much time being spent traveling between facilities for meetings. We installed an open-source AccessGrid multi-media-conferencing system using (largely) consumer-grade equipment, connecting 6 sites at 5 separate facilities. The system was accepted rapidly and enthusiastically, and was inexpensive compared to alternative approaches. Security was addressed by aspects of the AG software and by local network administrative practices. The chief obstacles to deployment arose from security restrictions imposed by multiple independent network administration regimes, requiring a drastically reduced list of network ports employed by AG components.

The Pixhawk Open-Source Computer Vision Framework for Mavs

NASA Astrophysics Data System (ADS)

Meier, L.; Tanskanen, P.; Fraundorfer, F.; Pollefeys, M.

2011-09-01

Unmanned aerial vehicles (UAV) and micro air vehicles (MAV) are already intensively used in geodetic applications. State of the art autonomous systems are however geared towards the application area in safe and obstacle-free altitudes greater than 30 meters. Applications at lower altitudes still require a human pilot. A new application field will be the reconstruction of structures and buildings, including the facades and roofs, with semi-autonomous MAVs. Ongoing research in the MAV robotics field is focusing on enabling this system class to operate at lower altitudes in proximity to nearby obstacles and humans. PIXHAWK is an open source and open hardware toolkit for this purpose. The quadrotor design is optimized for onboard computer vision and can connect up to four cameras to its onboard computer. The validity of the system design is shown with a fully autonomous capture flight along a building.

Cellular-enabled water quality measurements

NASA Astrophysics Data System (ADS)

Zhao, Y.; Kerkez, B.

2013-12-01

While the past decade has seen significant improvements in our ability to measure nutrients and other water quality parameters, the use of these sensors has yet to gain traction due to their costprohibitive nature and deployment expertise required on the part of researchers. Furthermore, an extra burden is incurred when real-time data access becomes an experimental requirement. We present an open-source hardware design to facilitate the real-time, low-cost, and robust measurements of water quality across large urbanized areas. Our hardware platform interfaces an embedded, vastly configurable, high-precision, ultra-low power measurement system, with a low-power cellular module. Each sensor station is configured with an IP address, permitting reliable streaming of sensor data to off-site locations as measurements are made. We discuss the role of high-quality hardware components during extreme event scenarios, and present preliminary performance metrics that validate the ability of the platform to provide streaming access to sensor measurements.

Arduino: a low-cost multipurpose lab equipment.

PubMed

D'Ausilio, Alessandro

2012-06-01

Typical experiments in psychological and neurophysiological settings often require the accurate control of multiple input and output signals. These signals are often generated or recorded via computer software and/or external dedicated hardware. Dedicated hardware is usually very expensive and requires additional software to control its behavior. In the present article, I present some accuracy tests on a low-cost and open-source I/O board (Arduino family) that may be useful in many lab environments. One of the strengths of Arduinos is the possibility they afford to load the experimental script on the board's memory and let it run without interfacing with computers or external software, thus granting complete independence, portability, and accuracy. Furthermore, a large community has arisen around the Arduino idea and offers many hardware add-ons and hundreds of free scripts for different projects. Accuracy tests show that Arduino boards may be an inexpensive tool for many psychological and neurophysiological labs.

Measuring the RC time constant with Arduino

NASA Astrophysics Data System (ADS)

Pereira, N. S. A.

2016-11-01

In this work we use the Arduino UNO R3 open source hardware platform to assemble an experimental apparatus for the measurement of the time constant of an RC circuit. With adequate programming, the Arduino is used as a signal generator, a data acquisition system and a basic signal visualisation tool. Theoretical calculations are compared with direct observations from an analogue oscilloscope. Data processing and curve fitting is performed on a spreadsheet. The results obtained for the six RC test circuits are within the expected interval of values defined by the tolerance of the components. The hardware and software prove to be adequate to the proposed measurements and therefore adaptable to a laboratorial teaching and learning context.

Advanced Shutter Control for a Molecular Beam Epitaxy Reactor

DTIC Science & Technology

An open-source hardware and software-based shutter controller solution was developed that communicates over Ethernet with our original equipment...manufacturer (OEM) molecular beam epitaxy (MBE) reactor control software. An Arduino Mega microcontroller is the used for the brain of the shutter... controller , while a custom-designed circuit board distributes 24-V power to each of the 16 shutter solenoids available on the MBE. Using Ethernet

SmartSIM - a virtual reality simulator for laparoscopy training using a generic physics engine.

PubMed

Khan, Zohaib Amjad; Kamal, Nabeel; Hameed, Asad; Mahmood, Amama; Zainab, Rida; Sadia, Bushra; Mansoor, Shamyl Bin; Hasan, Osman

2017-09-01

Virtual reality (VR) training simulators have started playing a vital role in enhancing surgical skills, such as hand-eye coordination in laparoscopy, and practicing surgical scenarios that cannot be easily created using physical models. We describe a new VR simulator for basic training in laparoscopy, i.e. SmartSIM, which has been developed using a generic open-source physics engine called the simulation open framework architecture (SOFA). This paper describes the systems perspective of SmartSIM including design details of both hardware and software components, while highlighting the critical design decisions. Some of the distinguishing features of SmartSIM include: (i) an easy-to-fabricate custom-built hardware interface; (ii) use of a generic physics engine to facilitate wider accessibility of our work and flexibility in terms of using various graphical modelling algorithms and their implementations; and (iii) an intelligent and smart evaluation mechanism that facilitates unsupervised and independent learning. Copyright © 2016 John Wiley & Sons, Ltd.

Waggle: A Framework for Intelligent Attentive Sensing and Actuation

NASA Astrophysics Data System (ADS)

Sankaran, R.; Jacob, R. L.; Beckman, P. H.; Catlett, C. E.; Keahey, K.

2014-12-01

Advances in sensor-driven computation and computationally steered sensing will greatly enable future research in fields including environmental and atmospheric sciences. We will present "Waggle," an open-source hardware and software infrastructure developed with two goals: (1) reducing the separation and latency between sensing and computing and (2) improving the reliability and longevity of sensing-actuation platforms in challenging and costly deployments. Inspired by "deep-space probe" systems, the Waggle platform design includes features that can support longitudinal studies, deployments with varying communication links, and remote management capabilities. Waggle lowers the barrier for scientists to incorporate real-time data from their sensors into their computations and to manipulate the sensors or provide feedback through actuators. A standardized software and hardware design allows quick addition of new sensors/actuators and associated software in the nodes and enables them to be coupled with computational codes both insitu and on external compute infrastructure. The Waggle framework currently drives the deployment of two observational systems - a portable and self-sufficient weather platform for study of small-scale effects in Chicago's urban core and an open-ended distributed instrument in Chicago that aims to support several research pursuits across a broad range of disciplines including urban planning, microbiology and computer science. Built around open-source software, hardware, and Linux OS, the Waggle system comprises two components - the Waggle field-node and Waggle cloud-computing infrastructure. Waggle field-node affords a modular, scalable, fault-tolerant, secure, and extensible platform for hosting sensors and actuators in the field. It supports insitu computation and data storage, and integration with cloud-computing infrastructure. The Waggle cloud infrastructure is designed with the goal of scaling to several hundreds of thousands of Waggle nodes. It supports aggregating data from sensors hosted by the nodes, staging computation, relaying feedback to the nodes and serving data to end-users. We will discuss the Waggle design principles and their applicability to various observational research pursuits, and demonstrate its capabilities.

Inexpensive, Low Power, Open-Source Data Logging hardware development

NASA Astrophysics Data System (ADS)

Sandell, C. T.; Schulz, B.; Wickert, A. D.

2017-12-01

Over the past six years, we have developed a suite of open-source, low-cost, and lightweight data loggers for scientific research. These loggers employ the popular and easy-to-use Arduino programming environment, but consist of custom hardware optimized for field research. They may be connected to a broad and expanding range of off-the-shelf sensors, with software support built in directly to the "ALog" library. Three main models exist: The ALog (for Autonomous or Arduino Logger) is the extreme low-power model for years-long deployments with only primary AA or D batteries. The ALog shield is a stripped-down ALog that nests with a standard Arduino board for prototyping or education. The TLog (for Telemetering Logger) contains an embedded radio with 500 m range and a GPS for communications and precision timekeeping. This enables meshed networks of loggers that can send their data back to an internet-connected "home base" logger for near-real-time field data retrieval. All boards feature feature a high-precision clock, full size SD card slot for high-volume data storage, large screw terminals to connect sensors, interrupts, SPI and I2C communication capability, and 3.3V/5V power outputs. The ALog and TLog have fourteen 16-bit analog inputs with a precision voltage reference for precise analog measurements. Their components are rated -40 to +85 degrees C, and they have been tested in harsh field conditions. These low-cost and open-source data loggers have enabled our research group to collect field data across North and South America on a limited budget, support student projects, and build toward better future scientific data systems.

Open Source High Content Analysis Utilizing Automated Fluorescence Lifetime Imaging Microscopy.

PubMed

Görlitz, Frederik; Kelly, Douglas J; Warren, Sean C; Alibhai, Dominic; West, Lucien; Kumar, Sunil; Alexandrov, Yuriy; Munro, Ian; Garcia, Edwin; McGinty, James; Talbot, Clifford; Serwa, Remigiusz A; Thinon, Emmanuelle; da Paola, Vincenzo; Murray, Edward J; Stuhmeier, Frank; Neil, Mark A A; Tate, Edward W; Dunsby, Christopher; French, Paul M W

2017-01-18

We present an open source high content analysis instrument utilizing automated fluorescence lifetime imaging (FLIM) for assaying protein interactions using Förster resonance energy transfer (FRET) based readouts of fixed or live cells in multiwell plates. This provides a means to screen for cell signaling processes read out using intramolecular FRET biosensors or intermolecular FRET of protein interactions such as oligomerization or heterodimerization, which can be used to identify binding partners. We describe here the functionality of this automated multiwell plate FLIM instrumentation and present exemplar data from our studies of HIV Gag protein oligomerization and a time course of a FRET biosensor in live cells. A detailed description of the practical implementation is then provided with reference to a list of hardware components and a description of the open source data acquisition software written in µManager. The application of FLIMfit, an open source MATLAB-based client for the OMERO platform, to analyze arrays of multiwell plate FLIM data is also presented. The protocols for imaging fixed and live cells are outlined and a demonstration of an automated multiwell plate FLIM experiment using cells expressing fluorescent protein-based FRET constructs is presented. This is complemented by a walk-through of the data analysis for this specific FLIM FRET data set.

Open Source High Content Analysis Utilizing Automated Fluorescence Lifetime Imaging Microscopy

PubMed Central

Warren, Sean C.; Alibhai, Dominic; West, Lucien; Kumar, Sunil; Alexandrov, Yuriy; Munro, Ian; Garcia, Edwin; McGinty, James; Talbot, Clifford; Serwa, Remigiusz A.; Thinon, Emmanuelle; da Paola, Vincenzo; Murray, Edward J.; Stuhmeier, Frank; Neil, Mark A. A.; Tate, Edward W.; Dunsby, Christopher; French, Paul M. W.

2017-01-01

We present an open source high content analysis instrument utilizing automated fluorescence lifetime imaging (FLIM) for assaying protein interactions using Förster resonance energy transfer (FRET) based readouts of fixed or live cells in multiwell plates. This provides a means to screen for cell signaling processes read out using intramolecular FRET biosensors or intermolecular FRET of protein interactions such as oligomerization or heterodimerization, which can be used to identify binding partners. We describe here the functionality of this automated multiwell plate FLIM instrumentation and present exemplar data from our studies of HIV Gag protein oligomerization and a time course of a FRET biosensor in live cells. A detailed description of the practical implementation is then provided with reference to a list of hardware components and a description of the open source data acquisition software written in µManager. The application of FLIMfit, an open source MATLAB-based client for the OMERO platform, to analyze arrays of multiwell plate FLIM data is also presented. The protocols for imaging fixed and live cells are outlined and a demonstration of an automated multiwell plate FLIM experiment using cells expressing fluorescent protein-based FRET constructs is presented. This is complemented by a walk-through of the data analysis for this specific FLIM FRET data set. PMID:28190060

4onse: four times open & non-conventional technology for sensing the environment

NASA Astrophysics Data System (ADS)

Cannata, Massimiliano; Ratnayake, Rangageewa; Antonovic, Milan; Strigaro, Daniele; Cardoso, Mirko; Hoffmann, Marcus

2017-04-01

The availability of complete, quality and dense monitoring hydro-meteorological data is essential to address a number of practical issues including, but not limited to, flood-water and urban drainage management, climate change impact assessment, early warning and risk management, now-casting and weather predictions. Thanks to the recent technological advances such as Internet Of Things, Big Data and Ubiquitous Internet, non-conventional monitoring systems based on open technologies and low cost sensors may represent a great opportunity either as a complement of authoritative monitoring network or as a vital source of information wherever existing monitoring networks are in decline or completely missing. Nevertheless, scientific literature on such a kind of open and non-conventional monitoring systems is still limited and often relates to prototype engineering and testing in rather limited case studies. For this reason the 4onse project aims at integrating existing open technologies in the field of Free & Open Source Software, Open Hardware, Open Data, and Open Standards and evaluate this kind of system in a real case (about 30 stations) for a medium period of 2 years to better scientifically understand strengths, criticalities and applicabilities in terms of data quality; system durability; management costs; performances; sustainability. The ultimate objective is to contribute in non-conventional monitoring systems adoption based on four open technologies.

MARVIN: a medical research application framework based on open source software.

PubMed

Rudolph, Tobias; Puls, Marc; Anderegg, Christoph; Ebert, Lars; Broehan, Martina; Rudin, Adrian; Kowal, Jens

2008-08-01

This paper describes the open source framework MARVIN for rapid application development in the field of biomedical and clinical research. MARVIN applications consist of modules that can be plugged together in order to provide the functionality required for a specific experimental scenario. Application modules work on a common patient database that is used to store and organize medical data as well as derived data. MARVIN provides a flexible input/output system with support for many file formats including DICOM, various 2D image formats and surface mesh data. Furthermore, it implements an advanced visualization system and interfaces to a wide range of 3D tracking hardware. Since it uses only highly portable libraries, MARVIN applications run on Unix/Linux, Mac OS X and Microsoft Windows.

Advanced capabilities for materials modelling with Quantum ESPRESSO

NASA Astrophysics Data System (ADS)

Giannozzi, P.; Andreussi, O.; Brumme, T.; Bunau, O.; Buongiorno Nardelli, M.; Calandra, M.; Car, R.; Cavazzoni, C.; Ceresoli, D.; Cococcioni, M.; Colonna, N.; Carnimeo, I.; Dal Corso, A.; de Gironcoli, S.; Delugas, P.; DiStasio, R. A., Jr.; Ferretti, A.; Floris, A.; Fratesi, G.; Fugallo, G.; Gebauer, R.; Gerstmann, U.; Giustino, F.; Gorni, T.; Jia, J.; Kawamura, M.; Ko, H.-Y.; Kokalj, A.; Küçükbenli, E.; Lazzeri, M.; Marsili, M.; Marzari, N.; Mauri, F.; Nguyen, N. L.; Nguyen, H.-V.; Otero-de-la-Roza, A.; Paulatto, L.; Poncé, S.; Rocca, D.; Sabatini, R.; Santra, B.; Schlipf, M.; Seitsonen, A. P.; Smogunov, A.; Timrov, I.; Thonhauser, T.; Umari, P.; Vast, N.; Wu, X.; Baroni, S.

2017-11-01

Quantum EXPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudopotential and projector-augmented-wave approaches. Quantum EXPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement their ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.

Advanced capabilities for materials modelling with Quantum ESPRESSO.

PubMed

Giannozzi, P; Andreussi, O; Brumme, T; Bunau, O; Buongiorno Nardelli, M; Calandra, M; Car, R; Cavazzoni, C; Ceresoli, D; Cococcioni, M; Colonna, N; Carnimeo, I; Dal Corso, A; de Gironcoli, S; Delugas, P; DiStasio, R A; Ferretti, A; Floris, A; Fratesi, G; Fugallo, G; Gebauer, R; Gerstmann, U; Giustino, F; Gorni, T; Jia, J; Kawamura, M; Ko, H-Y; Kokalj, A; Küçükbenli, E; Lazzeri, M; Marsili, M; Marzari, N; Mauri, F; Nguyen, N L; Nguyen, H-V; Otero-de-la-Roza, A; Paulatto, L; Poncé, S; Rocca, D; Sabatini, R; Santra, B; Schlipf, M; Seitsonen, A P; Smogunov, A; Timrov, I; Thonhauser, T; Umari, P; Vast, N; Wu, X; Baroni, S

2017-10-24

Quantum EXPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudopotential and projector-augmented-wave approaches. Quantum EXPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement their ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.

Advanced capabilities for materials modelling with Quantum ESPRESSO.

PubMed

Andreussi, Oliviero; Brumme, Thomas; Bunau, Oana; Buongiorno Nardelli, Marco; Calandra, Matteo; Car, Roberto; Cavazzoni, Carlo; Ceresoli, Davide; Cococcioni, Matteo; Colonna, Nicola; Carnimeo, Ivan; Dal Corso, Andrea; de Gironcoli, Stefano; Delugas, Pietro; DiStasio, Robert; Ferretti, Andrea; Floris, Andrea; Fratesi, Guido; Fugallo, Giorgia; Gebauer, Ralph; Gerstmann, Uwe; Giustino, Feliciano; Gorni, Tommaso; Jia, Junteng; Kawamura, Mitsuaki; Ko, Hsin-Yu; Kokalj, Anton; Küçükbenli, Emine; Lazzeri, Michele; Marsili, Margherita; Marzari, Nicola; Mauri, Francesco; Nguyen, Ngoc Linh; Nguyen, Huy-Viet; Otero-de-la-Roza, Alberto; Paulatto, Lorenzo; Poncé, Samuel; Giannozzi, Paolo; Rocca, Dario; Sabatini, Riccardo; Santra, Biswajit; Schlipf, Martin; Seitsonen, Ari Paavo; Smogunov, Alexander; Timrov, Iurii; Thonhauser, Timo; Umari, Paolo; Vast, Nathalie; Wu, Xifan; Baroni, Stefano

2017-09-27

Quantum ESPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudo-potential and projector-augmented-wave approaches. Quantum ESPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement theirs ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software. © 2017 IOP Publishing Ltd.

Closed-Loop, Multichannel Experimentation Using the Open-Source NeuroRighter Electrophysiology Platform

PubMed Central

Newman, Jonathan P.; Zeller-Townson, Riley; Fong, Ming-Fai; Arcot Desai, Sharanya; Gross, Robert E.; Potter, Steve M.

2013-01-01

Single neuron feedback control techniques, such as voltage clamp and dynamic clamp, have enabled numerous advances in our understanding of ion channels, electrochemical signaling, and neural dynamics. Although commercially available multichannel recording and stimulation systems are commonly used for studying neural processing at the network level, they provide little native support for real-time feedback. We developed the open-source NeuroRighter multichannel electrophysiology hardware and software platform for closed-loop multichannel control with a focus on accessibility and low cost. NeuroRighter allows 64 channels of stimulation and recording for around US $10,000, along with the ability to integrate with other software and hardware. Here, we present substantial enhancements to the NeuroRighter platform, including a redesigned desktop application, a new stimulation subsystem allowing arbitrary stimulation patterns, low-latency data servers for accessing data streams, and a new application programming interface (API) for creating closed-loop protocols that can be inserted into NeuroRighter as plugin programs. This greatly simplifies the design of sophisticated real-time experiments without sacrificing the power and speed of a compiled programming language. Here we present a detailed description of NeuroRighter as a stand-alone application, its plugin API, and an extensive set of case studies that highlight the system’s abilities for conducting closed-loop, multichannel interfacing experiments. PMID:23346047

Anser EMT: the first open-source electromagnetic tracking platform for image-guided interventions.

PubMed

Jaeger, Herman Alexander; Franz, Alfred Michael; O'Donoghue, Kilian; Seitel, Alexander; Trauzettel, Fabian; Maier-Hein, Lena; Cantillon-Murphy, Pádraig

2017-06-01

Electromagnetic tracking is the gold standard for instrument tracking and navigation in the clinical setting without line of sight. Whilst clinical platforms exist for interventional bronchoscopy and neurosurgical navigation, the limited flexibility and high costs of electromagnetic tracking (EMT) systems for research investigations mitigate against a better understanding of the technology's characterisation and limitations. The Anser project provides an open-source implementation for EMT with particular application to image-guided interventions. This work provides implementation schematics for our previously reported EMT system which relies on low-cost acquisition and demodulation techniques using both National Instruments and Arduino hardware alongside MATLAB support code. The system performance is objectively compared to other commercial tracking platforms using the Hummel assessment protocol. Positional accuracy of 1.14 mm and angular rotation accuracy of [Formula: see text] are reported. Like other EMT platforms, Anser is susceptible to tracking errors due to eddy current and ferromagnetic distortion. The system is compatible with commercially available EMT sensors as well as the Open Network Interface for image-guided therapy (OpenIGTLink) for easy communication with visualisation and medical imaging toolkits such as MITK and 3D Slicer. By providing an open-source platform for research investigations, we believe that novel and collaborative approaches can overcome the limitations of current EMT technology.

A ROSE-based OpenMP 3.0 Research Compiler Supporting Multiple Runtime Libraries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liao, C; Quinlan, D; Panas, T

2010-01-25

OpenMP is a popular and evolving programming model for shared-memory platforms. It relies on compilers for optimal performance and to target modern hardware architectures. A variety of extensible and robust research compilers are key to OpenMP's sustainable success in the future. In this paper, we present our efforts to build an OpenMP 3.0 research compiler for C, C++, and Fortran; using the ROSE source-to-source compiler framework. Our goal is to support OpenMP research for ourselves and others. We have extended ROSE's internal representation to handle all of the OpenMP 3.0 constructs and facilitate their manipulation. Since OpenMP research is oftenmore » complicated by the tight coupling of the compiler translations and the runtime system, we present a set of rules to define a common OpenMP runtime library (XOMP) on top of multiple runtime libraries. These rules additionally define how to build a set of translations targeting XOMP. Our work demonstrates how to reuse OpenMP translations across different runtime libraries. This work simplifies OpenMP research by decoupling the problematic dependence between the compiler translations and the runtime libraries. We present an evaluation of our work by demonstrating an analysis tool for OpenMP correctness. We also show how XOMP can be defined using both GOMP and Omni and present comparative performance results against other OpenMP compilers.« less

SEnviro: a sensorized platform proposal using open hardware and open standards.

PubMed

Trilles, Sergio; Luján, Alejandro; Belmonte, Óscar; Montoliu, Raúl; Torres-Sospedra, Joaquín; Huerta, Joaquín

2015-03-06

The need for constant monitoring of environmental conditions has produced an increase in the development of wireless sensor networks (WSN). The drive towards smart cities has produced the need for smart sensors to be able to monitor what is happening in our cities. This, combined with the decrease in hardware component prices and the increase in the popularity of open hardware, has favored the deployment of sensor networks based on open hardware. The new trends in Internet Protocol (IP) communication between sensor nodes allow sensor access via the Internet, turning them into smart objects (Internet of Things and Web of Things). Currently, WSNs provide data in different formats. There is a lack of communication protocol standardization, which turns into interoperability issues when connecting different sensor networks or even when connecting different sensor nodes within the same network. This work presents a sensorized platform proposal that adheres to the principles of the Internet of Things and theWeb of Things. Wireless sensor nodes were built using open hardware solutions, and communications rely on the HTTP/IP Internet protocols. The Open Geospatial Consortium (OGC) SensorThings API candidate standard was used as a neutral format to avoid interoperability issues. An environmental WSN developed following the proposed architecture was built as a proof of concept. Details on how to build each node and a study regarding energy concerns are presented.

SEnviro: A Sensorized Platform Proposal Using Open Hardware and Open Standards

PubMed Central

Trilles, Sergio; Luján, Alejandro; Belmonte, Óscar; Montoliu, Raúl; Torres-Sospedra, Joaquín; Huerta, Joaquín

2015-01-01

The need for constant monitoring of environmental conditions has produced an increase in the development of wireless sensor networks (WSN). The drive towards smart cities has produced the need for smart sensors to be able to monitor what is happening in our cities. This, combined with the decrease in hardware component prices and the increase in the popularity of open hardware, has favored the deployment of sensor networks based on open hardware. The new trends in Internet Protocol (IP) communication between sensor nodes allow sensor access via the Internet, turning them into smart objects (Internet of Things and Web of Things). Currently, WSNs provide data in different formats. There is a lack of communication protocol standardization, which turns into interoperability issues when connecting different sensor networks or even when connecting different sensor nodes within the same network. This work presents a sensorized platform proposal that adheres to the principles of the Internet of Things and the Web of Things. Wireless sensor nodes were built using open hardware solutions, and communications rely on the HTTP/IP Internet protocols. The Open Geospatial Consortium (OGC) SensorThings API candidate standard was used as a neutral format to avoid interoperability issues. An environmental WSN developed following the proposed architecture was built as a proof of concept. Details on how to build each node and a study regarding energy concerns are presented. PMID:25756864

ACQ4: an open-source software platform for data acquisition and analysis in neurophysiology research.

PubMed

Campagnola, Luke; Kratz, Megan B; Manis, Paul B

2014-01-01

The complexity of modern neurophysiology experiments requires specialized software to coordinate multiple acquisition devices and analyze the collected data. We have developed ACQ4, an open-source software platform for performing data acquisition and analysis in experimental neurophysiology. This software integrates the tasks of acquiring, managing, and analyzing experimental data. ACQ4 has been used primarily for standard patch-clamp electrophysiology, laser scanning photostimulation, multiphoton microscopy, intrinsic imaging, and calcium imaging. The system is highly modular, which facilitates the addition of new devices and functionality. The modules included with ACQ4 provide for rapid construction of acquisition protocols, live video display, and customizable analysis tools. Position-aware data collection allows automated construction of image mosaics and registration of images with 3-dimensional anatomical atlases. ACQ4 uses free and open-source tools including Python, NumPy/SciPy for numerical computation, PyQt for the user interface, and PyQtGraph for scientific graphics. Supported hardware includes cameras, patch clamp amplifiers, scanning mirrors, lasers, shutters, Pockels cells, motorized stages, and more. ACQ4 is available for download at http://www.acq4.org.

A Cloud-based, Open-Source, Command-and-Control Software Paradigm for Space Situational Awareness (SSA)

NASA Astrophysics Data System (ADS)

Melton, R.; Thomas, J.

With the rapid growth in the number of space actors, there has been a marked increase in the complexity and diversity of software systems utilized to support SSA target tracking, indication, warning, and collision avoidance. Historically, most SSA software has been constructed with "closed" proprietary code, which limits interoperability, inhibits the code transparency that some SSA customers need to develop domain expertise, and prevents the rapid injection of innovative concepts into these systems. Open-source aerospace software, a rapidly emerging, alternative trend in code development, is based on open collaboration, which has the potential to bring greater transparency, interoperability, flexibility, and reduced development costs. Open-source software is easily adaptable, geared to rapidly changing mission needs, and can generally be delivered at lower costs to meet mission requirements. This paper outlines Ball's COSMOS C2 system, a fully open-source, web-enabled, command-and-control software architecture which provides several unique capabilities to move the current legacy SSA software paradigm to an open source model that effectively enables pre- and post-launch asset command and control. Among the unique characteristics of COSMOS is the ease with which it can integrate with diverse hardware. This characteristic enables COSMOS to serve as the command-and-control platform for the full life-cycle development of SSA assets, from board test, to box test, to system integration and test, to on-orbit operations. The use of a modern scripting language, Ruby, also permits automated procedures to provide highly complex decision making for the tasking of SSA assets based on both telemetry data and data received from outside sources. Detailed logging enables quick anomaly detection and resolution. Integrated real-time and offline data graphing renders the visualization of the both ground and on-orbit assets simple and straightforward.

A novel low-cost open-hardware platform for monitoring soil water content and multiple soil-air-vegetation parameters.

PubMed

Bitella, Giovanni; Rossi, Roberta; Bochicchio, Rocco; Perniola, Michele; Amato, Mariana

2014-10-21

Monitoring soil water content at high spatio-temporal resolution and coupled to other sensor data is crucial for applications oriented towards water sustainability in agriculture, such as precision irrigation or phenotyping root traits for drought tolerance. The cost of instrumentation, however, limits measurement frequency and number of sensors. The objective of this work was to design a low cost "open hardware" platform for multi-sensor measurements including water content at different depths, air and soil temperatures. The system is based on an open-source ARDUINO microcontroller-board, programmed in a simple integrated development environment (IDE). Low cost high-frequency dielectric probes were used in the platform and lab tested on three non-saline soils (ECe1: 2.5 < 0.1 mS/cm). Empirical calibration curves were subjected to cross-validation (leave-one-out method), and normalized root mean square error (NRMSE) were respectively 0.09 for the overall model, 0.09 for the sandy soil, 0.07 for the clay loam and 0.08 for the sandy loam. The overall model (pooled soil data) fitted the data very well (R2 = 0.89) showing a high stability, being able to generate very similar RMSEs during training and validation (RMSE(training) = 2.63; RMSE(validation) = 2.61). Data recorded on the card were automatically sent to a remote server allowing repeated field-data quality checks. This work provides a framework for the replication and upgrading of a customized low cost platform, consistent with the open source approach whereby sharing information on equipment design and software facilitates the adoption and continuous improvement of existing technologies.

Quality Test of Flexible Flat Cable (FFC) With Short Open Test Using Law Ohm Approach through Embedded Fuzzy Logic Based On Open Source Arduino Data Logger

NASA Astrophysics Data System (ADS)

Rohmanu, Ajar; Everhard, Yan

2017-04-01

A technological development, especially in the field of electronics is very fast. One of the developments in the electronics hardware device is Flexible Flat Cable (FFC), which serves as a media liaison between the main boards with other hardware parts. The production of Flexible Flat Cable (FFC) will go through the process of testing and measuring of the quality Flexible Flat Cable (FFC). Currently, the testing and measurement is still done manually by observing the Light Emitting Diode (LED) by the operator, so there were many problems. This study will be made of test quality Flexible Flat Cable (FFC) computationally utilize Open Source Embedded System. The method used is the measurement with Short Open Test method using Ohm’s Law approach to 4-wire (Kelvin) and fuzzy logic as a decision maker measurement results based on Open Source Arduino Data Logger. This system uses a sensor current INA219 as a sensor to read the voltage value thus obtained resistance value Flexible Flat Cable (FFC). To get a good system we will do the Black-box testing as well as testing the accuracy and precision with the standard deviation method. In testing the system using three models samples were obtained the test results in the form of standard deviation for the first model of 1.921 second model of 4.567 and 6.300 for the third model. While the value of the Standard Error of Mean (SEM) for the first model of the model 0.304 second at 0.736 and 0.996 of the third model. In testing this system, we will also obtain the average value of the measurement tolerance resistance values for the first model of - 3.50% 4.45% second model and the third model of 5.18% with the standard measurement of prisoners and improve productivity becomes 118.33%. From the results of the testing system is expected to improve the quality and productivity in the process of testing Flexible Flat Cable (FFC).

3Dmol.js: molecular visualization with WebGL.

PubMed

Rego, Nicholas; Koes, David

2015-04-15

3Dmol.js is a modern, object-oriented JavaScript library that uses the latest web technologies to provide interactive, hardware-accelerated three-dimensional representations of molecular data without the need to install browser plugins or Java. 3Dmol.js provides a full featured API for developers as well as a straightforward declarative interface that lets users easily share and embed molecular data in websites. 3Dmol.js is distributed under the permissive BSD open source license. Source code and documentation can be found at http://3Dmol.csb.pitt.edu dkoes@pitt.edu. © The Author 2014. Published by Oxford University Press.

FormScanner: Open-Source Solution for Grading Multiple-Choice Exams

NASA Astrophysics Data System (ADS)

Young, Chadwick; Lo, Glenn; Young, Kaisa; Borsetta, Alberto

2016-01-01

The multiple-choice exam remains a staple for many introductory physics courses. In the past, people have graded these by hand or even flaming needles. Today, one usually grades the exams with a form scanner that utilizes optical mark recognition (OMR). Several companies provide these scanners and particular forms, such as the eponymous "Scantron." OMR scanners combine hardware and software—a scanner and OMR program—to read and grade student-filled forms.

Digital time stamping system based on open source technologies.

PubMed

Miskinis, Rimantas; Smirnov, Dmitrij; Urba, Emilis; Burokas, Andrius; Malysko, Bogdan; Laud, Peeter; Zuliani, Francesco

2010-03-01

A digital time stamping system based on open source technologies (LINUX-UBUNTU, OpenTSA, OpenSSL, MySQL) is described in detail, including all important testing results. The system, called BALTICTIME, was developed under a project sponsored by the European Commission under the Program FP 6. It was designed to meet the requirements posed to the systems of legal and accountable time stamping and to be applicable to the hardware commonly used by the national time metrology laboratories. The BALTICTIME system is intended for the use of governmental and other institutions as well as personal bodies. Testing results demonstrate that the time stamps issued to the user by BALTICTIME and saved in BALTICTIME's archives (which implies that the time stamps are accountable) meet all the regulatory requirements. Moreover, the BALTICTIME in its present implementation is able to issue more than 10 digital time stamps per second. The system can be enhanced if needed. The test version of the BALTICTIME service is free and available at http://baltictime. pfi.lt:8080/btws/ and http://baltictime.lnmc.lv:8080/btws/.

Vision Based Autonomous Robotic Control for Advanced Inspection and Repair

NASA Technical Reports Server (NTRS)

Wehner, Walter S.

2014-01-01

The advanced inspection system is an autonomous control and analysis system that improves the inspection and remediation operations for ground and surface systems. It uses optical imaging technology with intelligent computer vision algorithms to analyze physical features of the real-world environment to make decisions and learn from experience. The advanced inspection system plans to control a robotic manipulator arm, an unmanned ground vehicle and cameras remotely, automatically and autonomously. There are many computer vision, image processing and machine learning techniques available as open source for using vision as a sensory feedback in decision-making and autonomous robotic movement. My responsibilities for the advanced inspection system are to create a software architecture that integrates and provides a framework for all the different subsystem components; identify open-source algorithms and techniques; and integrate robot hardware.

PyGaze: an open-source, cross-platform toolbox for minimal-effort programming of eyetracking experiments.

PubMed

Dalmaijer, Edwin S; Mathôt, Sebastiaan; Van der Stigchel, Stefan

2014-12-01

The PyGaze toolbox is an open-source software package for Python, a high-level programming language. It is designed for creating eyetracking experiments in Python syntax with the least possible effort, and it offers programming ease and script readability without constraining functionality and flexibility. PyGaze can be used for visual and auditory stimulus presentation; for response collection via keyboard, mouse, joystick, and other external hardware; and for the online detection of eye movements using a custom algorithm. A wide range of eyetrackers of different brands (EyeLink, SMI, and Tobii systems) are supported. The novelty of PyGaze lies in providing an easy-to-use layer on top of the many different software libraries that are required for implementing eyetracking experiments. Essentially, PyGaze is a software bridge for eyetracking research.

CSNS computing environment Based on OpenStack

NASA Astrophysics Data System (ADS)

Li, Yakang; Qi, Fazhi; Chen, Gang; Wang, Yanming; Hong, Jianshu

2017-10-01

Cloud computing can allow for more flexible configuration of IT resources and optimized hardware utilization, it also can provide computing service according to the real need. We are applying this computing mode to the China Spallation Neutron Source(CSNS) computing environment. So, firstly, CSNS experiment and its computing scenarios and requirements are introduced in this paper. Secondly, the design and practice of cloud computing platform based on OpenStack are mainly demonstrated from the aspects of cloud computing system framework, network, storage and so on. Thirdly, some improvments to openstack we made are discussed further. Finally, current status of CSNS cloud computing environment are summarized in the ending of this paper.

Design of PI Controlled Non Isolated Bidirectional DC to DC Converter for Electric Vehicle Application

NASA Astrophysics Data System (ADS)

Geetha, A.; Subramani, C.; Thamizh Thentral, T. M.; Krithika, V.; Usha, S.

2018-04-01

Non isolated Bidirectional DC-DC Converter (NIBDDC) is a good interface between DC source and inverter Fed induction motor drive. This paper deals with comparison between open loop and PI controlled Bidirectional DC to DC Converter Inverter System (BDDCIS). The modelling and control of BDDC is becomes an important issue. Open loop BDDCIS and closed loop PI controlled BDDCIS are designed, modelled and simulated using Matlab- simulink and their results are presented. The investigations indicate superior performance of PI controlled BDDCIS. The proposed BDDCIS has advantages like bidirectional power transfer ability, reduced hardware count and improved dynamic response.

Open-WiSe: a solar powered wireless sensor network platform.

PubMed

González, Apolinar; Aquino, Raúl; Mata, Walter; Ochoa, Alberto; Saldaña, Pedro; Edwards, Arthur

2012-01-01

Because battery-powered nodes are required in wireless sensor networks and energy consumption represents an important design consideration, alternate energy sources are needed to provide more effective and optimal function. The main goal of this work is to present an energy harvesting wireless sensor network platform, the Open Wireless Sensor node (WiSe). The design and implementation of the solar powered wireless platform is described including the hardware architecture, firmware, and a POSIX Real-Time Kernel. A sleep and wake up strategy was implemented to prolong the lifetime of the wireless sensor network. This platform was developed as a tool for researchers investigating Wireless sensor network or system integrators.

PACS for Bhutan: a cost effective open source architecture for emerging countries.

PubMed

Ratib, Osman; Roduit, Nicolas; Nidup, Dechen; De Geer, Gerard; Rosset, Antoine; Geissbuhler, Antoine

2016-10-01

This paper reports the design and implementation of an innovative and cost-effective imaging management infrastructure suitable for radiology centres in emerging countries. It was implemented in the main referring hospital of Bhutan equipped with a CT, an MRI, digital radiology, and a suite of several ultrasound units. They lacked the necessary informatics infrastructure for image archiving and interpretation and needed a system for distribution of images to clinical wards. The solution developed for this project combines several open source software platforms in a robust and versatile archiving and communication system connected to analysis workstations equipped with a FDA-certified version of the highly popular Open-Source software. The whole system was implemented on standard off-the-shelf hardware. The system was installed in three days, and training of the radiologists as well as the technical and IT staff was provided onsite to ensure full ownership of the system by the local team. Radiologists were rapidly capable of reading and interpreting studies on the diagnostic workstations, which had a significant benefit on their workflow and ability to perform diagnostic tasks more efficiently. Furthermore, images were also made available to several clinical units on standard desktop computers through a web-based viewer. • Open source imaging informatics platforms can provide cost-effective alternatives for PACS • Robust and cost-effective open architecture can provide adequate solutions for emerging countries • Imaging informatics is often lacking in hospitals equipped with digital modalities.

Open-source point-of-care electronic medical records for use in resource-limited settings: systematic review and questionnaire surveys

PubMed Central

Bru, Juan; Berger, Christopher A

2012-01-01

Background Point-of-care electronic medical records (EMRs) are a key tool to manage chronic illness. Several EMRs have been developed for use in treating HIV and tuberculosis, but their applicability to primary care, technical requirements and clinical functionalities are largely unknown. Objectives This study aimed to address the needs of clinicians from resource-limited settings without reliable internet access who are considering adopting an open-source EMR. Study eligibility criteria Open-source point-of-care EMRs suitable for use in areas without reliable internet access. Study appraisal and synthesis methods The authors conducted a comprehensive search of all open-source EMRs suitable for sites without reliable internet access. The authors surveyed clinician users and technical implementers from a single site and technical developers of each software product. The authors evaluated availability, cost and technical requirements. Results The hardware and software for all six systems is easily available, but they vary considerably in proprietary components, installation requirements and customisability. Limitations This study relied solely on self-report from informants who developed and who actively use the included products. Conclusions and implications of key findings Clinical functionalities vary greatly among the systems, and none of the systems yet meet minimum requirements for effective implementation in a primary care resource-limited setting. The safe prescribing of medications is a particular concern with current tools. The dearth of fully functional EMR systems indicates a need for a greater emphasis by global funding agencies to move beyond disease-specific EMR systems and develop a universal open-source health informatics platform. PMID:22763661

Development of a low cost pupillometer-eyetracker and applications

NASA Astrophysics Data System (ADS)

Bianchetti, Arturo; Perez, Liliana I.; Comastri, Silvia A.

2013-11-01

The determination of ocular pupil diameter and gaze direction is important in various psychophysical and cognitive tests and can be accomplished using commercial, academic or open-source devices. In this work we develop a table-top pupillometer eyetracker termed Blick, the hardware costs 50 dollars and the software is open source (https://github.com/abianchetti/blick). The hardware is mounted in a portable holder and comprises an illumination system (two infrared LEDs generating 0.13 W/m2 at 22 cm) and a detection system (containing an USB camera, an infrared filter and a 16mm lens system) The software, programmed in C++ using OpenCV and cvblob libraries, processes eye images in real time and supplies plots and tables of pupil diameter and gaze direction and a video of the eye. As applications, capturing the right eye of six young emmetropes and after performing the pixel-mm and homographic calibrations (required to determine diameter in mm and gaze direction), we conduct three tests. The corresponding tasks are to detect mistakes in three series of four poker cards, to recognize letters F between distractors and to write a sentence via eye movements using Blick as eye tracker and the tool Dasher (MacKayśs Cambridge Group). We obtain that Blicḱs performance is satisfactory (errors being 0.05 mm in pupil diameter and 1 degree in gaze direction); that there are slight pupil dilations when subjects used to playing cards find mistakes and when some subjects find targets and, finally, that Blick can be employed as eyetracker to allow communication of disabled persons.

CATOS (Computer Aided Training/Observing System): Automating animal observation and training.

PubMed

Oh, Jinook; Fitch, W Tecumseh

2017-02-01

In animal behavioral biology, an automated observing/training system may be useful for several reasons: (a) continuous observation of animals for documentation of specific, irregular events, (b) long-term intensive training of animals in preparation for behavioral experiments, (c) elimination of potential cues and biases induced by humans during training and testing. Here, we describe an open-source-based system named CATOS (Computer Aided Training/Observing System) developed for such situations. There are several notable features in this system. CATOS is flexible and low cost because it is based on free open-source software libraries, common hardware parts, and open-system electronics based on Arduino. Automated video condensation is applied, leading to significantly reduced video data storage compared to the total active hours of the system. A data-viewing utility program helps a user browse recorded data quickly and more efficiently. With these features, CATOS has the potential to be applied to many different animal species in various environments such as laboratories, zoos, or even private homes. Also, an animal's free access to the device without constraint, and a gamified learning process, enhance the animal's welfare and enriches their environment. As a proof of concept, the system was built and tested with two different species. Initially, the system was tested for approximately 10 months with a domesticated cat. The cat was successfully and fully automatically trained to discriminate three different spoken words. Then, in order to test the system's adaptability to other species and hardware components, we used it to train a laboratory rat for 3 weeks.

Open-Source Assisted Laboratory Automation through Graphical User Interfaces and 3D Printers: Application to Equipment Hyphenation for Higher-Order Data Generation.

PubMed

Siano, Gabriel G; Montemurro, Milagros; Alcaráz, Mirta R; Goicoechea, Héctor C

2017-10-17

Higher-order data generation implies some automation challenges, which are mainly related to the hidden programming languages and electronic details of the equipment. When techniques and/or equipment hyphenation are the key to obtaining higher-order data, the required simultaneous control of them demands funds for new hardware, software, and licenses, in addition to very skilled operators. In this work, we present Design of Inputs-Outputs with Sikuli (DIOS), a free and open-source code program that provides a general framework for the design of automated experimental procedures without prior knowledge of programming or electronics. Basically, instruments and devices are considered as nodes in a network, and every node is associated both with physical and virtual inputs and outputs. Virtual components, such as graphical user interfaces (GUIs) of equipment, are handled by means of image recognition tools provided by Sikuli scripting language, while handling of their physical counterparts is achieved using an adapted open-source three-dimensional (3D) printer. Two previously reported experiments of our research group, related to fluorescence matrices derived from kinetics and high-performance liquid chromatography, were adapted to be carried out in a more automated fashion. Satisfactory results, in terms of analytical performance, were obtained. Similarly, advantages derived from open-source tools assistance could be appreciated, mainly in terms of lesser intervention of operators and cost savings.

A national upgrade of the climate monitoring grid in Sri Lanka. The place of Open Design, OSHW and FOSS.

NASA Astrophysics Data System (ADS)

Chemin, Yann; Bandara, Niroshan; Eriyagama, Nishadi

2015-04-01

The National Climate Observatory of Sri lanka is a proposition designed for the Government of Sri Lanka in September and discussed with private and public stakeholders in November 2014. The idea was initially to install a networked grid of weather instruments from locally-made open source hardware technology, on land and seas, that report live the state of climate. After initial stakeholder meetings, it was agreed to first try to connect any existing weather stations from different governmental and private sector agencies. This would bring existing information to a common ground through the Internet. At this point, it was realized that extracting information from various vendors set up would take a large amount of efforts, that is still the best and fastest anyway, as considerations from ownership and maintenance are the most important issues in a tropical humid country as Sri Lanka. Thus, the question of Open Design, open source hardware (OSHW) and free and open source software (FOSS) became a pivotal element in considering operationalization of any future elements of a national grid. Reasons range from ownership, to low-cost and customization, but prominently it is about technology ownership, royalty-free and local availability. Building on previous work from (Chemin and Bandara, 2014) we proposed to open design specifications and prototypes for weather monitoring for various kinds of needs, the Meteorological Department clearly specified that the highest variability observed spatially in Sri Lanka is rainfall, and their willingness to investigate OSHW electronics using their new team of electronics and sensors specialists. A local manufacturer is providing an OSHW micro-controller product, a start up is providing additional sensor boards under OSHW specifications and local manufacture of the sensors (tipping-bucket and other wind sensors) is under development and blueprints have been made available in the Public Domain for CNC machine, 3D printing or Plastic Molding. The Lanka Rainwater Harvesting Forum was in need of volumetric estimation of rainfall-runoff contributed to recharge of the aquifers. Regular reporting of high quality rainfall events and intensity is still a challenge to be addressed in Sri Lanka. A combination of OSHW and FOSS is being used to created a royalty-free, cheap raingauge design, with full control of on-board data collection and statistics. Development of an initial 15 raingauges include capacity-building, joint set up from the ground to scouting and installation, and full ownership of all aspects (hardware sourcing locally, software modification, communication troubleshooting, etc.). The Irrigation Department in Malwatu Oya had a requirement for real time rainfall information to manage reservoirs in cascade ("daisy chain") and mitigate flooding consequences downstream. 5 generic prototypes are now reporting to reservoir managers, and the reservoir management model is now rerun as often as needed to re-assess decision-requirements from any new rainfall about certain, already-known, dangerous intensity. The irrigation department capacity-building was provided in two trainings, one for engineers (decision-making support) and technicians (reporting and maintenance). Interest for further level of control in the system is low. Reporting online is following several potential routes, and an open design GPRS protocol is being developed, to simplify future weather stations design specifications in Sri Lanka.

Fluorescence Behavioral Imaging (FBI) Tracks Identity in Heterogeneous Groups of Drosophila

PubMed Central

Ramdya, Pavan; Schaffter, Thomas; Floreano, Dario; Benton, Richard

2012-01-01

Distinguishing subpopulations in group behavioral experiments can reveal the impact of differences in genetic, pharmacological and life-histories on social interactions and decision-making. Here we describe Fluorescence Behavioral Imaging (FBI), a toolkit that uses transgenic fluorescence to discriminate subpopulations, imaging hardware that simultaneously records behavior and fluorescence expression, and open-source software for automated, high-accuracy determination of genetic identity. Using FBI, we measure courtship partner choice in genetically mixed groups of Drosophila. PMID:23144871

Fluorescence behavioral imaging (FBI) tracks identity in heterogeneous groups of Drosophila.

PubMed

Ramdya, Pavan; Schaffter, Thomas; Floreano, Dario; Benton, Richard

2012-01-01

Distinguishing subpopulations in group behavioral experiments can reveal the impact of differences in genetic, pharmacological and life-histories on social interactions and decision-making. Here we describe Fluorescence Behavioral Imaging (FBI), a toolkit that uses transgenic fluorescence to discriminate subpopulations, imaging hardware that simultaneously records behavior and fluorescence expression, and open-source software for automated, high-accuracy determination of genetic identity. Using FBI, we measure courtship partner choice in genetically mixed groups of Drosophila.

Optical interferometer testbed

NASA Technical Reports Server (NTRS)

Blackwood, Gary H.

1991-01-01

Viewgraphs on optical interferometer testbed presented at the MIT Space Research Engineering Center 3rd Annual Symposium are included. Topics covered include: space-based optical interferometer; optical metrology; sensors and actuators; real time control hardware; controlled structures technology (CST) design methodology; identification for MIMO control; FEM/ID correlation for the naked truss; disturbance modeling; disturbance source implementation; structure design: passive damping; low authority control; active isolation of lightweight mirrors on flexible structures; open loop transfer function of mirror; and global/high authority control.

Cyber Defence in the Armed Forces of the Czech Republic

DTIC Science & Technology

2010-11-01

undesirable action backward discovery. This solution is based on special tools using NetFlow protocol. Active network elements or specialized hardware...probes attached to the backbone network using a tap can be the sources of NetFlow data. The principal advantage of NetFlow protocol is the fact that it...provides primary data in the open form, which can be easily utilized in the subsequent operations. The FlowMon Probe 4000 is mostly used NetFlow

Large-scale virtual screening on public cloud resources with Apache Spark.

PubMed

Capuccini, Marco; Ahmed, Laeeq; Schaal, Wesley; Laure, Erwin; Spjuth, Ola

2017-01-01

Structure-based virtual screening is an in-silico method to screen a target receptor against a virtual molecular library. Applying docking-based screening to large molecular libraries can be computationally expensive, however it constitutes a trivially parallelizable task. Most of the available parallel implementations are based on message passing interface, relying on low failure rate hardware and fast network connection. Google's MapReduce revolutionized large-scale analysis, enabling the processing of massive datasets on commodity hardware and cloud resources, providing transparent scalability and fault tolerance at the software level. Open source implementations of MapReduce include Apache Hadoop and the more recent Apache Spark. We developed a method to run existing docking-based screening software on distributed cloud resources, utilizing the MapReduce approach. We benchmarked our method, which is implemented in Apache Spark, docking a publicly available target receptor against [Formula: see text]2.2 M compounds. The performance experiments show a good parallel efficiency (87%) when running in a public cloud environment. Our method enables parallel Structure-based virtual screening on public cloud resources or commodity computer clusters. The degree of scalability that we achieve allows for trying out our method on relatively small libraries first and then to scale to larger libraries. Our implementation is named Spark-VS and it is freely available as open source from GitHub (https://github.com/mcapuccini/spark-vs).Graphical abstract.

Performance Evaluation of Block Acquisition and Tracking Algorithms Using an Open Source GPS Receiver Platform

NASA Technical Reports Server (NTRS)

Ramachandran, Ganesh K.; Akopian, David; Heckler, Gregory W.; Winternitz, Luke B.

2011-01-01

Location technologies have many applications in wireless communications, military and space missions, etc. US Global Positioning System (GPS) and other existing and emerging Global Navigation Satellite Systems (GNSS) are expected to provide accurate location information to enable such applications. While GNSS systems perform very well in strong signal conditions, their operation in many urban, indoor, and space applications is not robust or even impossible due to weak signals and strong distortions. The search for less costly, faster and more sensitive receivers is still in progress. As the research community addresses more and more complicated phenomena there exists a demand on flexible multimode reference receivers, associated SDKs, and development platforms which may accelerate and facilitate the research. One of such concepts is the software GPS/GNSS receiver (GPS SDR) which permits a facilitated access to algorithmic libraries and a possibility to integrate more advanced algorithms without hardware and essential software updates. The GNU-SDR and GPS-SDR open source receiver platforms are such popular examples. This paper evaluates the performance of recently proposed block-corelator techniques for acquisition and tracking of GPS signals using open source GPS-SDR platform.

ACQ4: an open-source software platform for data acquisition and analysis in neurophysiology research

PubMed Central

Campagnola, Luke; Kratz, Megan B.; Manis, Paul B.

2014-01-01

The complexity of modern neurophysiology experiments requires specialized software to coordinate multiple acquisition devices and analyze the collected data. We have developed ACQ4, an open-source software platform for performing data acquisition and analysis in experimental neurophysiology. This software integrates the tasks of acquiring, managing, and analyzing experimental data. ACQ4 has been used primarily for standard patch-clamp electrophysiology, laser scanning photostimulation, multiphoton microscopy, intrinsic imaging, and calcium imaging. The system is highly modular, which facilitates the addition of new devices and functionality. The modules included with ACQ4 provide for rapid construction of acquisition protocols, live video display, and customizable analysis tools. Position-aware data collection allows automated construction of image mosaics and registration of images with 3-dimensional anatomical atlases. ACQ4 uses free and open-source tools including Python, NumPy/SciPy for numerical computation, PyQt for the user interface, and PyQtGraph for scientific graphics. Supported hardware includes cameras, patch clamp amplifiers, scanning mirrors, lasers, shutters, Pockels cells, motorized stages, and more. ACQ4 is available for download at http://www.acq4.org. PMID:24523692

New virtual laboratories presenting advanced motion control concepts

NASA Astrophysics Data System (ADS)

Goubej, Martin; Krejčí, Alois; Reitinger, Jan

2015-11-01

The paper deals with development of software framework for rapid generation of remote virtual laboratories. Client-server architecture is chosen in order to employ real-time simulation core which is running on a dedicated server. Ordinary web browser is used as a final renderer to achieve hardware independent solution which can be run on different target platforms including laptops, tablets or mobile phones. The provided toolchain allows automatic generation of the virtual laboratory source code from the configuration file created in the open- source Inkscape graphic editor. Three virtual laboratories presenting advanced motion control algorithms have been developed showing the applicability of the proposed approach.

Pulseq: A rapid and hardware-independent pulse sequence prototyping framework.

PubMed

Layton, Kelvin J; Kroboth, Stefan; Jia, Feng; Littin, Sebastian; Yu, Huijun; Leupold, Jochen; Nielsen, Jon-Fredrik; Stöcker, Tony; Zaitsev, Maxim

2017-04-01

Implementing new magnetic resonance experiments, or sequences, often involves extensive programming on vendor-specific platforms, which can be time consuming and costly. This situation is exacerbated when research sequences need to be implemented on several platforms simultaneously, for example, at different field strengths. This work presents an alternative programming environment that is hardware-independent, open-source, and promotes rapid sequence prototyping. A novel file format is described to efficiently store the hardware events and timing information required for an MR pulse sequence. Platform-dependent interpreter modules convert the file to appropriate instructions to run the sequence on MR hardware. Sequences can be designed in high-level languages, such as MATLAB, or with a graphical interface. Spin physics simulation tools are incorporated into the framework, allowing for comparison between real and virtual experiments. Minimal effort is required to implement relatively advanced sequences using the tools provided. Sequences are executed on three different MR platforms, demonstrating the flexibility of the approach. A high-level, flexible and hardware-independent approach to sequence programming is ideal for the rapid development of new sequences. The framework is currently not suitable for large patient studies or routine scanning although this would be possible with deeper integration into existing workflows. Magn Reson Med 77:1544-1552, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

An inexpensive Arduino-based LED stimulator system for vision research.

PubMed

Teikari, Petteri; Najjar, Raymond P; Malkki, Hemi; Knoblauch, Kenneth; Dumortier, Dominique; Gronfier, Claude; Cooper, Howard M

2012-11-15

Light emitting diodes (LEDs) are being used increasingly as light sources in life sciences applications such as in vision research, fluorescence microscopy and in brain-computer interfacing. Here we present an inexpensive but effective visual stimulator based on light emitting diodes (LEDs) and open-source Arduino microcontroller prototyping platform. The main design goal of our system was to use off-the-shelf and open-source components as much as possible, and to reduce design complexity allowing use of the system to end-users without advanced electronics skills. The main core of the system is a USB-connected Arduino microcontroller platform designed initially with a specific emphasis on the ease-of-use creating interactive physical computing environments. The pulse-width modulation (PWM) signal of Arduino was used to drive LEDs allowing linear light intensity control. The visual stimulator was demonstrated in applications such as murine pupillometry, rodent models for cognitive research, and heterochromatic flicker photometry in human psychophysics. These examples illustrate some of the possible applications that can be easily implemented and that are advantageous for students, educational purposes and universities with limited resources. The LED stimulator system was developed as an open-source project. Software interface was developed using Python with simplified examples provided for Matlab and LabVIEW. Source code and hardware information are distributed under the GNU General Public Licence (GPL, version 3). Copyright © 2012 Elsevier B.V. All rights reserved.

FUX-Sim: Implementation of a fast universal simulation/reconstruction framework for X-ray systems.

PubMed

Abella, Monica; Serrano, Estefania; Garcia-Blas, Javier; García, Ines; de Molina, Claudia; Carretero, Jesus; Desco, Manuel

2017-01-01

The availability of digital X-ray detectors, together with advances in reconstruction algorithms, creates an opportunity for bringing 3D capabilities to conventional radiology systems. The downside is that reconstruction algorithms for non-standard acquisition protocols are generally based on iterative approaches that involve a high computational burden. The development of new flexible X-ray systems could benefit from computer simulations, which may enable performance to be checked before expensive real systems are implemented. The development of simulation/reconstruction algorithms in this context poses three main difficulties. First, the algorithms deal with large data volumes and are computationally expensive, thus leading to the need for hardware and software optimizations. Second, these optimizations are limited by the high flexibility required to explore new scanning geometries, including fully configurable positioning of source and detector elements. And third, the evolution of the various hardware setups increases the effort required for maintaining and adapting the implementations to current and future programming models. Previous works lack support for completely flexible geometries and/or compatibility with multiple programming models and platforms. In this paper, we present FUX-Sim, a novel X-ray simulation/reconstruction framework that was designed to be flexible and fast. Optimized implementation for different families of GPUs (CUDA and OpenCL) and multi-core CPUs was achieved thanks to a modularized approach based on a layered architecture and parallel implementation of the algorithms for both architectures. A detailed performance evaluation demonstrates that for different system configurations and hardware platforms, FUX-Sim maximizes performance with the CUDA programming model (5 times faster than other state-of-the-art implementations). Furthermore, the CPU and OpenCL programming models allow FUX-Sim to be executed over a wide range of hardware platforms.

Specifications and implementation of the RT MHD control system for the EC launcher of FTU

NASA Astrophysics Data System (ADS)

Galperti, C.; Alessi, E.; Boncagni, L.; Bruschi, A.; Granucci, G.; Grosso, A.; Iannone, F.; Marchetto, C.; Nowak, S.; Panella, M.; Sozzi, C.; Tilia, B.

2012-09-01

To perform real time plasma control experiments using EC heating waves by using the new fast launcher installed on FTU a dedicated data acquisition and elaboration system has been designed recently. A prototypical version of the acquisition/control system has been recently developed and will be tested on FTU machine in its next experimental campaign. The open-source framework MARTe (Multi-threaded Application Real-Time executor) on Linux/RTAI real-time operating system has been chosen as software platform to realize the control system. Standard open-architecture industrial PCs, based either on VME bus and CompactPCI bus equipped with standard input/output cards are the chosen hardware platform.

Open-WiSe: A Solar Powered Wireless Sensor Network Platform

PubMed Central

González, Apolinar; Aquino, Raúl; Mata, Walter; Ochoa, Alberto; Saldaña, Pedro; Edwards, Arthur

2012-01-01

Because battery-powered nodes are required in wireless sensor networks and energy consumption represents an important design consideration, alternate energy sources are needed to provide more effective and optimal function. The main goal of this work is to present an energy harvesting wireless sensor network platform, the Open Wireless Sensor node (WiSe). The design and implementation of the solar powered wireless platform is described including the hardware architecture, firmware, and a POSIX Real-Time Kernel. A sleep and wake up strategy was implemented to prolong the lifetime of the wireless sensor network. This platform was developed as a tool for researchers investigating Wireless sensor network or system integrators. PMID:22969396

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chamana, Manohar; Prabakar, Kumaraguru; Palmintier, Bryan

A software process is developed to convert distribution network models from a quasi-static time-series tool (OpenDSS) to a real-time dynamic phasor simulator (ePHASORSIM). The description of this process in this paper would be helpful for researchers who intend to perform similar conversions. The converter could be utilized directly by users of real-time simulators who intend to perform software-in-the-loop or hardware-in-the-loop tests on large distribution test feeders for a range of use cases, including testing functions of advanced distribution management systems against a simulated distribution system. In the future, the developers intend to release the conversion tool as open source tomore » enable use by others.« less

A freely available real-time operating system well suited for astronomy and the physical sciences

NASA Astrophysics Data System (ADS)

Pedretti, Ettore; Monnier, John D.; Thureau, Nathalie D.; Berger, David H.

2006-06-01

This paper wants to be a practical example in building a real-time data-acquisition and control system from scratch using relatively non-expensive PC hardware and open-source software. The practical example of building the control system for the Michigan Infrared Combiner (MIRC) at the CHARA interferometer will be used to give the reader a 'hands-on' experience in installing and configuring the RTAI-Fusion real-time operating system and developing a complete control system with it.

Real time wind farm emulation using SimWindFarm toolbox

NASA Astrophysics Data System (ADS)

Topor, Marcel

2016-06-01

This paper presents a wind farm emulation solution using an open source Matlab/Simulink toolbox and the National Instruments cRIO platform. This work is based on the Aeolus SimWindFarm (SWF) toolbox models developed at Aalborg university, Denmark. Using the Matlab Simulink models developed in SWF, the modeling code can be exported to a real time model using the NI Veristand model framework and the resulting code is integrated as a hardware in the loop control on the NI 9068 platform.

Analyzing huge pathology images with open source software.

PubMed

Deroulers, Christophe; Ameisen, David; Badoual, Mathilde; Gerin, Chloé; Granier, Alexandre; Lartaud, Marc

2013-06-06

Digital pathology images are increasingly used both for diagnosis and research, because slide scanners are nowadays broadly available and because the quantitative study of these images yields new insights in systems biology. However, such virtual slides build up a technical challenge since the images occupy often several gigabytes and cannot be fully opened in a computer's memory. Moreover, there is no standard format. Therefore, most common open source tools such as ImageJ fail at treating them, and the others require expensive hardware while still being prohibitively slow. We have developed several cross-platform open source software tools to overcome these limitations. The NDPITools provide a way to transform microscopy images initially in the loosely supported NDPI format into one or several standard TIFF files, and to create mosaics (division of huge images into small ones, with or without overlap) in various TIFF and JPEG formats. They can be driven through ImageJ plugins. The LargeTIFFTools achieve similar functionality for huge TIFF images which do not fit into RAM. We test the performance of these tools on several digital slides and compare them, when applicable, to standard software. A statistical study of the cells in a tissue sample from an oligodendroglioma was performed on an average laptop computer to demonstrate the efficiency of the tools. Our open source software enables dealing with huge images with standard software on average computers. They are cross-platform, independent of proprietary libraries and very modular, allowing them to be used in other open source projects. They have excellent performance in terms of execution speed and RAM requirements. They open promising perspectives both to the clinician who wants to study a single slide and to the research team or data centre who do image analysis of many slides on a computer cluster. The virtual slide(s) for this article can be found here:http://www.diagnosticpathology.diagnomx.eu/vs/5955513929846272.

Analyzing huge pathology images with open source software

PubMed Central

2013-01-01

Background Digital pathology images are increasingly used both for diagnosis and research, because slide scanners are nowadays broadly available and because the quantitative study of these images yields new insights in systems biology. However, such virtual slides build up a technical challenge since the images occupy often several gigabytes and cannot be fully opened in a computer’s memory. Moreover, there is no standard format. Therefore, most common open source tools such as ImageJ fail at treating them, and the others require expensive hardware while still being prohibitively slow. Results We have developed several cross-platform open source software tools to overcome these limitations. The NDPITools provide a way to transform microscopy images initially in the loosely supported NDPI format into one or several standard TIFF files, and to create mosaics (division of huge images into small ones, with or without overlap) in various TIFF and JPEG formats. They can be driven through ImageJ plugins. The LargeTIFFTools achieve similar functionality for huge TIFF images which do not fit into RAM. We test the performance of these tools on several digital slides and compare them, when applicable, to standard software. A statistical study of the cells in a tissue sample from an oligodendroglioma was performed on an average laptop computer to demonstrate the efficiency of the tools. Conclusions Our open source software enables dealing with huge images with standard software on average computers. They are cross-platform, independent of proprietary libraries and very modular, allowing them to be used in other open source projects. They have excellent performance in terms of execution speed and RAM requirements. They open promising perspectives both to the clinician who wants to study a single slide and to the research team or data centre who do image analysis of many slides on a computer cluster. Virtual slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/5955513929846272 PMID:23829479

Architecture and Implementation of OpenPET Firmware and Embedded Software

PubMed Central

Abu-Nimeh, Faisal T.; Ito, Jennifer; Moses, William W.; Peng, Qiyu; Choong, Woon-Seng

2016-01-01

OpenPET is an open source, modular, extendible, and high-performance platform suitable for multi-channel data acquisition and analysis. Due to the flexibility of the hardware, firmware, and software architectures, the platform is capable of interfacing with a wide variety of detector modules not only in medical imaging but also in homeland security applications. Analog signals from radiation detectors share similar characteristics – a pulse whose area is proportional to the deposited energy and whose leading edge is used to extract a timing signal. As a result, a generic design method of the platform is adopted for the hardware, firmware, and software architectures and implementations. The analog front-end is hosted on a module called a Detector Board, where each board can filter, combine, timestamp, and process multiple channels independently. The processed data is formatted and sent through a backplane bus to a module called Support Board, where 1 Support Board can host up to eight Detector Board modules. The data in the Support Board, coming from 8 Detector Board modules, can be aggregated or correlated (if needed) depending on the algorithm implemented or runtime mode selected. It is then sent out to a computer workstation for further processing. The number of channels (detector modules), to be processed, mandates the overall OpenPET System Configuration, which is designed to handle up to 1,024 channels using 16-channel Detector Boards in the Standard System Configuration and 16,384 channels using 32-channel Detector Boards in the Large System Configuration. PMID:27110034

MVO Automation Platform: Addressing Unmet Needs in Clinical Laboratories with Microcontrollers, 3D Printing, and Open-Source Hardware/Software.

PubMed

Iglehart, Brian

2018-05-01

Laboratory automation improves test reproducibility, which is vital to patient care in clinical laboratories. Many small and specialty laboratories are excluded from the benefits of automation due to low sample number, cost, space, and/or lack of automation expertise. The Minimum Viable Option (MVO) automation platform was developed to address these hurdles and fulfill an unmet need. Consumer 3D printing enabled rapid iterative prototyping to allow for a variety of instrumentation and assay setups and procedures. Three MVO versions have been produced. MVOv1.1 successfully performed part of a clinical assay, and results were comparable to those of commercial automation. Raspberry Pi 3 Model B (RPI3) single-board computers with Sense Hardware Attached on Top (HAT) and Raspberry Pi Camera Module V2 hardware were remotely accessed and evaluated for their suitability to qualify the latest MVOv1.2 platform. Sense HAT temperature, barometric pressure, and relative humidity sensors were stable in climate-controlled environments and are useful in identifying appropriate laboratory spaces for automation placement. The RPI3 with camera plus digital dial indicator logged axis travel experiments. RPI3 with camera and Sense HAT as a light source showed promise when used for photometric dispensing tests. Individual well standard curves were necessary for well-to-well light and path length compensations.

BigDataScript: a scripting language for data pipelines.

PubMed

Cingolani, Pablo; Sladek, Rob; Blanchette, Mathieu

2015-01-01

The analysis of large biological datasets often requires complex processing pipelines that run for a long time on large computational infrastructures. We designed and implemented a simple script-like programming language with a clean and minimalist syntax to develop and manage pipeline execution and provide robustness to various types of software and hardware failures as well as portability. We introduce the BigDataScript (BDS) programming language for data processing pipelines, which improves abstraction from hardware resources and assists with robustness. Hardware abstraction allows BDS pipelines to run without modification on a wide range of computer architectures, from a small laptop to multi-core servers, server farms, clusters and clouds. BDS achieves robustness by incorporating the concepts of absolute serialization and lazy processing, thus allowing pipelines to recover from errors. By abstracting pipeline concepts at programming language level, BDS simplifies implementation, execution and management of complex bioinformatics pipelines, resulting in reduced development and debugging cycles as well as cleaner code. BigDataScript is available under open-source license at http://pcingola.github.io/BigDataScript. © The Author 2014. Published by Oxford University Press.

Proof of concept of an artificial muscle: theoretical model, numerical model, and hardware experiment.

PubMed

Haeufle, D F B; Günther, M; Blickhan, R; Schmitt, S

2011-01-01

Recently, the hyperbolic Hill-type force-velocity relation was derived from basic physical components. It was shown that a contractile element CE consisting of a mechanical energy source (active element AE), a parallel damper element (PDE), and a serial element (SE) exhibits operating points with hyperbolic force-velocity dependency. In this paper, the contraction dynamics of this CE concept were analyzed in a numerical simulation of quick release experiments against different loads. A hyperbolic force-velocity relation was found. The results correspond to measurements of the contraction dynamics of a technical prototype. Deviations from the theoretical prediction could partly be explained by the low stiffness of the SE, which was modeled analog to the metal spring in the hardware prototype. The numerical model and hardware prototype together, are a proof of this CE concept and can be seen as a well-founded starting point for the development of Hill-type artificial muscles. This opens up new vistas for the technical realization of natural movements with rehabilitation devices. © 2011 IEEE

BigDataScript: a scripting language for data pipelines

PubMed Central

Cingolani, Pablo; Sladek, Rob; Blanchette, Mathieu

2015-01-01

Motivation: The analysis of large biological datasets often requires complex processing pipelines that run for a long time on large computational infrastructures. We designed and implemented a simple script-like programming language with a clean and minimalist syntax to develop and manage pipeline execution and provide robustness to various types of software and hardware failures as well as portability. Results: We introduce the BigDataScript (BDS) programming language for data processing pipelines, which improves abstraction from hardware resources and assists with robustness. Hardware abstraction allows BDS pipelines to run without modification on a wide range of computer architectures, from a small laptop to multi-core servers, server farms, clusters and clouds. BDS achieves robustness by incorporating the concepts of absolute serialization and lazy processing, thus allowing pipelines to recover from errors. By abstracting pipeline concepts at programming language level, BDS simplifies implementation, execution and management of complex bioinformatics pipelines, resulting in reduced development and debugging cycles as well as cleaner code. Availability and implementation: BigDataScript is available under open-source license at http://pcingola.github.io/BigDataScript. Contact: pablo.e.cingolani@gmail.com PMID:25189778

Hard real-time closed-loop electrophysiology with the Real-Time eXperiment Interface (RTXI)

PubMed Central

George, Ansel; Dorval, Alan D.; Christini, David J.

2017-01-01

The ability to experimentally perturb biological systems has traditionally been limited to static pre-programmed or operator-controlled protocols. In contrast, real-time control allows dynamic probing of biological systems with perturbations that are computed on-the-fly during experimentation. Real-time control applications for biological research are available; however, these systems are costly and often restrict the flexibility and customization of experimental protocols. The Real-Time eXperiment Interface (RTXI) is an open source software platform for achieving hard real-time data acquisition and closed-loop control in biological experiments while retaining the flexibility needed for experimental settings. RTXI has enabled users to implement complex custom closed-loop protocols in single cell, cell network, animal, and human electrophysiology studies. RTXI is also used as a free and open source, customizable electrophysiology platform in open-loop studies requiring online data acquisition, processing, and visualization. RTXI is easy to install, can be used with an extensive range of external experimentation and data acquisition hardware, and includes standard modules for implementing common electrophysiology protocols. PMID:28557998

OSG-GEM: Gene Expression Matrix Construction Using the Open Science Grid.

PubMed

Poehlman, William L; Rynge, Mats; Branton, Chris; Balamurugan, D; Feltus, Frank A

2016-01-01

High-throughput DNA sequencing technology has revolutionized the study of gene expression while introducing significant computational challenges for biologists. These computational challenges include access to sufficient computer hardware and functional data processing workflows. Both these challenges are addressed with our scalable, open-source Pegasus workflow for processing high-throughput DNA sequence datasets into a gene expression matrix (GEM) using computational resources available to U.S.-based researchers on the Open Science Grid (OSG). We describe the usage of the workflow (OSG-GEM), discuss workflow design, inspect performance data, and assess accuracy in mapping paired-end sequencing reads to a reference genome. A target OSG-GEM user is proficient with the Linux command line and possesses basic bioinformatics experience. The user may run this workflow directly on the OSG or adapt it to novel computing environments.

OSG-GEM: Gene Expression Matrix Construction Using the Open Science Grid

PubMed Central

Poehlman, William L.; Rynge, Mats; Branton, Chris; Balamurugan, D.; Feltus, Frank A.

2016-01-01

High-throughput DNA sequencing technology has revolutionized the study of gene expression while introducing significant computational challenges for biologists. These computational challenges include access to sufficient computer hardware and functional data processing workflows. Both these challenges are addressed with our scalable, open-source Pegasus workflow for processing high-throughput DNA sequence datasets into a gene expression matrix (GEM) using computational resources available to U.S.-based researchers on the Open Science Grid (OSG). We describe the usage of the workflow (OSG-GEM), discuss workflow design, inspect performance data, and assess accuracy in mapping paired-end sequencing reads to a reference genome. A target OSG-GEM user is proficient with the Linux command line and possesses basic bioinformatics experience. The user may run this workflow directly on the OSG or adapt it to novel computing environments. PMID:27499617

HPC Programming on Intel Many-Integrated-Core Hardware with MAGMA Port to Xeon Phi

DOE PAGES

Dongarra, Jack; Gates, Mark; Haidar, Azzam; ...

2015-01-01

This paper presents the design and implementation of several fundamental dense linear algebra (DLA) algorithms for multicore with Intel Xeon Phi coprocessors. In particular, we consider algorithms for solving linear systems. Further, we give an overview of the MAGMA MIC library, an open source, high performance library, that incorporates the developments presented here and, more broadly, provides the DLA functionality equivalent to that of the popular LAPACK library while targeting heterogeneous architectures that feature a mix of multicore CPUs and coprocessors. The LAPACK-compliance simplifies the use of the MAGMA MIC library in applications, while providing them with portably performant DLA.more » High performance is obtained through the use of the high-performance BLAS, hardware-specific tuning, and a hybridization methodology whereby we split the algorithm into computational tasks of various granularities. Execution of those tasks is properly scheduled over the heterogeneous hardware by minimizing data movements and mapping algorithmic requirements to the architectural strengths of the various heterogeneous hardware components. Our methodology and programming techniques are incorporated into the MAGMA MIC API, which abstracts the application developer from the specifics of the Xeon Phi architecture and is therefore applicable to algorithms beyond the scope of DLA.« less

Openstage: A Low-Cost Motorized Microscope Stage with Sub-Micron Positioning Accuracy

PubMed Central

Campbell, Robert A. A.; Eifert, Robert W.; Turner, Glenn C.

2014-01-01

Recent progress in intracellular calcium sensors and other fluorophores has promoted the widespread adoption of functional optical imaging in the life sciences. Home-built multiphoton microscopes are easy to build, highly customizable, and cost effective. For many imaging applications a 3-axis motorized stage is critical, but commercially available motorization hardware (motorized translators, controller boxes, etc) are often very expensive. Furthermore, the firmware on commercial motor controllers cannot easily be altered and is not usually designed with a microscope stage in mind. Here we describe an open-source motorization solution that is simple to construct, yet far cheaper and more customizable than commercial offerings. The cost of the controller and motorization hardware are under $1000. Hardware costs are kept low by replacing linear actuators with high quality stepper motors. Electronics are assembled from commonly available hobby components, which are easy to work with. Here we describe assembly of the system and quantify the positioning accuracy of all three axes. We obtain positioning repeatability of the order of in X/Y and in Z. A hand-held control-pad allows the user to direct stage motion precisely over a wide range of speeds ( to ), rapidly store and return to different locations, and execute “jumps” of a fixed size. In addition, the system can be controlled from a PC serial port. Our “OpenStage” controller is sufficiently flexible that it could be used to drive other devices, such as micro-manipulators, with minimal modifications. PMID:24586468

Integrating new Storage Technologies into EOS

NASA Astrophysics Data System (ADS)

Peters, Andreas J.; van der Ster, Dan C.; Rocha, Joaquim; Lensing, Paul

2015-12-01

The EOS[1] storage software was designed to cover CERN disk-only storage use cases in the medium-term trading scalability against latency. To cover and prepare for long-term requirements the CERN IT data and storage services group (DSS) is actively conducting R&D and open source contributions to experiment with a next generation storage software based on CEPH[3] and ethernet enabled disk drives. CEPH provides a scale-out object storage system RADOS and additionally various optional high-level services like S3 gateway, RADOS block devices and a POSIX compliant file system CephFS. The acquisition of CEPH by Redhat underlines the promising role of CEPH as the open source storage platform of the future. CERN IT is running a CEPH service in the context of OpenStack on a moderate scale of 1 PB replicated storage. Building a 100+PB storage system based on CEPH will require software and hardware tuning. It is of capital importance to demonstrate the feasibility and possibly iron out bottlenecks and blocking issues beforehand. The main idea behind this R&D is to leverage and contribute to existing building blocks in the CEPH storage stack and implement a few CERN specific requirements in a thin, customisable storage layer. A second research topic is the integration of ethernet enabled disks. This paper introduces various ongoing open source developments, their status and applicability.

Real-time control using open source RTOS

NASA Astrophysics Data System (ADS)

Irwin, Philip C.; Johnson, Richard L., Jr.

2002-12-01

Complex telescope systems such as interferometers tend to rely heavily on hard real-time operating systems (RTOS). It has been standard practice at NASA's Jet Propulsion Laboratory (JPL) and many other institutions to use costly commercial RTOSs and hardware. After developing a real-time toolkit for VxWorks on the PowerPC platform (dubbed RTC), the interferometry group at JPL is porting this code to the real-time Application Interface (RTAI), an open source RTOS that is essentially an extension to the Linux kernel. This port has the potential to reduce software and hardware costs for future projects, while increasing the level of performance. The goals of this paper are to briefly describe the RTC toolkit, highlight the successes and pitfalls of porting the toolkit from VxWorks to Linux-RTAI, and to discuss future enhancements that will be implemented as a direct result of this port. The first port of any body of code is always the most difficult since it uncovers the OS-specific calls and forces "red flags" into those portions of the code. For this reason, It has also been a huge benefit that the project chose a generic, platform independent OS extension, ACE, and its CORBA counterpart, TAO. This port of RTC will pave the way for conversions to other environments, the most interesting of which is a non-real-time simulation environment, currently being considered by the Space Interferometry Mission (SIM) and the Terrestrial Planet Finder (TPF) Projects.

A novel design for sap flux data acquisition in large research plots using open source components

NASA Astrophysics Data System (ADS)

Hawthorne, D. A.; Oishi, A. C.

2017-12-01

Sap flux sensors are a widely-used tool for estimating in-situ, tree-level transpiration rates. These probes are installed in the stems of multiple trees within a study area and are typically left in place throughout the year. Sensors vary in their design and theory of operation, but all require electrical power for a heating element and produce at least one analog signal that must be digitized for storage. There are two topologies traditionally adopted to energize these sensors and gather the data from them. In one, a single data logger and power source are used. Dedicated cables radiate out from the logger to supply power to each of the probes and retrieve analog signals. In the other layout, a standalone data logger is located at each monitored tree. Batteries must then be distributed throughout the plot to service these loggers. We present a hybrid solution based on industrial control systems that employs a central data logger and battery, but co-locates digitizing hardware with the sensors at each tree. Each hardware node is able to communicate and share power over wire links with neighboring nodes. The resulting network provides a fault-tolerant path between the logger and each sensor. The approach is optimized to limit disturbance of the study plot, protect signal integrity and to enhance system reliability. This open-source implementation is built on the Arduino micro-controller system and employs RS485 and Modbus communications protocols. It is supported by laptop based management software coded in Python. The system is designed to be readily fabricated and programmed by non-experts. It works with a variety of sap-flux measurement techniques and it is able to interface to additional environmental sensors.

OpenSQUID: A Flexible Open-Source Software Framework for the Control of SQUID Electronics

DOE PAGES

Jaeckel, Felix T.; Lafler, Randy J.; Boyd, S. T. P.

2013-02-06

We report commercially available computer-controlled SQUID electronics are usually delivered with software providing a basic user interface for adjustment of SQUID tuning parameters, such as bias current, flux offset, and feedback loop settings. However, in a research context it would often be useful to be able to modify this code and/or to have full control over all these parameters from researcher-written software. In the case of the STAR Cryoelectronics PCI/PFL family of SQUID control electronics, the supplied software contains modules for automatic tuning and noise characterization, but does not provide an interface for user code. On the other hand, themore » Magnicon SQUIDViewer software package includes a public application programming interface (API), but lacks auto-tuning and noise characterization features. To overcome these and other limitations, we are developing an "open-source" framework for controlling SQUID electronics which should provide maximal interoperability with user software, a unified user interface for electronics from different manufacturers, and a flexible platform for the rapid development of customized SQUID auto-tuning and other advanced features. Finally, we have completed a first implementation for the STAR Cryoelectronics hardware and have made the source code for this ongoing project available to the research community on SourceForge (http://opensquid.sourceforge.net) under the GNU public license.« less

An open-source wireless sensor stack: from Arduino to SDI-12 to Water One Flow

NASA Astrophysics Data System (ADS)

Hicks, S.; Damiano, S. G.; Smith, K. M.; Olexy, J.; Horsburgh, J. S.; Mayorga, E.; Aufdenkampe, A. K.

2013-12-01

Implementing a large-scale streaming environmental sensor network has previously been limited by the high cost of the datalogging and data communication infrastructure. The Christina River Basin Critical Zone Observatory (CRB-CZO) is overcoming the obstacles to large near-real-time data collection networks by using Arduino, an open source electronics platform, in combination with XBee ZigBee wireless radio modules. These extremely low-cost and easy-to-use open source electronics are at the heart of the new DIY movement and have provided solutions to countless projects by over half a million users worldwide. However, their use in environmental sensing is in its infancy. At present a primary limitation to widespread deployment of open-source electronics for environmental sensing is the lack of a simple, open-source software stack to manage streaming data from heterogeneous sensor networks. Here we present a functioning prototype software stack that receives sensor data over a self-meshing ZigBee wireless network from over a hundred sensors, stores the data locally and serves it on demand as a CUAHSI Water One Flow (WOF) web service. We highlight a few new, innovative components, including: (1) a versatile open data logger design based the Arduino electronics platform and ZigBee radios; (2) a software library implementing SDI-12 communication protocol between any Arduino platform and SDI12-enabled sensors without the need for additional hardware (https://github.com/StroudCenter/Arduino-SDI-12); and (3) 'midStream', a light-weight set of Python code that receives streaming sensor data, appends it with metadata on the fly by querying a relational database structured on an early version of the Observations Data Model version 2.0 (ODM2), and uses the WOFpy library to serve the data as WaterML via SOAP and REST web services.

Open Source 3D Multipurpose Measurement System with Submillimetre Fidelity and First Application in Magnetic Resonance.

PubMed

Han, Haopeng; Moritz, Raphael; Oberacker, Eva; Waiczies, Helmar; Niendorf, Thoralf; Winter, Lukas

2017-10-18

Magnetic resonance imaging (MRI) is the mainstay of diagnostic imaging, a versatile instrument for clinical science and the subject of intense research interest. Advancing clinical science, research and technology of MRI requires high fidelity measurements in quantity, location and time of the given physical property. To meet this goal a broad spectrum of commercial measurement systems has been made available. These instruments frequently share in common that they are costly and typically employ closed proprietary hardware and software. This shortcoming makes any adjustment for a specified application difficult if not prohibitive. Recognizing this limitation this work presents COSI Measure, an automated open source measurement system that provides submillimetre resolution, robust configuration and a large working volume to support a versatile range of applications. The submillimetre fidelity and reproducibility/backlash performance were evaluated experimentally. Magnetic field mapping of a single ring Halbach magnet, a 3.0 T and a 7.0 T MR scanner as well as temperature mapping of a radio frequency coil were successfully conducted. Due to its open source nature and versatile construction, the system can be easily modified for other applications. In a resource limited research setting, COSI Measure makes efficient use of laboratory space, financial resources and collaborative efforts.

GNSS CORS hardware and software enabling new science

NASA Astrophysics Data System (ADS)

Drummond, P.

2009-12-01

GNSS CORS networks are enabling new opportunities for science and public and private sector business. This paper will explore how the newest geodetic monitoring software and GNSS receiver hardware from Trimble Navigation Ltd are enabling new science. Technology trends and science opportunities will be explored. These trends include the installation of active GNSS control, automation of observations and processing, and the advantages of multi-observable and multi-constellation observations, all performed with the use of off the shelf products and industry standard open-source data formats. Also the possibilities with moving science from an after-the-fact postprocessed model to a real-time epoch-by-epoch solution will be explored. This presentation will also discuss the combination of existing GNSS CORS networks with project specific installations used for monitoring. Experience is showing GNSS is able to provide higher resolution data than previous methods, providing new tools for science, decision makers and financial planners.

An open ecosystem engagement strategy through the lens of global food safety

PubMed Central

Stacey, Paul; Fons, Garin; Bernardo, Theresa M

2015-01-01

The Global Food Safety Partnership (GFSP) is a public/private partnership established through the World Bank to improve food safety systems through a globally coordinated and locally-driven approach. This concept paper aims to establish a framework to help GFSP fully leverage the potential of open models. In preparing this paper the authors spoke to many different GFSP stakeholders who asked questions about open models such as: what is it?what’s in it for me?why use an open rather than a proprietary model?how will open models generate equivalent or greater sustainable revenue streams compared to the current “traditional” approaches?  This last question came up many times with assertions that traditional service providers need to see opportunity for equivalent or greater revenue dollars before they will buy-in. This paper identifies open value propositions for GFSP stakeholders and proposes a framework for creating and structuring that value. Open Educational Resources (OER) were the primary open practice GFSP partners spoke to us about, as they provide a logical entry point for collaboration. Going forward, funders should consider requiring that educational resources and concomitant data resulting from their sponsorship should be open, as a public good. There are, however, many other forms of open practice that bring value to the GFSP. Nine different open strategies and tactics (Appendix A) are described, including: open content (including OER and open courseware), open data, open access (research), open government, open source software, open standards, open policy, open licensing and open hardware. It is recommended that all stakeholders proactively pursue "openness" as an operating principle. This paper presents an overall GFSP Open Ecosystem Engagement Strategy within which specific local case examples can be situated. Two different case examples, China and Colombia, are presented to show both project-based and crowd-sourced, direct-to-public paths through this ecosystem. PMID:26213614

OpenSoC Fabric

DOE Office of Scientific and Technical Information (OSTI.GOV)

2014-08-21

Recent advancements in technology scaling have shown a trend towards greater integration with large-scale chips containing thousands of processors connected to memories and other I/O devices using non-trivial network topologies. Software simulation proves insufficient to study the tradeoffs in such complex systems due to slow execution time, whereas hardware RTL development is too time-consuming. We present OpenSoC Fabric, an on-chip network generation infrastructure which aims to provide a parameterizable and powerful on-chip network generator for evaluating future high performance computing architectures based on SoC technology. OpenSoC Fabric leverages a new hardware DSL, Chisel, which contains powerful abstractions provided by itsmore » base language, Scala, and generates both software (C++) and hardware (Verilog) models from a single code base. The OpenSoC Fabric2 infrastructure is modeled after existing state-of-the-art simulators, offers large and powerful collections of configuration options, and follows object-oriented design and functional programming to make functionality extension as easy as possible.« less

Demonstration of Supervisory Control and Data Acquisition (SCADA) Virtualization Capability in the US Army Research Laboratory (ARL)/Sustaining Base Network Assurance Branch (SBNAB) US Army Cyber Analytics Laboratory (ACAL) SCADA Hardware Testbed

DTIC Science & Technology

2015-05-01

application ,1 while the simulated PLC software is the open source ModbusPal Java application . When queried using the Modbus TCP protocol, ModbusPal reports...and programmable logic controller ( PLC ) components. The HMI and PLC components were instantiated with software and installed in multiple virtual...creating and capturing HMI– PLC network traffic over a 24-h period in the virtualized network and inspect the packets for errors.  Test the

Architecture and Implementation of OpenPET Firmware and Embedded Software

DOE PAGES

Abu-Nimeh, Faisal T.; Ito, Jennifer; Moses, William W.; ...

2016-01-11

OpenPET is an open source, modular, extendible, and high-performance platform suitable for multi-channel data acquisition and analysis. Due to the versatility of the hardware, firmware, and software architectures, the platform is capable of interfacing with a wide variety of detector modules not only in medical imaging but also in homeland security applications. Analog signals from radiation detectors share similar characteristics-a pulse whose area is proportional to the deposited energy and whose leading edge is used to extract a timing signal. As a result, a generic design method of the platform is adopted for the hardware, firmware, and software architectures andmore » implementations. The analog front-end is hosted on a module called a Detector Board, where each board can filter, combine, timestamp, and process multiple channels independently. The processed data is formatted and sent through a backplane bus to a module called Support Board, where 1 Support Board can host up to eight Detector Board modules. The data in the Support Board, coming from 8 Detector Board modules, can be aggregated or correlated (if needed) depending on the algorithm implemented or runtime mode selected. It is then sent out to a computer workstation for further processing. The number of channels (detector modules), to be processed, mandates the overall OpenPET System Configuration, which is designed to handle up to 1,024 channels using 16-channel Detector Boards in the Standard System Configuration and 16,384 channels using 32-channel Detector Boards in the Large System Configuration.« less

Low Cost, Scalable Proteomics Data Analysis Using Amazon's Cloud Computing Services and Open Source Search Algorithms

PubMed Central

Halligan, Brian D.; Geiger, Joey F.; Vallejos, Andrew K.; Greene, Andrew S.; Twigger, Simon N.

2009-01-01

One of the major difficulties for many laboratories setting up proteomics programs has been obtaining and maintaining the computational infrastructure required for the analysis of the large flow of proteomics data. We describe a system that combines distributed cloud computing and open source software to allow laboratories to set up scalable virtual proteomics analysis clusters without the investment in computational hardware or software licensing fees. Additionally, the pricing structure of distributed computing providers, such as Amazon Web Services, allows laboratories or even individuals to have large-scale computational resources at their disposal at a very low cost per run. We provide detailed step by step instructions on how to implement the virtual proteomics analysis clusters as well as a list of current available preconfigured Amazon machine images containing the OMSSA and X!Tandem search algorithms and sequence databases on the Medical College of Wisconsin Proteomics Center website (http://proteomics.mcw.edu/vipdac). PMID:19358578

Low cost, scalable proteomics data analysis using Amazon's cloud computing services and open source search algorithms.

PubMed

Halligan, Brian D; Geiger, Joey F; Vallejos, Andrew K; Greene, Andrew S; Twigger, Simon N

2009-06-01

One of the major difficulties for many laboratories setting up proteomics programs has been obtaining and maintaining the computational infrastructure required for the analysis of the large flow of proteomics data. We describe a system that combines distributed cloud computing and open source software to allow laboratories to set up scalable virtual proteomics analysis clusters without the investment in computational hardware or software licensing fees. Additionally, the pricing structure of distributed computing providers, such as Amazon Web Services, allows laboratories or even individuals to have large-scale computational resources at their disposal at a very low cost per run. We provide detailed step-by-step instructions on how to implement the virtual proteomics analysis clusters as well as a list of current available preconfigured Amazon machine images containing the OMSSA and X!Tandem search algorithms and sequence databases on the Medical College of Wisconsin Proteomics Center Web site ( http://proteomics.mcw.edu/vipdac ).

SWARM: A Compact High Resolution Correlator and Wideband VLBI Phased Array Upgrade for SMA

NASA Astrophysics Data System (ADS)

Weintroub, Jonathan

2014-06-01

A new digital back end (DBE) is being commissioned on Mauna Kea. The “SMA Wideband Astronomical ROACH2 Machine”, or SWARM, processes a 4 GHz usable band in single polarization mode and is flexibly reconfigurable for 2 GHz full Stokes dual polarization. The hardware is based on the open source Reconfigurable Open Architecture Computing Hardware 2 (ROACH2) platform from the Collaboration for Astronomy Signal Processing and Electronics Research (CASPER). A 5 GSps quad-core analog-to-digital converter board uses a commercial chip from e2v installed on a CASPER-standard printed circuit board designed by Homin Jiang’s group at ASIAA. Two ADC channels are provided per ROACH2, each sampling a 2.3 GHz Nyquist band generated by a custom wideband block downconverter (BDC). The ROACH2 logic includes 16k-channel Polyphase Filterbank (F-engine) per input followed by a 10 GbE switch based corner-turn which feeds into correlator-accumulator logic (X-engines) co-located with the F-engines. This arrangement makes very effective use of a small amount of digital hardware (just 8 ROACH2s in 1U rack mount enclosures). The primary challenge now is to meet timing at full speed for a large and very complex FPGA bit code. Design of the VLBI phased sum and recorder interface logic is also in process. Our poster will describe the instrument design, with the focus on the particular challenges of ultra wideband signal processing. Early connected commissioning and science verification data will be presented.

Psynteract: A flexible, cross-platform, open framework for interactive experiments.

PubMed

Henninger, Felix; Kieslich, Pascal J; Hilbig, Benjamin E

2017-10-01

We introduce a novel platform for interactive studies, that is, any form of study in which participants' experiences depend not only on their own responses, but also on those of other participants who complete the same study in parallel, for example a prisoner's dilemma or an ultimatum game. The software thus especially serves the rapidly growing field of strategic interaction research within psychology and behavioral economics. In contrast to all available software packages, our platform does not handle stimulus display and response collection itself. Instead, we provide a mechanism to extend existing experimental software to incorporate interactive functionality. This approach allows us to draw upon the capabilities already available, such as accuracy of temporal measurement, integration with auxiliary hardware such as eye-trackers or (neuro-)physiological apparatus, and recent advances in experimental software, for example capturing response dynamics through mouse-tracking. Through integration with OpenSesame, an open-source graphical experiment builder, studies can be assembled via a drag-and-drop interface requiring little or no further programming skills. In addition, by using the same communication mechanism across software packages, we also enable interoperability between systems. Our source code, which provides support for all major operating systems and several popular experimental packages, can be freely used and distributed under an open source license. The communication protocols underlying its functionality are also well documented and easily adapted to further platforms. Code and documentation are available at https://github.com/psynteract/ .

Exploring Infiniband Hardware Virtualization in OpenNebula towards Efficient High-Performance Computing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pais Pitta de Lacerda Ruivo, Tiago; Bernabeu Altayo, Gerard; Garzoglio, Gabriele

2014-11-11

has been widely accepted that software virtualization has a big negative impact on high-performance computing (HPC) application performance. This work explores the potential use of Infiniband hardware virtualization in an OpenNebula cloud towards the efficient support of MPI-based workloads. We have implemented, deployed, and tested an Infiniband network on the FermiCloud private Infrastructure-as-a-Service (IaaS) cloud. To avoid software virtualization towards minimizing the virtualization overhead, we employed a technique called Single Root Input/Output Virtualization (SRIOV). Our solution spanned modifications to the Linux’s Hypervisor as well as the OpenNebula manager. We evaluated the performance of the hardware virtualization on up to 56more » virtual machines connected by up to 8 DDR Infiniband network links, with micro-benchmarks (latency and bandwidth) as well as w a MPI-intensive application (the HPL Linpack benchmark).« less

Surgeon Training in Telerobotic Surgery via a Hardware-in-the-Loop Simulator

PubMed Central

Alemzadeh, Homa; Chen, Daniel; Kalbarczyk, Zbigniew; Iyer, Ravishankar K.; Kesavadas, Thenkurussi

2017-01-01

This work presents a software and hardware framework for a telerobotic surgery safety and motor skill training simulator. The aims are at providing trainees a comprehensive simulator for acquiring essential skills to perform telerobotic surgery. Existing commercial robotic surgery simulators lack features for safety training and optimal motion planning, which are critical factors in ensuring patient safety and efficiency in operation. In this work, we propose a hardware-in-the-loop simulator directly introducing these two features. The proposed simulator is built upon the Raven-II™ open source surgical robot, integrated with a physics engine and a safety hazard injection engine. Also, a Fast Marching Tree-based motion planning algorithm is used to help trainee learn the optimal instrument motion patterns. The main contributions of this work are (1) reproducing safety hazards events, related to da Vinci™ system, reported to the FDA MAUDE database, with a novel haptic feedback strategy to provide feedback to the operator when the underlying dynamics differ from the real robot's states so that the operator will be aware and can mitigate the negative impact of the safety-critical events, and (2) using motion planner to generate semioptimal path in an interactive robotic surgery training environment. PMID:29065635

Mousetrap: An integrated, open-source mouse-tracking package.

PubMed

Kieslich, Pascal J; Henninger, Felix

2017-10-01

Mouse-tracking - the analysis of mouse movements in computerized experiments - is becoming increasingly popular in the cognitive sciences. Mouse movements are taken as an indicator of commitment to or conflict between choice options during the decision process. Using mouse-tracking, researchers have gained insight into the temporal development of cognitive processes across a growing number of psychological domains. In the current article, we present software that offers easy and convenient means of recording and analyzing mouse movements in computerized laboratory experiments. In particular, we introduce and demonstrate the mousetrap plugin that adds mouse-tracking to OpenSesame, a popular general-purpose graphical experiment builder. By integrating with this existing experimental software, mousetrap allows for the creation of mouse-tracking studies through a graphical interface, without requiring programming skills. Thus, researchers can benefit from the core features of a validated software package and the many extensions available for it (e.g., the integration with auxiliary hardware such as eye-tracking, or the support of interactive experiments). In addition, the recorded data can be imported directly into the statistical programming language R using the mousetrap package, which greatly facilitates analysis. Mousetrap is cross-platform, open-source and available free of charge from https://github.com/pascalkieslich/mousetrap-os .

Software solution for autonomous observations with H2RG detectors and SIDECAR ASICs for the RATIR camera

NASA Astrophysics Data System (ADS)

Klein, Christopher R.; Kubánek, Petr; Butler, Nathaniel R.; Fox, Ori D.; Kutyrev, Alexander S.; Rapchun, David A.; Bloom, Joshua S.; Farah, Alejandro; Gehrels, Neil; Georgiev, Leonid; González, J. Jesús; Lee, William H.; Lotkin, Gennadiy N.; Moseley, Samuel H.; Prochaska, J. Xavier; Ramirez-Ruiz, Enrico; Richer, Michael G.; Robinson, Frederick D.; Román-Zúñiga, Carlos; Samuel, Mathew V.; Sparr, Leroy M.; Tucker, Corey; Watson, Alan M.

2012-07-01

The Reionization And Transients InfraRed (RATIR) camera has been built for rapid Gamma-Ray Burst (GRB) followup and will provide quasi-simultaneous imaging in ugriZY JH. The optical component uses two 2048 × 2048 pixel Finger Lakes Imaging ProLine detectors, one optimized for the SDSS u, g, and r bands and one optimized for the SDSS i band. The infrared portion incorporates two 2048 × 2048 pixel Teledyne HgCdTe HAWAII-2RG detectors, one with a 1.7-micron cutoff and one with a 2.5-micron cutoff. The infrared detectors are controlled by Teledyne's SIDECAR (System for Image Digitization Enhancement Control And Retrieval) ASICs (Application Specific Integrated Circuits). While other ground-based systems have used the SIDECAR before, this system also utilizes Teledyne's JADE2 (JWST ASIC Drive Electronics) interface card and IDE (Integrated Development Environment). Here we present a summary of the software developed to interface the RATIR detectors with Remote Telescope System, 2nd Version (RTS2) software. RTS2 is an integrated open source package for remote observatory control under the Linux operating system and will autonomously coordinate observatory dome, telescope pointing, detector, filter wheel, focus stage, and dewar vacuum compressor operations. Where necessary we have developed custom interfaces between RTS2 and RATIR hardware, most notably for cryogenic focus stage motor drivers and temperature controllers. All detector and hardware interface software developed for RATIR is freely available and open source as part of the RTS2 distribution.

Conversion and Validation of Distribution System Model from a QSTS-Based Tool to a Real-Time Dynamic Phasor Simulator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chamana, Manohar; Prabakar, Kumaraguru; Palmintier, Bryan

A software process is developed to convert distribution network models from a quasi-static time-series tool (OpenDSS) to a real-time dynamic phasor simulator (ePHASORSIM). The description of this process in this paper would be helpful for researchers who intend to perform similar conversions. The converter could be utilized directly by users of real-time simulators who intend to perform software-in-the-loop or hardware-in-the-loop tests on large distribution test feeders for a range of use cases, including testing functions of advanced distribution management systems against a simulated distribution system. In the future, the developers intend to release the conversion tool as open source tomore » enable use by others.« less

Conversion and Validation of Distribution System Model from a QSTS-Based Tool to a Real-Time Dynamic Phasor Simulator: Preprint

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chamana, Manohar; Prabakar, Kumaraguru; Palmintier, Bryan

A software process is developed to convert distribution network models from a quasi-static time-series tool (OpenDSS) to a real-time dynamic phasor simulator (ePHASORSIM). The description of this process in this paper would be helpful for researchers who intend to perform similar conversions. The converter could be utilized directly by users of real-time simulators who intend to perform software-in-the-loop or hardware-in-the-loop tests on large distribution test feeders for a range of use cases, including testing functions of advanced distribution management systems against a simulated distribution system. In the future, the developers intend to release the conversion tool as open source tomore » enable use by others.« less

Novel algorithm implementations in DARC: the Durham AO real-time controller

NASA Astrophysics Data System (ADS)

Basden, Alastair; Bitenc, Urban; Jenkins, David

2016-07-01

The Durham AO Real-time Controller has been used on-sky with the CANARY AO demonstrator instrument since 2010, and is also used to provide control for several AO test-benches, including DRAGON. Over this period, many new real-time algorithms have been developed, implemented and demonstrated, leading to performance improvements for CANARY. Additionally, the computational performance of this real-time system has continued to improve. Here, we provide details about recent updates and changes made to DARC, and the relevance of these updates, including new algorithms, to forthcoming AO systems. We present the computational performance of DARC when used on different hardware platforms, including hardware accelerators, and determine the relevance and potential for ELT scale systems. Recent updates to DARC have included algorithms to handle elongated laser guide star images, including correlation wavefront sensing, with options to automatically update references during AO loop operation. Additionally, sub-aperture masking options have been developed to increase signal to noise ratio when operating with non-symmetrical wavefront sensor images. The development of end-user tools has progressed with new options for configuration and control of the system. New wavefront sensor camera models and DM models have been integrated with the system, increasing the number of possible hardware configurations available, and a fully open-source AO system is now a reality, including drivers necessary for commercial cameras and DMs. The computational performance of DARC makes it suitable for ELT scale systems when implemented on suitable hardware. We present tests made on different hardware platforms, along with the strategies taken to optimise DARC for these systems.

Advantages and Disadvantages in Image Processing with Free Software in Radiology.

PubMed

Mujika, Katrin Muradas; Méndez, Juan Antonio Juanes; de Miguel, Andrés Framiñan

2018-01-15

Currently, there are sophisticated applications that make it possible to visualize medical images and even to manipulate them. These software applications are of great interest, both from a teaching and a radiological perspective. In addition, some of these applications are known as Free Open Source Software because they are free and the source code is freely available, and therefore it can be easily obtained even on personal computers. Two examples of free open source software are Osirix Lite® and 3D Slicer®. However, this last group of free applications have limitations in its use. For the radiological field, manipulating and post-processing images is increasingly important. Consequently, sophisticated computing tools that combine software and hardware to process medical images are needed. In radiology, graphic workstations allow their users to process, review, analyse, communicate and exchange multidimensional digital images acquired with different image-capturing radiological devices. These radiological devices are basically CT (Computerised Tomography), MRI (Magnetic Resonance Imaging), PET (Positron Emission Tomography), etc. Nevertheless, the programs included in these workstations have a high cost which always depends on the software provider and is always subject to its norms and requirements. With this study, we aim to present the advantages and disadvantages of these radiological image visualization systems in the advanced management of radiological studies. We will compare the features of the VITREA2® and AW VolumeShare 5® radiology workstation with free open source software applications like OsiriX® and 3D Slicer®, with examples from specific studies.

Hardware Removal in Craniomaxillofacial Trauma

PubMed Central

Cahill, Thomas J.; Gandhi, Rikesh; Allori, Alexander C.; Marcus, Jeffrey R.; Powers, David; Erdmann, Detlev; Hollenbeck, Scott T.; Levinson, Howard

2015-01-01

Background Craniomaxillofacial (CMF) fractures are typically treated with open reduction and internal fixation. Open reduction and internal fixation can be complicated by hardware exposure or infection. The literature often does not differentiate between these 2 entities; so for this study, we have considered all hardware exposures as hardware infections. Approximately 5% of adults with CMF trauma are thought to develop hardware infections. Management consists of either removing the hardware versus leaving it in situ. The optimal approach has not been investigated. Thus, a systematic review of the literature was undertaken and a resultant evidence-based approach to the treatment and management of CMF hardware infections was devised. Materials and Methods A comprehensive search of journal articles was performed in parallel using MEDLINE, Web of Science, and ScienceDirect electronic databases. Keywords and phrases used were maxillofacial injuries; facial bones; wounds and injuries; fracture fixation, internal; wound infection; and infection. Our search yielded 529 articles. To focus on CMF fractures with hardware infections, the full text of English-language articles was reviewed to identify articles focusing on the evaluation and management of infected hardware in CMF trauma. Each article’s reference list was manually reviewed and citation analysis performed to identify articles missed by the search strategy. There were 259 articles that met the full inclusion criteria and form the basis of this systematic review. The articles were rated based on the level of evidence. There were 81 grade II articles included in the meta-analysis. Result Our meta-analysis revealed that 7503 patients were treated with hardware for CMF fractures in the 81 grade II articles. Hardware infection occurred in 510 (6.8%) of these patients. Of those infections, hardware removal occurred in 264 (51.8%) patients; hardware was left in place in 166 (32.6%) patients; and in 80 (15.6%) cases, there was no report as to hardware management. Finally, our review revealed that there were no reported differences in outcomes between groups. Conclusions Management of CMF hardware infections should be performed in a sequential and consistent manner to optimize outcome. An evidence-based algorithm for management of CMF hardware infections based on this critical review of the literature is presented and discussed. PMID:25393499

Creating an open environment software infrastructure

NASA Technical Reports Server (NTRS)

Jipping, Michael J.

1992-01-01

As the development of complex computer hardware accelerates at increasing rates, the ability of software to keep pace is essential. The development of software design tools, however, is falling behind the development of hardware for several reasons, the most prominent of which is the lack of a software infrastructure to provide an integrated environment for all parts of a software system. The research was undertaken to provide a basis for answering this problem by investigating the requirements of open environments.

OpenControl: a free opensource software for video tracking and automated control of behavioral mazes.

PubMed

Aguiar, Paulo; Mendonça, Luís; Galhardo, Vasco

2007-10-15

Operant animal behavioral tests require the interaction of the subject with sensors and actuators distributed in the experimental environment of the arena. In order to provide user independent reliable results and versatile control of these devices it is vital to use an automated control system. Commercial systems for control of animal mazes are usually based in software implementations that restrict their application to the proprietary hardware of the vendor. In this paper we present OpenControl: an opensource Visual Basic software that permits a Windows-based computer to function as a system to run fully automated behavioral experiments. OpenControl integrates video-tracking of the animal, definition of zones from the video signal for real-time assignment of animal position in the maze, control of the maze actuators from either hardware sensors or from the online video tracking, and recording of experimental data. Bidirectional communication with the maze hardware is achieved through the parallel-port interface, without the need for expensive AD-DA cards, while video tracking is attained using an inexpensive Firewire digital camera. OpenControl Visual Basic code is structurally general and versatile allowing it to be easily modified or extended to fulfill specific experimental protocols and custom hardware configurations. The Visual Basic environment was chosen in order to allow experimenters to easily adapt the code and expand it at their own needs.

Use of Open Standards and Technologies at the Lunar Mapping and Modeling Project

NASA Astrophysics Data System (ADS)

Law, E.; Malhotra, S.; Bui, B.; Chang, G.; Goodale, C. E.; Ramirez, P.; Kim, R. M.; Sadaqathulla, S.; Rodriguez, L.

2011-12-01

The Lunar Mapping and Modeling Project (LMMP), led by the Marshall Space Flight center (MSFC), is tasked by NASA. The project is responsible for the development of an information system to support lunar exploration activities. It provides lunar explorers a set of tools and lunar map and model products that are predominantly derived from present lunar missions (e.g., the Lunar Reconnaissance Orbiter (LRO)) and from historical missions (e.g., Apollo). At Jet Propulsion Laboratory (JPL), we have built the LMMP interoperable geospatial information system's underlying infrastructure and a single point of entry - the LMMP Portal by employing a number of open standards and technologies. The Portal exposes a set of services to users to allow search, visualization, subset, and download of lunar data managed by the system. Users also have access to a set of tools that visualize, analyze and annotate the data. The infrastructure and Portal are based on web service oriented architecture. We designed the system to support solar system bodies in general including asteroids, earth and planets. We employed a combination of custom software, commercial and open-source components, off-the-shelf hardware and pay-by-use cloud computing services. The use of open standards and web service interfaces facilitate platform and application independent access to the services and data, offering for instances, iPad and Android mobile applications and large screen multi-touch with 3-D terrain viewing functions, for a rich browsing and analysis experience from a variety of platforms. The web services made use of open standards including: Representational State Transfer (REST); and Open Geospatial Consortium (OGC)'s Web Map Service (WMS), Web Coverage Service (WCS), Web Feature Service (WFS). Its data management services have been built on top of a set of open technologies including: Object Oriented Data Technology (OODT) - open source data catalog, archive, file management, data grid framework; openSSO - open source access management and federation platform; solr - open source enterprise search platform; redmine - open source project collaboration and management framework; GDAL - open source geospatial data abstraction library; and others. Its data products are compliant with Federal Geographic Data Committee (FGDC) metadata standard. This standardization allows users to access the data products via custom written applications or off-the-shelf applications such as GoogleEarth. We will demonstrate this ready-to-use system for data discovery and visualization by walking through the data services provided through the portal such as browse, search, and other tools. We will further demonstrate image viewing and layering of lunar map images from the Internet, via mobile devices such as Apple's iPad.

Performance of the High Sensitivity Open Source Multi-GNSS Assisted GNSS Reference Server.

NASA Astrophysics Data System (ADS)

Sarwar, Ali; Rizos, Chris; Glennon, Eamonn

2015-06-01

The Open Source GNSS Reference Server (OSGRS) exploits the GNSS Reference Interface Protocol (GRIP) to provide assistance data to GPS receivers. Assistance can be in terms of signal acquisition and in the processing of the measurement data. The data transfer protocol is based on Extensible Mark-up Language (XML) schema. The first version of the OSGRS required a direct hardware connection to a GPS device to acquire the data necessary to generate the appropriate assistance. Scenarios of interest for the OSGRS users are weak signal strength indoors, obstructed outdoors or heavy multipath environments. This paper describes an improved version of OSGRS that provides alternative assistance support from a number of Global Navigation Satellite Systems (GNSS). The underlying protocol to transfer GNSS assistance data from global casters is the Networked Transport of RTCM (Radio Technical Commission for Maritime Services) over Internet Protocol (NTRIP), and/or the RINEX (Receiver Independent Exchange) format. This expands the assistance and support model of the OSGRS to globally available GNSS data servers connected via internet casters. A variety of formats and versions of RINEX and RTCM streams become available, which strengthens the assistance provisioning capability of the OSGRS platform. The prime motivation for this work was to enhance the system architecture of the OSGRS to take advantage of globally available GNSS data sources. Open source software architectures and assistance models provide acquisition and data processing assistance for GNSS receivers operating in weak signal environments. This paper describes test scenarios to benchmark the OSGRSv2 performance against other Assisted-GNSS solutions. Benchmarking devices include the SPOT satellite messenger, MS-Based & MS-Assisted GNSS, HSGNSS (SiRFstar-III) and Wireless Sensor Networks Assisted-GNSS. Benchmarked parameters include the number of tracked satellites, the Time to Fix First (TTFF), navigation availability and accuracy. Three different configurations of Multi-GNSS assistance servers were used, namely Cloud-Client-Server, the Demilitarized Zone (DMZ) Client-Server and PC-Client-Server; with respect to the connectivity location of client and server. The impact on the performance based on server and/or client initiation, hardware capability, network latency, processing delay and computation times with their storage, scalability, processing and load sharing capabilities, were analysed. The performance of the OSGRS is compared against commercial GNSS, Assisted-GNSS and WSN-enabled GNSS devices. The OSGRS system demonstrated lower TTFF and higher availability.

An open source solution for an in-house built dynamic platform for the validation of stereotactic ablative body radiotherapy for VMAT and IMRT.

PubMed

Munoz, Luis; Ziebell, Amy; Morton, Jason; Bhat, Madhava

2016-12-01

An in-house solution for the verification of dose delivered to a moving phantom as required for the clinical implementation of lung stereotactic ablative body radiation therapy was developed. The superior-inferior movement required to simulate tumour motion during a normal breathing cycle was achieved via the novel use of an Arduino Uno™, a low-cost open-source microcontroller board connected to a high torque servo motor. Slow CT imaging was used to acquire the image set and a 4D cone beam CT (4D-CBCT) verified the efficacy of contoured margins before treatment on the moving phantom. Treatment fields were delivered to a section of a CIRS™ anthropomorphic phantom. Dose verification to the dynamic phantom with Gafchromic EBT3 film using 3 %-1 mm gamma analysis acceptance criteria registered an absolute dose pass rate for IMRT and VMAT of 98 and 96.6 %, respectively. It was verified that 100 % of the PTV received the prescribed dose of 12 Gy per fraction using the dynamic phantom, and no major discrepancy between planned and measured results due to interplay between multileaf collimator sequences and target motion was observed. This study confirmed that the use of an in-house solution using open source hardware and software with existing quality assurance equipment was appropriate in validating a new treatment technique.

Biosignal PI, an Affordable Open-Source ECG and Respiration Measurement System

PubMed Central

Abtahi, Farhad; Snäll, Jonatan; Aslamy, Benjamin; Abtahi, Shirin; Seoane, Fernando; Lindecrantz, Kaj

2015-01-01

Bioimedical pilot projects e.g., telemedicine, homecare, animal and human trials usually involve several physiological measurements. Technical development of these projects is time consuming and in particular costly. A versatile but affordable biosignal measurement platform can help to reduce time and risk while keeping the focus on the important goal and making an efficient use of resources. In this work, an affordable and open source platform for development of physiological signals is proposed. As a first step an 8–12 leads electrocardiogram (ECG) and respiration monitoring system is developed. Chips based on iCoupler technology have been used to achieve electrical isolation as required by IEC 60601 for patient safety. The result shows the potential of this platform as a base for prototyping compact, affordable, and medically safe measurement systems. Further work involves both hardware and software development to develop modules. These modules may require development of front-ends for other biosignals or just collect data wirelessly from different devices e.g., blood pressure, weight, bioimpedance spectrum, blood glucose, e.g., through Bluetooth. All design and development documents, files and source codes will be available for non-commercial use through project website, BiosignalPI.org. PMID:25545268

Building Energy Management Open Source Software

DOE Office of Scientific and Technical Information (OSTI.GOV)

This is the repository for Building Energy Management Open Source Software (BEMOSS), which is an open source operating system that is engineered to improve sensing and control of equipment in small- and medium-sized commercial buildings. BEMOSS offers the following key features: (1) Open source, open architecture – BEMOSS is an open source operating system that is built upon VOLTTRON – a distributed agent platform developed by Pacific Northwest National Laboratory (PNNL). BEMOSS was designed to make it easy for hardware manufacturers to seamlessly interface their devices with BEMOSS. Software developers can also contribute to adding additional BEMOSS functionalities and applications.more » (2) Plug & play – BEMOSS was designed to automatically discover supported load controllers (including smart thermostats, VAV/RTUs, lighting load controllers and plug load controllers) in commercial buildings. (3) Interoperability – BEMOSS was designed to work with load control devices form different manufacturers that operate on different communication technologies and data exchange protocols. (4) Cost effectiveness – Implementation of BEMOSS deemed to be cost-effective as it was built upon a robust open source platform that can operate on a low-cost single-board computer, such as Odroid. This feature could contribute to its rapid deployment in small- or medium-sized commercial buildings. (5) Scalability and ease of deployment – With its multi-node architecture, BEMOSS provides a distributed architecture where load controllers in a multi-floor and high occupancy building could be monitored and controlled by multiple single-board computers hosting BEMOSS. This makes it possible for a building engineer to deploy BEMOSS in one zone of a building, be comfortable with its operation, and later on expand the deployment to the entire building to make it more energy efficient. (6) Ability to provide local and remote monitoring – BEMOSS provides both local and remote monitoring ability with role-based access control. (7) Security – In addition to built-in security features provided by VOLTTRON, BEMOSS provides enhanced security features, including BEMOSS discovery approval process, encrypted core-to-node communication, thermostat anti-tampering feature and many more. (8) Support from the Advisory Committee – BEMOSS was developed in consultation with an advisory committee from the beginning of the project. BEMOSS advisory committee comprises representatives from 22 organizations from government and industry.« less

How to create successful Open Hardware projects — About White Rabbits and open fields

NASA Astrophysics Data System (ADS)

van der Bij, E.; Arruat, M.; Cattin, M.; Daniluk, G.; Gonzalez Cobas, J. D.; Gousiou, E.; Lewis, J.; Lipinski, M. M.; Serrano, J.; Stana, T.; Voumard, N.; Wlostowski, T.

2013-12-01

CERN's accelerator control group has embraced ''Open Hardware'' (OH) to facilitate peer review, avoid vendor lock-in and make support tasks scalable. A web-based tool for easing collaborative work was set up and the CERN OH Licence was created. New ADC, TDC, fine delay and carrier cards based on VITA and PCI-SIG standards were designed and drivers for Linux were written. Often industry was paid for developments, while quality and documentation was controlled by CERN. An innovative timing network was also developed with the OH paradigm. Industry now sells and supports these designs that find their way into new fields.

Hardware platforms for MEMS gyroscope tuning based on evolutionary computation using open-loop and closed -loop frequency response

NASA Technical Reports Server (NTRS)

Keymeulen, Didier; Ferguson, Michael I.; Fink, Wolfgang; Oks, Boris; Peay, Chris; Terrile, Richard; Cheng, Yen; Kim, Dennis; MacDonald, Eric; Foor, David

2005-01-01

We propose a tuning method for MEMS gyroscopes based on evolutionary computation to efficiently increase the sensitivity of MEMS gyroscopes through tuning. The tuning method was tested for the second generation JPL/Boeing Post-resonator MEMS gyroscope using the measurement of the frequency response of the MEMS device in open-loop operation. We also report on the development of a hardware platform for integrated tuning and closed loop operation of MEMS gyroscopes. The control of this device is implemented through a digital design on a Field Programmable Gate Array (FPGA). The hardware platform easily transitions to an embedded solution that allows for the miniaturization of the system to a single chip.

Web-based access, aggregation, and visualization of future climate projections with emphasis on agricultural assessments

NASA Astrophysics Data System (ADS)

Villoria, Nelson B.; Elliott, Joshua; Müller, Christoph; Shin, Jaewoo; Zhao, Lan; Song, Carol

2018-01-01

Access to climate and spatial datasets by non-specialists is restricted by technical barriers involving hardware, software and data formats. We discuss an open-source online tool that facilitates downloading the climate data from the global circulation models used by the Inter-Sectoral Impacts Model Intercomparison Project. The tool also offers temporal and spatial aggregation capabilities for incorporating future climate scenarios in applications where spatial aggregation is important. We hope that streamlined access to these data facilitates analysis of climate related issues while considering the uncertainties derived from future climate projections and temporal aggregation choices.

Using Cesium for 3D Thematic Visualisations on the Web

NASA Astrophysics Data System (ADS)

Gede, Mátyás

2018-05-01

Cesium (http://cesiumjs.org) is an open source, WebGL-based JavaScript library for virtual globes and 3D maps. It is an excellent tool for 3D thematic visualisations, but to use its full functionality it has to be feed with its own file format, CZML. Unfortunately, this format is not yet supported by any major GIS software. This paper intro- duces a plugin for QGIS, developed by the author, which facilitates the creation of CZML file for various types of visualisations. The usability of Cesium is also examined in various hardware/software environments.

Solar wind monitor—a school geophysics project

NASA Astrophysics Data System (ADS)

Robinson, Ian

2018-05-01

Described is an established geophysics project to construct a solar wind monitor based on a nT resolution fluxgate magnetometer. Low-cost and appropriate from school to university level it incorporates elements of astrophysics, geophysics, electronics, programming, computer networking and signal processing. The system monitors the earth’s field in real-time uploading data and graphs to a website every few minutes. Modular design encourages construction and testing by teams of students as well as expansion and refinement. The system has been tested running unattended for months at a time. Both the hardware design and software is published as open-source [1, 10].

From evolutionary computation to the evolution of things.

PubMed

Eiben, Agoston E; Smith, Jim

2015-05-28

Evolution has provided a source of inspiration for algorithm designers since the birth of computers. The resulting field, evolutionary computation, has been successful in solving engineering tasks ranging in outlook from the molecular to the astronomical. Today, the field is entering a new phase as evolutionary algorithms that take place in hardware are developed, opening up new avenues towards autonomous machines that can adapt to their environment. We discuss how evolutionary computation compares with natural evolution and what its benefits are relative to other computing approaches, and we introduce the emerging area of artificial evolution in physical systems.

Build and Execute Environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guan, Qiang

At exascale, the challenge becomes to develop applications that run at scale and use exascale platforms reliably, efficiently, and flexibly. Workflows become much more complex because they must seamlessly integrate simulation and data analytics. They must include down-sampling, post-processing, feature extraction, and visualization. Power and data transfer limitations require these analysis tasks to be run in-situ or in-transit. We expect successful workflows will comprise multiple linked simulations along with tens of analysis routines. Users will have limited development time at scale and, therefore, must have rich tools to develop, debug, test, and deploy applications. At this scale, successful workflows willmore » compose linked computations from an assortment of reliable, well-defined computation elements, ones that can come and go as required, based on the needs of the workflow over time. We propose a novel framework that utilizes both virtual machines (VMs) and software containers to create a workflow system that establishes a uniform build and execution environment (BEE) beyond the capabilities of current systems. In this environment, applications will run reliably and repeatably across heterogeneous hardware and software. Containers, both commercial (Docker and Rocket) and open-source (LXC and LXD), define a runtime that isolates all software dependencies from the machine operating system. Workflows may contain multiple containers that run different operating systems, different software, and even different versions of the same software. We will run containers in open-source virtual machines (KVM) and emulators (QEMU) so that workflows run on any machine entirely in user-space. On this platform of containers and virtual machines, we will deliver workflow software that provides services, including repeatable execution, provenance, checkpointing, and future proofing. We will capture provenance about how containers were launched and how they interact to annotate workflows for repeatable and partial re-execution. We will coordinate the physical snapshots of virtual machines with parallel programming constructs, such as barriers, to automate checkpoint and restart. We will also integrate with HPC-specific container runtimes to gain access to accelerators and other specialized hardware to preserve native performance. Containers will link development to continuous integration. When application developers check code in, it will automatically be tested on a suite of different software and hardware architectures.« less

BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics.

PubMed

Ayres, Daniel L; Darling, Aaron; Zwickl, Derrick J; Beerli, Peter; Holder, Mark T; Lewis, Paul O; Huelsenbeck, John P; Ronquist, Fredrik; Swofford, David L; Cummings, Michael P; Rambaut, Andrew; Suchard, Marc A

2012-01-01

Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emergence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently exploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software.

BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics

PubMed Central

Ayres, Daniel L.; Darling, Aaron; Zwickl, Derrick J.; Beerli, Peter; Holder, Mark T.; Lewis, Paul O.; Huelsenbeck, John P.; Ronquist, Fredrik; Swofford, David L.; Cummings, Michael P.; Rambaut, Andrew; Suchard, Marc A.

2012-01-01

Abstract Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emergence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently exploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software. PMID:21963610

OsiriX: an open-source software for navigating in multidimensional DICOM images.

PubMed

Rosset, Antoine; Spadola, Luca; Ratib, Osman

2004-09-01

A multidimensional image navigation and display software was designed for display and interpretation of large sets of multidimensional and multimodality images such as combined PET-CT studies. The software is developed in Objective-C on a Macintosh platform under the MacOS X operating system using the GNUstep development environment. It also benefits from the extremely fast and optimized 3D graphic capabilities of the OpenGL graphic standard widely used for computer games optimized for taking advantage of any hardware graphic accelerator boards available. In the design of the software special attention was given to adapt the user interface to the specific and complex tasks of navigating through large sets of image data. An interactive jog-wheel device widely used in the video and movie industry was implemented to allow users to navigate in the different dimensions of an image set much faster than with a traditional mouse or on-screen cursors and sliders. The program can easily be adapted for very specific tasks that require a limited number of functions, by adding and removing tools from the program's toolbar and avoiding an overwhelming number of unnecessary tools and functions. The processing and image rendering tools of the software are based on the open-source libraries ITK and VTK. This ensures that all new developments in image processing that could emerge from other academic institutions using these libraries can be directly ported to the OsiriX program. OsiriX is provided free of charge under the GNU open-source licensing agreement at http://homepage.mac.com/rossetantoine/osirix.

ScanImage: flexible software for operating laser scanning microscopes.

PubMed

Pologruto, Thomas A; Sabatini, Bernardo L; Svoboda, Karel

2003-05-17

Laser scanning microscopy is a powerful tool for analyzing the structure and function of biological specimens. Although numerous commercial laser scanning microscopes exist, some of the more interesting and challenging applications demand custom design. A major impediment to custom design is the difficulty of building custom data acquisition hardware and writing the complex software required to run the laser scanning microscope. We describe a simple, software-based approach to operating a laser scanning microscope without the need for custom data acquisition hardware. Data acquisition and control of laser scanning are achieved through standard data acquisition boards. The entire burden of signal integration and image processing is placed on the CPU of the computer. We quantitate the effectiveness of our data acquisition and signal conditioning algorithm under a variety of conditions. We implement our approach in an open source software package (ScanImage) and describe its functionality. We present ScanImage, software to run a flexible laser scanning microscope that allows easy custom design.

Neighbour lists for smoothed particle hydrodynamics on GPUs

NASA Astrophysics Data System (ADS)

Winkler, Daniel; Rezavand, Massoud; Rauch, Wolfgang

2018-04-01

The efficient iteration of neighbouring particles is a performance critical aspect of any high performance smoothed particle hydrodynamics (SPH) solver. SPH solvers that implement a constant smoothing length generally divide the simulation domain into a uniform grid to reduce the computational complexity of the neighbour search. Based on this method, particle neighbours are either stored per grid cell or for each individual particle, denoted as Verlet list. While the latter approach has significantly higher memory requirements, it has the potential for a significant computational speedup. A theoretical comparison is performed to estimate the potential improvements of the method based on unknown hardware dependent factors. Subsequently, the computational performance of both approaches is empirically evaluated on graphics processing units. It is shown that the speedup differs significantly for different hardware, dimensionality and floating point precision. The Verlet list algorithm is implemented as an alternative to the cell linked list approach in the open-source SPH solver DualSPHysics and provided as a standalone software package.

Developing information technology at the Medical Research Unit of the Albert Schweitzer Hospital in Lambaréné, Gabon.

PubMed

Dibacka, Paterne Lessihuin; Bounda, Yann; Nguema, Davy Ondo; Lell, Bertrand

2010-03-01

Information technology has become a key resource for research institutions, providing services such as hardware, software and network maintenance, as well as data management services. The IT department of the Medical Research Unit (MRU) of the Albert Schweitzer Hospital in Lambaréné, Gabon is a good example of how IT has developed at African Research Centres in recent years and demonstrates the scope of work that a modern research centre needs to offer. It illustrates the development in the past 15 years--from single computers maintained by investigators to the present situation of a group of well-trained local IT personal who are in charge of a variety of hardware and software and who also develop applications for use in a research environment. Open source applications are particularly suited for these needs and various applications are used in data management, data analysis, accounting, administration and quality management.

An Open Hardware seismic data recorder - a solid basis for citizen science

NASA Astrophysics Data System (ADS)

Mertl, Stefan

2015-04-01

"Ruwai" is a 24-Bit Open Hardware seismic data recorder. It is built up of four stackable printed circuit boards fitting the Arduino Mega 2560 microcontroller prototyping platform. An interface to the BeagleBone Black single-board computer enables extensive data storage, -processing and networking capabilities. The four printed circuit boards provide a uBlox Lea-6T GPS module and real-time clock (GPS Timing shield), an Texas Instruments ADS1274 24-Bit analog to digital converter (ADC main shield), an analog input section with a Texas Instruments PGA281 programmable gain amplifier and an analog anti-aliasing filter (ADC analog interface pga) and the power conditioning based on 9-36V DC input (power supply shield). The Arduino Mega 2560 is used for controlling the hardware components, timestamping sampled data using the GPS timing information and transmitting the data to the BeagleBone Black single-board computer. The BeagleBone Black provides local data storage, wireless mesh networking using the optimized link state routing daemon and differential GNSS positioning using the RTKLIB software. The complete hardware and software is published under free software - or open hardware licenses and only free software (e.g. KiCad) was used for the development to facilitate the reusability of the design and increases the sustainability of the project. "Ruwai" was developed within the framework of the "Community Environmental Observation Network (CEON)" (http://www.mertl-research.at/ceon/) which was supported by the Internet Foundation Austria (IPA) within the NetIdee 2013 call.

Reduction of Background Noise in the NASA Ames 40- by 80-Foot Wind Tunnel

NASA Technical Reports Server (NTRS)

Jaeger, Stephen M.; Allen, Christopher S.; Soderman, Paul T.; Olson, Larry E. (Technical Monitor)

1995-01-01

Background noise in both open-jet and closed wind tunnels adversely affects the signal-to-noise ratio of acoustic measurements. To measure the noise of increasingly quieter aircraft models, the background noise will have to be reduced by physical means or through signal processing. In a closed wind tunnel, such as the NASA Ames 40- by 80- Foot Wind Tunnel, the principle background noise sources can be classified as: (1) fan drive noise; (2) microphone self-noise; (3) aerodynamically induced noise from test-dependent hardware such as model struts and junctions; and (4) noise from the test section walls and vane set. This paper describes the steps taken to minimize the influence of each of these background noise sources in the 40 x 80.

Open-source web-enabled data management, analyses, and visualization of very large data in geosciences using Jupyter, Apache Spark, and community tools

NASA Astrophysics Data System (ADS)

Chaudhary, A.

2017-12-01

Current simulation models and sensors are producing high-resolution, high-velocity data in geosciences domain. Knowledge discovery from these complex and large size datasets require tools that are capable of handling very large data and providing interactive data analytics features to researchers. To this end, Kitware and its collaborators are producing open-source tools GeoNotebook, GeoJS, Gaia, and Minerva for geosciences that are using hardware accelerated graphics and advancements in parallel and distributed processing (Celery and Apache Spark) and can be loosely coupled to solve real-world use-cases. GeoNotebook (https://github.com/OpenGeoscience/geonotebook) is co-developed by Kitware and NASA-Ames and is an extension to the Jupyter Notebook. It provides interactive visualization and python-based analysis of geospatial data and depending the backend (KTile or GeoPySpark) can handle data sizes of Hundreds of Gigabytes to Terabytes. GeoNotebook uses GeoJS (https://github.com/OpenGeoscience/geojs) to render very large geospatial data on the map using WebGL and Canvas2D API. GeoJS is more than just a GIS library as users can create scientific plots such as vector and contour and can embed InfoVis plots using D3.js. GeoJS aims for high-performance visualization and interactive data exploration of scientific and geospatial location aware datasets and supports features such as Point, Line, Polygon, and advanced features such as Pixelmap, Contour, Heatmap, and Choropleth. Our another open-source tool Minerva ((https://github.com/kitware/minerva) is a geospatial application that is built on top of open-source web-based data management system Girder (https://github.com/girder/girder) which provides an ability to access data from HDFS or Amazon S3 buckets and provides capabilities to perform visualization and analyses on geosciences data in a web environment using GDAL and GeoPandas wrapped in a unified API provided by Gaia (https://github.com/OpenDataAnalytics/gaia). In this presentation, we will discuss core features of each of these tools and will present lessons learned on handling large data in the context of data management, analyses and visualization.

A Fault-Oblivious Extreme-Scale Execution Environment (FOX)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van Hensbergen, Eric; Speight, William; Xenidis, Jimi

IBM Research’s contribution to the Fault Oblivious Extreme-scale Execution Environment (FOX) revolved around three core research deliverables: • collaboration with Boston University around the Kittyhawk cloud infrastructure which both enabled a development and deployment platform for the project team and provided a fault-injection testbed to evaluate prototypes • operating systems research focused on exploring role-based operating system technologies through collaboration with Sandia National Labs on the NIX research operating system and collaboration with the broader IBM Research community around a hybrid operating system model which became known as FusedOS • IBM Research also participated in an advisory capacity with themore » Boston University SESA project, the core of which was derived from the K42 operating system research project funded in part by DARPA’s HPCS program. Both of these contributions were built on a foundation of previous operating systems research funding by the Department of Energy’s FastOS Program. Through the course of the X-stack funding we were able to develop prototypes, deploy them on production clusters at scale, and make them available to other researchers. As newer hardware, in the form of BlueGene/Q, came online, we were able to port the prototypes to the new hardware and release the source code for the resulting prototypes as open source to the community. In addition to the open source coded for the Kittyhawk and NIX prototypes, we were able to bring the BlueGene/Q Linux patches up to a more recent kernel and contribute them for inclusion by the broader Linux community. The lasting impact of the IBM Research work on FOX can be seen in its effect on the shift of IBM’s approach to HPC operating systems from Linux and Compute Node Kernels to role-based approaches as prototyped by the NIX and FusedOS work. This impact can be seen beyond IBM in follow-on ideas being incorporated into the proposals for the Exasacale Operating Systems/Runtime program.« less

Track-A-Worm, An Open-Source System for Quantitative Assessment of C. elegans Locomotory and Bending Behavior

PubMed Central

Wang, Sijie Jason; Wang, Zhao-Wen

2013-01-01

A major challenge of neuroscience is to understand the circuit and gene bases of behavior. C. elegans is commonly used as a model system to investigate how various gene products function at specific tissue, cellular, and synaptic foci to produce complicated locomotory and bending behavior. The investigation generally requires quantitative behavioral analyses using an automated single-worm tracker, which constantly records and analyzes the position and body shape of a freely moving worm at a high magnification. Many single-worm trackers have been developed to meet lab-specific needs, but none has been widely implemented for various reasons, such as hardware difficult to assemble, and software lacking sufficient functionality, having closed source code, or using a programming language that is not broadly accessible. The lack of a versatile system convenient for wide implementation makes data comparisons difficult and compels other labs to develop new worm trackers. Here we describe Track-A-Worm, a system rich in functionality, open in source code, and easy to use. The system includes plug-and-play hardware (a stereomicroscope, a digital camera and a motorized stage), custom software written to run with Matlab in Windows 7, and a detailed user manual. Grayscale images are automatically converted to binary images followed by head identification and placement of 13 markers along a deduced spline. The software can extract and quantify a variety of parameters, including distance traveled, average speed, distance/time/speed of forward and backward locomotion, frequency and amplitude of dominant bends, overall bending activities measured as root mean square, and sum of all bends. It also plots worm travel path, bend trace, and bend frequency spectrum. All functionality is performed through graphical user interfaces and data is exported to clearly-annotated and documented Excel files. These features make Track-A-Worm a good candidate for implementation in other labs. PMID:23922769

Low cost open data acquisition system for biomedical applications

NASA Astrophysics Data System (ADS)

Zabolotny, Wojciech M.; Laniewski-Wollk, Przemyslaw; Zaworski, Wojciech

2005-09-01

In the biomedical applications it is often necessary to collect measurement data from different devices. It is relatively easy, if the devices are equipped with a MIB or Ethernet interface, however often they feature only the asynchronous serial link, and sometimes the measured values are available only as the analog signals. The system presented in the paper is a low cost alternative to commercially available data acquisition systems. The hardware and software architecture of the system is fully open, so it is possible to customize it for particular needs. The presented system offers various possibilities to connect it to the computer based data processing unit - e.g. using the USB or Ethernet ports. Both interfaces allow also to use many such systems in parallel to increase amount of serial and analog inputs. The open source software used in the system makes possible to process the acquired data with standard tools like MATLAB, Scilab or Octave, or with a dedicated, user supplied application.

The New Meteor Radar at Penn State: Design and First Observations

NASA Technical Reports Server (NTRS)

Urbina, J.; Seal, R.; Dyrud, L.

2011-01-01

In an effort to provide new and improved meteor radar sensing capabilities, Penn State has been developing advanced instruments and technologies for future meteor radars, with primary objectives of making such instruments more capable and more cost effective in order to study the basic properties of the global meteor flux, such as average mass, velocity, and chemical composition. Using low-cost field programmable gate arrays (FPGAs), combined with open source software tools, we describe a design methodology enabling one to develop state-of-the art radar instrumentation, by developing a generalized instrumentation core that can be customized using specialized output stage hardware. Furthermore, using object-oriented programming (OOP) techniques and open-source tools, we illustrate a technique to provide a cost-effective, generalized software framework to uniquely define an instrument s functionality through a customizable interface, implemented by the designer. The new instrument is intended to provide instantaneous profiles of atmospheric parameters and climatology on a daily basis throughout the year. An overview of the instrument design concepts and some of the emerging technologies developed for this meteor radar are presented.

GREEN SUPERCOMPUTING IN A DESKTOP BOX

DOE Office of Scientific and Technical Information (OSTI.GOV)

HSU, CHUNG-HSING; FENG, WU-CHUN; CHING, AVERY

2007-01-17

The computer workstation, introduced by Sun Microsystems in 1982, was the tool of choice for scientists and engineers as an interactive computing environment for the development of scientific codes. However, by the mid-1990s, the performance of workstations began to lag behind high-end commodity PCs. This, coupled with the disappearance of BSD-based operating systems in workstations and the emergence of Linux as an open-source operating system for PCs, arguably led to the demise of the workstation as we knew it. Around the same time, computational scientists started to leverage PCs running Linux to create a commodity-based (Beowulf) cluster that provided dedicatedmore » computer cycles, i.e., supercomputing for the rest of us, as a cost-effective alternative to large supercomputers, i.e., supercomputing for the few. However, as the cluster movement has matured, with respect to cluster hardware and open-source software, these clusters have become much more like their large-scale supercomputing brethren - a shared (and power-hungry) datacenter resource that must reside in a machine-cooled room in order to operate properly. Consequently, the above observations, when coupled with the ever-increasing performance gap between the PC and cluster supercomputer, provide the motivation for a 'green' desktop supercomputer - a turnkey solution that provides an interactive and parallel computing environment with the approximate form factor of a Sun SPARCstation 1 'pizza box' workstation. In this paper, they present the hardware and software architecture of such a solution as well as its prowess as a developmental platform for parallel codes. In short, imagine a 12-node personal desktop supercomputer that achieves 14 Gflops on Linpack but sips only 185 watts of power at load, resulting in a performance-power ratio that is over 300% better than their reference SMP platform.« less

Putting tools in the toolbox: Development of a free, open-source toolbox for quantitative image analysis of porous media.

NASA Astrophysics Data System (ADS)

Iltis, G.; Caswell, T. A.; Dill, E.; Wilkins, S.; Lee, W. K.

2014-12-01

X-ray tomographic imaging of porous media has proven to be a valuable tool for investigating and characterizing the physical structure and state of both natural and synthetic porous materials, including glass bead packs, ceramics, soil and rock. Given that most synchrotron facilities have user programs which grant academic researchers access to facilities and x-ray imaging equipment free of charge, a key limitation or hindrance for small research groups interested in conducting x-ray imaging experiments is the financial cost associated with post-experiment data analysis. While the cost of high performance computing hardware continues to decrease, expenses associated with licensing commercial software packages for quantitative image analysis continue to increase, with current prices being as high as $24,000 USD, for a single user license. As construction of the Nation's newest synchrotron accelerator nears completion, a significant effort is being made here at the National Synchrotron Light Source II (NSLS-II), Brookhaven National Laboratory (BNL), to provide an open-source, experiment-to-publication toolbox that reduces the financial and technical 'activation energy' required for performing sophisticated quantitative analysis of multidimensional porous media data sets, collected using cutting-edge x-ray imaging techniques. Implementation focuses on leveraging existing open-source projects and developing additional tools for quantitative analysis. We will present an overview of the software suite that is in development here at BNL including major design decisions, a demonstration of several test cases illustrating currently available quantitative tools for analysis and characterization of multidimensional porous media image data sets and plans for their future development.

FocusStack and StimServer: a new open source MATLAB toolchain for visual stimulation and analysis of two-photon calcium neuronal imaging data.

PubMed

Muir, Dylan R; Kampa, Björn M

2014-01-01

Two-photon calcium imaging of neuronal responses is an increasingly accessible technology for probing population responses in cortex at single cell resolution, and with reasonable and improving temporal resolution. However, analysis of two-photon data is usually performed using ad-hoc solutions. To date, no publicly available software exists for straightforward analysis of stimulus-triggered two-photon imaging experiments. In addition, the increasing data rates of two-photon acquisition systems imply increasing cost of computing hardware required for in-memory analysis. Here we present a Matlab toolbox, FocusStack, for simple and efficient analysis of two-photon calcium imaging stacks on consumer-level hardware, with minimal memory footprint. We also present a Matlab toolbox, StimServer, for generation and sequencing of visual stimuli, designed to be triggered over a network link from a two-photon acquisition system. FocusStack is compatible out of the box with several existing two-photon acquisition systems, and is simple to adapt to arbitrary binary file formats. Analysis tools such as stack alignment for movement correction, automated cell detection and peri-stimulus time histograms are already provided, and further tools can be easily incorporated. Both packages are available as publicly-accessible source-code repositories.

FocusStack and StimServer: a new open source MATLAB toolchain for visual stimulation and analysis of two-photon calcium neuronal imaging data

PubMed Central

Muir, Dylan R.; Kampa, Björn M.

2015-01-01

Two-photon calcium imaging of neuronal responses is an increasingly accessible technology for probing population responses in cortex at single cell resolution, and with reasonable and improving temporal resolution. However, analysis of two-photon data is usually performed using ad-hoc solutions. To date, no publicly available software exists for straightforward analysis of stimulus-triggered two-photon imaging experiments. In addition, the increasing data rates of two-photon acquisition systems imply increasing cost of computing hardware required for in-memory analysis. Here we present a Matlab toolbox, FocusStack, for simple and efficient analysis of two-photon calcium imaging stacks on consumer-level hardware, with minimal memory footprint. We also present a Matlab toolbox, StimServer, for generation and sequencing of visual stimuli, designed to be triggered over a network link from a two-photon acquisition system. FocusStack is compatible out of the box with several existing two-photon acquisition systems, and is simple to adapt to arbitrary binary file formats. Analysis tools such as stack alignment for movement correction, automated cell detection and peri-stimulus time histograms are already provided, and further tools can be easily incorporated. Both packages are available as publicly-accessible source-code repositories1. PMID:25653614

Advancing global marine biogeography research with open-source GIS software and cloud-computing

USGS Publications Warehouse

Fujioka, Ei; Vanden Berghe, Edward; Donnelly, Ben; Castillo, Julio; Cleary, Jesse; Holmes, Chris; McKnight, Sean; Halpin, patrick

2012-01-01

Across many scientific domains, the ability to aggregate disparate datasets enables more meaningful global analyses. Within marine biology, the Census of Marine Life served as the catalyst for such a global data aggregation effort. Under the Census framework, the Ocean Biogeographic Information System was established to coordinate an unprecedented aggregation of global marine biogeography data. The OBIS data system now contains 31.3 million observations, freely accessible through a geospatial portal. The challenges of storing, querying, disseminating, and mapping a global data collection of this complexity and magnitude are significant. In the face of declining performance and expanding feature requests, a redevelopment of the OBIS data system was undertaken. Following an Open Source philosophy, the OBIS technology stack was rebuilt using PostgreSQL, PostGIS, GeoServer and OpenLayers. This approach has markedly improved the performance and online user experience while maintaining a standards-compliant and interoperable framework. Due to the distributed nature of the project and increasing needs for storage, scalability and deployment flexibility, the entire hardware and software stack was built on a Cloud Computing environment. The flexibility of the platform, combined with the power of the application stack, enabled rapid re-development of the OBIS infrastructure, and ensured complete standards-compliance.

Open source platform for collaborative construction of wearable sensor datasets for human motion analysis and an application for gait analysis.

PubMed

Llamas, César; González, Manuel A; Hernández, Carmen; Vegas, Jesús

2016-10-01

Nearly every practical improvement in modeling human motion is well founded in a properly designed collection of data or datasets. These datasets must be made publicly available for the community could validate and accept them. It is reasonable to concede that a collective, guided enterprise could serve to devise solid and substantial datasets, as a result of a collaborative effort, in the same sense as the open software community does. In this way datasets could be complemented, extended and expanded in size with, for example, more individuals, samples and human actions. For this to be possible some commitments must be made by the collaborators, being one of them sharing the same data acquisition platform. In this paper, we offer an affordable open source hardware and software platform based on inertial wearable sensors in a way that several groups could cooperate in the construction of datasets through common software suitable for collaboration. Some experimental results about the throughput of the overall system are reported showing the feasibility of acquiring data from up to 6 sensors with a sampling frequency no less than 118Hz. Also, a proof-of-concept dataset is provided comprising sampled data from 12 subjects suitable for gait analysis. Copyright © 2016 Elsevier Inc. All rights reserved.

Hierarchical image-based rendering using texture mapping hardware

DOE Office of Scientific and Technical Information (OSTI.GOV)

Max, N

1999-01-15

Multi-layered depth images containing color and normal information for subobjects in a hierarchical scene model are precomputed with standard z-buffer hardware for six orthogonal views. These are adaptively selected according to the proximity of the viewpoint, and combined using hardware texture mapping to create ''reprojected'' output images for new viewpoints. (If a subobject is too close to the viewpoint, the polygons in the original model are rendered.) Specific z-ranges are selected from the textures with the hardware alpha test to give accurate 3D reprojection. The OpenGL color matrix is used to transform the precomputed normals into their orientations in themore » final view, for hardware shading.« less

Computerized Workstation for Tsunami Hazard Monitoring

NASA Astrophysics Data System (ADS)

Lavrentiev-Jr, Mikhail; Marchuk, Andrey; Romanenko, Alexey; Simonov, Konstantin; Titov, Vasiliy

2010-05-01

We present general structure and functionality of the proposed Computerized Workstation for Tsunami Hazard Monitoring (CWTHM). The tool allows interactive monitoring of hazard, tsunami risk assessment, and mitigation - at all stages, from the period of strong tsunamigenic earthquake preparation to inundation of the defended coastal areas. CWTHM is a software-hardware complex with a set of software applications, optimized to achieve best performance on hardware platforms in use. The complex is calibrated for selected tsunami source zone(s) and coastal zone(s) to be defended. The number of zones (both source and coastal) is determined, or restricted, by available hardware resources. The presented complex performs monitoring of selected tsunami source zone via the Internet. The authors developed original algorithms, which enable detection of the preparation zone of the strong underwater earthquake automatically. For the so-determined zone the event time, magnitude and spatial location of tsunami source are evaluated by means of energy of the seismic precursors (foreshocks) analysis. All the above parameters are updated after each foreshock. Once preparing event is detected, several scenarios are forecasted for wave amplitude parameters as well as the inundation zone. Estimations include the lowest and the highest wave amplitudes and the least and the most inundation zone. In addition to that, the most probable case is calculated. In case of multiple defended coastal zones, forecasts and estimates can be done in parallel. Each time the simulated model wave reaches deep ocean buoys or tidal gauge, expected values of wave parameters and inundation zones are updated with historical events information and pre-calculated scenarios. The Method of Splitting Tsunami (MOST) software package is used for mathematical simulation. The authors suggest code acceleration for deep water wave propagation. As a result, performance is 15 times faster compared to MOST, original version. Performance gain is achieved by compiler options, use of optimized libraries, and advantages of OpenMP parallel technology. Moreover, it is possible to achieve 100 times code acceleration by using modern Graphics Processing Units (GPU). Parallel evaluation of inundation zones for multiple coastal zones is also available. All computer codes can be easily assembled under MS Windows and Unix OS family. Although software is virtually platform independent, the most performance gain is achieved while using the recommended hardware components. When the seismic event occurs, all valuable parameters are updated with seismic data and wave propagation monitoring is enabled. As soon as the wave passes each deep ocean tsunameter, parameters of the initial displacement at source are updated from direct calculations based on original algorithms. For better source reconstruction, a combination of two methods is used: optimal unit source linear combination from preliminary calculated database and direct numerical inversion along the wave ray between real source and particular measurement buoys. Specific dissipation parameter along with the wave ray is also taken into account. During the entire wave propagation process the expected wave parameters and inundation zone(s) characteristics are updated with all available information. If recommended hardware components are used, monitoring results are available in real time. The suggested version of CWTHM has been tested by analyzing seismic precursors (foreshocks) and the measured tsunami waves at North Pacific for the Central Kuril's tsunamigenic earthquake of November 15, 2006.

Post hoc support vector machine learning for impedimetric biosensors based on weak protein-ligand interactions.

PubMed

Rong, Y; Padron, A V; Hagerty, K J; Nelson, N; Chi, S; Keyhani, N O; Katz, J; Datta, S P A; Gomes, C; McLamore, E S

2018-04-30

Impedimetric biosensors for measuring small molecules based on weak/transient interactions between bioreceptors and target analytes are a challenge for detection electronics, particularly in field studies or in the analysis of complex matrices. Protein-ligand binding sensors have enormous potential for biosensing, but achieving accuracy in complex solutions is a major challenge. There is a need for simple post hoc analytical tools that are not computationally expensive, yet provide near real time feedback on data derived from impedance spectra. Here, we show the use of a simple, open source support vector machine learning algorithm for analyzing impedimetric data in lieu of using equivalent circuit analysis. We demonstrate two different protein-based biosensors to show that the tool can be used for various applications. We conclude with a mobile phone-based demonstration focused on the measurement of acetone, an important biomarker related to the onset of diabetic ketoacidosis. In all conditions tested, the open source classifier was capable of performing as well as, or better, than the equivalent circuit analysis for characterizing weak/transient interactions between a model ligand (acetone) and a small chemosensory protein derived from the tsetse fly. In addition, the tool has a low computational requirement, facilitating use for mobile acquisition systems such as mobile phones. The protocol is deployed through Jupyter notebook (an open source computing environment available for mobile phone, tablet or computer use) and the code was written in Python. For each of the applications, we provide step-by-step instructions in English, Spanish, Mandarin and Portuguese to facilitate widespread use. All codes were based on scikit-learn, an open source software machine learning library in the Python language, and were processed in Jupyter notebook, an open-source web application for Python. The tool can easily be integrated with the mobile biosensor equipment for rapid detection, facilitating use by a broad range of impedimetric biosensor users. This post hoc analysis tool can serve as a launchpad for the convergence of nanobiosensors in planetary health monitoring applications based on mobile phone hardware.

Open Data and Open Science for better Research in the Geo and Space Domain

NASA Astrophysics Data System (ADS)

Ritschel, B.; Seelus, C.; Neher, G.; Iyemori, T.; Koyama, Y.; Yatagai, A. I.; Murayama, Y.; King, T. A.; Hughes, S.; Fung, S. F.; Galkin, I. A.; Hapgood, M. A.; Belehaki, A.

2015-12-01

Main open data principles had been worked out in the run-up and finally adopted in the Open Data Charta at the G8 summit in Lough Erne, Northern Ireland in June 2013. Important principles are also valid for science data, such as Open Data by Default, Quality and Quantity, Useable by All, Releasing Data for Improved Governance, Releasing Data for Innovation. There is also an explicit relationship to such areas of high values as earth observation, education and geospatial data. The European union implementation plan of the Open Data Charta identifies among other things objectives such as making data available in an open format, enabling semantic interoperability, ensuring quality, documentation and where appropriate reconciliation across different data sources, implementing software solutionsallowing easy management, publication or visualization of datasets and simplifying clearance of intellectual property rights.Open Science is not just a list of already for a longer time known principles but stands for a lot of initiatives and projects around a better handling of scientific data and openly shared scientific knowledge. It is also about transparency in methodology and collection of data, availability and reuse of scientific data, public accessibility to scientific communication and using of social media to facility scientific collaboration. Some projects are concentrating on open sharing of free and open source software and even further hardware in kind of processing capabilities. In addition question about the mashup of data and publication and an open peer review process are addressed.Following the principles of open data and open science the newest results of the collaboration efforts in mashing up the data servers related to the Japanese IUGONET, the European Union ESPAS and the GFZ ISDC semantic Web projects will be presented here. The semantic Web based approach for the mashup is focusing on the design and implementation of a common but still distributed data catalog based on semantical interoperability including the transparent access to data in relational data bases. References: https://www.gov.uk/government/uploads/system/uploads/attachment_data/file/207772/Open_Data_Charter.pdfhttp://www.openscience.org/blog/wp-content/uploads/2013/06/OpenSciencePoster.pdf

ProjectQ Software Framework

NASA Astrophysics Data System (ADS)

Steiger, Damian S.; Haener, Thomas; Troyer, Matthias

Quantum computers promise to transform our notions of computation by offering a completely new paradigm. A high level quantum programming language and optimizing compilers are essential components to achieve scalable quantum computation. In order to address this, we introduce the ProjectQ software framework - an open source effort to support both theorists and experimentalists by providing intuitive tools to implement and run quantum algorithms. Here, we present our ProjectQ quantum compiler, which compiles a quantum algorithm from our high-level Python-embedded language down to low-level quantum gates available on the target system. We demonstrate how this compiler can be used to control actual hardware and to run high-performance simulations.

Tracking PACS usage with open source tools.

PubMed

French, Todd L; Langer, Steve G

2011-08-01

A typical choice faced by Picture Archiving and Communication System (PACS) administrators is deciding how many PACS workstations are needed and where they should be sited. Oftentimes, the social consequences of having too few are severe enough to encourage oversupply and underutilization. This is costly, at best in terms of hardware and electricity, and at worst (depending on the PACS licensing and support model) in capital costs and maintenance fees. The PACS administrator needs tools to asses accurately the use to which her fleet is being subjected, and thus make informed choices before buying more workstations. Lacking a vended solution for this challenge, we developed our own.

Verification of OpenSSL version via hardware performance counters

NASA Astrophysics Data System (ADS)

Bruska, James; Blasingame, Zander; Liu, Chen

2017-05-01

Many forms of malware and security breaches exist today. One type of breach downgrades a cryptographic program by employing a man-in-the-middle attack. In this work, we explore the utilization of hardware events in conjunction with machine learning algorithms to detect which version of OpenSSL is being run during the encryption process. This allows for the immediate detection of any unknown downgrade attacks in real time. Our experimental results indicated this detection method is both feasible and practical. When trained with normal TLS and SSL data, our classifier was able to detect which protocol was being used with 99.995% accuracy. After the scope of the hardware event recording was enlarged, the accuracy diminished greatly, but to 53.244%. Upon removal of TLS 1.1 from the data set, the accuracy returned to 99.905%.

A Versatile and Reproducible Multi-Frequency Electrical Impedance Tomography System

PubMed Central

Avery, James; Dowrick, Thomas; Faulkner, Mayo; Goren, Nir; Holder, David

2017-01-01

A highly versatile Electrical Impedance Tomography (EIT) system, nicknamed the ScouseTom, has been developed. The system allows control over current amplitude, frequency, number of electrodes, injection protocol and data processing. Current is injected using a Keithley 6221 current source, and voltages are recorded with a 24-bit EEG system with minimum bandwidth of 3.2 kHz. Custom PCBs interface with a PC to control the measurement process, electrode addressing and triggering of external stimuli. The performance of the system was characterised using resistor phantoms to represent human scalp recordings, with an SNR of 77.5 dB, stable across a four hour recording and 20 Hz to 20 kHz. In studies of both haeomorrhage using scalp electrodes, and evoked activity using epicortical electrode mats in rats, it was possible to reconstruct images matching established literature at known areas of onset. Data collected using scalp electrode in humans matched known tissue impedance spectra and was stable over frequency. The experimental procedure is software controlled and is readily adaptable to new paradigms. Where possible, commercial or open-source components were used, to minimise the complexity in reproduction. The hardware designs and software for the system have been released under an open source licence, encouraging contributions and allowing for rapid replication. PMID:28146122

OpenCL Implementation of NeuroIsing

NASA Astrophysics Data System (ADS)

Zapart, C. A.

Recent advances in graphics card hardware combined with anintroduction of the OpenCL standard promise to accelerate numerical simulations across diverse scientific disciplines. One such field benefiting from new hardware/software paradigms is econophysics. The paper describes an OpenCL implementation of a selected econophysics model: NeuroIsing, which has been designed to execute in parallel on a vendor-independent graphics card. Originally introduced in the paper [C.~A.~Zapart, ``Econophysics in Financial Time Series Prediction'', PhD thesis, Graduate University for Advanced Studies, Japan (2009)], at first it was implemented on a CELL processor running inside a SONY PS3 games console. The NeuroIsing framework can be applied to predicting and trading foreign exchange as well as stock market index futures.

On the relevance of using open wireless sensor networks in environment monitoring.

PubMed

Bagula, Antoine B; Inggs, Gordon; Scott, Simon; Zennaro, Marco

2009-01-01

This paper revisits the problem of the readiness for field deployments of wireless sensor networks by assessing the relevance of using Open Hardware and Software motes for environment monitoring. We propose a new prototype wireless sensor network that fine-tunes SquidBee motes to improve the life-time and sensing performance of an environment monitoring system that measures temperature, humidity and luminosity. Building upon two outdoor sensing scenarios, we evaluate the performance of the newly proposed energy-aware prototype solution in terms of link quality when expressed by the Received Signal Strength, Packet Loss and the battery lifetime. The experimental results reveal the relevance of using the Open Hardware and Software motes when setting up outdoor wireless sensor networks.

Science in the Wild: Adventure Citizen Science in the Arctic and Himalaya

NASA Astrophysics Data System (ADS)

Horodyskyj, U. N.; Rufat-Latre, J.; Reimuller, J. D.; Rowe, P.; Pothier, B.; Thapa, A.

2016-12-01

Science in the Wild provides educational hands-on adventure science expeditions for the everyday person, blending athletics and academics in remote regions of the planet. Participants receive training on field data collection techniques in order to be able to help scientists in the field while on expedition with them. At SITW, we also involve our participants in analyzing and interpreting the data, thus teaching them about data quality and sources of error and uncertainty. SITW teaches citizens the art of science storytelling, aims to make science more open and transparent, and utilizes open source software and hardware in projects. Open science serves both the research community and the greater public. For the former, it makes science reproducible, transparent and more impactful by mobilizing multidisciplinary and international collaborative research efforts. For the latter, it minimizes mistrust in the sciences by allowing the public a `behind-the-scenes' look into how scientific research is conducted, raw and unfiltered. We present results from a citizen-science expedition to Baffin Island (Canadian Arctic), which successfully skied and sampled snow for dust and black carbon concentration from the Penny Ice Cap, down the 25-mile length of Coronation Glacier, and back to the small Arctic town of Qikitarjuaq. From a May/June 2016 citizen-science expedition to Nepal (Himalaya), we present results comparing 2014/16 depth and lake floor compositional data from supraglacial lakes on Ngozumpa glacier while using open-source surface and underwater robotics. The Sherpa-Scientist Initiative, a program aimed at empowering locals in data collection and interpretation, successfully trained half a dozen Sherpas during this expedition and demonstrates the value of local engagement. In future expeditions to the region, efforts will be made to scale up the number of trainees and expand our spatial reach in the Himalaya.

Efficacy of a Virtual Teaching Assistant in an Open Laboratory Environment for Electric Circuits

ERIC Educational Resources Information Center

Saleheen, Firdous; Wang, Zicong; Picone, Joseph; Butz, Brian P.; Won, Chang-Hee

2018-01-01

In order to provide an on-demand, open electrical engineering laboratory, we developed an innovative software-based Virtual Open Laboratory Teaching Assistant (VOLTA). This web-based virtual assistant provides laboratory instructions, equipment usage videos, circuit simulation assistance, and hardware implementation diagnostics. VOLTA allows…

Machine Cleans And Degreases Without Toxic Solvents

NASA Technical Reports Server (NTRS)

Gurguis, Kamal S.; Higginson, Gregory A.

1993-01-01

Appliance uses hot water and biodegradable chemicals to degrease and clean hardware. Spray chamber essentially industrial-scale dishwasher. Front door tilts open, and hardware to be cleaned placed on basket-like tray. During cleaning process, basket-like tray rotates as high-pressure "V" jets deliver steam, hot water, detergent solution, and rust inhibitor as required.

Open ISEmeter: An open hardware high-impedance interface for potentiometric detection.

PubMed

Salvador, C; Mesa, M S; Durán, E; Alvarez, J L; Carbajo, J; Mozo, J D

2016-05-01

In this work, a new open hardware interface based on Arduino to read electromotive force (emf) from potentiometric detectors is presented. The interface has been fully designed with the open code philosophy and all documentation will be accessible on web. The paper describes a comprehensive project including the electronic design, the firmware loaded on Arduino, and the Java-coded graphical user interface to load data in a computer (PC or Mac) for processing. The prototype was tested by measuring the calibration curve of a detector. As detection element, an active poly(vinyl chloride)-based membrane was used, doped with cetyltrimethylammonium dodecylsulphate (CTA(+)-DS(-)). The experimental measures of emf indicate Nernstian behaviour with the CTA(+) content of test solutions, as it was described in the literature, proving the validity of the developed prototype. A comparative analysis of performance was made by using the same chemical detector but changing the measurement instrumentation.

Photon-HDF5: An Open File Format for Timestamp-Based Single-Molecule Fluorescence Experiments.

PubMed

Ingargiola, Antonino; Laurence, Ted; Boutelle, Robert; Weiss, Shimon; Michalet, Xavier

2016-01-05

We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long-term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode, photomultiplier tube, or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel number, etc.) from any acquisition hardware, but also setup and sample description, information on provenance, authorship and other metadata, and is flexible enough to include any kind of custom data. The format specifications are hosted on a public website, which is open to contributions by the biophysics community. As an initial resource, the website provides code examples to read Photon-HDF5 files in several programming languages and a reference Python library (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Photon-HDF5. To encourage adoption by the academic and commercial communities, all software is released under the MIT open source license. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Photon-HDF5: An Open File Format for Timestamp-Based Single-Molecule Fluorescence Experiments

PubMed Central

Ingargiola, Antonino; Laurence, Ted; Boutelle, Robert; Weiss, Shimon; Michalet, Xavier

2016-01-01

We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long-term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode, photomultiplier tube, or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel number, etc.) from any acquisition hardware, but also setup and sample description, information on provenance, authorship and other metadata, and is flexible enough to include any kind of custom data. The format specifications are hosted on a public website, which is open to contributions by the biophysics community. As an initial resource, the website provides code examples to read Photon-HDF5 files in several programming languages and a reference Python library (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Photon-HDF5. To encourage adoption by the academic and commercial communities, all software is released under the MIT open source license. PMID:26745406

Photon-HDF5: an open file format for single-molecule fluorescence experiments using photon-counting detectors

DOE PAGES

Ingargiola, A.; Laurence, T. A.; Boutelle, R.; ...

2015-12-23

We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode (SPAD), photomultiplier tube (PMT) or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel number, etc) from any acquisition hardware, but also setup and sample description, information on provenance, authorship and other metadata, and is flexible enough to include any kind of custom data. Themore » format specifications are hosted on a public website, which is open to contributions by the biophysics community. As an initial resource, the website provides code examples to read Photon-HDF5 files in several programming languages and a reference python library (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Photon-HDF5. As a result, to encourage adoption by the academic and commercial communities, all software is released under the MIT open source license.« less

A 868MHz-based wireless sensor network for ground truthing of soil moisture for a hyperspectral remote sensing campaign - design and preliminary results

NASA Astrophysics Data System (ADS)

Näthe, Paul; Becker, Rolf

2014-05-01

Soil moisture and plant available water are important environmental parameters that affect plant growth and crop yield. Hence, they are significant parameters for vegetation monitoring and precision agriculture. However, validation through ground-based soil moisture measurements is necessary for accessing soil moisture, plant canopy temperature, soil temperature and soil roughness with airborne hyperspectral imaging systems in a corresponding hyperspectral imaging campaign as a part of the INTERREG IV A-Project SMART INSPECTORS. At this point, commercially available sensors for matric potential, plant available water and volumetric water content are utilized for automated measurements with smart sensor nodes which are developed on the basis of open-source 868MHz radio modules, featuring a full-scale microcontroller unit that allows an autarkic operation of the sensor nodes on batteries in the field. The generated data from each of these sensor nodes is transferred wirelessly with an open-source protocol to a central node, the so-called "gateway". This gateway collects, interprets and buffers the sensor readings and, eventually, pushes the data-time series onto a server-based database. The entire data processing chain from the sensor reading to the final storage of data-time series on a server is realized with open-source hardware and software in such a way that the recorded data can be accessed from anywhere through the internet. It will be presented how this open-source based wireless sensor network is developed and specified for the application of ground truthing. In addition, the system's perspectives and potentials with respect to usability and applicability for vegetation monitoring and precision agriculture shall be pointed out. Regarding the corresponding hyperspectral imaging campaign, results from ground measurements will be discussed in terms of their contributing aspects to the remote sensing system. Finally, the significance of the wireless sensor network for the application of ground truthing shall be determined.

The hobbyist phenomenon in physical security.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Michaud, E. C.

Pro-Ams (professional amateurs) are groups of people who work on a problem as amateurs or unpaid persons in a given field at professional levels of competence. Astronomy is a good example of Pro-Am activity. At Galaxy Zoo, Pro-Ams evaluate data generated by professional observatories and are able to evaluate the millions of galaxies that have been observed but not classified, and report their findings at professional levels for fun. To allow the archiving of millions of galaxies that have been observed but not classified, the website has been engineered so that the public can view and classify galaxies even ifmore » they are not professional astronomers. In this endeavor, it has been found that amateurs can easily outperform automated vision systems. Today in the world of physical security, Pro-Ams are playing an ever-increasing role. Traditionally, locksmiths, corporations, and government organizations have been largely responsible for developing standards, uncovering vulnerabilities, and devising best security practices. Increasingly, however, nonprofit sporting organizations and clubs are doing this. They can be found all over the world, from Europe to the US and now South East Asia. Examples include TOOOL (The Open Organization of Lockpickers), the Longhorn Lockpicking Club, Sportsfreunde der Sperrtechnik - Deustcheland e.V., though there are many others. Members of these groups have been getting together weekly to discuss many elements of security, with some groups specializing in specific areas of security. When members are asked why they participate in these hobbyist groups, they usually reply (with gusto) that they do it for fun, and that they view defeating locks and other security devices as an interesting and entertaining puzzle. A lot of what happens at these clubs would not be possible if it weren't for 'Super Abundance', the ability to easily acquire (at little or no cost) the products, security tools, technologies, and intellectual resources traditionally limited to corporations, government organizations, or wealthy individuals. With this new access comes new discoveries. For example, hobbyist sport lockpicking groups discovered - and publicized - a number of new vulnerabilities between 2004 and 2009 that resulted in the majority of high-security lock manufacturers having to make changes and improvements to their products. A decade ago, amateur physical security discoveries were rare, at least those discussed publicly. In the interim, Internet sites such as lockpicking.org, lockpicking101.com and others have provided an online meeting place for people to trade tips, find friends with similar interests, and develop tools. The open, public discussion of software vulnerabilities, in contrast, has been going on for a long time. These two industries, physical security and software, have very different upgrade mechanisms. With software, a patch can typically be deployed quickly to fix a serious vulnerability, whereas a hardware fix for a physical security device or system can take upwards of months to implement in the field, especially if (as is often the case) hardware integrators are involved. Even when responding to publicly announced security vulnerabilities, manufacturers of physical security devices such as locks, intrusion detectors, or access control devices rarely view hobbyists as a positive resource. This is most unfortunate. In the field of software, it is common to speak of Open Source versus Closed Source. An Open Source software company may choose to distribute their software with a particular license, and give it away openly, with full details and all the lines of source code made available. Linux is a very popular example of this. A Close Source company, in contrast, chooses not to reveal its source code and will license its software products in a restrictive manor. Slowly, the idea of Open Source is now coming to the world of physical security. In the case of locks, it provides an alternative to the traditional Closed Source world of locksmiths. Now locks are physical objects, and can therefore be disassembled. As such, they have always been Open Source in a limited sense. Secrecy, in fact, is very difficult to maintain for a lock that is widely distributed. Having direct access to the lock design provides the hobbyist with a very open environment for finding security flaws, even if the lock manufacturer attempts to follow a Close Source model. It is clear that the field of physical security is going the digital route with companies such as Medeco, Mul-T-Lock, and Abloy manufacturing electromechanical locks. Various companies have already begun to add microcontrollers, cryptographic chip sets, solid-state sensors, and a number of other high-tech improvements to their product lineup in an effort to thwart people from defeating their security products.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hornung, Richard D.; Hones, Holger E.

The RAJA Performance Suite is designed to evaluate performance of the RAJA performance portability library on a wide variety of important high performance computing (HPC) algorithmic lulmels. These kernels assess compiler optimizations and various parallel programming model backends accessible through RAJA, such as OpenMP, CUDA, etc. The Initial version of the suite contains 25 computational kernels, each of which appears in 6 variants: Baseline SequcntiaJ, RAJA SequentiaJ, Baseline OpenMP, RAJA OpenMP, Baseline CUDA, RAJA CUDA. All variants of each kernel perform essentially the same mathematical operations and the loop body code for each kernel is identical across all variants. Theremore » are a few kernels, such as those that contain reduction operations, that require CUDA-specific coding for their CUDA variants. ActuaJ computer instructions executed and how they run in parallel differs depending on the parallel programming model backend used and which optimizations are perfonned by the compiler used to build the Perfonnance Suite executable. The Suite will be used primarily by RAJA developers to perform regular assessments of RAJA performance across a range of hardware platforms and compilers as RAJA features are being developed. It will also be used by LLNL hardware and software vendor panners for new defining requirements for future computing platform procurements and acceptance testing. In particular, the RAJA Performance Suite will be used for compiler acceptance testing of the upcoming CORAUSierra machine {initial LLNL delivery expected in late-2017/early 2018) and the CORAL-2 procurement. The Suite will aJso be used to generate concise source code reproducers of compiler and runtime issues we uncover so that we may provide them to relevant vendors to be fixed.« less

Multi-Level Secure Information Sharing Between Smart Cloud Systems of Systems

DTIC Science & Technology

2014-03-01

implementation of virtual hardware (VMWare), along with a commercial implementation of virtual networking (VPN), such as OpenVPN . 1. VMWare Virtualization...en.wikipedia.org/wiki/MongoDB. Wikipedia. 2014b. Accessed February 26. s.v. “Open VPN,” http://en.wikipedia.org/wiki/ OpenVPN . Wikipedia. 2014c. Accessed

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barbara Chapman

OpenMP was not well recognized at the beginning of the project, around year 2003, because of its limited use in DoE production applications and the inmature hardware support for an efficient implementation. Yet in the recent years, it has been graduately adopted both in HPC applications, mostly in the form of MPI+OpenMP hybrid code, and in mid-scale desktop applications for scientific and experimental studies. We have observed this trend and worked deligiently to improve our OpenMP compiler and runtimes, as well as to work with the OpenMP standard organization to make sure OpenMP are evolved in the direction close tomore » DoE missions. In the Center for Programming Models for Scalable Parallel Computing project, the HPCTools team at the University of Houston (UH), directed by Dr. Barbara Chapman, has been working with project partners, external collaborators and hardware vendors to increase the scalability and applicability of OpenMP for multi-core (and future manycore) platforms and for distributed memory systems by exploring different programming models, language extensions, compiler optimizations, as well as runtime library support.« less

Tools for DIY site-testing

NASA Astrophysics Data System (ADS)

Flores, Federico; Rondanelli, Roberto; Abarca, Accel; Diaz, Marcos; Querel, Richard

2012-09-01

Our group has designed, sourced and constructed a radiosonde/ground-station pair using inexpensive opensource hardware. Based on the Arduino platform, the easy to build radiosonde allows the atmospheric science community to test and deploy instrumentation packages that can be fully customized to their individual sensing requirements. This sensing/transmitter package has been successfully deployed on a tethered-balloon, a weather balloon, a UAV airplane, and is currently being integrated into a UAV quadcopter and a student-built rocket. In this paper, the system, field measurements and potential applications will be described. As will the science drivers of having full control and open access to a measurement system in an age when commercial solutions have become popular but are restrictive in terms of proprietary sensor specifications, "black-box" calibration operations or data handling routines, etc. The ability to modify and experiment with both the hardware and software tools is an essential part of the scientific process. Without an understanding of the intrinsic biases or limitations in your instruments and system, it becomes difficult to improve them or advance the knowledge in any given field.

U.S. Reliance on Foreign IT: Mitigating Risks Associated with Foreign Sources of Hardware Components, Summer 2008 - Project 08-03

DTIC Science & Technology

2008-08-01

REPORT MAY 2008 - AUGUST 2008 U.S. Reliance on Foreign IT: Mitigating Risks Associated with Foreign Sources of Hardware Components N/A N/A N/A 08...Clinger-Cohen Act CIA Central Intelligence Agency CIO Chief Information Officer CMOS Complimentary Metal -Oxide Semiconductor DARPA Defense Advanced

OpenPET Hardware, Firmware, Software, and Board Design Files

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abu-Nimeh, Faisal; Choong, Woon-Sengq; Moses, William W.

OpenPET is an open source, flexible, high-performance, and modular data acquisition system for a variety of applications. The OpenPET electronics are capable of reading analog voltage or current signals from a wide variety of sensors. The electronics boards make extensive use of field programmable gate arrays (FPGAs) to provide flexibility and scalability. Firmware and software for the FPGAs and computer are used to control and acquire data from the system. The command and control flow is similar to the data flow, however, the commands are initiated from the computer similar to a tree topology (i.e., from top-to-bottom). Each node inmore » the tree discovers its parent and children, and all addresses are configured accordingly. A user (or a script) initiates a command from the computer. This command will be translated and encoded to the corresponding child (e.g., SB, MB, DB, etc.). Consecutively, each node will pass the command to its corresponding child(ren) by looking at the destination address. Finally, once the command reaches its desired destination(s) the corresponding node(s) execute(s) the command and send(s) a reply, if required. All the firmware, software, and the electronics board design files are distributed through the OpenPET website (http://openpet.lbl.gov).« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ingargiola, A.; Laurence, T. A.; Boutelle, R.

We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode (SPAD), photomultiplier tube (PMT) or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel number, etc) from any acquisition hardware, but also setup and sample description, information on provenance, authorship and other metadata, and is flexible enough to include any kind of custom data. Themore » format specifications are hosted on a public website, which is open to contributions by the biophysics community. As an initial resource, the website provides code examples to read Photon-HDF5 files in several programming languages and a reference python library (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Photon-HDF5. As a result, to encourage adoption by the academic and commercial communities, all software is released under the MIT open source license.« less

Implementation of a departmental picture archiving and communication system: a productivity and cost analysis.

PubMed

Macyszyn, Luke; Lega, Brad; Bohman, Leif-Erik; Latefi, Ahmad; Smith, Michelle J; Malhotra, Neil R; Welch, William; Grady, Sean M

2013-09-01

Digital radiology enhances productivity and results in long-term cost savings. However, the viewing, storage, and sharing of outside imaging studies on compact discs at ambulatory offices and hospitals pose a number of unique challenges to a surgeon's efficiency and clinical workflow. To improve the efficiency and clinical workflow of an academic neurosurgical practice when evaluating patients with outside radiological studies. Open-source software and commercial hardware were used to design and implement a departmental picture archiving and communications system (PACS). The implementation of a departmental PACS system significantly improved productivity and enhanced collaboration in a variety of clinical settings. Using published data on the rate of information technology problems associated with outside studies on compact discs, this system produced a cost savings ranging from $6250 to $33600 and from $43200 to $72000 for 2 cohorts, urgent transfer and spine clinic patients, respectively, therefore justifying the costs of the system in less than a year. The implementation of a departmental PACS system using open-source software is straightforward and cost-effective and results in significant gains in surgeon productivity when evaluating patients with outside imaging studies.

OASYS (OrAnge SYnchrotron Suite): an open-source graphical environment for x-ray virtual experiments

NASA Astrophysics Data System (ADS)

Rebuffi, Luca; Sanchez del Rio, Manuel

2017-08-01

The evolution of the hardware platforms, the modernization of the software tools, the access to the codes of a large number of young people and the popularization of the open source software for scientific applications drove us to design OASYS (ORange SYnchrotron Suite), a completely new graphical environment for modelling X-ray experiments. The implemented software architecture allows to obtain not only an intuitive and very-easy-to-use graphical interface, but also provides high flexibility and rapidity for interactive simulations, making configuration changes to quickly compare multiple beamline configurations. Its purpose is to integrate in a synergetic way the most powerful calculation engines available. OASYS integrates different simulation strategies via the implementation of adequate simulation tools for X-ray Optics (e.g. ray tracing and wave optics packages). It provides a language to make them to communicate by sending and receiving encapsulated data. Python has been chosen as main programming language, because of its universality and popularity in scientific computing. The software Orange, developed at the University of Ljubljana (SLO), is the high level workflow engine that provides the interaction with the user and communication mechanisms.

Data Applicability of Heritage and New Hardware for Launch Vehicle System Reliability Models

NASA Technical Reports Server (NTRS)

Al Hassan Mohammad; Novack, Steven

2015-01-01

Many launch vehicle systems are designed and developed using heritage and new hardware. In most cases, the heritage hardware undergoes modifications to fit new functional system requirements, impacting the failure rates and, ultimately, the reliability data. New hardware, which lacks historical data, is often compared to like systems when estimating failure rates. Some qualification of applicability for the data source to the current system should be made. Accurately characterizing the reliability data applicability and quality under these circumstances is crucial to developing model estimations that support confident decisions on design changes and trade studies. This presentation will demonstrate a data-source classification method that ranks reliability data according to applicability and quality criteria to a new launch vehicle. This method accounts for similarities/dissimilarities in source and applicability, as well as operating environments like vibrations, acoustic regime, and shock. This classification approach will be followed by uncertainty-importance routines to assess the need for additional data to reduce uncertainty.

Meta-image navigation augmenters for unmanned aircraft systems (MINA for UAS)

NASA Astrophysics Data System (ADS)

Òªelik, Koray; Somani, Arun K.; Schnaufer, Bernard; Hwang, Patrick Y.; McGraw, Gary A.; Nadke, Jeremy

2013-05-01

GPS is a critical sensor for Unmanned Aircraft Systems (UASs) due to its accuracy, global coverage and small hardware footprint, but is subject to denial due to signal blockage or RF interference. When GPS is unavailable, position, velocity and attitude (PVA) performance from other inertial and air data sensors is not sufficient, especially for small UASs. Recently, image-based navigation algorithms have been developed to address GPS outages for UASs, since most of these platforms already include a camera as standard equipage. Performing absolute navigation with real-time aerial images requires georeferenced data, either images or landmarks, as a reference. Georeferenced imagery is readily available today, but requires a large amount of storage, whereas collections of discrete landmarks are compact but must be generated by pre-processing. An alternative, compact source of georeferenced data having large coverage area is open source vector maps from which meta-objects can be extracted for matching against real-time acquired imagery. We have developed a novel, automated approach called MINA (Meta Image Navigation Augmenters), which is a synergy of machine-vision and machine-learning algorithms for map aided navigation. As opposed to existing image map matching algorithms, MINA utilizes publicly available open-source geo-referenced vector map data, such as OpenStreetMap, in conjunction with real-time optical imagery from an on-board, monocular camera to augment the UAS navigation computer when GPS is not available. The MINA approach has been experimentally validated with both actual flight data and flight simulation data and results are presented in the paper.

Moose: An Open-Source Framework to Enable Rapid Development of Collaborative, Multi-Scale, Multi-Physics Simulation Tools

NASA Astrophysics Data System (ADS)

Slaughter, A. E.; Permann, C.; Peterson, J. W.; Gaston, D.; Andrs, D.; Miller, J.

2014-12-01

The Idaho National Laboratory (INL)-developed Multiphysics Object Oriented Simulation Environment (MOOSE; www.mooseframework.org), is an open-source, parallel computational framework for enabling the solution of complex, fully implicit multiphysics systems. MOOSE provides a set of computational tools that scientists and engineers can use to create sophisticated multiphysics simulations. Applications built using MOOSE have computed solutions for chemical reaction and transport equations, computational fluid dynamics, solid mechanics, heat conduction, mesoscale materials modeling, geomechanics, and others. To facilitate the coupling of diverse and highly-coupled physical systems, MOOSE employs the Jacobian-free Newton-Krylov (JFNK) method when solving the coupled nonlinear systems of equations arising in multiphysics applications. The MOOSE framework is written in C++, and leverages other high-quality, open-source scientific software packages such as LibMesh, Hypre, and PETSc. MOOSE uses a "hybrid parallel" model which combines both shared memory (thread-based) and distributed memory (MPI-based) parallelism to ensure efficient resource utilization on a wide range of computational hardware. MOOSE-based applications are inherently modular, which allows for simulation expansion (via coupling of additional physics modules) and the creation of multi-scale simulations. Any application developed with MOOSE supports running (in parallel) any other MOOSE-based application. Each application can be developed independently, yet easily communicate with other applications (e.g., conductivity in a slope-scale model could be a constant input, or a complete phase-field micro-structure simulation) without additional code being written. This method of development has proven effective at INL and expedites the development of sophisticated, sustainable, and collaborative simulation tools.

Feeding Experimentation Device (FED): A flexible open-source device for measuring feeding behavior.

PubMed

Nguyen, Katrina P; O'Neal, Timothy J; Bolonduro, Olurotimi A; White, Elecia; Kravitz, Alexxai V

2016-07-15

Measuring food intake in rodents is a conceptually simple yet labor-intensive and temporally-imprecise task. Most commonly, food is weighed manually, with an interval of hours or days between measurements. Commercial feeding monitors are excellent, but are costly and require specialized caging and equipment. We have developed the Feeding Experimentation Device (FED): a low-cost, open-source, home cage-compatible feeding system. FED utilizes an Arduino microcontroller and open-source software and hardware. FED dispenses a single food pellet into a food well where it is monitored by an infrared beam. When the mouse removes the pellet, FED logs the timestamp to a secure digital (SD) card and dispenses a new pellet into the well. Post-hoc analyses of pellet retrieval timestamps reveal high-resolution details about feeding behavior. FED is capable of accurately measuring food intake, identifying discrete trends during light and dark-cycle feeding. Additionally, we show the utility of FED for measuring increases in feeding resulting from optogenetic stimulation of agouti-related peptide neurons in the arcuate nucleus of the hypothalamus. With a cost of ∼$350 per device, FED is >10× cheaper than commercially available feeding systems. FED is also self-contained, battery powered, and designed to be placed in standard colony rack cages, allowing for monitoring of true home cage feeding behavior. Moreover, FED is highly adaptable and can be synchronized with emerging techniques in neuroscience, such as optogenetics, as we demonstrate here. FED allows for accurate, precise monitoring of feeding behavior in a home cage setting. Published by Elsevier B.V.

Quantum neuromorphic hardware for quantum artificial intelligence

NASA Astrophysics Data System (ADS)

Prati, Enrico

2017-08-01

The development of machine learning methods based on deep learning boosted the field of artificial intelligence towards unprecedented achievements and application in several fields. Such prominent results were made in parallel with the first successful demonstrations of fault tolerant hardware for quantum information processing. To which extent deep learning can take advantage of the existence of a hardware based on qubits behaving as a universal quantum computer is an open question under investigation. Here I review the convergence between the two fields towards implementation of advanced quantum algorithms, including quantum deep learning.

18F-FDG PET/CT evaluation of children and young adults with suspected spinal fusion hardware infection.

PubMed

Bagrosky, Brian M; Hayes, Kari L; Koo, Phillip J; Fenton, Laura Z

2013-08-01

Evaluation of the child with spinal fusion hardware and concern for infection is challenging because of hardware artifact with standard imaging (CT and MRI) and difficult physical examination. Studies using (18)F-FDG PET/CT combine the benefit of functional imaging with anatomical localization. To discuss a case series of children and young adults with spinal fusion hardware and clinical concern for hardware infection. These people underwent FDG PET/CT imaging to determine the site of infection. We performed a retrospective review of whole-body FDG PET/CT scans at a tertiary children's hospital from December 2009 to January 2012 in children and young adults with spinal hardware and suspected hardware infection. The PET/CT scan findings were correlated with pertinent clinical information including laboratory values of inflammatory markers, postoperative notes and pathology results to evaluate the diagnostic accuracy of FDG PET/CT. An exempt status for this retrospective review was approved by the Institution Review Board. Twenty-five FDG PET/CT scans were performed in 20 patients. Spinal fusion hardware infection was confirmed surgically and pathologically in six patients. The most common FDG PET/CT finding in patients with hardware infection was increased FDG uptake in the soft tissue and bone immediately adjacent to the posterior spinal fusion rods at multiple contiguous vertebral levels. Noninfectious hardware complications were diagnosed in ten patients and proved surgically in four. Alternative sources of infection were diagnosed by FDG PET/CT in seven patients (five with pneumonia, one with pyonephrosis and one with superficial wound infections). FDG PET/CT is helpful in evaluation of children and young adults with concern for spinal hardware infection. Noninfectious hardware complications and alternative sources of infection, including pneumonia and pyonephrosis, can be diagnosed. FDG PET/CT should be the first-line cross-sectional imaging study in patients with suspected spinal hardware infection. Because pneumonia was diagnosed as often as spinal hardware infection, initial chest radiography should also be performed.

Software for real-time localization of baleen whale calls using directional sonobuoys: A case study on Antarctic blue whales.

PubMed

Miller, Brian S; Calderan, Susannah; Gillespie, Douglas; Weatherup, Graham; Leaper, Russell; Collins, Kym; Double, Michael C

2016-03-01

Directional frequency analysis and recording (DIFAR) sonobuoys can allow real-time acoustic localization of baleen whales for underwater tracking and remote sensing, but limited availability of hardware and software has prevented wider usage. These software limitations were addressed by developing a module in the open-source software PAMGuard. A case study is presented demonstrating that this software provides greater efficiency and accessibility than previous methods for detecting, localizing, and tracking Antarctic blue whales in real time. Additionally, this software can easily be extended to track other low and mid frequency sounds including those from other cetaceans, pinnipeds, icebergs, shipping, and seismic airguns.

An Open-Source Arduino-based Controller for Mechanical Rain Simulators

NASA Astrophysics Data System (ADS)

Cantilina, K. K.

2017-12-01

Many commercial rain simulators currently used in hydrology rely on inflexible and outdated controller designs. These analog controllers typically only allow a handful of discrete parameter options, and do not support internal timing functions or continuously-changing parameters. A desire for finer control of rain simulation events necessitated the design and construction of a microcontroller-based controller, using widely available off-the-shelf components. A menu driven interface allows users to fine-tune simulation parameters without the need for training or experience with microcontrollers, and the accessibility of the Arduino IDE allows users with a minimum of programming and hardware experience to modify the controller program to suit the needs of individual experiments.

Real-time Experiment Interface for Biological Control Applications

PubMed Central

Lin, Risa J.; Bettencourt, Jonathan; White, John A.; Christini, David J.; Butera, Robert J.

2013-01-01

The Real-time Experiment Interface (RTXI) is a fast and versatile real-time biological experimentation system based on Real-Time Linux. RTXI is open source and free, can be used with an extensive range of experimentation hardware, and can be run on Linux or Windows computers (when using the Live CD). RTXI is currently used extensively for two experiment types: dynamic patch clamp and closed-loop stimulation pattern control in neural and cardiac single cell electrophysiology. RTXI includes standard plug-ins for implementing commonly used electrophysiology protocols with synchronized stimulation, event detection, and online analysis. These and other user-contributed plug-ins can be found on the website (http://www.rtxi.org). PMID:21096883

FreeTure: A Free software to capTure meteors for FRIPON

NASA Astrophysics Data System (ADS)

Audureau, Yoan; Marmo, Chiara; Bouley, Sylvain; Kwon, Min-Kyung; Colas, François; Vaubaillon, Jérémie; Birlan, Mirel; Zanda, Brigitte; Vernazza, Pierre; Caminade, Stephane; Gattecceca, Jérôme

2014-02-01

The Fireball Recovery and Interplanetary Observation Network (FRIPON) is a French project started in 2014 which will monitor the sky, using 100 all-sky cameras to detect meteors and to retrieve related meteorites on the ground. There are several detection software all around. Some of them are proprietary. Also, some of them are hardware dependent. We present here the open source software for meteor detection to be installed on the FRIPON network's stations. The software will run on Linux with gigabit Ethernet cameras and we plan to make it cross platform. This paper is focused on the meteor detection method used for the pipeline development and the present capabilities.

Ising Processing Units: Potential and Challenges for Discrete Optimization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Coffrin, Carleton James; Nagarajan, Harsha; Bent, Russell Whitford

The recent emergence of novel computational devices, such as adiabatic quantum computers, CMOS annealers, and optical parametric oscillators, presents new opportunities for hybrid-optimization algorithms that leverage these kinds of specialized hardware. In this work, we propose the idea of an Ising processing unit as a computational abstraction for these emerging tools. Challenges involved in using and bench- marking these devices are presented, and open-source software tools are proposed to address some of these challenges. The proposed benchmarking tools and methodology are demonstrated by conducting a baseline study of established solution methods to a D-Wave 2X adiabatic quantum computer, one examplemore » of a commercially available Ising processing unit.« less

Development and characteristics of the hardware for Skylab experiment S015

NASA Technical Reports Server (NTRS)

Thirolf, R. G.

1975-01-01

Details are given regarding the hardware for the Skylab S015 experiment, which was designed to detect the effects of zero gravity on cell growth rates. Experience gained in hardware-related considerations is presented for use of researchers concerned with future research of this type and further study of the S015 results. Brief descriptions are given of the experiment hardware, the hardware configuration for the critical design review, the major configuration changes, the final configuration, and the postflight review and analysis. An appendix describes pertinent documentation, film, and hardware that are available to qualified researchers; sources for additional or special information are given.

Architecture for Survivable System Processing (ASSP)

NASA Astrophysics Data System (ADS)

Wood, Richard J.

1991-11-01

The Architecture for Survivable System Processing (ASSP) Program is a multi-phase effort to implement Department of Defense (DOD) and commercially developed high-tech hardware, software, and architectures for reliable space avionics and ground based systems. System configuration options provide processing capabilities to address Time Dependent Processing (TDP), Object Dependent Processing (ODP), and Mission Dependent Processing (MDP) requirements through Open System Architecture (OSA) alternatives that allow for the enhancement, incorporation, and capitalization of a broad range of development assets. High technology developments in hardware, software, and networking models, address technology challenges of long processor life times, fault tolerance, reliability, throughput, memories, radiation hardening, size, weight, power (SWAP) and security. Hardware and software design, development, and implementation focus on the interconnectivity/interoperability of an open system architecture and is being developed to apply new technology into practical OSA components. To insure for widely acceptable architecture capable of interfacing with various commercial and military components, this program provides for regular interactions with standardization working groups (e.g.) the International Standards Organization (ISO), American National Standards Institute (ANSI), Society of Automotive Engineers (SAE), and Institute of Electrical and Electronic Engineers (IEEE). Selection of a viable open architecture is based on the widely accepted standards that implement the ISO/OSI Reference Model.

Architecture for Survivable System Processing (ASSP)

NASA Technical Reports Server (NTRS)

Wood, Richard J.

1991-01-01

The Architecture for Survivable System Processing (ASSP) Program is a multi-phase effort to implement Department of Defense (DOD) and commercially developed high-tech hardware, software, and architectures for reliable space avionics and ground based systems. System configuration options provide processing capabilities to address Time Dependent Processing (TDP), Object Dependent Processing (ODP), and Mission Dependent Processing (MDP) requirements through Open System Architecture (OSA) alternatives that allow for the enhancement, incorporation, and capitalization of a broad range of development assets. High technology developments in hardware, software, and networking models, address technology challenges of long processor life times, fault tolerance, reliability, throughput, memories, radiation hardening, size, weight, power (SWAP) and security. Hardware and software design, development, and implementation focus on the interconnectivity/interoperability of an open system architecture and is being developed to apply new technology into practical OSA components. To insure for widely acceptable architecture capable of interfacing with various commercial and military components, this program provides for regular interactions with standardization working groups (e.g.) the International Standards Organization (ISO), American National Standards Institute (ANSI), Society of Automotive Engineers (SAE), and Institute of Electrical and Electronic Engineers (IEEE). Selection of a viable open architecture is based on the widely accepted standards that implement the ISO/OSI Reference Model.

Benchmarking and Evaluating Unified Memory for OpenMP GPU Offloading

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mishra, Alok; Li, Lingda; Kong, Martin

Here, the latest OpenMP standard offers automatic device offloading capabilities which facilitate GPU programming. Despite this, there remain many challenges. One of these is the unified memory feature introduced in recent GPUs. GPUs in current and future HPC systems have enhanced support for unified memory space. In such systems, CPU and GPU can access each other's memory transparently, that is, the data movement is managed automatically by the underlying system software and hardware. Memory over subscription is also possible in these systems. However, there is a significant lack of knowledge about how this mechanism will perform, and how programmers shouldmore » use it. We have modified several benchmarks codes, in the Rodinia benchmark suite, to study the behavior of OpenMP accelerator extensions and have used them to explore the impact of unified memory in an OpenMP context. We moreover modified the open source LLVM compiler to allow OpenMP programs to exploit unified memory. The results of our evaluation reveal that, while the performance of unified memory is comparable with that of normal GPU offloading for benchmarks with little data reuse, it suffers from significant overhead when GPU memory is over subcribed for benchmarks with large amount of data reuse. Based on these results, we provide several guidelines for programmers to achieve better performance with unified memory.« less

Cost efficient CFD simulations: Proper selection of domain partitioning strategies

NASA Astrophysics Data System (ADS)

Haddadi, Bahram; Jordan, Christian; Harasek, Michael

2017-10-01

Computational Fluid Dynamics (CFD) is one of the most powerful simulation methods, which is used for temporally and spatially resolved solutions of fluid flow, heat transfer, mass transfer, etc. One of the challenges of Computational Fluid Dynamics is the extreme hardware demand. Nowadays super-computers (e.g. High Performance Computing, HPC) featuring multiple CPU cores are applied for solving-the simulation domain is split into partitions for each core. Some of the different methods for partitioning are investigated in this paper. As a practical example, a new open source based solver was utilized for simulating packed bed adsorption, a common separation method within the field of thermal process engineering. Adsorption can for example be applied for removal of trace gases from a gas stream or pure gases production like Hydrogen. For comparing the performance of the partitioning methods, a 60 million cell mesh for a packed bed of spherical adsorbents was created; one second of the adsorption process was simulated. Different partitioning methods available in OpenFOAM® (Scotch, Simple, and Hierarchical) have been used with different numbers of sub-domains. The effect of the different methods and number of processor cores on the simulation speedup and also energy consumption were investigated for two different hardware infrastructures (Vienna Scientific Clusters VSC 2 and VSC 3). As a general recommendation an optimum number of cells per processor core was calculated. Optimized simulation speed, lower energy consumption and consequently the cost effects are reported here.

HiCAT Software Infrastructure: Safe hardware control with object oriented Python

NASA Astrophysics Data System (ADS)

Moriarty, Christopher; Brooks, Keira; Soummer, Remi

2018-01-01

High contrast imaging for Complex Aperture Telescopes (HiCAT) is a testbed designed to demonstrate coronagraphy and wavefront control for segmented on-axis space telescopes such as envisioned for LUVOIR. To limit the air movements in the testbed room, software interfaces for several different hardware components were developed to completely automate operations. When developing software interfaces for many different pieces of hardware, unhandled errors are commonplace and can prevent the software from properly closing a hardware resource. Some fragile components (e.g. deformable mirrors) can be permanently damaged because of this. We present an object oriented Python-based infrastructure to safely automate hardware control and optical experiments. Specifically, conducting high-contrast imaging experiments while monitoring humidity and power status along with graceful shutdown processes even for unexpected errors. Python contains a construct called a “context manager” that allows you define code to run when a resource is opened or closed. Context managers ensure that a resource is properly closed, even when unhandled errors occur. Harnessing the context manager design, we also use Python’s multiprocessing library to monitor humidity and power status without interrupting the experiment. Upon detecting a safety problem, the master process sends an event to the child process that triggers the context managers to gracefully close any open resources. This infrastructure allows us to queue up several experiments and safely operate the testbed without a human in the loop.

Closed-loop thrust and pressure profile throttling of a nitrous oxide/hydroxyl-terminated polybutadiene hybrid rocket motor

NASA Astrophysics Data System (ADS)

Peterson, Zachary W.

Hybrid motors that employ non-toxic, non-explosive components with a liquid oxidizer and a solid hydrocarbon fuel grain have inherently safe operating characteristics. The inherent safety of hybrid rocket motors offers the potential to greatly reduce overall operating costs. Another key advantage of hybrid rocket motors is the potential for in-flight shutdown, restart, and throttle by controlling the pressure drop between the oxidizer tank and the injector. This research designed, developed, and ground tested a closed-loop throttle controller for a hybrid rocket motor using nitrous oxide and hydroxyl-terminated polybutadiene as propellants. The research simultaneously developed closed-loop throttle algorithms and lab scale motor hardware to evaluate the fidelity of the throttle simulations and algorithms. Initial open-loop motor tests were performed to better classify system parameters and to validate motor performance values. Deep-throttle open-loop tests evaluated limits of stable thrust that can be achieved on the test hardware. Open-loop tests demonstrated the ability to throttle the motor to less than 10% of maximum thrust with little reduction in effective specific impulse and acoustical stability. Following the open-loop development, closed-loop, hardware-in-the-loop tests were performed. The closed-loop controller successfully tracked prescribed step and ramp command profiles with a high degree of fidelity. Steady-state accuracy was greatly improved over uncontrolled thrust.

Using FastX on the Peregrine System | High-Performance Computing | NREL

Science.gov Websites

with full 3D hardware acceleration. The traditional method of displaying graphics applications to a remote X server (indirect rendering) supports 3D hardware acceleration, but this approach causes all of the OpenGL commands and 3D data to be sent over the network to be rendered on the client machine. With

A Linux Workstation for High Performance Graphics

NASA Technical Reports Server (NTRS)

Geist, Robert; Westall, James

2000-01-01

The primary goal of this effort was to provide a low-cost method of obtaining high-performance 3-D graphics using an industry standard library (OpenGL) on PC class computers. Previously, users interested in doing substantial visualization or graphical manipulation were constrained to using specialized, custom hardware most often found in computers from Silicon Graphics (SGI). We provided an alternative to expensive SGI hardware by taking advantage of third-party, 3-D graphics accelerators that have now become available at very affordable prices. To make use of this hardware our goal was to provide a free, redistributable, and fully-compatible OpenGL work-alike library so that existing bodies of code could simply be recompiled. for PC class machines running a free version of Unix. This should allow substantial cost savings while greatly expanding the population of people with access to a serious graphics development and viewing environment. This should offer a means for NASA to provide a spectrum of graphics performance to its scientists, supplying high-end specialized SGI hardware for high-performance visualization while fulfilling the requirements of medium and lower performance applications with generic, off-the-shelf components and still maintaining compatibility between the two.

Automatic Thread-Level Parallelization in the Chombo AMR Library

DOE Office of Scientific and Technical Information (OSTI.GOV)

Christen, Matthias; Keen, Noel; Ligocki, Terry

2011-05-26

The increasing on-chip parallelism has some substantial implications for HPC applications. Currently, hybrid programming models (typically MPI+OpenMP) are employed for mapping software to the hardware in order to leverage the hardware?s architectural features. In this paper, we present an approach that automatically introduces thread level parallelism into Chombo, a parallel adaptive mesh refinement framework for finite difference type PDE solvers. In Chombo, core algorithms are specified in the ChomboFortran, a macro language extension to F77 that is part of the Chombo framework. This domain-specific language forms an already used target language for an automatic migration of the large number ofmore » existing algorithms into a hybrid MPI+OpenMP implementation. It also provides access to the auto-tuning methodology that enables tuning certain aspects of an algorithm to hardware characteristics. Performance measurements are presented for a few of the most relevant kernels with respect to a specific application benchmark using this technique as well as benchmark results for the entire application. The kernel benchmarks show that, using auto-tuning, up to a factor of 11 in performance was gained with 4 threads with respect to the serial reference implementation.« less

Conversion of HSPF Legacy Model to a Platform-Independent, Open-Source Language

NASA Astrophysics Data System (ADS)

Heaphy, R. T.; Burke, M. P.; Love, J. T.

2015-12-01

Since its initial development over 30 years ago, the Hydrologic Simulation Program - FORTAN (HSPF) model has been used worldwide to support water quality planning and management. In the United States, HSPF receives widespread endorsement as a regulatory tool at all levels of government and is a core component of the EPA's Better Assessment Science Integrating Point and Nonpoint Sources (BASINS) system, which was developed to support nationwide Total Maximum Daily Load (TMDL) analysis. However, the model's legacy code and data management systems have limitations in their ability to integrate with modern software, hardware, and leverage parallel computing, which have left voids in optimization, pre-, and post-processing tools. Advances in technology and our scientific understanding of environmental processes that have occurred over the last 30 years mandate that upgrades be made to HSPF to allow it to evolve and continue to be a premiere tool for water resource planners. This work aims to mitigate the challenges currently facing HSPF through two primary tasks: (1) convert code to a modern widely accepted, open-source, high-performance computing (hpc) code; and (2) convert model input and output files to modern widely accepted, open-source, data model, library, and binary file format. Python was chosen as the new language for the code conversion. It is an interpreted, object-oriented, hpc code with dynamic semantics that has become one of the most popular open-source languages. While python code execution can be slow compared to compiled, statically typed programming languages, such as C and FORTRAN, the integration of Numba (a just-in-time specializing compiler) has allowed this challenge to be overcome. For the legacy model data management conversion, HDF5 was chosen to store the model input and output. The code conversion for HSPF's hydrologic and hydraulic modules has been completed. The converted code has been tested against HSPF's suite of "test" runs and shown good agreement and similar execution times while using the Numba compiler. Continued verification of the accuracy of the converted code against more complex legacy applications and improvement upon execution times by incorporating an intelligent network change detection tool is currently underway, and preliminary results will be presented.

Comparison of cooperative and non-cooperative adaptive optics reference performance for propagation with thermal blooming effects

NASA Astrophysics Data System (ADS)

Edwards, Brian E.; Nitkowski, Arthur; Lawrence, Ryan; Horton, Kasey; Higgs, Charles

2004-10-01

Atmospheric turbulence and laser-induced thermal blooming effects can degrade the beam quality of a high-energy laser (HEL) weapon, and ultimately limit the amount of energy deliverable to a target. Lincoln Laboratory has built a thermal blooming laboratory capable of emulating atmospheric thermal blooming and turbulence effects for tactical HEL systems. The HEL weapon emulation hardware includes an adaptive optics beam delivery system, which utilizes a Shack-Hartman wavefront sensor and a 349 actuator deformable mirror. For this experiment, the laboratory was configured to emulate an engagement scenario consisting of sea skimming target approaching directly toward the HEL weapon at a range of 10km. The weapon utilizes a 1.5m aperture and radiates at a 1.62 micron wavelength. An adaptive optics reference beam was provided as either a point source located at the target (cooperative) or a projected point source reflected from the target (uncooperative). Performance of the adaptive optics system was then compared between reference sources. Results show that, for operating conditions with a thermal blooming distortion number of 75 and weak turbulence (Rytov of 0.02 and D/ro of 3), cooperative beacon AO correction experiences Phase Compensation Instability, resulting in lower performance than a simple, open-loop condition. The uncooperative beacon resulted in slightly better performance than the open-loop condition.

Utilizing Commercial Hardware and Open Source Computer Vision Software to Perform Motion Capture for Reduced Gravity Flight

NASA Technical Reports Server (NTRS)

Humphreys, Brad; Bellisario, Brian; Gallo, Christopher; Thompson, William K.; Lewandowski, Beth

2016-01-01

Long duration space travel to Mars or to an asteroid will expose astronauts to extended periods of reduced gravity. Since gravity is not present to aid loading, astronauts will use resistive and aerobic exercise regimes for the duration of the space flight to minimize the loss of bone density, muscle mass and aerobic capacity that occurs during exposure to a reduced gravity environment. Unlike the International Space Station (ISS), the area available for an exercise device in the next generation of spacecraft is limited. Therefore, compact resistance exercise device prototypes are being developed. The NASA Digital Astronaut Project (DAP) is supporting the Advanced Exercise Concepts (AEC) Project, Exercise Physiology and Countermeasures (ExPC) project and the National Space Biomedical Research Institute (NSBRI) funded researchers by developing computational models of exercising with these new advanced exercise device concepts. To perform validation of these models and to support the Advanced Exercise Concepts Project, several candidate devices have been flown onboard NASAs Reduced Gravity Aircraft. In terrestrial laboratories, researchers typically have available to them motion capture systems for the measurement of subject kinematics. Onboard the parabolic flight aircraft it is not practical to utilize the traditional motion capture systems due to the large working volume they require and their relatively high replacement cost if damaged. To support measuring kinematics on board parabolic aircraft, a motion capture system is being developed utilizing open source computer vision code with commercial off the shelf (COTS) video camera hardware. While the systems accuracy is lower than lab setups, it provides a means to produce quantitative comparison motion capture kinematic data. Additionally, data such as required exercise volume for small spaces such as the Orion capsule can be determined. METHODS: OpenCV is an open source computer vision library that provides the ability to perform multi-camera 3 dimensional reconstruction. Utilizing OpenCV, via the Python programming language, a set of tools has been developed to perform motion capture in confined spaces using commercial cameras. Four Sony Video Cameras were intrinsically calibrated prior to flight. Intrinsic calibration provides a set of camera specific parameters to remove geometric distortion of the lens and sensor (specific to each individual camera). A set of high contrast markers were placed on the exercising subject (safety also necessitated that they be soft in case they become detached during parabolic flight); small yarn balls were used. Extrinsic calibration, the determination of camera location and orientation parameters, is performed using fixed landmark markers shared by the camera scenes. Additionally a wand calibration, the sweeping of the camera scenes simultaneously, was also performed. Techniques have been developed to perform intrinsic calibration, extrinsic calibration, isolation of the markers in the scene, calculation of marker 2D centroids, and 3D reconstruction from multiple cameras. These methods have been tested in the laboratory side-by-side comparison to a traditional motion capture system and also on a parabolic flight.

Open ISEmeter: An open hardware high-impedance interface for potentiometric detection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salvador, C.; Carbajo, J.; Mozo, J. D., E-mail: jdaniel.mozo@diq.uhu.es

In this work, a new open hardware interface based on Arduino to read electromotive force (emf) from potentiometric detectors is presented. The interface has been fully designed with the open code philosophy and all documentation will be accessible on web. The paper describes a comprehensive project including the electronic design, the firmware loaded on Arduino, and the Java-coded graphical user interface to load data in a computer (PC or Mac) for processing. The prototype was tested by measuring the calibration curve of a detector. As detection element, an active poly(vinyl chloride)-based membrane was used, doped with cetyltrimethylammonium dodecylsulphate (CTA{sup +}-DS{supmore » −}). The experimental measures of emf indicate Nernstian behaviour with the CTA{sup +} content of test solutions, as it was described in the literature, proving the validity of the developed prototype. A comparative analysis of performance was made by using the same chemical detector but changing the measurement instrumentation.« less

On the use of inexact, pruned hardware in atmospheric modelling

PubMed Central

Düben, Peter D.; Joven, Jaume; Lingamneni, Avinash; McNamara, Hugh; De Micheli, Giovanni; Palem, Krishna V.; Palmer, T. N.

2014-01-01

Inexact hardware design, which advocates trading the accuracy of computations in exchange for significant savings in area, power and/or performance of computing hardware, has received increasing prominence in several error-tolerant application domains, particularly those involving perceptual or statistical end-users. In this paper, we evaluate inexact hardware for its applicability in weather and climate modelling. We expand previous studies on inexact techniques, in particular probabilistic pruning, to floating point arithmetic units and derive several simulated set-ups of pruned hardware with reasonable levels of error for applications in atmospheric modelling. The set-up is tested on the Lorenz ‘96 model, a toy model for atmospheric dynamics, using software emulation for the proposed hardware. The results show that large parts of the computation tolerate the use of pruned hardware blocks without major changes in the quality of short- and long-time diagnostics, such as forecast errors and probability density functions. This could open the door to significant savings in computational cost and to higher resolution simulations with weather and climate models. PMID:24842031

A FPGA implementation for linearly unmixing a hyperspectral image using OpenCL

NASA Astrophysics Data System (ADS)

Guerra, Raúl; López, Sebastián.; Sarmiento, Roberto

2017-10-01

Hyperspectral imaging systems provide images in which single pixels have information from across the electromagnetic spectrum of the scene under analysis. These systems divide the spectrum into many contiguos channels, which may be even out of the visible part of the spectra. The main advantage of the hyperspectral imaging technology is that certain objects leave unique fingerprints in the electromagnetic spectrum, known as spectral signatures, which allow to distinguish between different materials that may look like the same in a traditional RGB image. Accordingly, the most important hyperspectral imaging applications are related with distinguishing or identifying materials in a particular scene. In hyperspectral imaging applications under real-time constraints, the huge amount of information provided by the hyperspectral sensors has to be rapidly processed and analysed. For such purpose, parallel hardware devices, such as Field Programmable Gate Arrays (FPGAs) are typically used. However, developing hardware applications typically requires expertise in the specific targeted device, as well as in the tools and methodologies which can be used to perform the implementation of the desired algorithms in the specific device. In this scenario, the Open Computing Language (OpenCL) emerges as a very interesting solution in which a single high-level synthesis design language can be used to efficiently develop applications in multiple and different hardware devices. In this work, the Fast Algorithm for Linearly Unmixing Hyperspectral Images (FUN) has been implemented into a Bitware Stratix V Altera FPGA using OpenCL. The obtained results demonstrate the suitability of OpenCL as a viable design methodology for quickly creating efficient FPGAs designs for real-time hyperspectral imaging applications.

SoundCompass: A Distributed MEMS Microphone Array-Based Sensor for Sound Source Localization

PubMed Central

Tiete, Jelmer; Domínguez, Federico; da Silva, Bruno; Segers, Laurent; Steenhaut, Kris; Touhafi, Abdellah

2014-01-01

Sound source localization is a well-researched subject with applications ranging from localizing sniper fire in urban battlefields to cataloging wildlife in rural areas. One critical application is the localization of noise pollution sources in urban environments, due to an increasing body of evidence linking noise pollution to adverse effects on human health. Current noise mapping techniques often fail to accurately identify noise pollution sources, because they rely on the interpolation of a limited number of scattered sound sensors. Aiming to produce accurate noise pollution maps, we developed the SoundCompass, a low-cost sound sensor capable of measuring local noise levels and sound field directionality. Our first prototype is composed of a sensor array of 52 Microelectromechanical systems (MEMS) microphones, an inertial measuring unit and a low-power field-programmable gate array (FPGA). This article presents the SoundCompass’s hardware and firmware design together with a data fusion technique that exploits the sensing capabilities of the SoundCompass in a wireless sensor network to localize noise pollution sources. Live tests produced a sound source localization accuracy of a few centimeters in a 25-m2 anechoic chamber, while simulation results accurately located up to five broadband sound sources in a 10,000-m2 open field. PMID:24463431

Tectonic Storytelling with Open Source and Digital Object Identifiers - a case study about Plate Tectonics and the Geopark Bergstraße-Odenwald

NASA Astrophysics Data System (ADS)

Löwe, Peter; Barmuta, Jan; Klump, Jens; Neumann, Janna; Plank, Margret

2014-05-01

The communication of advances in research to the common public for both education and decision making is an important aspect of scientific work. An even more crucial task is to gain recognition within the scientific community, which is judged by impact factor and citation counts. Recently, the latter concepts have been extended from textual publications to include data and software publications. This paper presents a case study for science communication and data citation. For this, tectonic models, Free and Open Source Software (FOSS), best practices for data citation and a multimedia online-portal for scientific content are combined. This approach creates mutual benefits for the stakeholders: Target audiences receive information on the latest research results, while the use of Digital Object Identifiers (DOI) increases the recognition and citation of underlying scientific data. This creates favourable conditions for every researcher as DOI names ensure citeability and long term availability of scientific research. In the developed application, the FOSS tool for tectonic modelling GPlates is used to visualise and manipulate plate-tectonic reconstructions and associated data through geological time. These capabilities are augmented by the Science on a Halfsphere project (SoaH) with a robust and intuitive visualisation hardware environment. The tectonic models used for science communication are provided by the AGH University of Science and Technology. They focus on the Silurian to Early Carboniferous evolution of Central Europe (Bohemian Massif) and were interpreted for the area of the Geopark Bergstraße Odenwald based on the GPlates/SoaH hardware- and software stack. As scientific story-telling is volatile by nature, recordings are a natural means of preservation for further use, reference and analysis. For this, the upcoming portal for audiovisual media of the German National Library of Science and Technology TIB is expected to become a critical service infrastructure. It allows complex search queries, including metadata such as DOI and media fragment identifiers (MFI), thereby linking data citation and science communication.

Exploiting current-generation graphics hardware for synthetic-scene generation

NASA Astrophysics Data System (ADS)

Tanner, Michael A.; Keen, Wayne A.

2010-04-01

Increasing seeker frame rate and pixel count, as well as the demand for higher levels of scene fidelity, have driven scene generation software for hardware-in-the-loop (HWIL) and software-in-the-loop (SWIL) testing to higher levels of parallelization. Because modern PC graphics cards provide multiple computational cores (240 shader cores for a current NVIDIA Corporation GeForce and Quadro cards), implementation of phenomenology codes on graphics processing units (GPUs) offers significant potential for simultaneous enhancement of simulation frame rate and fidelity. To take advantage of this potential requires algorithm implementation that is structured to minimize data transfers between the central processing unit (CPU) and the GPU. In this paper, preliminary methodologies developed at the Kinetic Hardware In-The-Loop Simulator (KHILS) will be presented. Included in this paper will be various language tradeoffs between conventional shader programming, Compute Unified Device Architecture (CUDA) and Open Computing Language (OpenCL), including performance trades and possible pathways for future tool development.

Space Telecommunications Radio Systems (STRS) Hardware Architecture Standard: Release 1.0 Hardware Section

NASA Technical Reports Server (NTRS)

Reinhart, Richard C.; Kacpura, Thomas J.; Smith, Carl R.; Liebetreu, John; Hill, Gary; Mortensen, Dale J.; Andro, Monty; Scardelletti, Maximilian C.; Farrington, Allen

2008-01-01

This report defines a hardware architecture approach for software-defined radios to enable commonality among NASA space missions. The architecture accommodates a range of reconfigurable processing technologies including general-purpose processors, digital signal processors, field programmable gate arrays, and application-specific integrated circuits (ASICs) in addition to flexible and tunable radiofrequency front ends to satisfy varying mission requirements. The hardware architecture consists of modules, radio functions, and interfaces. The modules are a logical division of common radio functions that compose a typical communication radio. This report describes the architecture details, the module definitions, the typical functions on each module, and the module interfaces. Tradeoffs between component-based, custom architecture and a functional-based, open architecture are described. The architecture does not specify a physical implementation internally on each module, nor does the architecture mandate the standards or ratings of the hardware used to construct the radios.

SafeConnect Solar - Final Scientific/Technical Report (Updated)

DOE Office of Scientific and Technical Information (OSTI.GOV)

McNish, Zachary

2016-02-03

Final Scientific/Technical Report from Tier 0 SunShot Incubator award for hardware-based solution to reducing soft costs of installed solar. The primary objective of this project was for SafeConnect Solar (“SafeConnect”) to create working proof-of-concept hardware prototypes from its proprietary intellectual property and business concepts for a plug-and-play, safety-oriented hardware solution for photovoltaic solar systems. Specifically, SafeConnect sought to build prototypes of its “SmartBox” and related cabling and connectors, as well as the firmware needed to run the hardware. This hardware is designed to ensure a residential PV system installed with it can address all safety concerns that currently form themore » basis of AHJ electrical permitting and licensing requirements, thereby reducing the amount of permitting and specialized labor required on a residential PV system, and also opening up new sales channels and customer acquisition opportunities.« less

World Reaction to Virtual Space

NASA Technical Reports Server (NTRS)

1999-01-01

DRaW Computing developed virtual reality software for the International Space Station. Open Worlds, as the software has been named, can be made to support Java scripting and virtual reality hardware devices. Open Worlds permits the use of VRML script nodes to add virtual reality capabilities to the user's applications.

The ORT Open Tech Robotics and Automation Literacy Course.

ERIC Educational Resources Information Center

Sharon, Dan; And Others

1987-01-01

Presents an overview of a course on robotics and automation developed by the Organization for Rehabilitation through Training (ORT) to be offered through an open learning environment in the United Kingdom. Highlights include hardware and software requirements, an educational model, design principles, and future developments. (LRW)

Development and programming of Geophonino: A low cost Arduino-based seismic recorder for vertical geophones

NASA Astrophysics Data System (ADS)

Soler-Llorens, J. L.; Galiana-Merino, J. J.; Giner-Caturla, J.; Jauregui-Eslava, P.; Rosa-Cintas, S.; Rosa-Herranz, J.

2016-09-01

The commercial data acquisition systems used for seismic exploration are usually expensive equipment. In this work, a low cost data acquisition system (Geophonino) has been developed for recording seismic signals from a vertical geophone. The signal goes first through an instrumentation amplifier, INA155, which is suitable for low amplitude signals like the seismic noise, and an anti-aliasing filter based on the MAX7404 switched-capacitor filter. After that, the amplified and filtered signal is digitized and processed by Arduino Due and registered in an SD memory card. Geophonino is configured for continuous registering, where the sampling frequency, the amplitude gain and the registering time are user-defined. The complete prototype is an open source and open hardware system. It has been tested by comparing the registered signals with the ones obtained through different commercial data recording systems and different kind of geophones. The obtained results show good correlation between the tested measurements, presenting Geophonino as a low-cost alternative system for seismic data recording.

Maker Cultures and the Prospects for Technological Action.

PubMed

Nascimento, Susana; Pólvora, Alexandre

2018-06-01

Supported by easier and cheaper access to tools and expanding communities, maker cultures are pointing towards the ideas of (almost) everyone designing, creating, producing and distributing renewed, new and improved products, machines, things or artefacts. A careful analysis of the assumptions and challenges of maker cultures emphasizes the relevance of what may be called technological action, that is, active and critical interventions regarding the purposes and applications of technologies within ordinary lives, thus countering the deterministic trends of current directions of technology. In such transformative potential, we will explore a set of elements what is and could be technological action through snapshots of maker cultures based on the empirical research conducted in three particular contexts: the Fab Lab Network, Maker Media core outputs and initiatives such as Maker Faires, and the Open Source Hardware Association (OSHWA). Elements such as control and empowerment through material engagement, openness and sharing, and social, cultural, political and ethical values of the common good in topics such as diversity, sustainability and transparency, are critically analysed.

GBU-X bounding requirements for highly flexible munitions

NASA Astrophysics Data System (ADS)

Bagby, Patrick T.; Shaver, Jonathan; White, Reed; Cafarelli, Sergio; Hébert, Anthony J.

2017-04-01

This paper will present the results of an investigation into requirements for existing software and hardware solutions for open digital communication architectures that support weapon subsystem integration. The underlying requirements of such a communication architecture would be to achieve the lowest latency possible at a reasonable cost point with respect to the mission objective of the weapon. The determination of the latency requirements of the open architecture software and hardware were derived through the use of control system and stability margins analyses. Studies were performed on the throughput and latency of different existing communication transport methods. The two architectures that were tested in this study include Data Distribution Service (DDS) and Modular Open Network Architecture (MONARCH). This paper defines what levels of latency can be achieved with current technology and how this capability may translate to future weapons. The requirements moving forward within communications solutions are discussed.

Sustainable and non-conventional monitoring systems to mitigate natural hazards in low income economies: the 4onse project approach.

NASA Astrophysics Data System (ADS)

Cannata, Massimiliano; Ratnayake, Rangajeewa; Antonovic, Milan; Strigaro, Daniele

2017-04-01

Environmental monitoring systems in low economies countries are often in decline, outdated or missing with the consequence that there is a very scarce availability and accessibility to these information that are vital for coping and mitigating natural hazards. Non-conventional monitoring systems based on open technologies may constitute a viable solution to create low cost and sustainable monitoring systems that may be fully developed, deployed and maintained at local level without lock-in dependances on copyrights or patents or high costs of replacements. The 4onse research project , funded under the Research for Development program of the Swiss National Science Foundation and the Swiss Office for Development and Cooperation, propose a complete monitoring system that integrates Free & Open Source Software, Open Hardware, Open Data, and Open Standards. After its engineering, it will be tested in the Deduru Oya catchment (Sri Lanka) to evaluate the system and develop a water management information system to optimize the regulation of artificial basins levels and mitigate flash floods. One of the objective is to better scientifically understand strengths, criticalities and applicabilities in terms of data quality; system durability; management costs; performances; sustainability. Results, challenges and experiences from the first six months of the projects will be presented with particular focus on the activities of synergies building and data collection and dissemination system advances.

An open and configurable embedded system for EMG pattern recognition implementation for artificial arms.

PubMed

Jun Liu; Fan Zhang; Huang, He Helen

2014-01-01

Pattern recognition (PR) based on electromyographic (EMG) signals has been developed for multifunctional artificial arms for decades. However, assessment of EMG PR control for daily prosthesis use is still limited. One of the major barriers is the lack of a portable and configurable embedded system to implement the EMG PR control. This paper aimed to design an open and configurable embedded system for EMG PR implementation so that researchers can easily modify and optimize the control algorithms upon our designed platform and test the EMG PR control outside of the lab environments. The open platform was built on an open source embedded Linux Operating System running a high-performance Gumstix board. Both the hardware and software system framework were openly designed. The system was highly flexible in terms of number of inputs/outputs and calibration interfaces used. Such flexibility enabled easy integration of our embedded system with different types of commercialized or prototypic artificial arms. Thus far, our system was portable for take-home use. Additionally, compared with previously reported embedded systems for EMG PR implementation, our system demonstrated improved processing efficiency and high system precision. Our long-term goals are (1) to develop a wearable and practical EMG PR-based control for multifunctional artificial arms, and (2) to quantify the benefits of EMG PR-based control over conventional myoelectric prosthesis control in a home setting.

Sensor Open System Architecture (SOSA) evolution for collaborative standards development

NASA Astrophysics Data System (ADS)

Collier, Charles Patrick; Lipkin, Ilya; Davidson, Steven A.; Baldwin, Rusty; Orlovsky, Michael C.; Ibrahim, Tim

2017-04-01

The Sensor Open System Architecture (SOSA) is a C4ISR-focused technical and economic collaborative effort between the Air Force, Navy, Army, the Department of Defense (DoD), Industry, and other Governmental agencies to develop (and incorporate) a technical Open Systems Architecture standard in order to maximize C4ISR sub-system, system, and platform affordability, re-configurability, and hardware/software/firmware re-use. The SOSA effort will effectively create an operational and technical framework for the integration of disparate payloads into C4ISR systems; with a focus on the development of a modular decomposition (defining functions and behaviors) and associated key interfaces (physical and logical) for common multi-purpose architecture for radar, EO/IR, SIGINT, EW, and Communications. SOSA addresses hardware, software, and mechanical/electrical interfaces. The modular decomposition will produce a set of re-useable components, interfaces, and sub-systems that engender reusable capabilities. This, in effect, creates a realistic and affordable ecosystem enabling mission effectiveness through systematic re-use of all available re-composed hardware, software, and electrical/mechanical base components and interfaces. To this end, SOSA will leverage existing standards as much as possible and evolve the SOSA architecture through modification, reuse, and enhancements to achieve C4ISR goals. This paper will present accomplishments over the first year of SOSA initiative.

Simulation verification techniques study

NASA Technical Reports Server (NTRS)

Schoonmaker, P. B.; Wenglinski, T. H.

1975-01-01

Results are summarized of the simulation verification techniques study which consisted of two tasks: to develop techniques for simulator hardware checkout and to develop techniques for simulation performance verification (validation). The hardware verification task involved definition of simulation hardware (hardware units and integrated simulator configurations), survey of current hardware self-test techniques, and definition of hardware and software techniques for checkout of simulator subsystems. The performance verification task included definition of simulation performance parameters (and critical performance parameters), definition of methods for establishing standards of performance (sources of reference data or validation), and definition of methods for validating performance. Both major tasks included definition of verification software and assessment of verification data base impact. An annotated bibliography of all documents generated during this study is provided.

Study of efficient video compression algorithms for space shuttle applications

NASA Technical Reports Server (NTRS)

Poo, Z.

1975-01-01

Results are presented of a study on video data compression techniques applicable to space flight communication. This study is directed towards monochrome (black and white) picture communication with special emphasis on feasibility of hardware implementation. The primary factors for such a communication system in space flight application are: picture quality, system reliability, power comsumption, and hardware weight. In terms of hardware implementation, these are directly related to hardware complexity, effectiveness of the hardware algorithm, immunity of the source code to channel noise, and data transmission rate (or transmission bandwidth). A system is recommended, and its hardware requirement summarized. Simulations of the study were performed on the improved LIM video controller which is computer-controlled by the META-4 CPU.

3D in the Fast Lane: Render as You Go with the Latest OpenGL Boards.

ERIC Educational Resources Information Center

Sauer, Jeff; Murphy, Sam

1997-01-01

NT OpenGL hardware allows modelers and animators to work at relatively inexpensive NT workstations in their own offices or homes previous to shared space and workstation time in expensive studios. Rates seven OpenGL boards and two QuickDraw 3D accelerator boards for Mac users on overall value, wireframe and texture rendering, 2D acceleration, and…

3D Printed Fluidic Hardware for DNA Assembly

DTIC Science & Technology

2015-04-10

A3909 stepper motor driver, were soldered onto the milled circuit board (Supplementary Figure 8). Custom Arduino - based firmware was written to take...initiatives such as the FabLab Foundation10. Access to digital fabrication tools and open electronics, such as Arduino and Raspberry Pi, enables access to...hardware for assembly of DNA- based genetic circuits. Solid-phase DNA synthesis has declined in price, enabling researchers to routinely design and

Development of hardwares and computer interface for a two-degree-of-freedom robot

NASA Technical Reports Server (NTRS)

Nguyen, Charles C.; Pooran, Farhad J.

1987-01-01

The research results that were obtained are reviewed. Then the robot actuator, the selection of the data acquisition system, and the design of the power amplifier will be discussed. The machine design of the robot manipulator will then be presented. After that, the integration of the developed hardware into the open-loop system will also be discussed. Current and future research work is addressed.

Fire protection for launch facilities using machine vision fire detection

NASA Astrophysics Data System (ADS)

Schwartz, Douglas B.

1993-02-01

Fire protection of critical space assets, including launch and fueling facilities and manned flight hardware, demands automatic sensors for continuous monitoring, and in certain high-threat areas, fast-reacting automatic suppression systems. Perhaps the most essential characteristic for these fire detection and suppression systems is high reliability; in other words, fire detectors should alarm only on actual fires and not be falsely activated by extraneous sources. Existing types of fire detectors have been greatly improved in the past decade; however, fundamental limitations of their method of operation leaves open a significant possibility of false alarms and restricts their usefulness. At the Civil Engineering Laboratory at Tyndall Air Force Base in Florida, a new type of fire detector is under development which 'sees' a fire visually, like a human being, and makes a reliable decision based on known visual characteristics of flames. Hardware prototypes of the Machine Vision (MV) Fire Detection System have undergone live fire tests and demonstrated extremely high accuracy in discriminating actual fires from false alarm sources. In fact, this technology promises to virtually eliminate false activations. This detector could be used to monitor fueling facilities, launch towers, clean rooms, and other high-value and high-risk areas. Applications can extend to space station and in-flight shuttle operations as well; fiber optics and remote camera heads enable the system to see around obstructed areas and crew compartments. The capability of the technology to distinguish fires means that fire detection can be provided even during maintenance operations, such as welding.

Fire protection for launch facilities using machine vision fire detection

NASA Technical Reports Server (NTRS)

Schwartz, Douglas B.

1993-01-01

Fire protection of critical space assets, including launch and fueling facilities and manned flight hardware, demands automatic sensors for continuous monitoring, and in certain high-threat areas, fast-reacting automatic suppression systems. Perhaps the most essential characteristic for these fire detection and suppression systems is high reliability; in other words, fire detectors should alarm only on actual fires and not be falsely activated by extraneous sources. Existing types of fire detectors have been greatly improved in the past decade; however, fundamental limitations of their method of operation leaves open a significant possibility of false alarms and restricts their usefulness. At the Civil Engineering Laboratory at Tyndall Air Force Base in Florida, a new type of fire detector is under development which 'sees' a fire visually, like a human being, and makes a reliable decision based on known visual characteristics of flames. Hardware prototypes of the Machine Vision (MV) Fire Detection System have undergone live fire tests and demonstrated extremely high accuracy in discriminating actual fires from false alarm sources. In fact, this technology promises to virtually eliminate false activations. This detector could be used to monitor fueling facilities, launch towers, clean rooms, and other high-value and high-risk areas. Applications can extend to space station and in-flight shuttle operations as well; fiber optics and remote camera heads enable the system to see around obstructed areas and crew compartments. The capability of the technology to distinguish fires means that fire detection can be provided even during maintenance operations, such as welding.

Barista: A Framework for Concurrent Speech Processing by USC-SAIL

PubMed Central

Can, Doğan; Gibson, James; Vaz, Colin; Georgiou, Panayiotis G.; Narayanan, Shrikanth S.

2016-01-01

We present Barista, an open-source framework for concurrent speech processing based on the Kaldi speech recognition toolkit and the libcppa actor library. With Barista, we aim to provide an easy-to-use, extensible framework for constructing highly customizable concurrent (and/or distributed) networks for a variety of speech processing tasks. Each Barista network specifies a flow of data between simple actors, concurrent entities communicating by message passing, modeled after Kaldi tools. Leveraging the fast and reliable concurrency and distribution mechanisms provided by libcppa, Barista lets demanding speech processing tasks, such as real-time speech recognizers and complex training workflows, to be scheduled and executed on parallel (and/or distributed) hardware. Barista is released under the Apache License v2.0. PMID:27610047

Embedded image processing engine using ARM cortex-M4 based STM32F407 microcontroller

DOE Office of Scientific and Technical Information (OSTI.GOV)

Samaiya, Devesh, E-mail: samaiya.devesh@gmail.com

2014-10-06

Due to advancement in low cost, easily available, yet powerful hardware and revolution in open source software, urge to make newer, more interactive machines and electronic systems have increased manifold among engineers. To make system more interactive, designers need easy to use sensor systems. Giving the boon of vision to machines was never easy, though it is not impossible these days; it is still not easy and expensive. This work presents a low cost, moderate performance and programmable Image processing engine. This Image processing engine is able to capture real time images, can store the images in the permanent storagemore » and can perform preprogrammed image processing operations on the captured images.« less

A control system of a mini survey facility for photometric monitoring

NASA Astrophysics Data System (ADS)

Tsutsui, Hironori; Yanagisawa, Kenshi; Izumiura, Hideyuki; Shimizu, Yasuhiro; Hanaue, Takumi; Ita, Yoshifusa; Ichikawa, Takashi; Komiyama, Takahiro

2016-08-01

We have built a control system for a mini survey facility dedicated to photometric monitoring of nearby bright (K<5) stars in the near-infrared region. The facility comprises a 4-m-diameter rotating dome and a small (30-mm aperture) wide-field (5 × 5 sq. deg. field of view) infrared (1.0-2.5 microns) camera on an equatorial fork mount, as well as power sources and other associated equipment. All the components other than the camera are controlled by microcomputerbased I/O boards that were developed in-house and are in many of the open-use instruments in our observatory. We present the specifications and configuration of the facility hardware, as well as the structure of its control software.

Bonsai: an event-based framework for processing and controlling data streams

PubMed Central

Lopes, Gonçalo; Bonacchi, Niccolò; Frazão, João; Neto, Joana P.; Atallah, Bassam V.; Soares, Sofia; Moreira, Luís; Matias, Sara; Itskov, Pavel M.; Correia, Patrícia A.; Medina, Roberto E.; Calcaterra, Lorenza; Dreosti, Elena; Paton, Joseph J.; Kampff, Adam R.

2015-01-01

The design of modern scientific experiments requires the control and monitoring of many different data streams. However, the serial execution of programming instructions in a computer makes it a challenge to develop software that can deal with the asynchronous, parallel nature of scientific data. Here we present Bonsai, a modular, high-performance, open-source visual programming framework for the acquisition and online processing of data streams. We describe Bonsai's core principles and architecture and demonstrate how it allows for the rapid and flexible prototyping of integrated experimental designs in neuroscience. We specifically highlight some applications that require the combination of many different hardware and software components, including video tracking of behavior, electrophysiology and closed-loop control of stimulation. PMID:25904861

Barista: A Framework for Concurrent Speech Processing by USC-SAIL.

PubMed

Can, Doğan; Gibson, James; Vaz, Colin; Georgiou, Panayiotis G; Narayanan, Shrikanth S

2014-05-01

We present Barista, an open-source framework for concurrent speech processing based on the Kaldi speech recognition toolkit and the libcppa actor library. With Barista, we aim to provide an easy-to-use, extensible framework for constructing highly customizable concurrent (and/or distributed) networks for a variety of speech processing tasks. Each Barista network specifies a flow of data between simple actors, concurrent entities communicating by message passing, modeled after Kaldi tools. Leveraging the fast and reliable concurrency and distribution mechanisms provided by libcppa, Barista lets demanding speech processing tasks, such as real-time speech recognizers and complex training workflows, to be scheduled and executed on parallel (and/or distributed) hardware. Barista is released under the Apache License v2.0.

Open source tracking and analysis of adult Drosophila locomotion in Buridan's paradigm with and without visual targets.

PubMed

Colomb, Julien; Reiter, Lutz; Blaszkiewicz, Jedrzej; Wessnitzer, Jan; Brembs, Bjoern

2012-01-01

Insects have been among the most widely used model systems for studying the control of locomotion by nervous systems. In Drosophila, we implemented a simple test for locomotion: in Buridan's paradigm, flies walk back and forth between two inaccessible visual targets [1]. Until today, the lack of easily accessible tools for tracking the fly position and analyzing its trajectory has probably contributed to the slow acceptance of Buridan's paradigm. We present here a package of open source software designed to track a single animal walking in a homogenous environment (Buritrack) and to analyze its trajectory. The Centroid Trajectory Analysis (CeTrAn) software is coded in the open source statistics project R. It extracts eleven metrics and includes correlation analyses and a Principal Components Analysis (PCA). It was designed to be easily customized to personal requirements. In combination with inexpensive hardware, these tools can readily be used for teaching and research purposes. We demonstrate the capabilities of our package by measuring the locomotor behavior of adult Drosophila melanogaster (whose wings were clipped), either in the presence or in the absence of visual targets, and comparing the latter to different computer-generated data. The analysis of the trajectories confirms that flies are centrophobic and shows that inaccessible visual targets can alter the orientation of the flies without changing their overall patterns of activity. Using computer generated data, the analysis software was tested, and chance values for some metrics (as well as chance value for their correlation) were set. Our results prompt the hypothesis that fixation behavior is observed only if negative phototaxis can overcome the propensity of the flies to avoid the center of the platform. Together with our companion paper, we provide new tools to promote Open Science as well as the collection and analysis of digital behavioral data.

Research on ARM Numerical Control System

NASA Astrophysics Data System (ADS)

Wei, Xu; JiHong, Chen

Computerized Numerical Control (CNC) machine tools is the foundation of modern manufacturing systems, whose advanced digital technology is the key to solve the problem of sustainable development of machine tool manufacturing industry. The paper is to design CNC system embedded on ARM and indicates the hardware design and the software systems supported. On the hardware side: the driving chip of the motor control unit, as the core of components, is MCX314AL of DSP motion control which is developed by NOVA Electronics Co., Ltd. of Japan. It make convenient to control machine because of its excellent performance, simple interface, easy programming. On the Software side, the uC/OS-2 is selected as the embedded operating system of the open source, which makes a detailed breakdown of the modules of the CNC system. Those priorities are designed according to their actual requirements. The ways of communication between the module and the interrupt response are so different that it guarantees real-time property and reliability of the numerical control system. Therefore, it not only meets the requirements of the current social precision machining, but has good man-machine interface and network support to facilitate a variety of craftsmen use.

The upgrade of the H.E.S.S. cameras

NASA Astrophysics Data System (ADS)

Giavitto, Gianluca; Ashton, Terry; Balzer, Arnim; Berge, David; Brun, Francois; Chaminade, Thomas; Delagnes, Eric; Fontaine, Gerard; Füßling, Matthias; Giebels, Berrie; Glicenstein, Jean-Francois; Gräber, Tobias; Hinton, Jim; Jahnke, Albert; Klepser, Stefan; Kossatz, Marko; Kretzschmann, Axel; Lefranc, Valentin; Leich, Holger; Lüdecke, Hartmut; Lypova, Iryna; Manigot, Pascal; Marandon, Vincent; Moulin, Emmanuel; de Naurois, Mathieu; Nayman, Patrick; Ohm, Stefan; Penno, Marek; Ross, Duncan; Salek, David; Schade, Markus; Schwab, Thomas; Simoni, Rachel; Stegmann, Christian; Steppa, Constantin; Thornhill, Julian; Toussnel, Francois

2017-01-01

The High Energy Stereoscopic System (H.E.S.S.) is an array of five imaging atmospheric Cherenkov telescopes (IACT) located in Namibia. In order to assure the continuous operation of H.E.S.S. at its full sensitivity until and possibly beyond the advent of CTA, the older cameras, installed in 2003, are currently undergoing an extensive upgrade. Its goals are reducing the system failure rate, reducing the dead time and improving the overall performance of the array. All camera components have been upgraded, except the mechanical structure and the photo-multiplier tubes (PMTs). Novel technical solutions have been introduced: the upgraded readout electronics is based on the NECTAr analog memory chip; the control of the hardware is carried out by an FPGA coupled to an embedded ARM computer; the control software was re-written from scratch and it is based on modern C++ open source libraries. These hardware and software solutions offer very good performance, robustness and flexibility. The first camera was fielded in July 2015 and has been successfully commissioned; the rest is scheduled to be upgraded in September 2016. The present contribution describes the design, the testing and the performance of the new H.E.S.S. camera and its components.

A one-piece 3D printed flexure translation stage for open-source microscopy

NASA Astrophysics Data System (ADS)

Sharkey, James P.; Foo, Darryl C. W.; Kabla, Alexandre; Baumberg, Jeremy J.; Bowman, Richard W.

2016-02-01

Open source hardware has the potential to revolutionise the way we build scientific instruments; with the advent of readily available 3D printers, mechanical designs can now be shared, improved, and replicated faster and more easily than ever before. However, printed parts are typically plastic and often perform poorly compared to traditionally machined mechanisms. We have overcome many of the limitations of 3D printed mechanisms by exploiting the compliance of the plastic to produce a monolithic 3D printed flexure translation stage, capable of sub-micron-scale motion over a range of 8 × 8 × 4 mm. This requires minimal post-print clean-up and can be automated with readily available stepper motors. The resulting plastic composite structure is very stiff and exhibits remarkably low drift, moving less than 20 μm over the course of a week, without temperature stabilisation. This enables us to construct a miniature microscope with excellent mechanical stability, perfect for time-lapse measurements in situ in an incubator or fume hood. The ease of manufacture lends itself to use in containment facilities where disposability is advantageous and to experiments requiring many microscopes in parallel. High performance mechanisms based on printed flexures need not be limited to microscopy, and we anticipate their use in other devices both within the laboratory and beyond.

SET: a pupil detection method using sinusoidal approximation

PubMed Central

Javadi, Amir-Homayoun; Hakimi, Zahra; Barati, Morteza; Walsh, Vincent; Tcheang, Lili

2015-01-01

Mobile eye-tracking in external environments remains challenging, despite recent advances in eye-tracking software and hardware engineering. Many current methods fail to deal with the vast range of outdoor lighting conditions and the speed at which these can change. This confines experiments to artificial environments where conditions must be tightly controlled. Additionally, the emergence of low-cost eye tracking devices calls for the development of analysis tools that enable non-technical researchers to process the output of their images. We have developed a fast and accurate method (known as “SET”) that is suitable even for natural environments with uncontrolled, dynamic and even extreme lighting conditions. We compared the performance of SET with that of two open-source alternatives by processing two collections of eye images: images of natural outdoor scenes with extreme lighting variations (“Natural”); and images of less challenging indoor scenes (“CASIA-Iris-Thousand”). We show that SET excelled in outdoor conditions and was faster, without significant loss of accuracy, indoors. SET offers a low cost eye-tracking solution, delivering high performance even in challenging outdoor environments. It is offered through an open-source MATLAB toolkit as well as a dynamic-link library (“DLL”), which can be imported into many programming languages including C# and Visual Basic in Windows OS (www.eyegoeyetracker.co.uk). PMID:25914641

A Low Cost/Low Power Open Source Sensor System for Automated Tuberculosis Drug Susceptibility Testing

PubMed Central

Kim, Kyukwang; Kim, Hyeong Keun; Lim, Hwijoon; Myung, Hyun

2016-01-01

In this research an open source, low power sensor node was developed to check the growth of mycobacteria in a culture bottle with a nitrate reductase assay method for a drug susceptibility test. The sensor system reports the temperature and color sensor output frequency change of the culture bottle when the device is triggered. After the culture process is finished, a nitrite ion detecting solution based on a commercial nitrite ion detection kit is injected into the culture bottle by a syringe pump to check bacterial growth by the formation of a pigment by the reaction between the solution and the color sensor. Sensor status and NRA results are broadcasted via a Bluetooth low energy beacon. An Android application was developed to collect the broadcasted data, classify the status of cultured samples from multiple devices, and visualize the data for the end users, circumventing the need to examine each culture bottle manually during a long culture period. The authors expect that usage of the developed sensor will decrease the cost and required labor for handling large amounts of patient samples in local health centers in developing countries. All 3D-printerable hardware parts, a circuit diagram, and software are available online. PMID:27338406

Informatics in radiology: web-based preliminary reporting system for radiology residents with PACS integration.

PubMed

O'Connell, Timothy; Chang, Debra

2012-01-01

While on call, radiology residents review imaging studies and issue preliminary reports to referring clinicians. In the absence of an integrated reporting system at the training sites of the authors' institution, residents were typing and faxing preliminary reports. To partially automate the on-call resident workflow, a Web-based system for resident reporting was developed by using the free open-source xAMP Web application framework and an open-source DICOM (Digital Imaging and Communications in Medicine) software toolkit, with the goals of reducing errors and lowering barriers to education. This reporting system integrates with the picture archiving and communication system to display a worklist of studies. Patient data are automatically entered in the preliminary report to prevent identification errors and simplify the report creation process. When the final report for a resident's on-call study is available, the reporting system queries the report broker for the final report, and then displays the preliminary report side by side with the final report, thus simplifying the review process and encouraging review of all of the resident's reports. The xAMP Web application framework should be considered for development of radiology department informatics projects owing to its zero cost, minimal hardware requirements, ease of programming, and large support community.

Megawatt-Scale Power Hardware-in-the-Loop Simulation Testing of a Power Conversion Module for Naval Applications

DTIC Science & Technology

2015-06-21

problem was detected . Protection elements were implemented to trigger on over- voltage , over-current, over/under-frequency, and zero-sequence voltage ...power hardware in the loop simulation of distribution networks with photovoltaic generation,” International Journal of Renewable Energy Research...source modules were intended to support both emulation of a representative gas turbine generator set, as well as a flexible, controllable voltage source

Mars Spark Source Prototype

NASA Technical Reports Server (NTRS)

Eichenberg, Dennis J.; Lindamood, Glenn R.; Weiland, Karen J.; VanderWal, Randall L.

1999-01-01

The Mars Spark Source Prototype (MSSP) hardware has been developed as part of a proof of concept system for the detection of trace metals such as lead, cadmium, and arsenic in Martian dusts and soils. A spark discharge produces plasma from a soil sample and detectors measure the optical emission from metals in the plasma that will allow their identification and quantification. Trace metal measurements are vital for the assessment of the potential toxicity of the Martian environment for human exploration. The current method of X-ray fluorescence can yield concentrations only of major species. Other instruments are incompatible with the volume, weight, and power constraints for a Mars mission. The instrument will be developed primarily for use in the Martian environment, but would be adaptable for terrestrial use in environmental monitoring. This paper describes the Mars Spark Source Prototype hardware, the results of the characterization tests, and future plans for hardware development.

Low Cost Real Time Autonomous Remote Monitoring Platform

NASA Astrophysics Data System (ADS)

Rodríguez, J. R.; Maldonado, P. M.; Pierson, J. J.; Harris, L.

2016-02-01

Environmental scientists have a need for gathering multiple parameters during specific time periods to answer their research questions. Most available monitoring systems are very expensive and closed systems, which limits the potential to scale up research projects. We developed a low cost, autonomous, real-time monitoring platform that is both open hardware/software and easy to build, deploy, manage and maintain. The hardware is built with off-the-shelf components and a credit card sized computer called Raspberry Pi, running an open source operating (Raspbian). The system runs off a set of batteries and a solar panel, which makes it ideal for remote locations. The software is divided into three parts: 1) a framework for abstracting the sensors (initializing, pooling and communications) designed in python and using a fully object-oriented design, making it easy for new sensor to be added with minimal code changes, 2) a web front end for managing the entire system, 3) a data store (database) framework for local and remote data retrieval and reporting services. Connectivity to the system can be accomplished through a Wi-Fi or cellular Internet connection. Scientists are being forced to do more with less, in response our platform will provide them with a flexible system that can improve the process of data gathering with an accessible, modular, low-cost, and efficient monitoring system. Currently, we have the required permits from the Department of Natural Resources in Puerto Rico to deploy the platform at the Laguna Grande Bioluminescence Lagoon in Fajardo, PR. This station will include probes for pH, DO, Conductivity and water temperature.

Global Dynamic Exposure and the OpenBuildingMap

NASA Astrophysics Data System (ADS)

Schorlemmer, D.; Beutin, T.; Hirata, N.; Hao, K. X.; Wyss, M.; Cotton, F.; Prehn, K.

2015-12-01

Detailed understanding of local risk factors regarding natural catastrophes requires in-depth characterization of the local exposure. Current exposure capture techniques have to find the balance between resolution and coverage. We aim at bridging this gap by employing a crowd-sourced approach to exposure capturing focusing on risk related to earthquake hazard. OpenStreetMap (OSM), the rich and constantly growing geographical database, is an ideal foundation for us. More than 2.5 billion geographical nodes, more than 150 million building footprints (growing by ~100'000 per day), and a plethora of information about school, hospital, and other critical facility locations allow us to exploit this dataset for risk-related computations. We will harvest this dataset by collecting exposure and vulnerability indicators from explicitly provided data (e.g. hospital locations), implicitly provided data (e.g. building shapes and positions), and semantically derived data, i.e. interpretation applying expert knowledge. With this approach, we can increase the resolution of existing exposure models from fragility classes distribution via block-by-block specifications to building-by-building vulnerability. To increase coverage, we will provide a framework for collecting building data by any person or community. We will implement a double crowd-sourced approach to bring together the interest and enthusiasm of communities with the knowledge of earthquake and engineering experts. The first crowd-sourced approach aims at collecting building properties in a community by local people and activists. This will be supported by tailored building capture tools for mobile devices for simple and fast building property capturing. The second crowd-sourced approach involves local experts in estimating building vulnerability that will provide building classification rules that translate building properties into vulnerability and exposure indicators as defined in the Building Taxonomy 2.0 developed by the Global Earthquake Model (GEM). These indicators will then be combined with a hazard model using the GEM OpenQuake engine to compute a risk model. The free/open framework we will provide can be used on commodity hardware for local to regional exposure capturing and for communities to understand their earthquake risk.

Architectural Improvements and New Processing Tools for the Open XAL Online Model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Allen, Christopher K; Pelaia II, Tom; Freed, Jonathan M

The online model is the component of Open XAL providing accelerator modeling, simulation, and dynamic synchronization to live hardware. Significant architectural changes and feature additions have been recently made in two separate areas: 1) the managing and processing of simulation data, and 2) the modeling of RF cavities. Simulation data and data processing have been completely decoupled. A single class manages all simulation data while standard tools were developed for processing the simulation results. RF accelerating cavities are now modeled as composite structures where parameter and dynamics computations are distributed. The beam and hardware models both maintain their relative phasemore » information, which allows for dynamic phase slip and elapsed time computation.« less

A Novel Low-Cost Open-Hardware Platform for Monitoring Soil Water Content and Multiple Soil-Air-Vegetation Parameters

PubMed Central

Bitella, Giovanni; Rossi, Roberta; Bochicchio, Rocco; Perniola, Michele; Amato, Mariana

2014-01-01

Monitoring soil water content at high spatio-temporal resolution and coupled to other sensor data is crucial for applications oriented towards water sustainability in agriculture, such as precision irrigation or phenotyping root traits for drought tolerance. The cost of instrumentation, however, limits measurement frequency and number of sensors. The objective of this work was to design a low cost “open hardware” platform for multi-sensor measurements including water content at different depths, air and soil temperatures. The system is based on an open-source ARDUINO microcontroller-board, programmed in a simple integrated development environment (IDE). Low cost high-frequency dielectric probes were used in the platform and lab tested on three non-saline soils (ECe1: 2.5 < 0.1 mS/cm). Empirical calibration curves were subjected to cross-validation (leave-one-out method), and normalized root mean square error (NRMSE) were respectively 0.09 for the overall model, 0.09 for the sandy soil, 0.07 for the clay loam and 0.08 for the sandy loam. The overall model (pooled soil data) fitted the data very well (R2 = 0.89) showing a high stability, being able to generate very similar RMSEs during training and validation (RMSEtraining = 2.63; RMSEvalidation = 2.61). Data recorded on the card were automatically sent to a remote server allowing repeated field-data quality checks. This work provides a framework for the replication and upgrading of a customized low cost platform, consistent with the open source approach whereby sharing information on equipment design and software facilitates the adoption and continuous improvement of existing technologies. PMID:25337742

Closed Loop Experiment Manager (CLEM)-An Open and Inexpensive Solution for Multichannel Electrophysiological Recordings and Closed Loop Experiments.

PubMed

Hazan, Hananel; Ziv, Noam E

2017-01-01

There is growing need for multichannel electrophysiological systems that record from and interact with neuronal systems in near real-time. Such systems are needed, for example, for closed loop, multichannel electrophysiological/optogenetic experimentation in vivo and in a variety of other neuronal preparations, or for developing and testing neuro-prosthetic devices, to name a few. Furthermore, there is a need for such systems to be inexpensive, reliable, user friendly, easy to set-up, open and expandable, and possess long life cycles in face of rapidly changing computing environments. Finally, they should provide powerful, yet reasonably easy to implement facilities for developing closed-loop protocols for interacting with neuronal systems. Here, we survey commercial and open source systems that address these needs to varying degrees. We then present our own solution, which we refer to as Closed Loop Experiments Manager (CLEM). CLEM is an open source, soft real-time, Microsoft Windows desktop application that is based on a single generic personal computer (PC) and an inexpensive, general-purpose data acquisition board. CLEM provides a fully functional, user-friendly graphical interface, possesses facilities for recording, presenting and logging electrophysiological data from up to 64 analog channels, and facilities for controlling external devices, such as stimulators, through digital and analog interfaces. Importantly, it includes facilities for running closed-loop protocols written in any programming language that can generate dynamic link libraries (DLLs). We describe the application, its architecture and facilities. We then demonstrate, using networks of cortical neurons growing on multielectrode arrays (MEA) that despite its reliance on generic hardware, its performance is appropriate for flexible, closed-loop experimentation at the neuronal network level.

Closed Loop Experiment Manager (CLEM)—An Open and Inexpensive Solution for Multichannel Electrophysiological Recordings and Closed Loop Experiments

PubMed Central

Hazan, Hananel; Ziv, Noam E.

2017-01-01

There is growing need for multichannel electrophysiological systems that record from and interact with neuronal systems in near real-time. Such systems are needed, for example, for closed loop, multichannel electrophysiological/optogenetic experimentation in vivo and in a variety of other neuronal preparations, or for developing and testing neuro-prosthetic devices, to name a few. Furthermore, there is a need for such systems to be inexpensive, reliable, user friendly, easy to set-up, open and expandable, and possess long life cycles in face of rapidly changing computing environments. Finally, they should provide powerful, yet reasonably easy to implement facilities for developing closed-loop protocols for interacting with neuronal systems. Here, we survey commercial and open source systems that address these needs to varying degrees. We then present our own solution, which we refer to as Closed Loop Experiments Manager (CLEM). CLEM is an open source, soft real-time, Microsoft Windows desktop application that is based on a single generic personal computer (PC) and an inexpensive, general-purpose data acquisition board. CLEM provides a fully functional, user-friendly graphical interface, possesses facilities for recording, presenting and logging electrophysiological data from up to 64 analog channels, and facilities for controlling external devices, such as stimulators, through digital and analog interfaces. Importantly, it includes facilities for running closed-loop protocols written in any programming language that can generate dynamic link libraries (DLLs). We describe the application, its architecture and facilities. We then demonstrate, using networks of cortical neurons growing on multielectrode arrays (MEA) that despite its reliance on generic hardware, its performance is appropriate for flexible, closed-loop experimentation at the neuronal network level. PMID:29093659

Open Source Dataturbine (OSDT) Android Sensorpod in Environmental Observing Systems

NASA Astrophysics Data System (ADS)

Fountain, T. R.; Shin, P.; Tilak, S.; Trinh, T.; Smith, J.; Kram, S.

2014-12-01

The OSDT Android SensorPod is a custom-designed mobile computing platform for assembling wireless sensor networks for environmental monitoring applications. Funded by an award from the Gordon and Betty Moore Foundation, the OSDT SensorPod represents a significant technological advance in the application of mobile and cloud computing technologies to near-real-time applications in environmental science, natural resources management, and disaster response and recovery. It provides a modular architecture based on open standards and open-source software that allows system developers to align their projects with industry best practices and technology trends, while avoiding commercial vendor lock-in to expensive proprietary software and hardware systems. The integration of mobile and cloud-computing infrastructure represents a disruptive technology in the field of environmental science, since basic assumptions about technology requirements are now open to revision, e.g., the roles of special purpose data loggers and dedicated site infrastructure. The OSDT Android SensorPod was designed with these considerations in mind, and the resulting system exhibits the following characteristics - it is flexible, efficient and robust. The system was developed and tested in the three science applications: 1) a fresh water limnology deployment in Wisconsin, 2) a near coastal marine science deployment at the UCSD Scripps Pier, and 3) a terrestrial ecological deployment in the mountains of Taiwan. As part of a public education and outreach effort, a Facebook page with daily ocean pH measurements from the UCSD Scripps pier was developed. Wireless sensor networks and the virtualization of data and network services is the future of environmental science infrastructure. The OSDT Android SensorPod was designed and developed to harness these new technology developments for environmental monitoring applications.

Current Concepts and Ongoing Research in the Prevention and Treatment of Open Fracture Infections

PubMed Central

Hannigan, Geoffrey D.; Pulos, Nicholas; Grice, Elizabeth A.; Mehta, Samir

2015-01-01

Significance: Open fractures are fractures in which the bone has violated the skin and soft tissue. Because of their severity, open fractures are associated with complications that can result in increased lengths of hospital stays, multiple operative interventions, and even amputation. One of the factors thought to influence the extent of these complications is exposure and contamination of the open fracture with environmental microorganisms, potentially those that are pathogenic in nature. Recent Advances: Current open fracture care aims to prevent infection by wound classification, prophylactic antibiotic administration, debridement and irrigation, and stable fracture fixation. Critical Issues: Despite these established treatment paradigms, infections and infection-related complications remain a significant clinical burden. To address this, improvements need to be made in our ability to detect bacterial infections, effectively remove wound contamination, eradicate infections, and treat and prevent biofilm formation associated with fracture fixation hardware. Future Directions: Current research is addressing these critical issues. While culture methods are of limited value, culture-independent molecular techniques are being developed to provide informative detection of bacterial contamination and infection. Other advanced contamination- and infection-detecting techniques are also being investigated. New hardware-coating methods are being developed to minimize the risk of biofilm formation in wounds, and immune stimulation techniques are being developed to prevent open fracture infections. PMID:25566415

Open hardware, low cost, air quality stations for monitoring ozone in coastal area

NASA Astrophysics Data System (ADS)

Lima, Marco; Donzella, Davide; Pintus, Fabio; Fedi, Adriano; Ferrari, Daniele; Massabò, Marco

2014-05-01

Ozone concentrations in urban and coastal area are a great concern for citizens and, consequently regulator. In the last 20 years the Ozone concentration is almost doubled and it has attracted the public attention because of the well know harmful impacts on human health and biosphere in general. Official monitoring networks usually comprise high precision, high accuracy observation stations, usually managed by public administrations and environmental agency; unfortunately due to their high costs of installation and maintenance, the monitoring stations are relatively sparse. This kind of monitoring networks have been recognized to be unsuitable to effectively characterize the high variability of air quality, especially in areas where pollution sources are various and often not static. We present a prototype of a low cost station for air quality monitoring, specifically developed for complementing the official monitoring stations improving the representation of air quality spatial distribution. We focused on a semi-professional product that could guarantee the highest reliability at the lowest possible cost, supported by a consistent infrastructure for data management. We test two type of Ozone sensor electrochemical and metal oxide. This work is integrated in the ACRONET Paradigm ® project: an open-hardware platform strongly oriented on environmental monitoring. All software and hardware sources will be available on the web. Thus, a computer and a small amount of work tools will be sufficient to create new monitoring networks, with the only constraint to share all the data obtained. It will so possible to create a real "sensing community". The prototype is currently able to measure ozone level, temperature and relative humidity, but soon, with the upcoming changes, it will be able also to monitor dust, carbon monoxide and nitrogen dioxide, always through the use of commercial sensors. The sensors are grouped in a compact board that interfaces with a data-logger able to transmit data to a dedicated server through a GPRS module (no ad hoc radio infrastructure needed). Due to the GPRS low latency transmission the data are transmitted in near-real time. The prototype has an independent power supply. The sensors outputs are directly compared with the measurement of the official fixed monitoring stations. We present preliminary tests of a ozone level assessment obtained without laboratory calibration during a first field campaign in Savona (Italy); the preliminary verification and test show reasonable agreement between low cost sensors and fixed monitoring station ozone level trends (low cost sensors detect gas concentration at ppb level). The preliminary results are promising for complementing the fixed official monitoring networks with low-cost sensors.

Interactive Internet Based Pendulum for Learning Mechatronics

NASA Astrophysics Data System (ADS)

Sethson, Magnus R.

2003-01-01

This paper describes an Internet based remote experimental setup of a double lined pendulum mechanism for students experiments at the M. Sc. Level. Some of the first year experience using this web-based setup in classes is referred. In most of the courses given at the division of mechanical engineering systems at Linkoeping Institute of Technology we provide experimental setups to enhance the teaching Of M.Sc. students. Many of these experimental setups involve mechatronical systems. Disciplines like fluid power, electronics, and mechanics and also software technologies are used in each experiment. As our campus has recently been split into two different cities some new concepts for distance learning have been studied. The one described here tries to implement remotely controlled mechatronic setups for teaching basic programming of real-time operating systems and analysis of the dynamics of mechanical systems. The students control the regulators for the pendulum through a web interface and get measurement results and a movie back through their email. The present setup uses a double linked pendulum that is controlled by a DC-motor and monitored through both camera and angular position sensors. All software needed is hosted on a double-processor PC running the RedHat 7.1. distribution complemented with real-time scheduling using DIAPM-RTAI 1.7. The Internet site is presented to the students using PHP, Apache and MySQL. All of the used software originates from the open source domain. The experience from integrating these technologies and security issues is discussed together with the web-camera interface. One of the important experiences from this project so far is the need for a good visual feedback. This is both in terms of video speed but also in resolution. It has been noticed that when the students makes misstates and wants to search the failure they want clear, large images with high resolution to support their personal believes in the cause of the failure. Even if the student does not need a high resolution image to get the idea of the mechanics and the function of the pendulum, they need such high quality images to get confidence in the hardware. It is important to support this when the ability to direct hand-on contact with the hardware is taken away. Some of the experiences in combining open source software; real-time scheduling and measurement hardware into a cost efficient way is also discussed. The pendulum has been available publicly on the Internet but has now been removed due to security issues.

Extended behavioural device modelling and circuit simulation with Qucs-S

NASA Astrophysics Data System (ADS)

Brinson, M. E.; Kuznetsov, V.

2018-03-01

Current trends in circuit simulation suggest a growing interest in open source software that allows access to more than one simulation engine while simultaneously supporting schematic drawing tools, behavioural Verilog-A and XSPICE component modelling, and output data post-processing. This article introduces a number of new features recently implemented in the 'Quite universal circuit simulator - SPICE variant' (Qucs-S), including structure and fundamental schematic capture algorithms, at the same time highlighting their use in behavioural semiconductor device modelling. Particular importance is placed on the interaction between Qucs-S schematics, equation-defined devices, SPICE B behavioural sources and hardware description language (HDL) scripts. The multi-simulator version of Qucs is a freely available tool that offers extended modelling and simulation features compared to those provided by legacy circuit simulators. The performance of a number of Qucs-S modelling extensions are demonstrated with a GaN HEMT compact device model and data obtained from tests using the Qucs-S/Ngspice/Xyce ©/SPICE OPUS multi-engine circuit simulator.

Fixed-target protein serial microcrystallography with an x-ray free electron laser

PubMed Central

Hunter, Mark S.; Segelke, Brent; Messerschmidt, Marc; Williams, Garth J.; Zatsepin, Nadia A.; Barty, Anton; Benner, W. Henry; Carlson, David B.; Coleman, Matthew; Graf, Alexander; Hau-Riege, Stefan P.; Pardini, Tommaso; Seibert, M. Marvin; Evans, James; Boutet, Sébastien; Frank, Matthias

2014-01-01

We present results from experiments at the Linac Coherent Light Source (LCLS) demonstrating that serial femtosecond crystallography (SFX) can be performed to high resolution (~2.5 Å) using protein microcrystals deposited on an ultra-thin silicon nitride membrane and embedded in a preservation medium at room temperature. Data can be acquired at a high acquisition rate using x-ray free electron laser sources to overcome radiation damage, while sample consumption is dramatically reduced compared to flowing jet methods. We achieved a peak data acquisition rate of 10 Hz with a hit rate of ~38%, indicating that a complete data set could be acquired in about one 12-hour LCLS shift using the setup described here, or in even less time using hardware optimized for fixed target SFX. This demonstration opens the door to ultra low sample consumption SFX using the technique of diffraction-before-destruction on proteins that exist in only small quantities and/or do not produce the copious quantities of microcrystals required for flowing jet methods. PMID:25113598

Influence of the spectral distribution of light on the characteristics of photovoltaic panel. Comparison between simulation and experimental

NASA Astrophysics Data System (ADS)

Chadel, Meriem; Bouzaki, Mohammed Moustafa; Chadel, Asma; Petit, Pierre; Sawicki, Jean-Paul; Aillerie, Michel; Benyoucef, Boumediene

2017-02-01

We present and analyze experimental results obtained with a laboratory setup based on a hardware and smart instrumentation for the complete study of performance of PV panels using for illumination an artificial radiation source (Halogen lamps). Associated to an accurate analysis, this global experimental procedure allows the determination of effective performance under standard conditions thanks to a simulation process originally developed under Matlab software environment. The uniformity of the irradiated surface was checked by simulation of the light field. We studied the response of standard commercial photovoltaic panels under enlightenment measured by a spectrometer with different spectra for two sources, halogen lamps and sunlight. Then, we bring a special attention to the influence of the spectral distribution of light on the characteristics of photovoltaic panel, that we have performed as a function of temperature and for different illuminations with dedicated measurements and studies of the open circuit voltage and short-circuit current.

Scale out databases for CERN use cases

NASA Astrophysics Data System (ADS)

Baranowski, Zbigniew; Grzybek, Maciej; Canali, Luca; Lanza Garcia, Daniel; Surdy, Kacper

2015-12-01

Data generation rates are expected to grow very fast for some database workloads going into LHC run 2 and beyond. In particular this is expected for data coming from controls, logging and monitoring systems. Storing, administering and accessing big data sets in a relational database system can quickly become a very hard technical challenge, as the size of the active data set and the number of concurrent users increase. Scale-out database technologies are a rapidly developing set of solutions for deploying and managing very large data warehouses on commodity hardware and with open source software. In this paper we will describe the architecture and tests on database systems based on Hadoop and the Cloudera Impala engine. We will discuss the results of our tests, including tests of data loading and integration with existing data sources and in particular with relational databases. We will report on query performance tests done with various data sets of interest at CERN, notably data from the accelerator log database.

Manned space flight nuclear system safety. Volume 1: base nuclear system safety

NASA Technical Reports Server (NTRS)

1972-01-01

The mission and terrestrial nuclear safety aspects of future long duration manned space missions in low earth orbit are discussed. Nuclear hazards of a typical low earth orbit Space Base mission (from natural sources and on-board nuclear hardware) have been identified and evaluated. Some of the principal nuclear safety design and procedural considerations involved in launch, orbital, and end of mission operations are presented. Areas of investigation include radiation interactions with the crew, subsystems, facilities, experiments, film, interfacing vehicles, nuclear hardware and the terrestrial populace. Results of the analysis indicate: (1) the natural space environment can be the dominant radiation source in a low earth orbit where reactors are effectively shielded, (2) with implementation of safety guidelines the reactor can present a low risk to the crew, support personnel, the terrestrial populace, flight hardware and the mission, (3) ten year missions are feasible without exceeding integrated radiation limits assigned to flight hardware, and (4) crew stay-times up to one year are feasible without storm shelter provisions.

Evaluation of Cathode Air Flow Transients in a SOFC/GT Hybrid System Using Hardware in the Loop Simulation.

PubMed

Zhou, Nana; Yang, Chen; Tucker, David

2015-02-01

Thermal management in the fuel cell component of a direct fired solid oxide fuel cell gas turbine (SOFC/GT) hybrid power system can be improved by effective management and control of the cathode airflow. The disturbances of the cathode airflow were accomplished by diverting air around the fuel cell system through the manipulation of a hot-air bypass valve in open loop experiments, using a hardware-based simulation facility designed and built by the U.S. Department of Energy, National Energy Technology Laboratory (NETL). The dynamic responses of the fuel cell component and hardware component of the hybrid system were studied in this paper.

E-Books Mediator: Nicholas Bogaty--Open Ebook Forum, New York

ERIC Educational Resources Information Center

Library Journal, 2004

2004-01-01

This article is about the work of Nick Bogaty, executive director of the Open eBook Forum. Nick Bogaty is not a librarian, but he plays nicely with them, along with publishers, hardware manufacturers, software producers, database vendors, and disability rights advocates. All are groups that share an interest in making e-books work for their…

Open architecture CNC system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tal, J.; Lopez, A.; Edwards, J.M.

1995-04-01

In this paper, an alternative solution to the traditional CNC machine tool controller has been introduced. Software and hardware modules have been described and their incorporation in a CNC control system has been outlined. This type of CNC machine tool controller demonstrates that technology is accessible and can be readily implemented into an open architecture machine tool controller. Benefit to the user is greater controller flexibility, while being economically achievable. PC based, motion as well as non-motion features will provide flexibility through a Windows environment. Up-grading this type of controller system through software revisions will keep the machine tool inmore » a competitive state with minimal effort. Software and hardware modules are mass produced permitting competitive procurement and incorporation. Open architecture CNC systems provide diagnostics thus enhancing maintainability, and machine tool up-time. A major concern of traditional CNC systems has been operator training time. Training time can be greatly minimized by making use of Windows environment features.« less

OpenDanubia - An integrated, modular simulation system to support regional water resource management

NASA Astrophysics Data System (ADS)

Muerth, M.; Waldmann, D.; Heinzeller, C.; Hennicker, R.; Mauser, W.

2012-04-01

The already completed, multi-disciplinary research project GLOWA-Danube has developed a regional scale, integrated modeling system, which was successfully applied on the 77,000 km2 Upper Danube basin to investigate the impact of Global Change on both the natural and anthropogenic water cycle. At the end of the last project phase, the integrated modeling system was transferred into the open source project OpenDanubia, which now provides both the core system as well as all major model components to the general public. First, this will enable decision makers from government, business and management to use OpenDanubia as a tool for proactive management of water resources in the context of global change. Secondly, the model framework to support integrated simulations and all simulation models developed for OpenDanubia in the scope of GLOWA-Danube are further available for future developments and research questions. OpenDanubia allows for the investigation of water-related scenarios considering different ecological and economic aspects to support both scientists and policy makers to design policies for sustainable environmental management. OpenDanubia is designed as a framework-based, distributed system. The model system couples spatially distributed physical and socio-economic process during run-time, taking into account their mutual influence. To simulate the potential future impacts of Global Change on agriculture, industrial production, water supply, households and tourism businesses, so-called deep actor models are implemented in OpenDanubia. All important water-related fluxes and storages in the natural environment are implemented in OpenDanubia as spatially explicit, process-based modules. This includes the land surface water and energy balance, dynamic plant water uptake, ground water recharge and flow as well as river routing and reservoirs. Although the complete system is relatively demanding on data requirements and hardware requirements, the modular structure and the generic core system (Core Framework, Actor Framework) allows the application in new regions and the selection of a reduced number of modules for simulation. As part of the Open Source Initiative in GLOWA-Danube (opendanubia.glowa-danube.de) a comprehensive documentation for the system installation was created and both the program code of the framework and of all major components is licensed under the GNU General Public License. In addition, some helpful programs and scripts necessary for the operation and processing of input and result data sets are provided.

X-LUNA: Extending Free/Open Source Real Time Executive for On-Board Space Applications

NASA Astrophysics Data System (ADS)

Braga, P.; Henriques, L.; Zulianello, M.

2008-08-01

In this paper we present xLuna, a system based on the RTEMS [1] Real-Time Operating System that is able to run on demand a GNU/Linux Operating System [2] as RTEMS' lowest priority task. Linux runs in user-mode and in a different memory partition. This allows running Hard Real-Time tasks and Linux applications on the same system sharing the Hardware resources while keeping a safe isolation and the Real-Time characteristics of RTEMS. Communication between both Systems is possible through a loose coupled mechanism based on message queues. Currently only SPARC LEON2 processor with Memory Management Unit (MMU) is supported. The advantage in having two isolated systems is that non critical components are quickly developed or simply ported reducing time-to-market and budget.

Development of the CLAES instrument aperture door system

NASA Technical Reports Server (NTRS)

Stubbs, D. M.

1990-01-01

The design, assembly, and test processes followed in developing a space-qualified aperture door system are described. A blackbody calibration source is mounted inside the door, requiring the assembly to open and close a minimum of 150 cycles for instrument recalibration. Within the door system are four separate mechanisms, three of which are redundant; a pyro launch latch, a hinge bearing assembly, and a pair of pivot mechanisms. Decoupling devices within the pivot mechanisms allow an active drive unit to automatically overdrive a failed drive unit. The door is also stowable for possible Shuttle retrieval and re-entry. Illustrations and photographs of the flight hardware help acquaint the reader with the design. The aim is to pass on lessons learned in all phases of developing this spaceflight mechanism.

Best kept secrets ... Source Data Systems, Inc. (SDS).

PubMed

Andrew, W F

1991-03-01

The SDS/MEDNET system is a cost-effective option for small- to medium-size hospitals (up to 400 beds). The parameter-driven system lets users control operations with only occasional SDS assistance. A full application set, available for modular selection to reduce upfront costs while facilitating steady growth and protecting client investment, is adaptable to multi-facility environments. The industry-standard, Intel-based multi-user processors, network communications and protocols assure high efficiency, low-cost solutions independent of any one hardware vendor. Sustained growth in both client base and product offerings point to a high level of responsiveness and healthcare industry commitment. Corporate emphasis on user involvement and open systems integration assures clients of leading-edge capabilities. SDS/MEDNET will be a strong contender in selected marketing environments.

Open Data, Open Specifications and Free and Open Source Software: A powerful mix to create distributed Web-based water information systems

NASA Astrophysics Data System (ADS)

Arias, Carolina; Brovelli, Maria Antonia; Moreno, Rafael

2015-04-01

We are in an age when water resources are increasingly scarce and the impacts of human activities on them are ubiquitous. These problems don't respect administrative or political boundaries and they must be addressed integrating information from multiple sources at multiple spatial and temporal scales. Communication, coordination and data sharing are critical for addressing the water conservation and management issues of the 21st century. However, different countries, provinces, local authorities and agencies dealing with water resources have diverse organizational, socio-cultural, economic, environmental and information technology (IT) contexts that raise challenges to the creation of information systems capable of integrating and distributing information across their areas of responsibility in an efficient and timely manner. Tight and disparate financial resources, and dissimilar IT infrastructures (data, hardware, software and personnel expertise) further complicate the creation of these systems. There is a pressing need for distributed interoperable water information systems that are user friendly, easily accessible and capable of managing and sharing large volumes of spatial and non-spatial data. In a distributed system, data and processes are created and maintained in different locations each with competitive advantages to carry out specific activities. Open Data (data that can be freely distributed) is available in the water domain, and it should be further promoted across countries and organizations. Compliance with Open Specifications for data collection, storage and distribution is the first step toward the creation of systems that are capable of interacting and exchanging data in a seamlessly (interoperable) way. The features of Free and Open Source Software (FOSS) offer low access cost that facilitate scalability and long-term viability of information systems. The World Wide Web (the Web) will be the platform of choice to deploy and access these systems. Geospatial capabilities for mapping, visualization, and spatial analysis will be important components of these new generation of Web-based interoperable information systems in the water domain. The purpose of this presentation is to increase the awareness of scientists, IT personnel and agency managers about the advantages offered by the combined use of Open Data, Open Specifications for geospatial and water-related data collection, storage and sharing, as well as mature FOSS projects for the creation of interoperable Web-based information systems in the water domain. A case study is used to illustrate how these principles and technologies can be integrated to create a system with the previously mentioned characteristics for managing and responding to flood events.

MUSCLEMOTION: A Versatile Open Software Tool to Quantify Cardiomyocyte and Cardiac Muscle Contraction In Vitro and In Vivo.

PubMed

Sala, Luca; van Meer, Berend J; Tertoolen, Leon G J; Bakkers, Jeroen; Bellin, Milena; Davis, Richard P; Denning, Chris; Dieben, Michel A E; Eschenhagen, Thomas; Giacomelli, Elisa; Grandela, Catarina; Hansen, Arne; Holman, Eduard R; Jongbloed, Monique R M; Kamel, Sarah M; Koopman, Charlotte D; Lachaud, Quentin; Mannhardt, Ingra; Mol, Mervyn P H; Mosqueira, Diogo; Orlova, Valeria V; Passier, Robert; Ribeiro, Marcelo C; Saleem, Umber; Smith, Godfrey L; Burton, Francis L; Mummery, Christine L

2018-02-02

There are several methods to measure cardiomyocyte and muscle contraction, but these require customized hardware, expensive apparatus, and advanced informatics or can only be used in single experimental models. Consequently, data and techniques have been difficult to reproduce across models and laboratories, analysis is time consuming, and only specialist researchers can quantify data. Here, we describe and validate an automated, open-source software tool (MUSCLEMOTION) adaptable for use with standard laboratory and clinical imaging equipment that enables quantitative analysis of normal cardiac contraction, disease phenotypes, and pharmacological responses. MUSCLEMOTION allowed rapid and easy measurement of movement from high-speed movies in (1) 1-dimensional in vitro models, such as isolated adult and human pluripotent stem cell-derived cardiomyocytes; (2) 2-dimensional in vitro models, such as beating cardiomyocyte monolayers or small clusters of human pluripotent stem cell-derived cardiomyocytes; (3) 3-dimensional multicellular in vitro or in vivo contractile tissues, such as cardiac "organoids," engineered heart tissues, and zebrafish and human hearts. MUSCLEMOTION was effective under different recording conditions (bright-field microscopy with simultaneous patch-clamp recording, phase contrast microscopy, and traction force microscopy). Outcomes were virtually identical to the current gold standards for contraction measurement, such as optical flow, post deflection, edge-detection systems, or manual analyses. Finally, we used the algorithm to quantify contraction in in vitro and in vivo arrhythmia models and to measure pharmacological responses. Using a single open-source method for processing video recordings, we obtained reliable pharmacological data and measures of cardiac disease phenotype in experimental cell, animal, and human models. © 2017 The Authors.

Hardware Architecture Study for NASA's Space Software Defined Radios

NASA Technical Reports Server (NTRS)

Reinhart, Richard C.; Scardelletti, Maximilian C.; Mortensen, Dale J.; Kacpura, Thomas J.; Andro, Monty; Smith, Carl; Liebetreu, John

2008-01-01

This study defines a hardware architecture approach for software defined radios to enable commonality among NASA space missions. The architecture accommodates a range of reconfigurable processing technologies including general purpose processors, digital signal processors, field programmable gate arrays (FPGAs), and application-specific integrated circuits (ASICs) in addition to flexible and tunable radio frequency (RF) front-ends to satisfy varying mission requirements. The hardware architecture consists of modules, radio functions, and and interfaces. The modules are a logical division of common radio functions that comprise a typical communication radio. This paper describes the architecture details, module definitions, and the typical functions on each module as well as the module interfaces. Trade-offs between component-based, custom architecture and a functional-based, open architecture are described. The architecture does not specify the internal physical implementation within each module, nor does the architecture mandate the standards or ratings of the hardware used to construct the radios.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hamilton, Kathleen E.; Humble, Travis S.

Using quantum annealing to solve an optimization problem requires minor embedding a logic graph into a known hardware graph. We introduce the minor set cover (MSC) of a known graph GG : a subset of graph minors which contain any remaining minor of the graph as a subgraph, in an effort to reduce the complexity of the minor embedding problem. Any graph that can be embedded into GG will be embeddable into a member of the MSC. Focusing on embedding into the hardware graph of commercially available quantum annealers, we establish the MSC for a particular known virtual hardware, whichmore » is a complete bipartite graph. Furthermore, we show that the complete bipartite graph K N,N has a MSC of N minors, from which K N+1 is identified as the largest clique minor of K N,N. In the case of determining the largest clique minor of hardware with faults we briefly discussed this open question.« less

A data-driven modeling approach to stochastic computation for low-energy biomedical devices.

PubMed

Lee, Kyong Ho; Jang, Kuk Jin; Shoeb, Ali; Verma, Naveen

2011-01-01

Low-power devices that can detect clinically relevant correlations in physiologically-complex patient signals can enable systems capable of closed-loop response (e.g., controlled actuation of therapeutic stimulators, continuous recording of disease states, etc.). In ultra-low-power platforms, however, hardware error sources are becoming increasingly limiting. In this paper, we present how data-driven methods, which allow us to accurately model physiological signals, also allow us to effectively model and overcome prominent hardware error sources with nearly no additional overhead. Two applications, EEG-based seizure detection and ECG-based arrhythmia-beat classification, are synthesized to a logic-gate implementation, and two prominent error sources are introduced: (1) SRAM bit-cell errors and (2) logic-gate switching errors ('stuck-at' faults). Using patient data from the CHB-MIT and MIT-BIH databases, performance similar to error-free hardware is achieved even for very high fault rates (up to 0.5 for SRAMs and 7 × 10(-2) for logic) that cause computational bit error rates as high as 50%.

24 CFR 208.112 - Cost.

Code of Federal Regulations, 2010 CFR

2010-04-01

... increases. (b) At the owner's option, the cost of the computer software may include service contracts to... requirements. (c) The source of funds for the purchase of hardware or software, or contracting for services for... formatted data, including either the purchase and maintenance of computer hardware or software, or both, the...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Halbgewachs, Ronald D.; Chavez, Adrian R.

Process Control System (PCS) and Industrial Control System (ICS) security is critical to our national security. But there are a number of technological, economic, and educational impediments to PCS owners implementing effective security on their systems. Sandia National Laboratories has performed the research and development of the OPSAID (Open PCS Security Architecture for Interoperable Design), a project sponsored by the US Department of Energy Office of Electricity Delivery and Energy Reliability (DOE/OE), to address this issue. OPSAID is an open-source architecture for PCS/ICS security that provides a design basis for vendors to build add-on security devices for legacy systems, whilemore » providing a path forward for the development of inherently-secure PCS elements in the future. Using standardized hardware, a proof-of-concept prototype system was also developed. This report describes the improvements and capabilities that have been added to OPSAID since an initial report was released. Testing and validation of this architecture has been conducted in another project, Lemnos Interoperable Security Project, sponsored by DOE/OE and managed by the National Energy Technology Laboratory (NETL).« less

PWM-switching pattern-based diagnosis scheme for single and multiple open-switch damages in VSI-fed induction motor drives.

PubMed

Trabelsi, Mohamed; Boussak, Mohamed; Gossa, Moncef

2012-03-01

This paper deals with a fault detection technique for insulated-gate bipolar transistors (IGBTs) open-circuit faults in voltage source inverter (VSI)-fed induction motor drives. The novelty of this idea consists in analyzing the pulse-width modulation (PWM) switching signals and the line-to-line voltage levels during the switching times, under both healthy and faulty operating conditions. The proposed method requires line-to-line voltage measurement, which provides information about switching states and is not affected by the load. The fault diagnosis scheme is achieved using simple hardware and can be included in the existing inverter system without any difficulty. In addition, it allows not only accurate single and multiple faults diagnosis but also minimization of the fault detection time to a maximum of one switching period (T(c)). Simulated and experimental results on a 3-kW squirrel-cage induction motor drive are displayed to validate the feasibility and the effectiveness of the proposed strategy. Crown Copyright © 2011. Published by Elsevier Ltd. All rights reserved.

GPU-accelerated Tersoff potentials for massively parallel Molecular Dynamics simulations

NASA Astrophysics Data System (ADS)

Nguyen, Trung Dac

2017-03-01

The Tersoff potential is one of the empirical many-body potentials that has been widely used in simulation studies at atomic scales. Unlike pair-wise potentials, the Tersoff potential involves three-body terms, which require much more arithmetic operations and data dependency. In this contribution, we have implemented the GPU-accelerated version of several variants of the Tersoff potential for LAMMPS, an open-source massively parallel Molecular Dynamics code. Compared to the existing MPI implementation in LAMMPS, the GPU implementation exhibits a better scalability and offers a speedup of 2.2X when run on 1000 compute nodes on the Titan supercomputer. On a single node, the speedup ranges from 2.0 to 8.0 times, depending on the number of atoms per GPU and hardware configurations. The most notable features of our GPU-accelerated version include its design for MPI/accelerator heterogeneous parallelism, its compatibility with other functionalities in LAMMPS, its ability to give deterministic results and to support both NVIDIA CUDA- and OpenCL-enabled accelerators. Our implementation is now part of the GPU package in LAMMPS and accessible for public use.

Global Dynamic Exposure and the OpenBuildingMap - Communicating Risk and Involving Communities

NASA Astrophysics Data System (ADS)

Schorlemmer, Danijel; Beutin, Thomas; Hirata, Naoshi; Hao, Ken; Wyss, Max; Cotton, Fabrice; Prehn, Karsten

2017-04-01

Detailed understanding of local risk factors regarding natural catastrophes requires in-depth characterization of the local exposure. Current exposure capture techniques have to find the balance between resolution and coverage. We aim at bridging this gap by employing a crowd-sourced approach to exposure capturing, focusing on risk related to earthquake hazard. OpenStreetMap (OSM), the rich and constantly growing geographical database, is an ideal foundation for this task. More than 3.5 billion geographical nodes, more than 200 million building footprints (growing by 100'000 per day), and a plethora of information about school, hospital, and other critical facilities allows us to exploit this dataset for risk-related computations. We are combining the strengths of crowd-sourced data collection with the knowledge of experts in extracting the most information from these data. Besides relying on the very active OpenStreetMap community and the Humanitarian OpenStreetMap Team, which are collecting building information at high pace, we are providing a tailored building capture tool for mobile devices. This tool is facilitating simple and fast building property capturing for OpenStreetMap by any person or interested community. With our OpenBuildingMap system, we are harvesting this dataset by processing every building in near-realtime. We are collecting exposure and vulnerability indicators from explicitly provided data (e.g. hospital locations), implicitly provided data (e.g. building shapes and positions), and semantically derived data, i.e. interpretation applying expert knowledge. The expert knowledge is needed to translate the simple building properties as captured by OpenStreetMap users into vulnerability and exposure indicators and subsequently into building classifications as defined in the Building Taxonomy 2.0 developed by the Global Earthquake Model (GEM) and the European Macroseismic Scale (EMS98). With this approach, we increase the resolution of existing exposure models from aggregated exposure information to building-by-building vulnerability. We report on our method, on the software development for the mobile application and the server-side analysis system, and on the OpenBuildingMap (www.openbuildingmap.org), our global Tile Map Service focusing on building properties. The free/open framework we provide can be used on commodity hardware for local to regional exposure capturing, for stakeholders in disaster management and mitigation for communicating risk, and for communities to understand their risk.

Open control/display system for a telerobotics work station

NASA Technical Reports Server (NTRS)

Keslowitz, Saul

1987-01-01

A working Advanced Space Cockpit was developed that integrated advanced control and display devices into a state-of-the-art multimicroprocessor hardware configuration, using window graphics and running under an object-oriented, multitasking real-time operating system environment. This Open Control/Display System supports the idea that the operator should be able to interactively monitor, select, control, and display information about many payloads aboard the Space Station using sets of I/O devices with a single, software-reconfigurable workstation. This is done while maintaining system consistency, yet the system is completely open to accept new additions and advances in hardware and software. The Advanced Space Cockpit, linked to Grumman's Hybrid Computing Facility and Large Amplitude Space Simulator (LASS), was used to test the Open Control/Display System via full-scale simulation of the following tasks: telerobotic truss assembly, RCS and thermal bus servicing, CMG changeout, RMS constrained motion and space constructible radiator assembly, HPA coordinated control, and OMV docking and tumbling satellite retrieval. The proposed man-machine interface standard discussed has evolved through many iterations of the tasks, and is based on feedback from NASA and Air Force personnel who performed those tasks in the LASS.

Technical note: RabbitCT--an open platform for benchmarking 3D cone-beam reconstruction algorithms.

PubMed

Rohkohl, C; Keck, B; Hofmann, H G; Hornegger, J

2009-09-01

Fast 3D cone beam reconstruction is mandatory for many clinical workflows. For that reason, researchers and industry work hard on hardware-optimized 3D reconstruction. Backprojection is a major component of many reconstruction algorithms that require a projection of each voxel onto the projection data, including data interpolation, before updating the voxel value. This step is the bottleneck of most reconstruction algorithms and the focus of optimization in recent publications. A crucial limitation, however, of these publications is that the presented results are not comparable to each other. This is mainly due to variations in data acquisitions, preprocessing, and chosen geometries and the lack of a common publicly available test dataset. The authors provide such a standardized dataset that allows for substantial comparison of hardware accelerated backprojection methods. They developed an open platform RabbitCT (www.rabbitCT.com) for worldwide comparison in backprojection performance and ranking on different architectures using a specific high resolution C-arm CT dataset of a rabbit. This includes a sophisticated benchmark interface, a prototype implementation in C++, and image quality measures. At the time of writing, six backprojection implementations are already listed on the website. Optimizations include multithreading using Intel threading building blocks and OpenMP, vectorization using SSE, and computation on the GPU using CUDA 2.0. There is a need for objectively comparing backprojection implementations for reconstruction algorithms. RabbitCT aims to provide a solution to this problem by offering an open platform with fair chances for all participants. The authors are looking forward to a growing community and await feedback regarding future evaluations of novel software- and hardware-based acceleration schemes.

A high performance, cost-effective, open-source microscope for scanning two-photon microscopy that is modular and readily adaptable.

PubMed

Rosenegger, David G; Tran, Cam Ha T; LeDue, Jeffery; Zhou, Ning; Gordon, Grant R

2014-01-01

Two-photon laser scanning microscopy has revolutionized the ability to delineate cellular and physiological function in acutely isolated tissue and in vivo. However, there exist barriers for many laboratories to acquire two-photon microscopes. Additionally, if owned, typical systems are difficult to modify to rapidly evolving methodologies. A potential solution to these problems is to enable scientists to build their own high-performance and adaptable system by overcoming a resource insufficiency. Here we present a detailed hardware resource and protocol for building an upright, highly modular and adaptable two-photon laser scanning fluorescence microscope that can be used for in vitro or in vivo applications. The microscope is comprised of high-end componentry on a skeleton of off-the-shelf compatible opto-mechanical parts. The dedicated design enabled imaging depths close to 1 mm into mouse brain tissue and a signal-to-noise ratio that exceeded all commercial two-photon systems tested. In addition to a detailed parts list, instructions for assembly, testing and troubleshooting, our plan includes complete three dimensional computer models that greatly reduce the knowledge base required for the non-expert user. This open-source resource lowers barriers in order to equip more laboratories with high-performance two-photon imaging and to help progress our understanding of the cellular and physiological function of living systems.

A High Performance, Cost-Effective, Open-Source Microscope for Scanning Two-Photon Microscopy that Is Modular and Readily Adaptable

PubMed Central

Rosenegger, David G.; Tran, Cam Ha T.; LeDue, Jeffery; Zhou, Ning; Gordon, Grant R.

2014-01-01

Two-photon laser scanning microscopy has revolutionized the ability to delineate cellular and physiological function in acutely isolated tissue and in vivo. However, there exist barriers for many laboratories to acquire two-photon microscopes. Additionally, if owned, typical systems are difficult to modify to rapidly evolving methodologies. A potential solution to these problems is to enable scientists to build their own high-performance and adaptable system by overcoming a resource insufficiency. Here we present a detailed hardware resource and protocol for building an upright, highly modular and adaptable two-photon laser scanning fluorescence microscope that can be used for in vitro or in vivo applications. The microscope is comprised of high-end componentry on a skeleton of off-the-shelf compatible opto-mechanical parts. The dedicated design enabled imaging depths close to 1 mm into mouse brain tissue and a signal-to-noise ratio that exceeded all commercial two-photon systems tested. In addition to a detailed parts list, instructions for assembly, testing and troubleshooting, our plan includes complete three dimensional computer models that greatly reduce the knowledge base required for the non-expert user. This open-source resource lowers barriers in order to equip more laboratories with high-performance two-photon imaging and to help progress our understanding of the cellular and physiological function of living systems. PMID:25333934

Using Selection Pressure as an Asset to Develop Reusable, Adaptable Software Systems

NASA Technical Reports Server (NTRS)

Berrick, Stephen; Lynnes, Christopher

2007-01-01

The Goddard Earth Sciences Data and Information Services Center (GES DISC) at NASA has over the years developed and honed several reusable architectural components for supporting large-scale data centers with a large customer base. These include a processing system (S4PM) and an archive system (S4PA) based upon a workflow engine called the Simple Scalable Script based Science Processor (S4P) and an online data visualization and analysis system (Giovanni). These subsystems are currently reused internally in a variety of combinations to implement customized data management on behalf of instrument science teams and other science investigators. Some of these subsystems (S4P and S4PM) have also been reused by other data centers for operational science processing. Our experience has been that development and utilization of robust interoperable and reusable software systems can actually flourish in environments defined by heterogeneous commodity hardware systems the emphasis on value-added customer service and the continual goal for achieving higher cost efficiencies. The repeated internal reuse that is fostered by such an environment encourages and even forces changes to the software that make it more reusable and adaptable. Allowing and even encouraging such selective pressures to software development has been a key factor In the success of S4P and S4PM which are now available to the open source community under the NASA Open source Agreement

Towards Guided Underwater Survey Using Light Visual Odometry

NASA Astrophysics Data System (ADS)

Nawaf, M. M.; Drap, P.; Royer, J. P.; Merad, D.; Saccone, M.

2017-02-01

A light distributed visual odometry method adapted to embedded hardware platform is proposed. The aim is to guide underwater surveys in real time. We rely on image stream captured using portable stereo rig attached to the embedded system. Taken images are analyzed on the fly to assess image quality in terms of sharpness and lightness, so that immediate actions can be taken accordingly. Images are then transferred over the network to another processing unit to compute the odometry. Relying on a standard ego-motion estimation approach, we speed up points matching between image quadruplets using a low level points matching scheme relying on fast Harris operator and template matching that is invariant to illumination changes. We benefit from having the light source attached to the hardware platform to estimate a priori rough depth belief following light divergence over distance low. The rough depth is used to limit points correspondence search zone as it linearly depends on disparity. A stochastic relative bundle adjustment is applied to minimize re-projection errors. The evaluation of the proposed method demonstrates the gain in terms of computation time w.r.t. other approaches that use more sophisticated feature descriptors. The built system opens promising areas for further development and integration of embedded computer vision techniques.

A Comparative Study of Point Cloud Data Collection and Processing

NASA Astrophysics Data System (ADS)

Pippin, J. E.; Matheney, M.; Gentle, J. N., Jr.; Pierce, S. A.; Fuentes-Pineda, G.

2016-12-01

Over the past decade, there has been dramatic growth in the acquisition of publicly funded high-resolution topographic data for scientific, environmental, engineering and planning purposes. These data sets are valuable for applications of interest across a large and varied user community. However, because of the large volumes of data produced by high-resolution mapping technologies and expense of aerial data collection, it is often difficult to collect and distribute these datasets. Furthermore, the data can be technically challenging to process, requiring software and computing resources not readily available to many users. This study presents a comparison of advanced computing hardware and software that is used to collect and process point cloud datasets, such as LIDAR scans. Activities included implementation and testing of open source libraries and applications for point cloud data processing such as, Meshlab, Blender, PDAL, and PCL. Additionally, a suite of commercial scale applications, Skanect and Cloudcompare, were applied to raw datasets. Handheld hardware solutions, a Structure Scanner and Xbox 360 Kinect V1, were tested for their ability to scan at three field locations. The resultant data projects successfully scanned and processed subsurface karst features ranging from small stalactites to large rooms, as well as a surface waterfall feature. Outcomes support the feasibility of rapid sensing in 3D at field scales.

Self-service for software development projects and HPC activities

NASA Astrophysics Data System (ADS)

Husejko, M.; Høimyr, N.; Gonzalez, A.; Koloventzos, G.; Asbury, D.; Trzcinska, A.; Agtzidis, I.; Botrel, G.; Otto, J.

2014-05-01

This contribution describes how CERN has implemented several essential tools for agile software development processes, ranging from version control (Git) to issue tracking (Jira) and documentation (Wikis). Running such services in a large organisation like CERN requires many administrative actions both by users and service providers, such as creating software projects, managing access rights, users and groups, and performing tool-specific customisation. Dealing with these requests manually would be a time-consuming task. Another area of our CERN computing services that has required dedicated manual support has been clusters for specific user communities with special needs. Our aim is to move all our services to a layered approach, with server infrastructure running on the internal cloud computing infrastructure at CERN. This contribution illustrates how we plan to optimise the management of our of services by means of an end-user facing platform acting as a portal into all the related services for software projects, inspired by popular portals for open-source developments such as Sourceforge, GitHub and others. Furthermore, the contribution will discuss recent activities with tests and evaluations of High Performance Computing (HPC) applications on different hardware and software stacks, and plans to offer a dynamically scalable HPC service at CERN, based on affordable hardware.

Embedded Volttron specification - benchmarking small footprint compute device for Volttron

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanyal, Jibonananda; Fugate, David L.; Woodworth, Ken

An embedded system is a small footprint computing unit that typically serves a specific purpose closely associated with measurements and control of hardware devices. These units are designed for reasonable durability and operations in a wide range of operating conditions. Some embedded systems support real-time operations and can demonstrate high levels of reliability. Many have failsafe mechanisms built to handle graceful shutdown of the device in exception conditions. The available memory, processing power, and network connectivity of these devices are limited due to the nature of their specific-purpose design and intended application. Industry practice is to carefully design the softwaremore » for the available hardware capability to suit desired deployment needs. Volttron is an open source agent development and deployment platform designed to enable researchers to interact with devices and appliances without having to write drivers themselves. Hosting Volttron on small footprint embeddable devices enables its demonstration for embedded use. This report details the steps required and the experience in setting up and running Volttron applications on three small footprint devices: the Intel Next Unit of Computing (NUC), the Raspberry Pi 2, and the BeagleBone Black. In addition, the report also details preliminary investigation of the execution performance of Volttron on these devices.« less

Multi-channel acoustic recording and automated analysis of Drosophila courtship songs

PubMed Central

2013-01-01

Background Drosophila melanogaster has served as a powerful model system for genetic studies of courtship songs. To accelerate research on the genetic and neural mechanisms underlying courtship song, we have developed a sensitive recording system to simultaneously capture the acoustic signals from 32 separate pairs of courting flies as well as software for automated segmentation of songs. Results Our novel hardware design enables recording of low amplitude sounds in most laboratory environments. We demonstrate the power of this system by collecting, segmenting and analyzing over 18 hours of courtship song from 75 males from five wild-type strains of Drosophila melanogaster. Our analysis reveals previously undetected modulation of courtship song features and extensive natural genetic variation for most components of courtship song. Despite having a large dataset with sufficient power to detect subtle modulations of song, we were unable to identify previously reported periodic rhythms in the inter-pulse interval of song. We provide detailed instructions for assembling the hardware and for using our open-source segmentation software. Conclusions Analysis of a large dataset of acoustic signals from Drosophila melanogaster provides novel insight into the structure and dynamics of species-specific courtship songs. Our new system for recording and analyzing fly acoustic signals should therefore greatly accelerate future studies of the genetics, neurobiology and evolution of courtship song. PMID:23369160

Distributed and Modular CAN-Based Architecture for Hardware Control and Sensor Data Integration

PubMed Central

Losada, Diego P.; Fernández, Joaquín L.; Paz, Enrique; Sanz, Rafael

2017-01-01

In this article, we present a CAN-based (Controller Area Network) distributed system to integrate sensors, actuators and hardware controllers in a mobile robot platform. With this work, we provide a robust, simple, flexible and open system to make hardware elements or subsystems communicate, that can be applied to different robots or mobile platforms. Hardware modules can be connected to or disconnected from the CAN bus while the system is working. It has been tested in our mobile robot Rato, based on a RWI (Real World Interface) mobile platform, to replace the old sensor and motor controllers. It has also been used in the design of two new robots: BellBot and WatchBot. Currently, our hardware integration architecture supports different sensors, actuators and control subsystems, such as motor controllers and inertial measurement units. The integration architecture was tested and compared with other solutions through a performance analysis of relevant parameters such as transmission efficiency and bandwidth usage. The results conclude that the proposed solution implements a lightweight communication protocol for mobile robot applications that avoids transmission delays and overhead. PMID:28467381

Distributed and Modular CAN-Based Architecture for Hardware Control and Sensor Data Integration.

PubMed

Losada, Diego P; Fernández, Joaquín L; Paz, Enrique; Sanz, Rafael

2017-05-03

In this article, we present a CAN-based (Controller Area Network) distributed system to integrate sensors, actuators and hardware controllers in a mobile robot platform. With this work, we provide a robust, simple, flexible and open system to make hardware elements or subsystems communicate, that can be applied to different robots or mobile platforms. Hardware modules can be connected to or disconnected from the CAN bus while the system is working. It has been tested in our mobile robot Rato, based on a RWI (Real World Interface) mobile platform, to replace the old sensor and motor controllers. It has also been used in the design of two new robots: BellBot and WatchBot. Currently, our hardware integration architecture supports different sensors, actuators and control subsystems, such as motor controllers and inertial measurement units. The integration architecture was tested and compared with other solutions through a performance analysis of relevant parameters such as transmission efficiency and bandwidth usage. The results conclude that the proposed solution implements a lightweight communication protocol for mobile robot applications that avoids transmission delays and overhead.

Managing coherence via put/get windows

DOEpatents

Blumrich, Matthias A [Ridgefield, CT; Chen, Dong [Croton on Hudson, NY; Coteus, Paul W [Yorktown Heights, NY; Gara, Alan G [Mount Kisco, NY; Giampapa, Mark E [Irvington, NY; Heidelberger, Philip [Cortlandt Manor, NY; Hoenicke, Dirk [Ossining, NY; Ohmacht, Martin [Yorktown Heights, NY

2011-01-11

A method and apparatus for managing coherence between two processors of a two processor node of a multi-processor computer system. Generally the present invention relates to a software algorithm that simplifies and significantly speeds the management of cache coherence in a message passing parallel computer, and to hardware apparatus that assists this cache coherence algorithm. The software algorithm uses the opening and closing of put/get windows to coordinate the activated required to achieve cache coherence. The hardware apparatus may be an extension to the hardware address decode, that creates, in the physical memory address space of the node, an area of virtual memory that (a) does not actually exist, and (b) is therefore able to respond instantly to read and write requests from the processing elements.

Managing coherence via put/get windows

DOEpatents

Blumrich, Matthias A [Ridgefield, CT; Chen, Dong [Croton on Hudson, NY; Coteus, Paul W [Yorktown Heights, NY; Gara, Alan G [Mount Kisco, NY; Giampapa, Mark E [Irvington, NY; Heidelberger, Philip [Cortlandt Manor, NY; Hoenicke, Dirk [Ossining, NY; Ohmacht, Martin [Yorktown Heights, NY

2012-02-21

A method and apparatus for managing coherence between two processors of a two processor node of a multi-processor computer system. Generally the present invention relates to a software algorithm that simplifies and significantly speeds the management of cache coherence in a message passing parallel computer, and to hardware apparatus that assists this cache coherence algorithm. The software algorithm uses the opening and closing of put/get windows to coordinate the activated required to achieve cache coherence. The hardware apparatus may be an extension to the hardware address decode, that creates, in the physical memory address space of the node, an area of virtual memory that (a) does not actually exist, and (b) is therefore able to respond instantly to read and write requests from the processing elements.

Experimental study of a valveless pulse detonation rocket engine using nontoxic hypergolic propellants

NASA Astrophysics Data System (ADS)

Kan, Brandon K.

A pulsed detonation rocket engine concept was explored through the use of hypergolic propellants in a fuel-centered pintle injector combustor. The combustor design yielded a simple open ended chamber with a pintle type injection element and pressure instrumentation. High-frequency pressure measurements from the first test series showed the presence of large pressure oscillations in excess of 2000 psia at frequencies between 400-600 hz during operation. High-speed video confirmed the high-frequency pulsed behavior and large amounts of after burning. Damaged hardware and instrumentation failure limited the amount of data gathered in the first test series, but the experiments met original test objectives of producing large over-pressures in an open chamber. A second test series proceeded by replacing hardware and instrumentation, and new data showed that pulsed events produced under expanded exhaust prior to pulsing, peak pressures around 8000 psi, and operating frequencies between 400-800 hz. Later hot-fires produced no pulsed behavior despite undamaged hardware. The research succeeded in producing pulsed combustion behavior using hypergolic fuels in a pintle injector setup and provided insights into design concepts that would assist future injector designs and experimental test setups.

Feature-based component model for design of embedded systems

NASA Astrophysics Data System (ADS)

Zha, Xuan Fang; Sriram, Ram D.

2004-11-01

An embedded system is a hybrid of hardware and software, which combines software's flexibility and hardware real-time performance. Embedded systems can be considered as assemblies of hardware and software components. An Open Embedded System Model (OESM) is currently being developed at NIST to provide a standard representation and exchange protocol for embedded systems and system-level design, simulation, and testing information. This paper proposes an approach to representing an embedded system feature-based model in OESM, i.e., Open Embedded System Feature Model (OESFM), addressing models of embedded system artifacts, embedded system components, embedded system features, and embedded system configuration/assembly. The approach provides an object-oriented UML (Unified Modeling Language) representation for the embedded system feature model and defines an extension to the NIST Core Product Model. The model provides a feature-based component framework allowing the designer to develop a virtual embedded system prototype through assembling virtual components. The framework not only provides a formal precise model of the embedded system prototype but also offers the possibility of designing variation of prototypes whose members are derived by changing certain virtual components with different features. A case study example is discussed to illustrate the embedded system model.

Exploiting IoT Technologies and Open Source Components for Smart Seismic Network Instrumentation

NASA Astrophysics Data System (ADS)

Germenis, N. G.; Koulamas, C. A.; Foundas, P. N.

2017-12-01

The data collection infrastructure of any seismic network poses a number of requirements and trade-offs related to accuracy, reliability, power autonomy and installation & operational costs. Having the right hardware design at the edge of this infrastructure, embedded software running inside the instruments is the heart of pre-processing and communication services implementation and their integration with the central storage and processing facilities of the seismic network. This work demonstrates the feasibility and benefits of exploiting software components from heterogeneous sources in order to realize a smart seismic data logger, achieving higher reliability, faster integration and less development and testing costs of critical functionality that is in turn responsible for the cost and power efficient operation of the device. The instrument's software builds on top of widely used open source components around the Linux kernel with real-time extensions, the core Debian Linux distribution, the earthworm and seiscomp tooling frameworks, as well as components from the Internet of Things (IoT) world, such as the CoAP and MQTT protocols for the signaling planes, besides the widely used de-facto standards of the application domain at the data plane, such as the SeedLink protocol. By using an innovative integration of features based on lower level GPL components of the seiscomp suite with higher level processing earthworm components, coupled with IoT protocol extensions to the latter, the instrument can implement smart functionality such as network controlled, event triggered data transmission in parallel with edge archiving and on demand, short term historical data retrieval.

Space Generic Open Avionics Architecture (SGOAA) reference model technical guide

NASA Technical Reports Server (NTRS)

Wray, Richard B.; Stovall, John R.

1993-01-01

This report presents a full description of the Space Generic Open Avionics Architecture (SGOAA). The SGOAA consists of a generic system architecture for the entities in spacecraft avionics, a generic processing architecture, and a six class model of interfaces in a hardware/software system. The purpose of the SGOAA is to provide an umbrella set of requirements for applying the generic architecture interface model to the design of specific avionics hardware/software systems. The SGOAA defines a generic set of system interface points to facilitate identification of critical interfaces and establishes the requirements for applying appropriate low level detailed implementation standards to those interface points. The generic core avionics system and processing architecture models provided herein are robustly tailorable to specific system applications and provide a platform upon which the interface model is to be applied.

Protecting Cryptographic Keys and Functions from Malware Attacks

DTIC Science & Technology

2010-12-01

registers. modifies RSA private key signing in OpenSSL to use the technique. The resulting system has the following features: 1. No special hardware is...the above method based on OpenSSL , by exploiting the Streaming SIMD Extension (SSE) XMM registers of modern Intel and AMD x86-compatible CPU’s [22...one can store a 2048-bit exponent.1 Our prototype is based on OpenSSL 0.9.8e, the Ubuntu 6.06 Linux distribution with a 2.6.15 kernel, and SSE2 which

Wireless Energy Harvesting Two-Way Relay Networks with Hardware Impairments.

PubMed

Peng, Chunling; Li, Fangwei; Liu, Huaping

2017-11-13

This paper considers a wireless energy harvesting two-way relay (TWR) network where the relay has energy-harvesting abilities and the effects of practical hardware impairments are taken into consideration. In particular, power splitting (PS) receiver is adopted at relay to harvests the power it needs for relaying the information between the source nodes from the signals transmitted by the source nodes, and hardware impairments is assumed suffered by each node. We analyze the effect of hardware impairments [-20]on both decode-and-forward (DF) relaying and amplify-and-forward (AF) relaying networks. By utilizing the obtained new expressions of signal-to-noise-plus-distortion ratios, the exact analytical expressions of the achievable sum rate and ergodic capacities for both DF and AF relaying protocols are derived. Additionally, the optimal power splitting (OPS) ratio that maximizes the instantaneous achievable sum rate is formulated and solved for both protocols. The performances of DF and AF protocols are evaluated via numerical results, which also show the effects of various network parameters on the system performance and on the OPS ratio design.

Research on starlight hardware-in-the-loop simulator

NASA Astrophysics Data System (ADS)

Zhang, Ying; Gao, Yang; Qu, Huiyang; Liu, Dongfang; Du, Huijie; Lei, Jie

2016-10-01

The starlight navigation is considered to be one of the most important methods for spacecraft navigation. Starlight simulation system is a high-precision system with large fields of view, designed to test the starlight navigation sensor performance on the ground. A complete hardware-in-the-loop simulation of the system has been built. The starlight simulator is made up of light source, light source controller, light filter, LCD, collimator and control computer. LCD is the key display component of the system, and is installed at the focal point of the collimator. For the LCD cannot emit light itself, so light source and light source power controller is specially designed for the brightness demanded by the LCD. Light filter is designed for the dark background which is also needed in the simulation.

Open core control software for surgical robots.

PubMed

Arata, Jumpei; Kozuka, Hiroaki; Kim, Hyung Wook; Takesue, Naoyuki; Vladimirov, B; Sakaguchi, Masamichi; Tokuda, Junichi; Hata, Nobuhiko; Chinzei, Kiyoyuki; Fujimoto, Hideo

2010-05-01

In these days, patients and doctors in operation room are surrounded by many medical devices as resulting from recent advancement of medical technology. However, these cutting-edge medical devices are working independently and not collaborating with each other, even though the collaborations between these devices such as navigation systems and medical imaging devices are becoming very important for accomplishing complex surgical tasks (such as a tumor removal procedure while checking the tumor location in neurosurgery). On the other hand, several surgical robots have been commercialized, and are becoming common. However, these surgical robots are not open for collaborations with external medical devices in these days. A cutting-edge "intelligent surgical robot" will be possible in collaborating with surgical robots, various kinds of sensors, navigation system and so on. On the other hand, most of the academic software developments for surgical robots are "home-made" in their research institutions and not open to the public. Therefore, open source control software for surgical robots can be beneficial in this field. From these perspectives, we developed Open Core Control software for surgical robots to overcome these challenges. In general, control softwares have hardware dependencies based on actuators, sensors and various kinds of internal devices. Therefore, these control softwares cannot be used on different types of robots without modifications. However, the structure of the Open Core Control software can be reused for various types of robots by abstracting hardware dependent parts. In addition, network connectivity is crucial for collaboration between advanced medical devices. The OpenIGTLink is adopted in Interface class which plays a role to communicate with external medical devices. At the same time, it is essential to maintain the stable operation within the asynchronous data transactions through network. In the Open Core Control software, several techniques for this purpose were introduced. Virtual fixture is well known technique as a "force guide" for supporting operators to perform precise manipulation by using a master-slave robot. The virtual fixture for precise and safety surgery was implemented on the system to demonstrate an idea of high-level collaboration between a surgical robot and a navigation system. The extension of virtual fixture is not a part of the Open Core Control system, however, the function such as virtual fixture cannot be realized without a tight collaboration between cutting-edge medical devices. By using the virtual fixture, operators can pre-define an accessible area on the navigation system, and the area information can be transferred to the robot. In this manner, the surgical console generates the reflection force when the operator tries to get out from the pre-defined accessible area during surgery. The Open Core Control software was implemented on a surgical master-slave robot and stable operation was observed in a motion test. The tip of the surgical robot was displayed on a navigation system by connecting the surgical robot with a 3D position sensor through the OpenIGTLink. The accessible area was pre-defined before the operation, and the virtual fixture was displayed as a "force guide" on the surgical console. In addition, the system showed stable performance in a duration test with network disturbance. In this paper, a design of the Open Core Control software for surgical robots and the implementation of virtual fixture were described. The Open Core Control software was implemented on a surgical robot system and showed stable performance in high-level collaboration works. The Open Core Control software is developed to be a widely used platform of surgical robots. Safety issues are essential for control software of these complex medical devices. It is important to follow the global specifications such as a FDA requirement "General Principles of Software Validation" or IEC62304. For following these regulations, it is important to develop a self-test environment. Therefore, a test environment is now under development to test various interference in operation room such as a noise of electric knife by considering safety and test environment regulations such as ISO13849 and IEC60508. The Open Core Control software is currently being developed software in open-source manner and available on the Internet. A communization of software interface is becoming a major trend in this field. Based on this perspective, the Open Core Control software can be expected to bring contributions in this field.

Open-source, small-animal magnetic resonance-guided focused ultrasound system.

PubMed

Poorman, Megan E; Chaplin, Vandiver L; Wilkens, Ken; Dockery, Mary D; Giorgio, Todd D; Grissom, William A; Caskey, Charles F

2016-01-01

MR-guided focused ultrasound or high-intensity focused ultrasound (MRgFUS/MRgHIFU) is a non-invasive therapeutic modality with many potential applications in areas such as cancer therapy, drug delivery, and blood-brain barrier opening. However, the large financial costs involved in developing preclinical MRgFUS systems represent a barrier to research groups interested in developing new techniques and applications. We aim to mitigate these challenges by detailing a validated, open-source preclinical MRgFUS system capable of delivering thermal and mechanical FUS in a quantifiable and repeatable manner under real-time MRI guidance. A hardware and software package was developed that includes closed-loop feedback controlled thermometry code and CAD drawings for a therapy table designed for a preclinical MRI scanner. For thermal treatments, the modular software uses a proportional integral derivative controller to maintain a precise focal temperature rise in the target given input from MR phase images obtained concurrently. The software computes the required voltage output and transmits it to a FUS transducer that is embedded in the delivery table within the magnet bore. The delivery table holds the FUS transducer, a small animal and its monitoring equipment, and a transmit/receive RF coil. The transducer is coupled to the animal via a water bath and is translatable in two dimensions from outside the magnet. The transducer is driven by a waveform generator and amplifier controlled by real-time software in Matlab. MR acoustic radiation force imaging is also implemented to confirm the position of the focus for mechanical and thermal treatments. The system was validated in tissue-mimicking phantoms and in vivo during murine tumor hyperthermia treatments. Sonications were successfully controlled over a range of temperatures and thermal doses for up to 20 min with minimal temperature overshoot. MR thermometry was validated with an optical temperature probe, and focus visualization was achieved with acoustic radiation force imaging. We developed an MRgFUS platform for small-animal treatments that robustly delivers accurate, precise, and controllable sonications over extended time periods. This system is an open source and could increase the availability of low-cost small-animal systems to interdisciplinary researchers seeking to develop new MRgFUS applications and technology.

Sustaining an Online, Shared Community Resource for Models, Robust Open source Software Tools and Data for Volcanology - the Vhub Experience

NASA Astrophysics Data System (ADS)

Patra, A. K.; Valentine, G. A.; Bursik, M. I.; Connor, C.; Connor, L.; Jones, M.; Simakov, N.; Aghakhani, H.; Jones-Ivey, R.; Kosar, T.; Zhang, B.

2015-12-01

Over the last 5 years we have created a community collaboratory Vhub.org [Palma et al, J. App. Volc. 3:2 doi:10.1186/2191-5040-3-2] as a place to find volcanology-related resources, and a venue for users to disseminate tools, teaching resources, data, and an online platform to support collaborative efforts. As the community (current active users > 6000 from an estimated community of comparable size) embeds the tools in the collaboratory into educational and research workflows it became imperative to: a) redesign tools into robust, open source reusable software for online and offline usage/enhancement; b) share large datasets with remote collaborators and other users seamlessly with security; c) support complex workflows for uncertainty analysis, validation and verification and data assimilation with large data. The focus on tool development/redevelopment has been twofold - firstly to use best practices in software engineering and new hardware like multi-core and graphic processing units. Secondly we wish to enhance capabilities to support inverse modeling, uncertainty quantification using large ensembles and design of experiments, calibration, validation. Among software engineering practices we practice are open source facilitating community contributions, modularity and reusability. Our initial targets are four popular tools on Vhub - TITAN2D, TEPHRA2, PUFF and LAVA. Use of tools like these requires many observation driven data sets e.g. digital elevation models of topography, satellite imagery, field observations on deposits etc. These data are often maintained in private repositories that are privately shared by "sneaker-net". As a partial solution to this we tested mechanisms using irods software for online sharing of private data with public metadata and access limits. Finally, we adapted use of workflow engines (e.g. Pegasus) to support the complex data and computing workflows needed for usage like uncertainty quantification for hazard analysis using physical models.

Encourage student learning of hydraulic matters by the use of Arduino platform

NASA Astrophysics Data System (ADS)

Rodriguez Sinobas, Leonor; Granja García, Javier; Sánchez Calvo, Raúl

2014-05-01

Arduino is an open-source electronics prototyping platform based on flexible, easy-to-use hardware and software. It's intended for several purposes to anyone interested in creating interactive objects or environments. The hydraulic matters teach at the Agricultural Engineering School at the Technical University of Madrid deal with practical issues regarding the measurement of variables such as pressure, discharge, temperature and soil water content. Most of the data loggers available in the market for these variables at expensive and not always affordable. On the other hand, current students are eager to manage new technological devices thus, their skills could be oriented not only to the application of an electronic platform as Arduino to build low cost data loggers for different purposes, but to encourage their learning in the hydraulic matters improving their self esteem

Sustainability of Recycled ABS and PA6 by Banana Fiber Reinforcement: Thermal, Mechanical and Morphological Properties

NASA Astrophysics Data System (ADS)

Singh, Rupinder; Kumar, Ranvijay; Ranjan, Nishant

2018-01-01

In the present study efforts have been made to prepare functional prototypes with improved thermal, mechanical and morphological properties from polymeric waste for sustainability. The primary recycled acrylonitrile butadiene styrene (ABS) and polyamide 6 (PA6) has been selected as matrix material with bio-degradable and bio-compatible banana fibers (BF) as reinforcement. The blend (in form of feed stock filament wire) of ABS/PA6 and BF was prepared in house by conventional twin screw extrusion (TSE) process. Finally feed stock filament of ABS/PA6 reinforced with BF was put to run on open source fused deposition modelling based three dimensional printer (without any change in hardware/software of the system) for printing of functional prototypes with improved thermal/mechanical/morphological properties. The results are supported by photomicrographs, thermographs and mechanical testing.

Presenting the master of all conductivity meters, and how it tastes streamflow

NASA Astrophysics Data System (ADS)

Weijs, S. V.; Parlange, M. B.

2012-04-01

For measuring streamflow in small Alpine streams, the salt dilution method is suitable and often used. By injecting a known mass of salt in the stream and measuring the downstream salt concentration as a function of time, we can obtain the streamflow by integration of the time signal. The underlying assumption is that the salt is well mixed within the stream cross-section. In this method, the salt concentration us usually measured through its relation with conductivity. Several commercial systems exist to do these conductivity measurements and automatically process the results. The problem we encountered when using these systems, however, is that uncertainty is often hidden under the hood. Because the processing happens onboard, researchers may be tempted to put too much trust in the final measurement outcomes. This is somewhat remediated by using a system with two probes which are individually processed to a streamflow outcome. We found that the salt-wave was differently shaped for the faster part of the stream compared to the sides, and therefore gave different readings for the discharge. To come a more probabilistic characterization of streamflow, and to know what is under the hood, we decided to build our own conductivity meter, equipped with eight probes covering the cross section. This enables quantifying some of the uncertainty in the streamflow measurements, which is important for testing hydrological models. This poster shows the first results and the hardware setup. We based our hardware on the open source hardware platform Arduino, and believe that by sharing both the design and the drawbacks, we contribute to the evolution of better measurement equipment or at least better understanding of its shortcomings.

Design, Fabrication, and Testing of a Hopper Spacecraft Simulator

NASA Astrophysics Data System (ADS)

Mucasey, Evan Phillip Krell

A robust test bed is needed to facilitate future development of guidance, navigation, and control software for future vehicles capable of vertical takeoff and landings. Specifically, this work aims to develop both a hardware and software simulator that can be used for future flight software development for extra-planetary vehicles. To achieve the program requirements of a high thrust to weight ratio with large payload capability, the vehicle is designed to have a novel combination of electric motors and a micro jet engine is used to act as the propulsion elements. The spacecraft simulator underwent several iterations of hardware development using different materials and fabrication methods. The final design used a combination of carbon fiber and fiberglass that was cured under vacuum to serve as the frame of the vehicle which provided a strong, lightweight platform for all flight components and future payloads. The vehicle also uses an open source software development platform, Arduino, to serve as the initial flight computer and has onboard accelerometers, gyroscopes, and magnetometers to sense the vehicles attitude. To prevent instability due to noise, a polynomial kalman filter was designed and this fed the sensed angles and rates into a robust attitude controller which autonomously control the vehicle' s yaw, pitch, and roll angles. In addition to the hardware development of the vehicle itself, both a software simulation and a real time data acquisition interface was written in MATLAB/SIMULINK so that real flight data could be taken and then correlated to the simulation to prove the accuracy of the analytical model. In result, the full scale vehicle was designed and own outside of the lab environment and data showed that the software model accurately predicted the flight dynamics of the vehicle.

A real-time biomimetic acoustic localizing system using time-shared architecture

NASA Astrophysics Data System (ADS)

Nourzad Karl, Marianne; Karl, Christian; Hubbard, Allyn

2008-04-01

In this paper a real-time sound source localizing system is proposed, which is based on previously developed mammalian auditory models. Traditionally, following the models, which use interaural time delay (ITD) estimates, the amount of parallel computations needed by a system to achieve real-time sound source localization is a limiting factor and a design challenge for hardware implementations. Therefore a new approach using a time-shared architecture implementation is introduced. The proposed architecture is a purely sample-base-driven digital system, and it follows closely the continuous-time approach described in the models. Rather than having dedicated hardware on a per frequency channel basis, a specialized core channel, shared for all frequency bands is used. Having an optimized execution time, which is much less than the system's sample rate, the proposed time-shared solution allows the same number of virtual channels to be processed as the dedicated channels in the traditional approach. Hence, the time-shared approach achieves a highly economical and flexible implementation using minimal silicon area. These aspects are particularly important in efficient hardware implementation of a real time biomimetic sound source localization system.

Acoustic Noise Prediction of the Amine Swingbed ISS ExPRESS Rack Payload

NASA Technical Reports Server (NTRS)

Welsh, David; Smith, Holly; Wang, Shuo

2010-01-01

Acoustics plays a vital role in maintaining the health, safety, and comfort of crew members aboard the International Space Station (ISS). In order to maintain this livable and workable environment, acoustic requirements have been established to ensure that ISS hardware and payload developers account for the acoustic emissions of their equipment and develop acoustic mitigations as necessary. These requirements are verified by an acoustic emissions test of the integrated hardware. The Amine Swingbed ExPRESS (Expedite the PRocessing of ExperimentS to Space) rack payload creates a unique challenge to the developers in that the payload hardware is transported to the ISS in phases, making an acoustic emissions test on the integrated flight hardware impossible. In addition, the payload incorporates a high back pressure fan and a diaphragm vacuum pump, which are recognized as significant and complex noise sources. In order to accurately predict the acoustic emissions of the integrated payload, the individual acoustic noise sources and paths are first characterized. These characterizations are conducted though a series of acoustic emissions tests on the individual payload components. Secondly, the individual acoustic noise sources and paths are incorporated into a virtual model of the integrated hardware. The virtual model is constructed with the use of hybrid method utilizing the Finite Element Acoustic (FEA) and Statistical Energy Analysis (SEA) techniques, which predict the overall acoustic emissions. Finally, the acoustic model is validated though an acoustic characterization test performed on an acoustically similar mock-up of the flight unit. The results of the validated acoustic model are then used to assess the acoustic emissions of the flight unit and define further acoustic mitigation efforts.

Towards fully analog hardware reservoir computing for speech recognition

NASA Astrophysics Data System (ADS)

Smerieri, Anteo; Duport, François; Paquot, Yvan; Haelterman, Marc; Schrauwen, Benjamin; Massar, Serge

2012-09-01

Reservoir computing is a very recent, neural network inspired unconventional computation technique, where a recurrent nonlinear system is used in conjunction with a linear readout to perform complex calculations, leveraging its inherent internal dynamics. In this paper we show the operation of an optoelectronic reservoir computer in which both the nonlinear recurrent part and the readout layer are implemented in hardware for a speech recognition application. The performance obtained is close to the one of to state-of-the-art digital reservoirs, while the analog architecture opens the way to ultrafast computation.

OSI for hardware/software interoperability

NASA Astrophysics Data System (ADS)

Wood, Richard J.; Harvey, Donald L.; Linderman, Richard W.; Gardener, Gary A.; Capraro, Gerard T.

1994-03-01

There is a need in public safety for real-time data collection and transmission from one or more sensors. The Rome Laboratory and the Ballistic Missile Defense Organization are pursuing an effort to bring the benefits of Open System Architectures (OSA) to embedded systems within the Department of Defense. When developed properly OSA provides interoperability, commonality, graceful upgradeability, survivability and hardware/software transportability to greatly minimize life cycle costs, integration and supportability. Architecture flexibility can be achieved to take advantage of commercial accomplishments by basing these developments on vendor-neutral commercially accepted standards and protocols.

Identifying the minor set cover of dense connected bipartite graphs via random matching edge sets

NASA Astrophysics Data System (ADS)

Hamilton, Kathleen E.; Humble, Travis S.

2017-04-01

Using quantum annealing to solve an optimization problem requires minor embedding a logic graph into a known hardware graph. In an effort to reduce the complexity of the minor embedding problem, we introduce the minor set cover (MSC) of a known graph G: a subset of graph minors which contain any remaining minor of the graph as a subgraph. Any graph that can be embedded into G will be embeddable into a member of the MSC. Focusing on embedding into the hardware graph of commercially available quantum annealers, we establish the MSC for a particular known virtual hardware, which is a complete bipartite graph. We show that the complete bipartite graph K_{N,N} has a MSC of N minors, from which K_{N+1} is identified as the largest clique minor of K_{N,N}. The case of determining the largest clique minor of hardware with faults is briefly discussed but remains an open question.

Identifying the minor set cover of dense connected bipartite graphs via random matching edge sets

DOE PAGES

Hamilton, Kathleen E.; Humble, Travis S.

2017-02-23

Using quantum annealing to solve an optimization problem requires minor embedding a logic graph into a known hardware graph. We introduce the minor set cover (MSC) of a known graph GG : a subset of graph minors which contain any remaining minor of the graph as a subgraph, in an effort to reduce the complexity of the minor embedding problem. Any graph that can be embedded into GG will be embeddable into a member of the MSC. Focusing on embedding into the hardware graph of commercially available quantum annealers, we establish the MSC for a particular known virtual hardware, whichmore » is a complete bipartite graph. Furthermore, we show that the complete bipartite graph K N,N has a MSC of N minors, from which K N+1 is identified as the largest clique minor of K N,N. In the case of determining the largest clique minor of hardware with faults we briefly discussed this open question.« less

Low-level rf control of Spallation Neutron Source: System and characterization

NASA Astrophysics Data System (ADS)

Ma, Hengjie; Champion, Mark; Crofford, Mark; Kasemir, Kay-Uwe; Piller, Maurice; Doolittle, Lawrence; Ratti, Alex

2006-03-01

The low-level rf control system currently commissioned throughout the Spallation Neutron Source (SNS) LINAC evolved from three design iterations over 1 yr intensive research and development. Its digital hardware implementation is efficient, and has succeeded in achieving a minimum latency of less than 150 ns which is the key for accomplishing an all-digital feedback control for the full bandwidth. The control bandwidth is analyzed in frequency domain and characterized by testing its transient response. The hardware implementation also includes the provision of a time-shared input channel for a superior phase differential measurement between the cavity field and the reference. A companion cosimulation system for the digital hardware was developed to ensure a reliable long-term supportability. A large effort has also been made in the operation software development for the practical issues such as the process automations, cavity filling, beam loading compensation, and the cavity mechanical resonance suppression.

Simplifying and speeding the management of intra-node cache coherence

DOEpatents

Blumrich, Matthias A [Ridgefield, CT; Chen, Dong [Croton on Hudson, NY; Coteus, Paul W [Yorktown Heights, NY; Gara, Alan G [Mount Kisco, NY; Giampapa, Mark E [Irvington, NY; Heidelberger, Phillip [Cortlandt Manor, NY; Hoenicke, Dirk [Ossining, NY; Ohmacht, Martin [Yorktown Heights, NY

2012-04-17

A method and apparatus for managing coherence between two processors of a two processor node of a multi-processor computer system. Generally the present invention relates to a software algorithm that simplifies and significantly speeds the management of cache coherence in a message passing parallel computer, and to hardware apparatus that assists this cache coherence algorithm. The software algorithm uses the opening and closing of put/get windows to coordinate the activated required to achieve cache coherence. The hardware apparatus may be an extension to the hardware address decode, that creates, in the physical memory address space of the node, an area of virtual memory that (a) does not actually exist, and (b) is therefore able to respond instantly to read and write requests from the processing elements.

Managing coherence via put/get windows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blumrich, Matthias A; Chen, Dong; Coteus, Paul W

A method and apparatus for managing coherence between two processors of a two processor node of a multi-processor computer system. Generally the present invention relates to a software algorithm that simplifies and significantly speeds the management of cache coherence in a message passing parallel computer, and to hardware apparatus that assists this cache coherence algorithm. The software algorithm uses the opening and closing of put/get windows to coordinate the activated required to achieve cache coherence. The hardware apparatus may be an extension to the hardware address decode, that creates, in the physical memory address space of the node, an areamore » of virtual memory that (a) does not actually exist, and (b) is therefore able to respond instantly to read and write requests from the processing elements.« less

CompactPCI/Linux Platform in FTU Slow Control System

NASA Astrophysics Data System (ADS)

Iannone, F.; Wang, L.; Centioli, C.; Panella, M.; Mazza, G.; Vitale, V.

2004-12-01

In large fusion experiments, such as tokamak devices, there is a common trend for slow control systems. Because of complexity of the plants, the so-called `Standard Model' (SM) in slow control has been adopted on several tokamak machines. This model is based on a three-level hierarchical control: 1) High-Level Control (HLC) with a supervisory function; 2) Medium-Level Control (MLC) to interface and concentrate I/O field equipments; 3) Low-Level Control (LLC) with hard real-time I/O function, often managed by PLCs. FTU control system designed with SM concepts has underwent several stages of developments in its fifteen years duration of runs. The latest evolution was inevitable, due to the obsolescence of the MLC CPUs, based on VME-MOTOROLA 68030 with OS9 operating system. A large amount of C code was developed for that platform to route the data flow from LLC, which is constituted by 24 Westinghouse Numalogic PC-700 PLCs with about 8000 field-points, to HLC, based on a commercial Object-Oriented Real-Time database on Alpha/CompaqTru64 platform. Therefore, we have to look for cost-effective solutions and finally a CompactPCI-Intel x86 platform with Linux operating system was chosen. A software porting has been done, taking into account the differences between OS9 and Linux operating system in terms of Inter/Network Processes Communications and I/O multi-ports serial driver. This paper describes the hardware/software architecture of the new MLC system, emphasizing the reliability and the low costs of the open source solutions. Moreover, a huge amount of software packages available in open source environment will assure a less painful maintenance, and will open the way to further improvements of the system itself.

Open Source Software Openfoam as a New Aerodynamical Simulation Tool for Rocket-Borne Measurements

NASA Astrophysics Data System (ADS)

Staszak, T.; Brede, M.; Strelnikov, B.

2015-09-01

The only way to do in-situ measurements, which are very important experimental studies for atmospheric science, in the mesoshere/lower thermosphere (MLT) is to use sounding rockets. The drawback of using rockets is the shock wave appearing because of the very high speed of the rocket motion (typically about 1000 mIs). This shock wave disturbs the density, the temperature and the velocity fields in the vicinity of the rocket, compared to undisturbed values of the atmosphere. This effect, however, can be quantified and the measured data has to be corrected not just to make it more precise but simply usable. The commonly accepted and widely used tool for this calculations is the Direct Simulation Monte Carlo (DSMC) technique developed by GA. Bird which is available as stand-alone program limited to use a single processor. Apart from complications with simulations of flows around bodies related to different flow regimes in the altitude range of MLT, that rise due to exponential density change by several orders of magnitude, a particular hardware configuration introduces significant difficulty for aerodynamical calculations due to choice of the grid sizes mainly depending on the demands on adequate DSMCs and good resolution of geometries with scale differences of factor of iO~. This makes either the calculation time unreasonably long or even prevents the calculation algorithm from converging. In this paper we apply the free open source software OpenFOAM (licensed under GNU GPL) for a three-dimensional CFD-Simulation of a flow around a sounding rocket instrumentation. An advantage of this software package, among other things, is that it can run on high performance clusters, which are easily scalable. We present the first results and discuss the potential of the new tool in applications for sounding rockets.

Whole earth modeling: developing and disseminating scientific software for computational geophysics.

NASA Astrophysics Data System (ADS)

Kellogg, L. H.

2016-12-01

Historically, a great deal of specialized scientific software for modeling and data analysis has been developed by individual researchers or small groups of scientists working on their own specific research problems. As the magnitude of available data and computer power has increased, so has the complexity of scientific problems addressed by computational methods, creating both a need to sustain existing scientific software, and expand its development to take advantage of new algorithms, new software approaches, and new computational hardware. To that end, communities like the Computational Infrastructure for Geodynamics (CIG) have been established to support the use of best practices in scientific computing for solid earth geophysics research and teaching. Working as a scientific community enables computational geophysicists to take advantage of technological developments, improve the accuracy and performance of software, build on prior software development, and collaborate more readily. The CIG community, and others, have adopted an open-source development model, in which code is developed and disseminated by the community in an open fashion, using version control and software repositories like Git. One emerging issue is how to adequately identify and credit the intellectual contributions involved in creating open source scientific software. The traditional method of disseminating scientific ideas, peer reviewed publication, was not designed for review or crediting scientific software, although emerging publication strategies such software journals are attempting to address the need. We are piloting an integrated approach in which authors are identified and credited as scientific software is developed and run. Successful software citation requires integration with the scholarly publication and indexing mechanisms as well, to assign credit, ensure discoverability, and provide provenance for software.

Cognitive IoT incorporating intelligence in building smart environment

NASA Astrophysics Data System (ADS)

Sarker, Dishari; Sumathy, S.

2017-11-01

The Internet of Things (IoT) is an invention of this century which also can be called as Internet which makes life more logical and electronic. According to research in the industrial field about which aspect in IoT contributes more for GDP is the concept which can be applied in various aspects of our life to make life logical and easier. We are very much aware of the increasing population and the pollution that is caused by the vehicles and many other sources such as harmful gas producers. So, this work focuses in determining the level of pollution in a specific area and predict how much more greenery has to be increased in that area. With its widespread application, this paper proposes an idea with a social cause in order to exhibit the concern towards the environment and mankind. This proposal will benefit farmers and others in polluted cities. The language to be used is Embedded C programming and Arduino IDE open source platform with both hardware and software interaction. The display will involve an android app called Blynk App.

Mobile Communication Via Satellite

NASA Technical Reports Server (NTRS)

Yan, Tsun-Yee; Naderi, Firouz M.

1988-01-01

System mixes real-time and delayed-transmission channels. Combination of L-band and SHF links connect fixed and mobile equipment on ground to satellite relay. Software and hardware architecture conforms structure of open-system-interconnection model suggested by International Standards Organization.

Open hardware: a role to play in wireless sensor networks?

PubMed

Fisher, Roy; Ledwaba, Lehlogonolo; Hancke, Gerhard; Kruger, Carel

2015-03-20

The concept of the Internet of Things is rapidly becoming a reality, with many applications being deployed within industrial and consumer sectors. At the 'thing' level-devices and inter-device network communication-the core technical building blocks are generally the same as those found in wireless sensor network implementations. For the Internet of Things to continue growing, we need more plentiful resources for building intelligent devices and sensor networks. Unfortunately, current commercial devices, e.g., sensor nodes and network gateways, tend to be expensive and proprietary, which presents a barrier to entry and arguably slows down further development. There are, however, an increasing number of open embedded platforms available and also a wide selection of off-the-shelf components that can quickly and easily be built into device and network gateway solutions. The question is whether these solutions measure up to built-for-purpose devices. In the paper, we provide a comparison of existing built-for-purpose devices against open source devices. For comparison, we have also designed and rapidly prototyped a sensor node based on off-the-shelf components. We show that these devices compare favorably to built-for-purpose devices in terms of performance, power and cost. Using open platforms and off-the-shelf components would allow more developers to build intelligent devices and sensor networks, which could result in a better overall development ecosystem, lower barriers to entry and rapid growth in the number of IoT applications.

Open Hardware: A Role to Play in Wireless Sensor Networks?

PubMed Central

Fisher, Roy; Ledwaba, Lehlogonolo; Hancke, Gerhard; Kruger, Carel

2015-01-01

The concept of the Internet of Things is rapidly becoming a reality, with many applications being deployed within industrial and consumer sectors. At the ‘thing’ level—devices and inter-device network communication—the core technical building blocks are generally the same as those found in wireless sensor network implementations. For the Internet of Things to continue growing, we need more plentiful resources for building intelligent devices and sensor networks. Unfortunately, current commercial devices, e.g., sensor nodes and network gateways, tend to be expensive and proprietary, which presents a barrier to entry and arguably slows down further development. There are, however, an increasing number of open embedded platforms available and also a wide selection of off-the-shelf components that can quickly and easily be built into device and network gateway solutions. The question is whether these solutions measure up to built-for-purpose devices. In the paper, we provide a comparison of existing built-for-purpose devices against open source devices. For comparison, we have also designed and rapidly prototyped a sensor node based on off-the-shelf components. We show that these devices compare favorably to built-for-purpose devices in terms of performance, power and cost. Using open platforms and off-the-shelf components would allow more developers to build intelligent devices and sensor networks, which could result in a better overall development ecosystem, lower barriers to entry and rapid growth in the number of IoT applications. PMID:25803706

Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms

PubMed Central

Stone, John E.; Hynninen, Antti-Pekka; Phillips, James C.; Schulten, Klaus

2017-01-01

All-atom molecular dynamics simulations of biomolecules provide a powerful tool for exploring the structure and dynamics of large protein complexes within realistic cellular environments. Unfortunately, such simulations are extremely demanding in terms of their computational requirements, and they present many challenges in terms of preparation, simulation methodology, and analysis and visualization of results. We describe our early experiences porting the popular molecular dynamics simulation program NAMD and the simulation preparation, analysis, and visualization tool VMD to GPU-accelerated OpenPOWER hardware platforms. We report our experiences with compiler-provided autovectorization and compare with hand-coded vector intrinsics for the POWER8 CPU. We explore the performance benefits obtained from unique POWER8 architectural features such as 8-way SMT and its value for particular molecular modeling tasks. Finally, we evaluate the performance of several GPU-accelerated molecular modeling kernels and relate them to other hardware platforms. PMID:29202130

Hacking for astronomy: can 3D printers and open-hardware enable low-cost sub-/millimeter instrumentation?

NASA Astrophysics Data System (ADS)

Ferkinhoff, Carl

2014-07-01

There have been several exciting developments in the technologies commonly used n in the hardware hacking community. Advances in low cost additive-manufacturing processes (i.e. 3D-printers) and the development of openhardware projects, which have produced inexpensive and easily programmable micro-controllers and micro-computers (i.e. Arduino and Raspberry Pi) have opened a new door for individuals seeking to make their own devices. Here we describe the potential for these technologies to reduce costs in construction and development of submillimeter/millimeter astronomical instrumentation. Specifically we have begun a program to measure the optical properties of the custom plastics used in 3D-printers as well as the printer accuracy and resolution to assess the feasibility of directly printing sub- /millimeter transmissive optics. We will also discuss low cost designs for cryogenic temperature measurement and control utilizing Arduino and Raspberry Pi.

The Need for Vendor Source Code at NAS. Revised

NASA Technical Reports Server (NTRS)

Carter, Russell; Acheson, Steve; Blaylock, Bruce; Brock, David; Cardo, Nick; Ciotti, Bob; Poston, Alan; Wong, Parkson; Chancellor, Marisa K. (Technical Monitor)

1997-01-01

The Numerical Aerodynamic Simulation (NAS) Facility has a long standing practice of maintaining buildable source code for installed hardware. There are two reasons for this: NAS's designated pathfinding role, and the need to maintain a smoothly running operational capacity given the widely diversified nature of the vendor installations. NAS has a need to maintain support capabilities when vendors are not able; diagnose and remedy hardware or software problems where applicable; and to support ongoing system software development activities whether or not the relevant vendors feel support is justified. This note provides an informal history of these activities at NAS, and brings together the general principles that drive the requirement that systems integrated into the NAS environment run binaries built from source code, onsite.

Checkpointing Shared Memory Programs at the Application-level

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bronevetsky, G; Schulz, M; Szwed, P

2004-09-08

Trends in high-performance computing are making it necessary for long-running applications to tolerate hardware faults. The most commonly used approach is checkpoint and restart(CPR)-the state of the computation is saved periodically on disk, and when a failure occurs, the computation is restarted from the last saved state. At present, it is the responsibility of the programmer to instrument applications for CPR. Our group is investigating the use of compiler technology to instrument codes to make them self-checkpointing and self-restarting, thereby providing an automatic solution to the problem of making long-running scientific applications resilient to hardware faults. Our previous work focusedmore » on message-passing programs. In this paper, we describe such a system for shared-memory programs running on symmetric multiprocessors. The system has two components: (i)a pre-compiler for source-to-source modification of applications, and (ii) a runtime system that implements a protocol for coordinating CPR among the threads of the parallel application. For the sake of concreteness, we focus on a non-trivial subset of OpenMP that includes barriers and locks. One of the advantages of this approach is that the ability to tolerate faults becomes embedded within the application itself, so applications become self-checkpointing and self-restarting on any platform. We demonstrate this by showing that our transformed benchmarks can checkpoint and restart on three different platforms (Windows/x86, Linux/x86, and Tru64/Alpha). Our experiments show that the overhead introduced by this approach is usually quite small; they also suggest ways in which the current implementation can be tuned to reduced overheads further.« less

Product Pipeline: Megan K. Fox Looks at the Latest Ebook Devices and What They Mean for Librarians

ERIC Educational Resources Information Center

Fox, Megan K.

2006-01-01

The standalone PDA seems to be dying, but the prominence of smart phones and similar devices are opening new doors for ebooks. The digital music and ipod phenomena bode well for what could happen with e-text publishing, with content and hardware easier to use just as new open standards are beginning to emerge. Mobile, portable, wireless, handheld,…

Evaluation of CHO Benchmarks on the Arria 10 FPGA using Intel FPGA SDK for OpenCL

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jin, Zheming; Yoshii, Kazutomo; Finkel, Hal

The OpenCL standard is an open programming model for accelerating algorithms on heterogeneous computing system. OpenCL extends the C-based programming language for developing portable codes on different platforms such as CPU, Graphics processing units (GPUs), Digital Signal Processors (DSPs) and Field Programmable Gate Arrays (FPGAs). The Intel FPGA SDK for OpenCL is a suite of tools that allows developers to abstract away the complex FPGA-based development flow for a high-level software development flow. Users can focus on the design of hardware-accelerated kernel functions in OpenCL and then direct the tools to generate the low-level FPGA implementations. The approach makes themore » FPGA-based development more accessible to software users as the needs for hybrid computing using CPUs and FPGAs are increasing. It can also significantly reduce the hardware development time as users can evaluate different ideas with high-level language without deep FPGA domain knowledge. Benchmarking of OpenCL-based framework is an effective way for analyzing the performance of system by studying the execution of the benchmark applications. CHO is a suite of benchmark applications that provides support for OpenCL [1]. The authors presented CHO as an OpenCL port of the CHStone benchmark. Using Altera OpenCL (AOCL) compiler to synthesize the benchmark applications, they listed the resource usage and performance of each kernel that can be successfully synthesized by the compiler. In this report, we evaluate the resource usage and performance of the CHO benchmark applications using the Intel FPGA SDK for OpenCL and Nallatech 385A FPGA board that features an Arria 10 FPGA device. The focus of the report is to have a better understanding of the resource usage and performance of the kernel implementations using Arria-10 FPGA devices compared to Stratix-5 FPGA devices. In addition, we also gain knowledge about the limitations of the current compiler when it fails to synthesize a benchmark application.« less

Bio-Inspired Controller on an FPGA Applied to Closed-Loop Diaphragmatic Stimulation

PubMed Central

Zbrzeski, Adeline; Bornat, Yannick; Hillen, Brian; Siu, Ricardo; Abbas, James; Jung, Ranu; Renaud, Sylvie

2016-01-01

Cervical spinal cord injury can disrupt connections between the brain respiratory network and the respiratory muscles which can lead to partial or complete loss of ventilatory control and require ventilatory assistance. Unlike current open-loop technology, a closed-loop diaphragmatic pacing system could overcome the drawbacks of manual titration as well as respond to changing ventilation requirements. We present an original bio-inspired assistive technology for real-time ventilation assistance, implemented in a digital configurable Field Programmable Gate Array (FPGA). The bio-inspired controller, which is a spiking neural network (SNN) inspired by the medullary respiratory network, is as robust as a classic controller while having a flexible, low-power and low-cost hardware design. The system was simulated in MATLAB with FPGA-specific constraints and tested with a computational model of rat breathing; the model reproduced experimentally collected respiratory data in eupneic animals. The open-loop version of the bio-inspired controller was implemented on the FPGA. Electrical test bench characterizations confirmed the system functionality. Open and closed-loop paradigm simulations were simulated to test the FPGA system real-time behavior using the rat computational model. The closed-loop system monitors breathing and changes in respiratory demands to drive diaphragmatic stimulation. The simulated results inform future acute animal experiments and constitute the first step toward the development of a neuromorphic, adaptive, compact, low-power, implantable device. The bio-inspired hardware design optimizes the FPGA resource and time costs while harnessing the computational power of spike-based neuromorphic hardware. Its real-time feature makes it suitable for in vivo applications. PMID:27378844

An open architecture for hybrid force-visual servo control of robotic manipulators in unstructured environments

NASA Astrophysics Data System (ADS)

Hassanzadeh, Iraj; Janabi-Sharifi, Farrokh

2005-12-01

In this paper, a new open architecture for visual servo control tasks is illustrated. A Puma-560 robotic manipulator is used to prove the concept. This design enables doing hybrid forcehisual servo control in an unstructured environment in different modes. Also, it can be controlled through Internet in teleoperation mode using a haptic device. Our proposed structure includes two major parts, hardware and software. In terms of hardware, it consists of a master (host) computer, a slave (target) computer, a Puma 560 manipulator, a CCD camera, a force sensor and a haptic device. There are five DAQ cards, interfacing Puma 560 and a slave computer. An open architecture package is developed using Matlab (R), Simulink (R) and XPC target toolbox. This package has the Hardware-In-the-Loop (HIL) property, i.e., enables one to readily implement different configurations of force, visual or hybrid control in real time. The implementation includes the following stages. First of all, retrofitting of puma was carried out. Then a modular joint controller for Puma 560 was realized using Simulink (R). Force sensor driver and force control implementation were written, using sjknction blocks of Simulink (R). Visual images were captured through Image Acquisition Toolbox of Matlab (R), and processed using Image Processing Toolbox. A haptic device interface was also written in Simulink (R). Thus, this setup could be readily reconfigured and accommodate any other robotic manipulator and/or other sensors without the trouble of the external issues relevant to the control, interface and software, while providing flexibility in components modification.

Potential Damage to Flight Hardware from MIL-STD-462 CS02 Setup

NASA Technical Reports Server (NTRS)

Harris, Patrick K.; Block, Nathan F.

2003-01-01

The MIL-STD-462 CS02 conducted susceptibility test setup includes an audio transformer, with the secondary used as an inductor, and a large capacitor. Together, these two components form an L-type low-pass filter to minimize the injected test signal input into the power source. Some flight hardware power input configurations are not compatible with this setup and break into oscillation when powered up. This, in turn, can damage flight hardware. Such an oscillation resulted in the catastrophic failure of an item tested in the Goddard Space Flight Center (GSFC) Large electromagnetic compatibility (EMC) Test Facility.

Potential Damage to Flight Hardware from MIL-STD-462 CS02 Setup

NASA Technical Reports Server (NTRS)

Harris, Patrick K.; Block, Nathan F.

2002-01-01

The MIL-STD-462 CS02 conducted susceptibility test setup, performed during electromagnetic compatibility (EMC) testing, consists of an audio transformer with the secondary used as an inductor and a large capacitor. Together, these two components form an L-type low-pass filter to minimize the injected test signal input into the power source. Some flight hardware power input configurations are not compatible with this setup and break into oscillation when powered up. This can damage flight hardware and caused a catastrophic failure to an item tested in the Goddard Space Flight Center (GSFC) Large EMC Test Facility.

Testing flight software on the ground: Introducing the hardware-in-the-loop simulation method to the Alpha Magnetic Spectrometer on the International Space Station

NASA Astrophysics Data System (ADS)

Sun, Wenhao; Cai, Xudong; Meng, Qiao

2016-04-01

Complex automatic protection functions are being added to the onboard software of the Alpha Magnetic Spectrometer. A hardware-in-the-loop simulation method has been introduced to overcome the difficulties of ground testing that are brought by hardware and environmental limitations. We invented a time-saving approach by reusing the flight data as the data source of the simulation system instead of mathematical models. This is easy to implement and it works efficiently. This paper presents the system framework, implementation details and some application examples.

Using Selection Pressure as an Asset to Develop Reusable, Adaptable Software Systems

NASA Astrophysics Data System (ADS)

Berrick, S. W.; Lynnes, C.

2007-12-01

The Goddard Earth Sciences Data and Information Services Center (GES DISC) at NASA has over the years developed and honed a number of reusable architectural components for supporting large-scale data centers with a large customer base. These include a processing system (S4PM) and an archive system (S4PA) based upon a workflow engine called the Simple, Scalable, Script-based Science Processor (S4P); an online data visualization and analysis system (Giovanni); and the radically simple and fast data search tool, Mirador. These subsystems are currently reused internally in a variety of combinations to implement customized data management on behalf of instrument science teams and other science investigators. Some of these subsystems (S4P and S4PM) have also been reused by other data centers for operational science processing. Our experience has been that development and utilization of robust, interoperable, and reusable software systems can actually flourish in environments defined by heterogeneous commodity hardware systems, the emphasis on value-added customer service, and continual cost reduction pressures. The repeated internal reuse that is fostered by such an environment encourages and even forces changes to the software that make it more reusable and adaptable. Allowing and even encouraging such selective pressures to software development has been a key factor in the success of S4P and S4PM, which are now available to the open source community under the NASA Open Source Agreement.

The ALMA common software: dispatch from the trenches

NASA Astrophysics Data System (ADS)

Schwarz, J.; Sommer, H.; Jeram, B.; Sekoranja, M.; Chiozzi, G.; Grimstrup, A.; Caproni, A.; Paredes, C.; Allaert, E.; Harrington, S.; Turolla, S.; Cirami, R.

2008-07-01

The ALMA Common Software (ACS) provides both an application framework and CORBA-based middleware for the distributed software system of the Atacama Large Millimeter Array. Building upon open-source tools such as the JacORB, TAO and OmniORB ORBs, ACS supports the development of component-based software in any of three languages: Java, C++ and Python. Now in its seventh major release, ACS has matured, both in its feature set as well as in its reliability and performance. However, it is only recently that the ALMA observatory's hardware and application software has reached a level at which it can exploit and challenge the infrastructure that ACS provides. In particular, the availability of an Antenna Test Facility(ATF) at the site of the Very Large Array in New Mexico has enabled us to exercise and test the still evolving end-to-end ALMA software under realistic conditions. The major focus of ACS, consequently, has shifted from the development of new features to consideration of how best to use those that already exist. Configuration details which could be neglected for the purpose of running unit tests or skeletal end-to-end simulations have turned out to be sensitive levers for achieving satisfactory performance in a real-world environment. Surprising behavior in some open-source tools has required us to choose between patching code that we did not write or addressing its deficiencies by implementing workarounds in our own software. We will discuss these and other aspects of our recent experience at the ATF and in simulation.

Real-Time Motion Capture Toolbox (RTMocap): an open-source code for recording 3-D motion kinematics to study action-effect anticipations during motor and social interactions.

PubMed

Lewkowicz, Daniel; Delevoye-Turrell, Yvonne

2016-03-01

We present here a toolbox for the real-time motion capture of biological movements that runs in the cross-platform MATLAB environment (The MathWorks, Inc., Natick, MA). It provides instantaneous processing of the 3-D movement coordinates of up to 20 markers at a single instant. Available functions include (1) the setting of reference positions, areas, and trajectories of interest; (2) recording of the 3-D coordinates for each marker over the trial duration; and (3) the detection of events to use as triggers for external reinforcers (e.g., lights, sounds, or odors). Through fast online communication between the hardware controller and RTMocap, automatic trial selection is possible by means of either a preset or an adaptive criterion. Rapid preprocessing of signals is also provided, which includes artifact rejection, filtering, spline interpolation, and averaging. A key example is detailed, and three typical variations are developed (1) to provide a clear understanding of the importance of real-time control for 3-D motion in cognitive sciences and (2) to present users with simple lines of code that can be used as starting points for customizing experiments using the simple MATLAB syntax. RTMocap is freely available (http://sites.google.com/site/RTMocap/) under the GNU public license for noncommercial use and open-source development, together with sample data and extensive documentation.

A New Arduino Datalogger Board for Simple, Low Cost Environmental Monitoring and the EnviroDIY Web Community

NASA Astrophysics Data System (ADS)

Hicks, S. D.; Aufdenkampe, A. K.; Montgomery, D. S.; Damiano, S. G.; Brooks, H. P.

2015-12-01

Scientists and educators around the world have been building their own dataloggers and devices using a variety of boards based on the Arduino open source electronics platform. While there have been several useful boards on the market in the past few years, they still required significant modification or additional components in order to use them with various sensors or deploy them in remote areas. Here we introduce our new custom datalogger board that makes it very easy to build a rugged environmental monitoring system. These custom boards contain all of the essential features of a solar-powered datalogger with radio telemetry, plus they have a very convenient and modular method for attaching a wide variety of sensors and devices. Various deployment options and installations are shown, as well as the online database that is used for capturing the live streaming data from the loggers and displaying graphs on custom web pages. Following the introduction last year of the EnviroDIY online community (http://enviroDIY.org), it continues to gain new members and share new ideas about open-source hardware and software solutions for observing our environment. EnviroDIY members can showcase their gadgets or describe their projects, ask questions, or follow along with helpful tutorials. Our new datalogger board, together with the EnviroDIY website, will make it easy for anyone to build and deploy their own environmental monitoring stations.

Treatment of hardware infection after osteosynthesis of lower leg using negative pressure wound therapy and transforming powder dressing.

PubMed

Marinović, Marin; Ivandcić, Aldo; Spanjol, Josip; Pina, Maja; Bakota, Bore; Bandalović, Ante; Cukeljs, Fabijan

2014-12-01

Fractures of the distal part of the lower leg are more common in everyday practice and traumatology. In young and active patients these injuries are mainly caused by high energy trauma. They are treated with external fixator in first step, and in second step, after sanation of the soft tissue, with open reduction and internal fixation (ORIF). It is very safe and effective method of treatment. Treatment of the infections that occur in the early postoperative period after open reduction and internal fixation represents a great problem and challenge for surgeons. It is widely accepted that the presence of deep infection can't be cured in the presence of hardware. However, removal of hardware in the presence of unhealed fractures significantly complicates sanation of infection and fracture itself We have decided to present a 35-years-old patient with a hardware infection with present chronic wound with hardware exposed eight months after the first operation and six months after second operation. The wound measured one centimeter in diameter with cell detritus and bad granulations tissue inside the wound. Hardwre was exposed in the depth of the wound.The secretion was minimal. Negative Pressure Wound Therapy (NPWT) was applicated after debridemet and lavage performed in ambulatory conditions. The starting therapy was continuously -125 mm Hg of vacuum. After five days of NPWT the defect was partially filled with granula- tion tissue. For another five days we continue with NPWT with the same values of-125 mm Hg pressure but in the inter- mitent mode. After that period we used transforming powder dressing for covering and protection of the wound with was filled with granulation tissue. Five days later, wound was completely healed with epithelisation. After four months of patient follow-up, we found the wound is completely repaired. The patient denies pain and has continued orderly flow of fracture healing, with no signs of infection.

Creative Uses of Custom Electronics for Environmental Monitoring

NASA Astrophysics Data System (ADS)

Hicks, S.; Aufdenkampe, A. K.; Montgomery, D. S.

2012-12-01

The ability to build custom electronic devices specifically suited to a unique task has gotten easier and cheaper, thanks to the recent popularity of open source electronics platforms like Arduino. Using Arduino-based processor boards, we have been creating a variety of helpful devices to perform functions that would have been too expensive to implement with standard methods and commercial hardware. The Christina River Basin CZO is currently operating dozens of homemade dataloggers that are connected to different types of environmental sensors. Most of these Arduino loggers have been deployed for over a year, so our experiences with them and their sensors have taught us a lot about the reliability and accuracy of both the loggers and the sensors. Some loggers also have the capability for wireless radio or ethernet data transmission for reporting live data to web sites for instant graphing or archiving. Other Arduino devices have the ability to be controlled remotely through web sites or telephones, making it easy to remotely trigger sample pumps or valves. The open-source nature of Arduino means collaboration is easy because the circuit schematics and source code for programming the boards can be shared between users. And because Arduino devices are easy to use and program, we developed an interface board that allows educators to easily connect a variety of inexpensive environmental sensors to an Arduino board. Then the students can write and upload simple programs to interact with the sensors, making it a very effective tool for teaching electronics and environmental science at the same time. The flexibility and capability of electronics prototyping platforms like Arduino mean these simple boards can cheaply and effectively perform a countless number of tasks for projects in environmental science and education.

50 years of physical growth and impressive technological advances unmatched by health human resources reform and cultural change.

PubMed

Scott, Graham W S

2012-01-01

The year 1962 was pre-medicare. The public was concerned about access and individual affordability of care. Funding involved public or private responsibility and the role of government. Physicians, the most influential providers, were concerned that government funding would result in the loss of their independence and their becoming state employees. The retrospective analysis "Looking Back 50 Years in Hospital Administration" by Graham and Sibbald is arresting as it underlines just how much progress we have made in what could be termed "hardware" in support of healthcare policy and hospital administration. From this perspective, the progress has been eye opening, given the advent of universal healthcare, the advancement in our physical facilities, the development of high-quality diagnostic equipment, the explosion of new research centres and new and complex clinical procedures. The development of this hardware has given our providers better weapons and contributed to a remarkable improvement in life expectancy. But progress in health administration and policy management involves more than hardware. If the hardware constitutes the tools, then the "software" of the healthcare system involves the human resources and the culture change that must be positioned to make maximum use of the hardware. In 2062, looking back at the 2012 experience, the legacy test may be whether we dealt with health human resources and culture change at a rate that matched our progress in hardware.

A pluggable framework for parallel pairwise sequence search.

PubMed

Archuleta, Jeremy; Feng, Wu-chun; Tilevich, Eli

2007-01-01

The current and near future of the computing industry is one of multi-core and multi-processor technology. Most existing sequence-search tools have been designed with a focus on single-core, single-processor systems. This discrepancy between software design and hardware architecture substantially hinders sequence-search performance by not allowing full utilization of the hardware. This paper presents a novel framework that will aid the conversion of serial sequence-search tools into a parallel version that can take full advantage of the available hardware. The framework, which is based on a software architecture called mixin layers with refined roles, enables modules to be plugged into the framework with minimal effort. The inherent modular design improves maintenance and extensibility, thus opening up a plethora of opportunities for advanced algorithmic features to be developed and incorporated while routine maintenance of the codebase persists.

A text input system developed by using lips image recognition based LabVIEW for the seriously disabled.

PubMed

Chen, S C; Shao, C L; Liang, C K; Lin, S W; Huang, T H; Hsieh, M C; Yang, C H; Luo, C H; Wuo, C M

2004-01-01

In this paper, we present a text input system for the seriously disabled by using lips image recognition based on LabVIEW. This system can be divided into the software subsystem and the hardware subsystem. In the software subsystem, we adopted the technique of image processing to recognize the status of mouth-opened or mouth-closed depending the relative distance between the upper lip and the lower lip. In the hardware subsystem, parallel port built in PC is used to transmit the recognized result of mouth status to the Morse-code text input system. Integrating the software subsystem with the hardware subsystem, we implement a text input system by using lips image recognition programmed in LabVIEW language. We hope the system can help the seriously disabled to communicate with normal people more easily.

Open Architecture Standard for NASA's Software-Defined Space Telecommunications Radio Systems

NASA Technical Reports Server (NTRS)

Reinhart, Richard C.; Johnson, Sandra K.; Kacpura, Thomas J.; Hall, Charles S.; Smith, Carl R.; Liebetreu, John

2008-01-01

NASA is developing an architecture standard for software-defined radios used in space- and ground-based platforms to enable commonality among radio developments to enhance capability and services while reducing mission and programmatic risk. Transceivers (or transponders) with functionality primarily defined in software (e.g., firmware) have the ability to change their functional behavior through software alone. This radio architecture standard offers value by employing common waveform software interfaces, method of instantiation, operation, and testing among different compliant hardware and software products. These common interfaces within the architecture abstract application software from the underlying hardware to enable technology insertion independently at either the software or hardware layer. This paper presents the initial Space Telecommunications Radio System (STRS) Architecture for NASA missions to provide the desired software abstraction and flexibility while minimizing the resources necessary to support the architecture.

Design of a 2-mm Wavelength KIDs Prototype Camera for the Large Millimeter Telescope

NASA Astrophysics Data System (ADS)

Velázquez, M.; Ferrusca, D.; Castillo-Dominguez, E.; Ibarra-Medel, E.; Ventura, S.; Gómez-Rivera, V.; Hughes, D.; Aretxaga, I.; Grant, W.; Doyle, S.; Mauskopf, P.

2016-08-01

A new camera is being developed for the Large Millimeter Telescope (Sierra Negra, México) by an international collaboration with the University of Massachusetts, the University of Cardiff, and Arizona State University. The camera is based on kinetic inductance detectors (KIDs), a very promising technology due to their sensitivity and especially, their compatibility with frequency domain multiplexing at microwave frequencies allowing large format arrays, in comparison with other detection technologies for mm-wavelength astronomy. The instrument will have a 100 pixels array of KIDs to image the 2-mm wavelength band and is designed for closed cycle operation using a pulse tube cryocooler along with a three-stage sub-kelvin 3He cooler to provide a 250 mK detector stage. RF cabling is used to readout the detectors from room temperature to 250 mK focal plane, and the amplification stage is achieved with a low-noise amplifier operating at 4 K. The readout electronics will be based on open-source reconfigurable open architecture computing hardware in order to perform real-time microwave transmission measurements and monitoring the resonance frequency of each detector, as well as the detection process.

SWARM: A 32 GHz Correlator and VLBI Beamformer for the Submillimeter Array

NASA Astrophysics Data System (ADS)

Primiani, Rurik A.; Young, Kenneth H.; Young, André; Patel, Nimesh; Wilson, Robert W.; Vertatschitsch, Laura; Chitwood, Billie B.; Srinivasan, Ranjani; MacMahon, David; Weintroub, Jonathan

2016-03-01

A 32GHz bandwidth VLBI capable correlator and phased array has been designed and deployeda at the Smithsonian Astrophysical Observatory’s Submillimeter Array (SMA). The SMA Wideband Astronomical ROACH2 Machine (SWARM) integrates two instruments: a correlator with 140kHz spectral resolution across its full 32GHz band, used for connected interferometric observations, and a phased array summer used when the SMA participates as a station in the Event Horizon Telescope (EHT) very long baseline interferometry (VLBI) array. For each SWARM quadrant, Reconfigurable Open Architecture Computing Hardware (ROACH2) units shared under open-source from the Collaboration for Astronomy Signal Processing and Electronics Research (CASPER) are equipped with a pair of ultra-fast analog-to-digital converters (ADCs), a field programmable gate array (FPGA) processor, and eight 10 Gigabit Ethernet (GbE) ports. A VLBI data recorder interface designated the SWARM digital back end, or SDBE, is implemented with a ninth ROACH2 per quadrant, feeding four Mark6 VLBI recorders with an aggregate recording rate of 64 Gbps. This paper describes the design and implementation of SWARM, as well as its deployment at SMA with reference to verification and science data.

Fiberfox: facilitating the creation of realistic white matter software phantoms.

PubMed

Neher, Peter F; Laun, Frederik B; Stieltjes, Bram; Maier-Hein, Klaus H

2014-11-01

Phantom-based validation of diffusion-weighted image processing techniques is an important key to innovation in the field and is widely used. Openly available and user friendly tools for the flexible generation of tailor-made datasets for the specific tasks at hand can greatly facilitate the work of researchers around the world. We present an open-source framework, Fiberfox, that enables (1) the intuitive definition of arbitrary artificial white matter fiber tracts, (2) signal generation from those fibers by means of the most recent multi-compartment modeling techniques, and (3) simulation of the actual MR acquisition that allows for the introduction of realistic MRI-related effects into the final image. We show that real acquisitions can be closely approximated by simulating the acquisition of the well-known FiberCup phantom. We further demonstrate the advantages of our framework by evaluating the effects of imaging artifacts and acquisition settings on the outcome of 12 tractography algorithms. Our findings suggest that experiments on a realistic software phantom might change the conclusions drawn from earlier hardware phantom experiments. Fiberfox may find application in validating and further developing methods such as tractography, super-resolution, diffusion modeling or artifact correction. Copyright © 2013 Wiley Periodicals, Inc.

Mass spectrometer output file format mzML.

PubMed

Deutsch, Eric W

2010-01-01

Mass spectrometry is an important technique for analyzing proteins and other biomolecular compounds in biological samples. Each of the vendors of these mass spectrometers uses a different proprietary binary output file format, which has hindered data sharing and the development of open source software for downstream analysis. The solution has been to develop, with the full participation of academic researchers as well as software and hardware vendors, an open XML-based format for encoding mass spectrometer output files, and then to write software to use this format for archiving, sharing, and processing. This chapter presents the various components and information available for this format, mzML. In addition to the XML schema that defines the file structure, a controlled vocabulary provides clear terms and definitions for the spectral metadata, and a semantic validation rules mapping file allows the mzML semantic validator to insure that an mzML document complies with one of several levels of requirements. Complete documentation and example files insure that the format may be uniformly implemented. At the time of release, there already existed several implementations of the format and vendors have committed to supporting the format in their products.

Software Productivity of Field Experiments Using the Mobile Agents Open Architecture with Workflow Interoperability

NASA Technical Reports Server (NTRS)

Clancey, William J.; Lowry, Michael R.; Nado, Robert Allen; Sierhuis, Maarten

2011-01-01

We analyzed a series of ten systematically developed surface exploration systems that integrated a variety of hardware and software components. Design, development, and testing data suggest that incremental buildup of an exploration system for long-duration capabilities is facilitated by an open architecture with appropriate-level APIs, specifically designed to facilitate integration of new components. This improves software productivity by reducing changes required for reconfiguring an existing system.

Open SHMEM Reference Implementation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pritchard, Howard; Curtis, Anthony; Welch, Aaron

2016-05-12

OpenSHMEM is an effort to create a specification for a standardized API for parallel programming in the Partitioned Global Address Space. Along with the specification the project is also creating a reference implementation of the API. This implementation attempts to be portable, to allow it to be deployed in multiple environments, and to be a starting point for implementations targeted to particular hardware platforms. It will also serve as a springboard for future development of the API.

NBodyLab: A Testbed for Undergraduates Utilizing a Web Interface to NEMO and MD-GRAPE2 Hardware

NASA Astrophysics Data System (ADS)

Johnson, V. L.; Teuben, P. J.; Penprase, B. E.

An N-body simulation testbed called NBodyLab was developed at Pomona College as a teaching tool for undergraduates. The testbed runs under Linux and provides a web interface to selected back-end NEMO modeling and analysis tools, and several integration methods which can optionally use an MD-GRAPE2 supercomputer card in the server to accelerate calculation of particle-particle forces. The testbed provides a framework for using and experimenting with the main components of N-body simulations: data models and transformations, numerical integration of the equations of motion, analysis and visualization products, and acceleration techniques (in this case, special purpose hardware). The testbed can be used by students with no knowledge of programming or Unix, freeing such students and their instructor to spend more time on scientific experimentation. The advanced student can extend the testbed software and/or more quickly transition to the use of more advanced Unix-based toolsets such as NEMO, Starlab and model builders such as GalactICS. Cosmology students at Pomona College used the testbed to study collisions of galaxies with different speeds, masses, densities, collision angles, angular momentum, etc., attempting to simulate, for example, the Tadpole Galaxy and the Antenna Galaxies. The testbed framework is available as open-source to assist other researchers and educators. Recommendations are made for testbed enhancements.

GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research

PubMed Central

Yeung, Ka Yee

2016-01-01

Reproducibility is vital in science. For complex computational methods, it is often necessary, not just to recreate the code, but also the software and hardware environment to reproduce results. Virtual machines, and container software such as Docker, make it possible to reproduce the exact environment regardless of the underlying hardware and operating system. However, workflows that use Graphical User Interfaces (GUIs) remain difficult to replicate on different host systems as there is no high level graphical software layer common to all platforms. GUIdock allows for the facile distribution of a systems biology application along with its graphics environment. Complex graphics based workflows, ubiquitous in systems biology, can now be easily exported and reproduced on many different platforms. GUIdock uses Docker, an open source project that provides a container with only the absolutely necessary software dependencies and configures a common X Windows (X11) graphic interface on Linux, Macintosh and Windows platforms. As proof of concept, we present a Docker package that contains a Bioconductor application written in R and C++ called networkBMA for gene network inference. Our package also includes Cytoscape, a java-based platform with a graphical user interface for visualizing and analyzing gene networks, and the CyNetworkBMA app, a Cytoscape app that allows the use of networkBMA via the user-friendly Cytoscape interface. PMID:27045593

Feasibility study on a strain based deflection monitoring system for wind turbine blades

NASA Astrophysics Data System (ADS)

Lee, Kyunghyun; Aihara, Aya; Puntsagdash, Ganbayar; Kawaguchi, Takayuki; Sakamoto, Hiraku; Okuma, Masaaki

2017-01-01

The bending stiffness of the wind turbine blades has decreased due to the trend of wind turbine upsizing. Consequently, the risk of blades breakage by hitting the tower has increased. In order to prevent such incidents, this study proposes a deflection monitoring system that can be installed to already operating wind turbine's blades. The monitoring system is composed of an estimation algorithm to detect blade deflection and a wireless sensor network as a hardware equipment. As for the estimation method for blade deflection, a strain-based estimation algorithm and an objective function for optimal sensor arrangement are proposed. Strain-based estimation algorithm is using a linear correlation between strain and deflections, which can be expressed in a form of a transformation matrix. The objective function includes the terms of strain sensitivity and condition number of the transformation matrix between strain and deflection. In order to calculate the objective function, a simplified experimental model of the blade is constructed by interpolating the mode shape of a blade from modal testing. The interpolation method is effective considering a practical use to operating wind turbines' blades since it is not necessary to establish a finite element model of a blade. On the other hand, a sensor network with wireless connection with an open source hardware is developed. It is installed to a 300 W scale wind turbine and vibration of the blade on operation is investigated.

GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research.

PubMed

Hung, Ling-Hong; Kristiyanto, Daniel; Lee, Sung Bong; Yeung, Ka Yee

2016-01-01

Reproducibility is vital in science. For complex computational methods, it is often necessary, not just to recreate the code, but also the software and hardware environment to reproduce results. Virtual machines, and container software such as Docker, make it possible to reproduce the exact environment regardless of the underlying hardware and operating system. However, workflows that use Graphical User Interfaces (GUIs) remain difficult to replicate on different host systems as there is no high level graphical software layer common to all platforms. GUIdock allows for the facile distribution of a systems biology application along with its graphics environment. Complex graphics based workflows, ubiquitous in systems biology, can now be easily exported and reproduced on many different platforms. GUIdock uses Docker, an open source project that provides a container with only the absolutely necessary software dependencies and configures a common X Windows (X11) graphic interface on Linux, Macintosh and Windows platforms. As proof of concept, we present a Docker package that contains a Bioconductor application written in R and C++ called networkBMA for gene network inference. Our package also includes Cytoscape, a java-based platform with a graphical user interface for visualizing and analyzing gene networks, and the CyNetworkBMA app, a Cytoscape app that allows the use of networkBMA via the user-friendly Cytoscape interface.

IQ-Station: A Low Cost Portable Immersive Environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eric Whiting; Patrick O'Leary; William Sherman

2010-11-01

The emergence of inexpensive 3D TV’s, affordable input and rendering hardware and open-source software has created a yeasty atmosphere for the development of low-cost immersive environments (IE). A low cost IE system, or IQ-station, fashioned from commercial off the shelf technology (COTS), coupled with a targeted immersive application can be a viable laboratory instrument for enhancing scientific workflow for exploration and analysis. The use of an IQ-station in a laboratory setting also has the potential of quickening the adoption of a more sophisticated immersive environment as a critical enabler in modern scientific and engineering workflows. Prior work in immersive environmentsmore » generally required either a head mounted display (HMD) system or a large projector-based implementation both of which have limitations in terms of cost, usability, or space requirements. The solution presented here provides an alternative platform providing a reasonable immersive experience that addresses those limitations. Our work brings together the needed hardware and software to create a fully integrated immersive display and interface system that can be readily deployed in laboratories and common workspaces. By doing so, it is now feasible for immersive technologies to be included in researchers’ day-to-day workflows. The IQ-Station sets the stage for much wider adoption of immersive environments outside the small communities of virtual reality centers.« less

Scalable digital hardware for a trapped ion quantum computer

NASA Astrophysics Data System (ADS)

Mount, Emily; Gaultney, Daniel; Vrijsen, Geert; Adams, Michael; Baek, So-Young; Hudek, Kai; Isabella, Louis; Crain, Stephen; van Rynbach, Andre; Maunz, Peter; Kim, Jungsang

2016-12-01

Many of the challenges of scaling quantum computer hardware lie at the interface between the qubits and the classical control signals used to manipulate them. Modular ion trap quantum computer architectures address scalability by constructing individual quantum processors interconnected via a network of quantum communication channels. Successful operation of such quantum hardware requires a fully programmable classical control system capable of frequency stabilizing the continuous wave lasers necessary for loading, cooling, initialization, and detection of the ion qubits, stabilizing the optical frequency combs used to drive logic gate operations on the ion qubits, providing a large number of analog voltage sources to drive the trap electrodes, and a scheme for maintaining phase coherence among all the controllers that manipulate the qubits. In this work, we describe scalable solutions to these hardware development challenges.

Analysis of a hardware and software fault tolerant processor for critical applications

NASA Technical Reports Server (NTRS)

Dugan, Joanne B.

1993-01-01

Computer systems for critical applications must be designed to tolerate software faults as well as hardware faults. A unified approach to tolerating hardware and software faults is characterized by classifying faults in terms of duration (transient or permanent) rather than source (hardware or software). Errors arising from transient faults can be handled through masking or voting, but errors arising from permanent faults require system reconfiguration to bypass the failed component. Most errors which are caused by software faults can be considered transient, in that they are input-dependent. Software faults are triggered by a particular set of inputs. Quantitative dependability analysis of systems which exhibit a unified approach to fault tolerance can be performed by a hierarchical combination of fault tree and Markov models. A methodology for analyzing hardware and software fault tolerant systems is applied to the analysis of a hypothetical system, loosely based on the Fault Tolerant Parallel Processor. The models consider both transient and permanent faults, hardware and software faults, independent and related software faults, automatic recovery, and reconfiguration.

Frugal Droplet Microfluidics Using Consumer Opto-Electronics.

PubMed

Frot, Caroline; Taccoen, Nicolas; Baroud, Charles N

2016-01-01

The maker movement has shown how off-the-shelf devices can be combined to perform operations that, until recently, required expensive specialized equipment. Applying this philosophy to microfluidic devices can play a fundamental role in disseminating these technologies outside specialist labs and into industrial use. Here we show how nanoliter droplets can be manipulated using a commercial DVD writer, interfaced with an Arduino electronic controller. We couple the optical setup with a droplet generation and manipulation device based on the "confinement gradients" approach. This device uses regions of different depths to generate and transport the droplets, which further simplifies the operation and reduces the need for precise flow control. The use of robust consumer electronics, combined with open source hardware, leads to a great reduction in the price of the device, as well as its footprint, without reducing its performance compared with the laboratory setup.

Ephus: Multipurpose Data Acquisition Software for Neuroscience Experiments

PubMed Central

Suter, Benjamin A.; O'Connor, Timothy; Iyer, Vijay; Petreanu, Leopoldo T.; Hooks, Bryan M.; Kiritani, Taro; Svoboda, Karel; Shepherd, Gordon M. G.

2010-01-01

Physiological measurements in neuroscience experiments often involve complex stimulus paradigms and multiple data channels. Ephus (http://www.ephus.org) is an open-source software package designed for general-purpose data acquisition and instrument control. Ephus operates as a collection of modular programs, including an ephys program for standard whole-cell recording with single or multiple electrodes in typical electrophysiological experiments, and a mapper program for synaptic circuit mapping experiments involving laser scanning photostimulation based on glutamate uncaging or channelrhodopsin-2 excitation. Custom user functions allow user-extensibility at multiple levels, including on-line analysis and closed-loop experiments, where experimental parameters can be changed based on recently acquired data, such as during in vivo behavioral experiments. Ephus is compatible with a variety of data acquisition and imaging hardware. This paper describes the main features and modules of Ephus and their use in representative experimental applications. PMID:21960959

Scintillation-Hardened GPS Receiver

NASA Technical Reports Server (NTRS)

Stephens, Donald R.

2015-01-01

CommLargo, Inc., has developed a scintillation-hardened Global Positioning System (GPS) receiver that improves reliability for low-orbit missions and complies with NASA's Space Telecommunications Radio System (STRS) architecture standards. A software-defined radio (SDR) implementation allows a single hardware element to function as either a conventional radio or as a GPS receiver, providing backup and redundancy for platforms such as the International Space Station (ISS) and high-value remote sensing platforms. The innovation's flexible SDR implementation reduces cost, weight, and power requirements. Scintillation hardening improves mission reliability and variability. In Phase I, CommLargo refactored an open-source GPS software package with Kalman filter-based tracking loops to improve performance during scintillation and also demonstrated improved navigation during a geomagnetic storm. In Phase II, the company generated a new field-programmable gate array (FPGA)-based GPS waveform to demonstrate on NASA's Space Communication and Navigation (SCaN) test bed.

Complex Geometric Models of Diffusion and Relaxation in Healthy and Damaged White Matter

PubMed Central

Farrell, Jonathan A.D.; Smith, Seth A.; Reich, Daniel S.; Calabresi, Peter A.; van Zijl, Peter C.M.

2010-01-01

Which aspects of tissue microstructure affect diffusion weighted MRI signals? Prior models, many of which use Monte-Carlo simulations, have focused on relatively simple models of the cellular microenvironment and have not considered important anatomic details. With the advent of higher-order analysis models for diffusion imaging, such as high-angular-resolution diffusion imaging (HARDI), more realistic models are necessary. This paper presents and evaluates the reproducibility of simulations of diffusion in complex geometries. Our framework is quantitative, does not require specialized hardware, is easily implemented with little programming experience, and is freely available as open-source software. Models may include compartments with different diffusivities, permeabilities, and T2 time constants using both parametric (e.g., spheres and cylinders) and arbitrary (e.g., mesh-based) geometries. Three-dimensional diffusion displacement-probability functions are mapped with high reproducibility, and thus can be readily used to assess reproducibility of diffusion-derived contrasts. PMID:19739233

Pybus -- A Python Software Bus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lavrijsen, Wim T.L.P.

2004-10-14

A software bus, just like its hardware equivalent, allows for the discovery, installation, configuration, loading, unloading, and run-time replacement of software components, as well as channeling of inter-component communication. Python, a popular open-source programming language, encourages a modular design on software written in it, but it offers little or no component functionality. However, the language and its interpreter provide sufficient hooks to implement a thin, integral layer of component support. This functionality can be presented to the developer in the form of a module, making it very easy to use. This paper describes a Pythonmodule, PyBus, with which the conceptmore » of a ''software bus'' can be realized in Python. It demonstrates, within the context of the ATLAS software framework Athena, how PyBus can be used for the installation and (run-time) configuration of software, not necessarily Python modules, from a Python application in a way that is transparent to the end-user.« less

Three-dimensional printing of complex biological structures by freeform reversible embedding of suspended hydrogels

PubMed Central

Hinton, Thomas J.; Jallerat, Quentin; Palchesko, Rachelle N.; Park, Joon Hyung; Grodzicki, Martin S.; Shue, Hao-Jan; Ramadan, Mohamed H.; Hudson, Andrew R.; Feinberg, Adam W.

2015-01-01

We demonstrate the additive manufacturing of complex three-dimensional (3D) biological structures using soft protein and polysaccharide hydrogels that are challenging or impossible to create using traditional fabrication approaches. These structures are built by embedding the printed hydrogel within a secondary hydrogel that serves as a temporary, thermoreversible, and biocompatible support. This process, termed freeform reversible embedding of suspended hydrogels, enables 3D printing of hydrated materials with an elastic modulus <500 kPa including alginate, collagen, and fibrin. Computer-aided design models of 3D optical, computed tomography, and magnetic resonance imaging data were 3D printed at a resolution of ~200 μm and at low cost by leveraging open-source hardware and software tools. Proof-of-concept structures based on femurs, branched coronary arteries, trabeculated embryonic hearts, and human brains were mechanically robust and recreated complex 3D internal and external anatomical architectures. PMID:26601312

RenderToolbox3: MATLAB tools that facilitate physically based stimulus rendering for vision research.

PubMed

Heasly, Benjamin S; Cottaris, Nicolas P; Lichtman, Daniel P; Xiao, Bei; Brainard, David H

2014-02-07

RenderToolbox3 provides MATLAB utilities and prescribes a workflow that should be useful to researchers who want to employ graphics in the study of vision and perhaps in other endeavors as well. In particular, RenderToolbox3 facilitates rendering scene families in which various scene attributes and renderer behaviors are manipulated parametrically, enables spectral specification of object reflectance and illuminant spectra, enables the use of physically based material specifications, helps validate renderer output, and converts renderer output to physical units of radiance. This paper describes the design and functionality of the toolbox and discusses several examples that demonstrate its use. We have designed RenderToolbox3 to be portable across computer hardware and operating systems and to be free and open source (except for MATLAB itself). RenderToolbox3 is available at https://github.com/DavidBrainard/RenderToolbox3.

Study on Huizhou architecture of point cloud registration based on optimized ICP algorithm

NASA Astrophysics Data System (ADS)

Zhang, Runmei; Wu, Yulu; Zhang, Guangbin; Zhou, Wei; Tao, Yuqian

2018-03-01

In view of the current point cloud registration software has high hardware requirements, heavy workload and moltiple interactive definition, the source of software with better processing effect is not open, a two--step registration method based on normal vector distribution feature and coarse feature based iterative closest point (ICP) algorithm is proposed in this paper. This method combines fast point feature histogram (FPFH) algorithm, define the adjacency region of point cloud and the calculation model of the distribution of normal vectors, setting up the local coordinate system for each key point, and obtaining the transformation matrix to finish rough registration, the rough registration results of two stations are accurately registered by using the ICP algorithm. Experimental results show that, compared with the traditional ICP algorithm, the method used in this paper has obvious time and precision advantages for large amount of point clouds.

Frugal Droplet Microfluidics Using Consumer Opto-Electronics

PubMed Central

Frot, Caroline; Taccoen, Nicolas; Baroud, Charles N.

2016-01-01

The maker movement has shown how off-the-shelf devices can be combined to perform operations that, until recently, required expensive specialized equipment. Applying this philosophy to microfluidic devices can play a fundamental role in disseminating these technologies outside specialist labs and into industrial use. Here we show how nanoliter droplets can be manipulated using a commercial DVD writer, interfaced with an Arduino electronic controller. We couple the optical setup with a droplet generation and manipulation device based on the “confinement gradients” approach. This device uses regions of different depths to generate and transport the droplets, which further simplifies the operation and reduces the need for precise flow control. The use of robust consumer electronics, combined with open source hardware, leads to a great reduction in the price of the device, as well as its footprint, without reducing its performance compared with the laboratory setup. PMID:27560139

Classification of hyperspectral imagery using MapReduce on a NVIDIA graphics processing unit (Conference Presentation)

NASA Astrophysics Data System (ADS)

Ramirez, Andres; Rahnemoonfar, Maryam

2017-04-01

A hyperspectral image provides multidimensional figure rich in data consisting of hundreds of spectral dimensions. Analyzing the spectral and spatial information of such image with linear and non-linear algorithms will result in high computational time. In order to overcome this problem, this research presents a system using a MapReduce-Graphics Processing Unit (GPU) model that can help analyzing a hyperspectral image through the usage of parallel hardware and a parallel programming model, which will be simpler to handle compared to other low-level parallel programming models. Additionally, Hadoop was used as an open-source version of the MapReduce parallel programming model. This research compared classification accuracy results and timing results between the Hadoop and GPU system and tested it against the following test cases: the CPU and GPU test case, a CPU test case and a test case where no dimensional reduction was applied.

Comparison of existing digital image analysis systems for the analysis of Thematic Mapper data

NASA Technical Reports Server (NTRS)

Likens, W. C.; Wrigley, R. C.

1984-01-01

Most existing image analysis systems were designed with the Landsat Multi-Spectral Scanner in mind, leaving open the question of whether or not these systems could adequately process Thematic Mapper data. In this report, both hardware and software systems have been evaluated for compatibility with TM data. Lack of spectral analysis capability was not found to be a problem, though techniques for spatial filtering and texture varied. Computer processing speed and data storage of currently existing mini-computer based systems may be less than adequate. Upgrading to more powerful hardware may be required for many TM applications.

Magnetic Nanoparticle Thermometer: An Investigation of Minimum Error Transmission Path and AC Bias Error

PubMed Central

Du, Zhongzhou; Su, Rijian; Liu, Wenzhong; Huang, Zhixing

2015-01-01

The signal transmission module of a magnetic nanoparticle thermometer (MNPT) was established in this study to analyze the error sources introduced during the signal flow in the hardware system. The underlying error sources that significantly affected the precision of the MNPT were determined through mathematical modeling and simulation. A transfer module path with the minimum error in the hardware system was then proposed through the analysis of the variations of the system error caused by the significant error sources when the signal flew through the signal transmission module. In addition, a system parameter, named the signal-to-AC bias ratio (i.e., the ratio between the signal and AC bias), was identified as a direct determinant of the precision of the measured temperature. The temperature error was below 0.1 K when the signal-to-AC bias ratio was higher than 80 dB, and other system errors were not considered. The temperature error was below 0.1 K in the experiments with a commercial magnetic fluid (Sample SOR-10, Ocean Nanotechnology, Springdale, AR, USA) when the hardware system of the MNPT was designed with the aforementioned method. PMID:25875188

Investigations of shot reproducibility for the SMP diode at 4.5 MV.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bennett, Nichelle; Crain, Marlon D.; Droemer, Darryl W.

In experiments conducted on the RITS-6 accelerator, the SMP diode exhibits sig- ni cant shot-to-shot variability. Speci cally, for identical hardware operated at the same voltage, some shots exhibit a catastrophic drop in diode impedance. A study is underway to identify sources of shot-to-shot variations which correlate with diode impedance collapse. To remove knob emission as a source, only data from a shot series conducted with a 4.5-MV peak voltage are considered. The scope of this report is limited to sources of variability which occur away from the diode, such as power ow emission and trajectory changes, variations in pulsedmore » power, dustbin and transmission line alignment, and di erent knob shapes. We nd no changes in the transmission line hardware, alignment, or hardware preparation methods which correlate with impedance collapse. However, in classifying good versus poor shots, we nd that there is not a continuous spectrum of diode impedance behavior but that the good and poor shots can be grouped into two distinct impedance pro les. This result forms the basis of a follow-on study focusing on the variability resulting from diode physics. 3« less

Sailfish: A flexible multi-GPU implementation of the lattice Boltzmann method

NASA Astrophysics Data System (ADS)

Januszewski, M.; Kostur, M.

2014-09-01

We present Sailfish, an open source fluid simulation package implementing the lattice Boltzmann method (LBM) on modern Graphics Processing Units (GPUs) using CUDA/OpenCL. We take a novel approach to GPU code implementation and use run-time code generation techniques and a high level programming language (Python) to achieve state of the art performance, while allowing easy experimentation with different LBM models and tuning for various types of hardware. We discuss the general design principles of the code, scaling to multiple GPUs in a distributed environment, as well as the GPU implementation and optimization of many different LBM models, both single component (BGK, MRT, ELBM) and multicomponent (Shan-Chen, free energy). The paper also presents results of performance benchmarks spanning the last three NVIDIA GPU generations (Tesla, Fermi, Kepler), which we hope will be useful for researchers working with this type of hardware and similar codes. Catalogue identifier: AETA_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AETA_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU Lesser General Public License, version 3 No. of lines in distributed program, including test data, etc.: 225864 No. of bytes in distributed program, including test data, etc.: 46861049 Distribution format: tar.gz Programming language: Python, CUDA C, OpenCL. Computer: Any with an OpenCL or CUDA-compliant GPU. Operating system: No limits (tested on Linux and Mac OS X). RAM: Hundreds of megabytes to tens of gigabytes for typical cases. Classification: 12, 6.5. External routines: PyCUDA/PyOpenCL, Numpy, Mako, ZeroMQ (for multi-GPU simulations), scipy, sympy Nature of problem: GPU-accelerated simulation of single- and multi-component fluid flows. Solution method: A wide range of relaxation models (LBGK, MRT, regularized LB, ELBM, Shan-Chen, free energy, free surface) and boundary conditions within the lattice Boltzmann method framework. Simulations can be run in single or double precision using one or more GPUs. Restrictions: The lattice Boltzmann method works for low Mach number flows only. Unusual features: The actual numerical calculations run exclusively on GPUs. The numerical code is built dynamically at run-time in CUDA C or OpenCL, using templates and symbolic formulas. The high-level control of the simulation is maintained by a Python process. Additional comments: !!!!! The distribution file for this program is over 45 Mbytes and therefore is not delivered directly when Download or Email is requested. Instead a html file giving details of how the program can be obtained is sent. !!!!! Running time: Problem-dependent, typically minutes (for small cases or short simulations) to hours (large cases or long simulations).

Web-Based Real-Time Emergency Monitoring

NASA Technical Reports Server (NTRS)

Harvey, Craig A.; Lawhead, Joel

2007-01-01

The Web-based Real-Time Asset Monitoring (RAM) module for emergency operations and facility management enables emergency personnel in federal agencies and local and state governments to monitor and analyze data in the event of a natural disaster or other crisis that threatens a large number of people and property. The software can manage many disparate sources of data within a facility, city, or county. It was developed on industry-standard Geo- Spatial software and is compliant with open GIS standards. RAM View can function as a standalone system, or as an integrated plugin module to Emergency Operations Center (EOC) software suites such as REACT (Real-time Emergency Action Coordination Tool), thus ensuring the widest possible distribution among potential users. RAM has the ability to monitor various data sources, including streaming data. Many disparate systems are included in the initial suite of supported hardware systems, such as mobile GPS units, ambient measurements of temperature, moisture and chemical agents, flow meters, air quality, asset location, and meteorological conditions. RAM View displays real-time data streams such as gauge heights from the U.S. Geological Survey gauging stations, flood crests from the National Weather Service, and meteorological data from numerous sources. Data points are clearly visible on the map interface, and attributes as specified in the user requirements can be viewed and queried.

What's New in Software? Current Sources of Information Boost Effectiveness of Computer-Assisted Instruction.

ERIC Educational Resources Information Center

Ellsworth, Nancy J.

1990-01-01

This article reviews current resources on computer-assisted instruction. Included are sources of software and hardware evaluations, advances in current technology, research, an information hotline, and inventories of available technological assistance. (DB)

Perceptron Genetic to Recognize Openning Strategy Ruy Lopez

NASA Astrophysics Data System (ADS)

Azmi, Zulfian; Mawengkang, Herman

2018-01-01

The application of Perceptron method is not effective for coding on hardware based systems because it is not real time learning. With Genetic algorithm approach in calculating and searching the best weight (fitness value) system will do learning only one iteration. And the results of this analysis were tested in the case of the introduction of the opening pattern of chess Ruy Lopez. The Analysis with Perceptron Model with Algorithm Approach Genetics from group Artificial Neural Network for open Ruy Lopez. The data is processed with base open chess, with step eight a position white Pion from end open chess. Using perceptron method have many input and one output process many weight and refraction until output equal goal. Data trained and test with software Matlab and system can recognize the chess opening Ruy Lopez or Not open Ruy Lopez with Real time.

Safecast: How disaster led to empowerment of crowdsourced citizen science for radiation measurement and communication after Fukushima

NASA Astrophysics Data System (ADS)

Brown, Azby; Franken, Peter; Bonner, Sean; Moross, Joe; Dolezal, Nick

2016-04-01

Safecast, an international, volunteer-based organization devoted to monitoring and openly sharing information on environmental radiation and other pollutants, was initiated on March 12, 2011, one day following the start of the Fukushima Daichi Nuclear Power Plant accident, in response to the lack of publicly available, accurate and trustworthy information about the spread of radioactive fallout. Since its inception, Safecast has grown in size, scope, and geographical reach, as well as in the technical sophistication of its citizen-science-based hardware and software systems. The focus of the group's work is to provide citizens worldwide with the tools they need to inform themselves by gathering and sharing accurate environmental data, in an open and participatory fashion. This effort combines hardware and software design for original radiation and air quality measurement devices; visualizations which are made available online and as applications for mobile and desktop; strong public outreach and education programs; and open forums for discussion of radiation, air pollution, and other hazards. The Safecast system is agile and flexible in terms of development and deployment, and all designs, software programs, and data is provided on an open-source basis. In addition, because the group takes no public stance either for or against nuclear power, it has become an important unbiased source of information regarding radiation risks. The Fukushima Daichi NPP disaster provided a crucial opportunity to evaluate the state of preparation on the part the powerplant operator, government agencies, and international oversight bodies, to gather necessary information on radiation risks quickly and to share it both with emergency responders and the general public. The inadequacy of this preparation and the chaotic nature of inter-agency and inter-governmental communication has been well noted in several official reports on the disaster, including those issued by The National Diet of Japan Fukushima Nuclear Accident Independent Investigation Commission (NAIIC) and by the International Atomic Energy Agency (IAEA). During the initial weeks of the disaster in particular, citizens were given little actionable information concerning actual radiation levels, and what was presented both by official spokespersons and in the media was often incomplete and /or contradictory. Many citizens stepped in to fill the gaps, share information and technical knowledge, and provide credible independent alternatives to official information, and Safecast has been held up as the most successful and noteworthy example. The experience of the Safecast project provides an extremely instructive opportunity to evaluate the potential for citizen scientists to make crucial public contributions in emergency situations as well as on a longterm basis, and to help formulate guidelines for the most mutually beneficial relationships between citizens' groups and government. This paper will describe the methodology and toolsets Safecast has developed and deployed, as well as a summary of the key results obtained to date, and lessons learned.

A Self-Provisioning Mechanism in OpenStack for IoT Devices.

PubMed

Solano, Antonio; Dormido, Raquel; Duro, Natividad; Sánchez, Juan Miguel

2016-08-17

The aim of this paper is to introduce a plug-and-play mechanism for an Internet of Things (IoT) device to instantiate a Software as a Service (SaaS) application in a private cloud, built up with OpenStack. The SaaS application is the digital avatar of a physical object connected to Internet. As a proof of concept, a Vending Machine is retrofitted and connected to Internet with and Arduino Open Hardware device. Once the self-configuration mechanism is completed, it is possible to order a product from a mobile communication device.

A Self-Provisioning Mechanism in OpenStack for IoT Devices

PubMed Central

Solano, Antonio; Dormido, Raquel; Duro, Natividad; Sánchez, Juan Miguel

2016-01-01

The aim of this paper is to introduce a plug-and-play mechanism for an Internet of Things (IoT) device to instantiate a Software as a Service (SaaS) application in a private cloud, built up with OpenStack. The SaaS application is the digital avatar of a physical object connected to Internet. As a proof of concept, a Vending Machine is retrofitted and connected to Internet with and Arduino Open Hardware device. Once the self-configuration mechanism is completed, it is possible to order a product from a mobile communication device. PMID:27548166

Simulation verification techniques study: Simulation self test hardware design and techniques report

NASA Technical Reports Server (NTRS)

1974-01-01

The final results are presented of the hardware verification task. The basic objectives of the various subtasks are reviewed along with the ground rules under which the overall task was conducted and which impacted the approach taken in deriving techniques for hardware self test. The results of the first subtask and the definition of simulation hardware are presented. The hardware definition is based primarily on a brief review of the simulator configurations anticipated for the shuttle training program. The results of the survey of current self test techniques are presented. The data sources that were considered in the search for current techniques are reviewed, and results of the survey are presented in terms of the specific types of tests that are of interest for training simulator applications. Specifically, these types of tests are readiness tests, fault isolation tests and incipient fault detection techniques. The most applicable techniques were structured into software flows that are then referenced in discussions of techniques for specific subsystems.

Design of a nickel-hydrogen battery simulator for the NASA EOS testbed

NASA Technical Reports Server (NTRS)

Gur, Zvi; Mang, Xuesi; Patil, Ashok R.; Sable, Dan M.; Cho, Bo H.; Lee, Fred C.

1992-01-01

The hardware and software design of a nickel-hydrogen (Ni-H2) battery simulator (BS) with application to the NASA Earth Observation System (EOS) satellite is presented. The battery simulator is developed as a part of a complete testbed for the EOS satellite power system. The battery simulator involves both hardware and software components. The hardware component includes the capability of sourcing and sinking current at a constant programmable voltage. The software component includes the capability of monitoring the battery's ampere-hours (Ah) and programming the battery voltage according to an empirical model of the nickel-hydrogen battery stored in a computer.

Computational System For Rapid CFD Analysis In Engineering

NASA Technical Reports Server (NTRS)

Barson, Steven L.; Ascoli, Edward P.; Decroix, Michelle E.; Sindir, Munir M.

1995-01-01

Computational system comprising modular hardware and software sub-systems developed to accelerate and facilitate use of techniques of computational fluid dynamics (CFD) in engineering environment. Addresses integration of all aspects of CFD analysis process, including definition of hardware surfaces, generation of computational grids, CFD flow solution, and postprocessing. Incorporates interfaces for integration of all hardware and software tools needed to perform complete CFD analysis. Includes tools for efficient definition of flow geometry, generation of computational grids, computation of flows on grids, and postprocessing of flow data. System accepts geometric input from any of three basic sources: computer-aided design (CAD), computer-aided engineering (CAE), or definition by user.

The Application of Acoustic Measurements and Audio Recordings for Diagnosis of In-Flight Hardware Anomalies

NASA Technical Reports Server (NTRS)

Welsh, David; Denham, Samuel; Allen, Christopher

2011-01-01

In many cases, an initial symptom of hardware malfunction is unusual or unexpected acoustic noise. Many industries such as automotive, heating and air conditioning, and petro-chemical processing use noise and vibration data along with rotating machinery analysis techniques to identify noise sources and correct hardware defects. The NASA/Johnson Space Center Acoustics Office monitors the acoustic environment of the International Space Station (ISS) through periodic sound level measurement surveys. Trending of the sound level measurement survey results can identify in-flight hardware anomalies. The crew of the ISS also serves as a "detection tool" in identifying unusual hardware noises; in these cases the spectral analysis of audio recordings made on orbit can be used to identify hardware defects that are related to rotating components such as fans, pumps, and compressors. In this paper, three examples of the use of sound level measurements and audio recordings for the diagnosis of in-flight hardware anomalies are discussed: identification of blocked inter-module ventilation (IMV) ducts, diagnosis of abnormal ISS Crew Quarters rack exhaust fan noise, and the identification and replacement of a defective flywheel assembly in the Treadmill with Vibration Isolation (TVIS) hardware. In each of these examples, crew time was saved by identifying the off nominal component or condition that existed and in directing in-flight maintenance activities to address and correct each of these problems.

Novel data visualizations of X-ray data for aviation security applications using the Open Threat Assessment Platform (OTAP)

NASA Astrophysics Data System (ADS)

Gittinger, Jaxon M.; Jimenez, Edward S.; Holswade, Erica A.; Nunna, Rahul S.

2017-02-01

This work will demonstrate the implementation of a traditional and non-traditional visualization of x-ray images for aviation security applications that will be feasible with open system architecture initiatives such as the Open Threat Assessment Platform (OTAP). Anomalies of interest to aviation security are fluid, where characteristic signals of anomalies of interest can evolve rapidly. OTAP is a limited scope open architecture baggage screening prototype that intends to allow 3rd-party vendors to develop and easily implement, integrate, and deploy detection algorithms and specialized hardware on a field deployable screening technology [13]. In this study, stereoscopic images were created using an unmodified, field-deployed system and rendered on the Oculus Rift, a commercial virtual reality video gaming headset. The example described in this work is not dependent on the Oculus Rift, and is possible using any comparable hardware configuration capable of rendering stereoscopic images. The depth information provided from viewing the images will aid in the detection of characteristic signals from anomalies of interest. If successful, OTAP has the potential to allow for aviation security to become more fluid in its adaptation to the evolution of anomalies of interest. This work demonstrates one example that is easily implemented using the OTAP platform, that could lead to the future generation of ATR algorithms and data visualization approaches.

Petascale computation of multi-physics seismic simulations

NASA Astrophysics Data System (ADS)

Gabriel, Alice-Agnes; Madden, Elizabeth H.; Ulrich, Thomas; Wollherr, Stephanie; Duru, Kenneth C.

2017-04-01

Capturing the observed complexity of earthquake sources in concurrence with seismic wave propagation simulations is an inherently multi-scale, multi-physics problem. In this presentation, we present simulations of earthquake scenarios resolving high-detail dynamic rupture evolution and high frequency ground motion. The simulations combine a multitude of representations of model complexity; such as non-linear fault friction, thermal and fluid effects, heterogeneous fault stress and fault strength initial conditions, fault curvature and roughness, on- and off-fault non-elastic failure to capture dynamic rupture behavior at the source; and seismic wave attenuation, 3D subsurface structure and bathymetry impacting seismic wave propagation. Performing such scenarios at the necessary spatio-temporal resolution requires highly optimized and massively parallel simulation tools which can efficiently exploit HPC facilities. Our up to multi-PetaFLOP simulations are performed with SeisSol (www.seissol.org), an open-source software package based on an ADER-Discontinuous Galerkin (DG) scheme solving the seismic wave equations in velocity-stress formulation in elastic, viscoelastic, and viscoplastic media with high-order accuracy in time and space. Our flux-based implementation of frictional failure remains free of spurious oscillations. Tetrahedral unstructured meshes allow for complicated model geometry. SeisSol has been optimized on all software levels, including: assembler-level DG kernels which obtain 50% peak performance on some of the largest supercomputers worldwide; an overlapping MPI-OpenMP parallelization shadowing the multiphysics computations; usage of local time stepping; parallel input and output schemes and direct interfaces to community standard data formats. All these factors enable aim to minimise the time-to-solution. The results presented highlight the fact that modern numerical methods and hardware-aware optimization for modern supercomputers are essential to further our understanding of earthquake source physics and complement both physic-based ground motion research and empirical approaches in seismic hazard analysis. Lastly, we will conclude with an outlook on future exascale ADER-DG solvers for seismological applications.

Operative treatment of early infection after internal fixation of limb fractures (exclusive of severe open fractures).

PubMed

Bonnevialle, P

2017-02-01

Early infection after open reduction and internal fixation (ORIF) of a limb bone is defined as bacteriologically documented, deep and/or superficial surgical-site infection (SSI) diagnosed within 6months after the surgical procedure. This interval is arbitrarily considered sufficient to obtain fracture healing. The treatment of early infection after ORIF should be decided by a multidisciplinary team. The principles are the same as for revision arthroplasty. Superficial SSIs should be differentiated from deep SSIs, based on the results of bacteriological specimens collected using flawless technique. A turning point in the local microbial ecology occurs around the third or fourth week, when a biofilm develops around metallic implants. This biofilm protects the bacteria. The treatment relies on both non-operative and operative measures, which are selected based on the time to occurrence of the infection, condition of the soft tissues, and stage of bone healing. Both the surgical strategy and the antibiotic regimen should be determined during a multidisciplinary discussion. When treating superficial SSIs after ORIF, soft-tissue management is the main challenge. The treatment differs according to whether the hardware is covered or exposed. Defects in the skin and/or fascia can be managed using reliable reconstructive surgery techniques, either immediately or after a brief period of vacuum-assisted closure. In deep SSIs, deciding whether to leave or to remove the hardware is difficult. If the hardware is removed, the fracture site can be stabilised provisionally using either external fixation or a cement rod. Once infection control is achieved, several measures can be taken to stimulate bone healing before the end of the classical 6-month interval. If the hardware was removed, then internal fixation must be performed once the infection is eradicated. Copyright © 2016. Published by Elsevier Masson SAS.

A superconducting large-angle magnetic suspension

NASA Technical Reports Server (NTRS)

Downer, James R.; Anastas, George V., Jr.; Bushko, Dariusz A.; Flynn, Frederick J.; Goldie, James H.; Gondhalekar, Vijay; Hawkey, Timothy J.; Hockney, Richard L.; Torti, Richard P.

1992-01-01

SatCon Technology Corporation has completed a Small Business Innovation Research (SBIR) Phase 2 program to develop a Superconducting Large-Angle Magnetic Suspension (LAMS) for the NASA Langley Research Center. The Superconducting LAMS was a hardware demonstration of the control technology required to develop an advanced momentum exchange effector. The Phase 2 research was directed toward the demonstration for the key technology required for the advanced concept CMG, the controller. The Phase 2 hardware consists of a superconducting solenoid ('source coils') suspended within an array of nonsuperconducting coils ('control coils'), a five-degree-of-freedom positioning sensing system, switching power amplifiers, and a digital control system. The results demonstrated the feasibility of suspending the source coil. Gimballing (pointing the axis of the source coil) was demonstrated over a limited range. With further development of the rotation sensing system, enhanced angular freedom should be possible.

A superconducting large-angle magnetic suspension

NASA Astrophysics Data System (ADS)

Downer, James R.; Anastas, George V., Jr.; Bushko, Dariusz A.; Flynn, Frederick J.; Goldie, James H.; Gondhalekar, Vijay; Hawkey, Timothy J.; Hockney, Richard L.; Torti, Richard P.

1992-12-01

SatCon Technology Corporation has completed a Small Business Innovation Research (SBIR) Phase 2 program to develop a Superconducting Large-Angle Magnetic Suspension (LAMS) for the NASA Langley Research Center. The Superconducting LAMS was a hardware demonstration of the control technology required to develop an advanced momentum exchange effector. The Phase 2 research was directed toward the demonstration for the key technology required for the advanced concept CMG, the controller. The Phase 2 hardware consists of a superconducting solenoid ('source coils') suspended within an array of nonsuperconducting coils ('control coils'), a five-degree-of-freedom positioning sensing system, switching power amplifiers, and a digital control system. The results demonstrated the feasibility of suspending the source coil. Gimballing (pointing the axis of the source coil) was demonstrated over a limited range. With further development of the rotation sensing system, enhanced angular freedom should be possible.

Compound simulator IR radiation characteristics test and calibration

NASA Astrophysics Data System (ADS)

Li, Yanhong; Zhang, Li; Li, Fan; Tian, Yi; Yang, Yang; Li, Zhuo; Shi, Rui

2015-10-01

The Hardware-in-the-loop simulation can establish the target/interference physical radiation and interception of product flight process in the testing room. In particular, the simulation of environment is more difficult for high radiation energy and complicated interference model. Here the development in IR scene generation produced by a fiber array imaging transducer with circumferential lamp spot sources is introduced. The IR simulation capability includes effective simulation of aircraft signatures and point-source IR countermeasures. Two point-sources as interference can move in two-dimension random directions. For simulation the process of interference release, the radiation and motion characteristic is tested. Through the zero calibration for optical axis of simulator, the radiation can be well projected to the product detector. The test and calibration results show the new type compound simulator can be used in the hardware-in-the-loop simulation trial.

Distance Learning in a Multimedia Networks Project: Main Results.

ERIC Educational Resources Information Center

Ruokamo, Heli; Pohjolainen, Seppo

2000-01-01

Discusses a goal-oriented project, focused on open learning environments using computer networks, called Distance Learning in Multimedia Networks that was part of the Finnish Multimedia Program. Describes the combined efforts of Finnish telecommunications companies, content providers, publishing houses, hardware companies, and educational…

An avionics scenario and command model description for Space Generic Open Avionics Architecture (SGOAA)

NASA Technical Reports Server (NTRS)

Stovall, John R.; Wray, Richard B.

1994-01-01

This paper presents a description of a model for a space vehicle operational scenario and the commands for avionics. This model will be used in developing a dynamic architecture simulation model using the Statemate CASE tool for validation of the Space Generic Open Avionics Architecture (SGOAA). The SGOAA has been proposed as an avionics architecture standard to NASA through its Strategic Avionics Technology Working Group (SATWG) and has been accepted by the Society of Automotive Engineers (SAE) for conversion into an SAE Avionics Standard. This architecture was developed for the Flight Data Systems Division (FDSD) of the NASA Johnson Space Center (JSC) by the Lockheed Engineering and Sciences Company (LESC), Houston, Texas. This SGOAA includes a generic system architecture for the entities in spacecraft avionics, a generic processing external and internal hardware architecture, and a nine class model of interfaces. The SGOAA is both scalable and recursive and can be applied to any hierarchical level of hardware/software processing systems.

Evaluation of Open-Source Hard Real Time Software Packages

NASA Technical Reports Server (NTRS)

Mattei, Nicholas S.

2004-01-01

Reliable software is, at times, hard to find. No piece of software can be guaranteed to work in every situation that may arise during its use here at Glenn Research Center or in space. The job of the Software Assurance (SA) group in the Risk Management Office is to rigorously test the software in an effort to ensure it matches the contract specifications. In some cases the SA team also researches new alternatives for selected software packages. This testing and research is an integral part of the department of Safety and Mission Assurance. Real Time operation in reference to a computer system is a particular style of handing the timing and manner with which inputs and outputs are handled. A real time system executes these commands and appropriate processing within a defined timing constraint. Within this definition there are two other classifications of real time systems: hard and soft. A soft real time system is one in which if the particular timing constraints are not rigidly met there will be no critical results. On the other hand, a hard real time system is one in which if the timing constraints are not met the results could be catastrophic. An example of a soft real time system is a DVD decoder. If the particular piece of data from the input is not decoded and displayed to the screen at exactly the correct moment nothing critical will become of it, the user may not even notice it. However, a hard real time system is needed to control the timing of fuel injections or steering on the Space Shuttle; a delay of even a fraction of a second could be catastrophic in such a complex system. The current real time system employed by most NASA projects is Wind River's VxWorks operating system. This is a proprietary operating system that can be configured to work with many of NASA s needs and it provides very accurate and reliable hard real time performance. The down side is that since it is a proprietary operating system it is also costly to implement. The prospect of replacing this somewhat costly implementation is the focus of one of the SA group s current research projects. The explosion of open source software in the last ten years has led to the development of a multitude of software solutions which were once only produced by major corporations. The benefits of these open projects include faster release and bug patching cycles as well as inexpensive if not free software solutions. The main packages for hard real time solutions under Linux are Real Time Application Interface (RTAI) and two varieties of Real Time Linux (RTL), RTLFree and RTLPro. During my time here at NASA I have been testing various hard real time solutions operating as layers on the Linux Operating System. All testing is being run on an Intel SBC 2590 which is a common embedded hardware platform. The test plan was provided to me by the Software Assurance group at the start of my internship and my job has been to test the systems by developing and executing the test cases on the hardware. These tests are constructed so that the Software Assurance group can get hard test data for a comparison between the open source and proprietary implementations of hard real time solutions.

Open core control software for surgical robots

PubMed Central

Kozuka, Hiroaki; Kim, Hyung Wook; Takesue, Naoyuki; Vladimirov, B.; Sakaguchi, Masamichi; Tokuda, Junichi; Hata, Nobuhiko; Chinzei, Kiyoyuki; Fujimoto, Hideo

2010-01-01

Object In these days, patients and doctors in operation room are surrounded by many medical devices as resulting from recent advancement of medical technology. However, these cutting-edge medical devices are working independently and not collaborating with each other, even though the collaborations between these devices such as navigation systems and medical imaging devices are becoming very important for accomplishing complex surgical tasks (such as a tumor removal procedure while checking the tumor location in neurosurgery). On the other hand, several surgical robots have been commercialized, and are becoming common. However, these surgical robots are not open for collaborations with external medical devices in these days. A cutting-edge “intelligent surgical robot” will be possible in collaborating with surgical robots, various kinds of sensors, navigation system and so on. On the other hand, most of the academic software developments for surgical robots are “home-made” in their research institutions and not open to the public. Therefore, open source control software for surgical robots can be beneficial in this field. From these perspectives, we developed Open Core Control software for surgical robots to overcome these challenges. Materials and methods In general, control softwares have hardware dependencies based on actuators, sensors and various kinds of internal devices. Therefore, these control softwares cannot be used on different types of robots without modifications. However, the structure of the Open Core Control software can be reused for various types of robots by abstracting hardware dependent parts. In addition, network connectivity is crucial for collaboration between advanced medical devices. The OpenIGTLink is adopted in Interface class which plays a role to communicate with external medical devices. At the same time, it is essential to maintain the stable operation within the asynchronous data transactions through network. In the Open Core Control software, several techniques for this purpose were introduced. Virtual fixture is well known technique as a “force guide” for supporting operators to perform precise manipulation by using a master–slave robot. The virtual fixture for precise and safety surgery was implemented on the system to demonstrate an idea of high-level collaboration between a surgical robot and a navigation system. The extension of virtual fixture is not a part of the Open Core Control system, however, the function such as virtual fixture cannot be realized without a tight collaboration between cutting-edge medical devices. By using the virtual fixture, operators can pre-define an accessible area on the navigation system, and the area information can be transferred to the robot. In this manner, the surgical console generates the reflection force when the operator tries to get out from the pre-defined accessible area during surgery. Results The Open Core Control software was implemented on a surgical master–slave robot and stable operation was observed in a motion test. The tip of the surgical robot was displayed on a navigation system by connecting the surgical robot with a 3D position sensor through the OpenIGTLink. The accessible area was pre-defined before the operation, and the virtual fixture was displayed as a “force guide” on the surgical console. In addition, the system showed stable performance in a duration test with network disturbance. Conclusion In this paper, a design of the Open Core Control software for surgical robots and the implementation of virtual fixture were described. The Open Core Control software was implemented on a surgical robot system and showed stable performance in high-level collaboration works. The Open Core Control software is developed to be a widely used platform of surgical robots. Safety issues are essential for control software of these complex medical devices. It is important to follow the global specifications such as a FDA requirement “General Principles of Software Validation” or IEC62304. For following these regulations, it is important to develop a self-test environment. Therefore, a test environment is now under development to test various interference in operation room such as a noise of electric knife by considering safety and test environment regulations such as ISO13849 and IEC60508. The Open Core Control software is currently being developed software in open-source manner and available on the Internet. A communization of software interface is becoming a major trend in this field. Based on this perspective, the Open Core Control software can be expected to bring contributions in this field. PMID:20033506

Power quality and protection of electric distribution systems with small, dispersed generation devices

NASA Astrophysics Data System (ADS)

Rizy, D. T.; Jewell, W. T.

1984-10-01

There are several operational problems associated with the connection of small power sources, such as wind turbines and photovoltaic (PV) arrays, to an electric distribution system. In one study the harmonic distortion produced by a subdivision of PV arrays connected through line-commutated inverters was simulated. A second simulation study evaluated protection problems associated with the operation of dispersed ac generators. The purpose of these studies was to examine the adequacy of the electric utility industry's traditional practices and hardware for the operation of dispersed power sources. The results of these simulation studies are discussed and recommendations are given for hardware and system operation needed for accommodating this new technology.

40 CFR Table 3 to Subpart Wwww of... - Organic HAP Emissions Limits for Existing Open Molding Sources, New Open Molding Sources Emitting...

Code of Federal Regulations, 2010 CFR

2010-07-01

... Existing Open Molding Sources, New Open Molding Sources Emitting Less Than 100 TPY of HAP, and New and... CATEGORIES National Emissions Standards for Hazardous Air Pollutants: Reinforced Plastic Composites... Existing Open Molding Sources, New Open Molding Sources Emitting Less Than 100 TPY of HAP, and New and...

Increasing the object recognition distance of compact open air on board vision system

NASA Astrophysics Data System (ADS)

Kirillov, Sergey; Kostkin, Ivan; Strotov, Valery; Dmitriev, Vladimir; Berdnikov, Vadim; Akopov, Eduard; Elyutin, Aleksey

2016-10-01

The aim of this work was developing an algorithm eliminating the atmospheric distortion and improves image quality. The proposed algorithm is entirely software without using additional hardware photographic equipment. . This algorithm does not required preliminary calibration. It can work equally effectively with the images obtained at a distances from 1 to 500 meters. An algorithm for the open air images improve designed for Raspberry Pi model B on-board vision systems is proposed. The results of experimental examination are given.

Flammability Configuration Analysis for Spacecraft Applications

NASA Technical Reports Server (NTRS)

Pedley, Michael D.

2014-01-01

Fire is one of the many potentially catastrophic hazards associated with the operation of crewed spacecraft. A major lesson learned by NASA from the Apollo 204 fire in 1966 was that ignition sources in an electrically powered vehicle should and can be minimized, but can never be eliminated completely. For this reason, spacecraft fire control is based on minimizing potential ignition sources and eliminating materials that can propagate fire. Fire extinguishers are always provided on crewed spacecraft, but are not considered as part of the fire control process. "Eliminating materials that can propagate fire" does not mean eliminating all flammable materials - the cost of designing and building spacecraft using only nonflammable materials is extraordinary and unnecessary. It means controlling the quantity and configuration of such materials to eliminate potential fire propagation paths and thus ensure that any fire would be small, localized, and isolated, and would self-extinguish without harm to the crew. Over the years, NASA has developed many solutions for controlling the configuration of flammable materials (and potentially flammable materials in commercial "off-the-shelf" hardware) so that they can be used safely in air and oxygen-enriched environments in crewed spacecraft. This document describes and explains these design solutions so payload customers and other organizations can use them in designing safe and cost-effective flight hardware. Proper application of these guidelines will produce acceptable flammability configurations for hardware located in any compartment of the International Space Station or other program crewed vehicles and habitats. However, use of these guidelines does not exempt hardware organizations of the responsibility for safety of the hardware under their control.

Public Access Workstations in the Library: New Trends.

ERIC Educational Resources Information Center

Beecher, Henry

1991-01-01

Discusses the use of microcomputer-based workstations that are provided for public access in libraries. Criteria for workstations are discussed, including standard hardware, open-design software, scalable interface, and connectivity options for networking; systems that provide full-text access are described; and the need for standards is…

Toward an automated parallel computing environment for geosciences

NASA Astrophysics Data System (ADS)

Zhang, Huai; Liu, Mian; Shi, Yaolin; Yuen, David A.; Yan, Zhenzhen; Liang, Guoping

2007-08-01

Software for geodynamic modeling has not kept up with the fast growing computing hardware and network resources. In the past decade supercomputing power has become available to most researchers in the form of affordable Beowulf clusters and other parallel computer platforms. However, to take full advantage of such computing power requires developing parallel algorithms and associated software, a task that is often too daunting for geoscience modelers whose main expertise is in geosciences. We introduce here an automated parallel computing environment built on open-source algorithms and libraries. Users interact with this computing environment by specifying the partial differential equations, solvers, and model-specific properties using an English-like modeling language in the input files. The system then automatically generates the finite element codes that can be run on distributed or shared memory parallel machines. This system is dynamic and flexible, allowing users to address different problems in geosciences. It is capable of providing web-based services, enabling users to generate source codes online. This unique feature will facilitate high-performance computing to be integrated with distributed data grids in the emerging cyber-infrastructures for geosciences. In this paper we discuss the principles of this automated modeling environment and provide examples to demonstrate its versatility.

An Exploration of Software-Based GNSS Signal Processing at Multiple Frequencies

NASA Astrophysics Data System (ADS)

Pasqual Paul, Manuel; Elosegui, Pedro; Lind, Frank; Vazquez, Antonio; Pankratius, Victor

2017-01-01

The Global Navigation Satellite System (GNSS; i.e., GPS, GLONASS, Galileo, and other constellations) has recently grown into numerous areas that go far beyond the traditional scope in navigation. In the geosciences, for example, high-precision GPS has become a powerful tool for a myriad of geophysical applications such as in geodynamics, seismology, paleoclimate, cryosphere, and remote sensing of the atmosphere. Positioning with millimeter-level accuracy can be achieved through carrier-phase-based, multi-frequency signal processing, which mitigates various biases and error sources such as those arising from ionospheric effects. Today, however, most receivers with multi-frequency capabilities are highly specialized hardware receiving systems with proprietary and closed designs, limited interfaces, and significant acquisition costs. This work explores alternatives that are entirely software-based, using Software-Defined Radio (SDR) receivers as a way to digitize the entire spectrum of interest. It presents an overview of existing open-source frameworks and outlines the next steps towards converting GPS software receivers from single-frequency to dual-frequency, geodetic-quality systems. In the future, this development will lead to a more flexible multi-constellation GNSS processing architecture that can be easily reused in different contexts, as well as to further miniaturization of receivers.

Development of a hardware-based AC microgrid for AC stability assessment

NASA Astrophysics Data System (ADS)

Swanson, Robert R.

As more power electronic-based devices enable the development of high-bandwidth AC microgrids, the topic of microgrid power distribution stability has become of increased interest. Recently, researchers have proposed a relatively straightforward method to assess the stability of AC systems based upon the time-constants of sources, the net bus capacitance, and the rate limits of sources. In this research, a focus has been to develop a hardware test system to evaluate AC system stability. As a first step, a time domain model of a two converter microgrid was established in which a three phase inverter acts as a power source and an active rectifier serves as an adjustable constant power AC load. The constant power load can be utilized to create rapid power flow transients to the generating system. As a second step, the inverter and active rectifier were designed using a Smart Power Module IGBT for switching and an embedded microcontroller as a processor for algorithm implementation. The inverter and active rectifier were designed to operate simultaneously using a synchronization signal to ensure each respective local controller operates in a common reference frame. Finally, the physical system was created and initial testing performed to validate the hardware functionality as a variable amplitude and variable frequency AC system.

Unique digital imagery interface between a silicon graphics computer and the kinetic kill vehicle hardware-in-the-loop simulator (KHILS) wideband infrared scene projector (WISP)

NASA Astrophysics Data System (ADS)

Erickson, Ricky A.; Moren, Stephen E.; Skalka, Marion S.

1998-07-01

Providing a flexible and reliable source of IR target imagery is absolutely essential for operation of an IR Scene Projector in a hardware-in-the-loop simulation environment. The Kinetic Kill Vehicle Hardware-in-the-Loop Simulator (KHILS) at Eglin AFB provides the capability, and requisite interfaces, to supply target IR imagery to its Wideband IR Scene Projector (WISP) from three separate sources at frame rates ranging from 30 - 120 Hz. Video can be input from a VCR source at the conventional 30 Hz frame rate. Pre-canned digital imagery and test patterns can be downloaded into stored memory from the host processor and played back as individual still frames or movie sequences up to a 120 Hz frame rate. Dynamic real-time imagery to the KHILS WISP projector system, at a 120 Hz frame rate, can be provided from a Silicon Graphics Onyx computer system normally used for generation of digital IR imagery through a custom CSA-built interface which is available for either the SGI/DVP or SGI/DD02 interface port. The primary focus of this paper is to describe our technical approach and experience in the development of this unique SGI computer and WISP projector interface.

Development of a Microphone Phased Array Capability for the Langley 14- by 22-Foot Subsonic Tunnel

NASA Technical Reports Server (NTRS)

Humphreys, William M.; Brooks, Thomas F.; Bahr, Christopher J.; Spalt, Taylor B.; Bartram, Scott M.; Culliton, William G.; Becker, Lawrence E.

2014-01-01

A new aeroacoustic measurement capability has been developed for use in open-jet testing in the NASA Langley 14- by 22-Foot Subsonic Tunnel (14x22 tunnel). A suite of instruments has been developed to characterize noise source strengths, locations, and directivity for both semi-span and full-span test articles in the facility. The primary instrument of the suite is a fully traversable microphone phased array for identification of noise source locations and strengths on models. The array can be mounted in the ceiling or on either side of the facility test section to accommodate various test article configurations. Complementing the phased array is an ensemble of streamwise traversing microphones that can be placed around the test section at defined locations to conduct noise source directivity studies along both flyover and sideline axes. A customized data acquisition system has been developed for the instrumentation suite that allows for command and control of all aspects of the array and microphone hardware, and is coupled with a comprehensive data reduction system to generate information in near real time. This information includes such items as time histories and spectral data for individual microphones and groups of microphones, contour presentations of noise source locations and strengths, and hemispherical directivity data. The data acquisition system integrates with the 14x22 tunnel data system to allow real time capture of facility parameters during acquisition of microphone data. The design of the phased array system has been vetted via a theoretical performance analysis based on conventional monopole beamforming and DAMAS deconvolution. The performance analysis provides the ability to compute figures of merit for the array as well as characterize factors such as beamwidths, sidelobe levels, and source discrimination for the types of noise sources anticipated in the 14x22 tunnel. The full paper will summarize in detail the design of the instrumentation suite, the construction of the hardware system, and the results of the performance analysis. Although the instrumentation suite is designed to characterize noise for a variety of test articles in the 14x22 tunnel, this paper will concentrate on description of the instruments for two specific test campaigns in the facility, namely a full-span NASA Hybrid Wing Body (HWB) model entry and a semi-span Gulfstream aircraft model entry, tested in the facility in the winter of 2012 and spring of 2013, respectively.

A Small Acoustic Goniometer for General Purpose Research

PubMed Central

Pook, Michael L.; Loo, Sin Ming

2016-01-01

Understanding acoustic events and monitoring their occurrence is a useful aspect of many research projects. In particular, acoustic goniometry allows researchers to determine the source of an event based solely on the sound it produces. The vast majority of acoustic goniometry research projects used custom hardware targeted to the specific application under test. Unfortunately, due to the wide range of sensing applications, a flexible general purpose hardware/firmware system does not exist for this purpose. This article focuses on the development of such a system which encourages the continued exploration of general purpose hardware/firmware and lowers barriers to research in projects requiring the use of acoustic goniometry. Simulations have been employed to verify system feasibility, and a complete hardware implementation of the acoustic goniometer has been designed and field tested. The results are reported, and suggested areas for improvement and further exploration are discussed. PMID:27136563

Exploring Surface Analysis Techniques for the Detection of Molecular Contaminants on Spacecraft

NASA Technical Reports Server (NTRS)

Rutherford, Gugu N.; Seasly, Elaine; Thornblom, Mark; Baughman, James

2016-01-01

Molecular contamination is a known area of concern for spacecraft. To mitigate this risk, projects involving space flight hardware set requirements in a contamination control plan that establishes an allocation budget for the exposure of non-volatile residues (NVR) onto critical surfaces. The purpose of this work will focus on non-contact surface analysis and in situ monitoring to mitigate molecular contamination on space flight hardware. By using Scanning Electron Microscopy and Energy Dispersive Spectroscopy (SEM-EDS) with Raman Spectroscopy, an unlikely contaminant was identified on space flight hardware. Using traditional and surface analysis methods provided the broader view of the contamination sources allowing for best fit solutions to prevent any future exposure.

A cost-effective and simple electronic solution to communication with patients with tracheostomy in a burns and intensive care setting.

PubMed

Javed, Muhammad; Dingley, John; Dickson, William; Shokrollahi, Kayvan

2014-02-01

Ventilated patients in ITU (intensive treatment unit) tend to be challenging to communicate with, especially patients who are being weaned. These patients usually have tracheostomy in situ and use means such as writing or letter boards to communicate. The situation becomes complex in patient groups that have burn injuries with bulky dressings and restricted upper limb function. We demonstrate a low cost, easy to use, potentially disposable system that can display words on any television screen via patient input device for such patient groups. The system consists of input device incorporated with Arduino microcontroller (an open-source electronics prototyping platform based on easy-to-use hardware and software intended for creating interactive environments) and 4 generously oversized control buttons. These are used to control the cursor movements (up, down, left, right) while a fifth has a "select" function. These are large enough to be pressed by an entire bandaged hand using gross upper limb movements only. A standard television is used to display menu containing the 26 letters of the alphabet and a flashing cursor. The patient selects the required letters/icon by moving the cursor and the words so created are displayed along the lower part of the screen for the carers to read. It is envisaged that anyone with basic craft skills should be able to construct this device. This device is a self-contained, cost-effective, simple, and open-source system that can be used effectively to bridge the communication gap with significant potential for patient care globally.

Automating mouse weighing in group homecages with Raspberry Pi micro-computers.

PubMed

Noorshams, Omid; Boyd, Jamie D; Murphy, Timothy H

2017-06-15

Operant training systems make use of water or food restriction and make it necessary to weigh animals to ensure compliance with experimental endpoints. In other applications periodic weighing is necessary to assess drug side-effects, or as an endpoint in feeding experiments. Periodic weighing while essential can disrupt animal circadian rhythms and social structure. Automatic weighing system within paired mouse homecages. Up to 10 mice freely move between two cages (28×18×9cm) which were connected by a weighing chamber mounted on a load cell. Each mouse was identified using an RFID tag placed under the skin of the neck. A single-board computer (Raspberry Pi; RPi) controls the task, logging RFID tag, load cell weights, and time stamps from each RFID detection until the animal leaves the chamber. Collected data were statistically analyzed to estimate mouse weights. We anticipate integration with tasks where automated imaging or behaviour is assessed in homecages. Mice frequently move between the two cages, an average of 42+-16 times/day/mouse at which time we obtained weights. We report accurate determination of mouse weight and long term monitoring over 53days. Comparison with existing methods Although commercial systems are available for automatically weighing rodents, they only work with single animals, or are not open source nor cost effective for specific custom application. This automated system permits automated weighing of mice ∼40 times per day. The system employs inexpensive hardware and open-source Python code. Copyright © 2017 Elsevier B.V. All rights reserved.

Enabling three-dimensional densitometric measurements using laboratory source X-ray micro-computed tomography

NASA Astrophysics Data System (ADS)

Pankhurst, M. J.; Fowler, R.; Courtois, L.; Nonni, S.; Zuddas, F.; Atwood, R. C.; Davis, G. R.; Lee, P. D.

2018-01-01

We present new software allowing significantly improved quantitative mapping of the three-dimensional density distribution of objects using laboratory source polychromatic X-rays via a beam characterisation approach (c.f. filtering or comparison to phantoms). One key advantage is that a precise representation of the specimen material is not required. The method exploits well-established, widely available, non-destructive and increasingly accessible laboratory-source X-ray tomography. Beam characterisation is performed in two stages: (1) projection data are collected through a range of known materials utilising a novel hardware design integrated into the rotation stage; and (2) a Python code optimises a spectral response model of the system. We provide hardware designs for use with a rotation stage able to be tilted, yet the concept is easily adaptable to virtually any laboratory system and sample, and implicitly corrects the image artefact known as beam hardening.

The Emergence of Open-Source Software in China

ERIC Educational Resources Information Center

Pan, Guohua; Bonk, Curtis J.

2007-01-01

The open-source software movement is gaining increasing momentum in China. Of the limited numbers of open-source software in China, "Red Flag Linux" stands out most strikingly, commanding 30 percent share of Chinese software market. Unlike the spontaneity of open-source movement in North America, open-source software development in…

A Study of Clinically Related Open Source Software Projects

PubMed Central

Hogarth, Michael A.; Turner, Stuart

2005-01-01

Open source software development has recently gained significant interest due to several successful mainstream open source projects. This methodology has been proposed as being similarly viable and beneficial in the clinical application domain as well. However, the clinical software development venue differs significantly from the mainstream software venue. Existing clinical open source projects have not been well characterized nor formally studied so the ‘fit’ of open source in this domain is largely unknown. In order to better understand the open source movement in the clinical application domain, we undertook a study of existing open source clinical projects. In this study we sought to characterize and classify existing clinical open source projects and to determine metrics for their viability. This study revealed several findings which we believe could guide the healthcare community in its quest for successful open source clinical software projects. PMID:16779056

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

PubMed Central

Swails, Jason; Zhao, Yutong; Beauchamp, Kyle A.; Wang, Lee-Ping; Stern, Chaya D.; Brooks, Bernard R.; Pande, Vijay S.

2017-01-01

OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It allows users to easily add new features, including forces with novel functional forms, new integration algorithms, and new simulation protocols. Those features automatically work on all supported hardware types (including both CPUs and GPUs) and perform well on all of them. In many cases they require minimal coding, just a mathematical description of the desired function. They also require no modification to OpenMM itself and can be distributed independently of OpenMM. This makes it an ideal tool for researchers developing new simulation methods, and also allows those new methods to be immediately available to the larger community. PMID:28746339

Open Access, Open Source and Digital Libraries: A Current Trend in University Libraries around the World

ERIC Educational Resources Information Center

Krishnamurthy, M.

2008-01-01

Purpose: The purpose of this paper is to describe the open access and open source movement in the digital library world. Design/methodology/approach: A review of key developments in the open access and open source movement is provided. Findings: Open source software and open access to research findings are of great use to scholars in developing…

Lessons Learned From Developing Three Generations of Remote Sensing Science Data Processing Systems

NASA Technical Reports Server (NTRS)

Tilmes, Curt; Fleig, Albert J.

2005-01-01

The Biospheric Information Systems Branch at NASA s Goddard Space Flight Center has developed three generations of Science Investigator-led Processing Systems for use with various remote sensing instruments. The first system is used for data from the MODIS instruments flown on NASA s Earth Observing Systems @OS) Terra and Aqua Spacecraft launched in 1999 and 2002 respectively. The second generation is for the Ozone Measuring Instrument flying on the EOS Aura spacecraft launched in 2004. We are now developing a third generation of the system for evaluation science data processing for the Ozone Mapping and Profiler Suite (OMPS) to be flown by the NPOESS Preparatory Project (NPP) in 2006. The initial system was based on large scale proprietary hardware, operating and database systems. The current OMI system and the OMPS system being developed are based on commodity hardware, the LINUX Operating System and on PostgreSQL, an Open Source RDBMS. The new system distributes its data archive across multiple server hosts and processes jobs on multiple processor boxes. We have created several instances of this system, including one for operational processing, one for testing and reprocessing and one for applications development and scientific analysis. Prior to receiving the first data from OMI we applied the system to reprocessing information from the Solar Backscatter Ultraviolet (SBUV) and Total Ozone Mapping Spectrometer (TOMS) instruments flown from 1978 until now. The system was able to process 25 years (108,000 orbits) of data and produce 800,000 files (400 GiB) of level 2 and level 3 products in less than a week. We will describe the lessons we have learned and tradeoffs between system design, hardware, operating systems, operational staffing, user support and operational procedures. During each generational phase, the system has become more generic and reusable. While the system is not currently shrink wrapped we believe it is to the point where it could be readily adopted, with substantial cost savings, for other similar tasks.

Visualization of planetary subsurface radar sounder data in three dimensions using stereoscopy

NASA Astrophysics Data System (ADS)

Frigeri, A.; Federico, C.; Pauselli, C.; Ercoli, M.; Coradini, A.; Orosei, R.

2010-12-01

Planetary subsurface sounding radar data extend the knowledge of planetary surfaces to a third dimension: the depth. The interpretation of delays of radar echoes converted into depth often requires the comparative analysis with other data, mainly topography, and radar data from different orbits can be used to investigate the spatial continuity of signals from subsurface geologic features. This scenario requires taking into account spatially referred information in three dimensions. Three dimensional objects are generally easier to understand if represented into a three dimensional space, and this representation can be improved by stereoscopic vision. Since its invention in the first half of 19th century, stereoscopy has been used in a broad range of application, including scientific visualization. The quick improvement of computer graphics and the spread of graphic rendering hardware allow to apply the basic principles of stereoscopy in the digital domain, allowing the stereoscopic projection of complex models. Specialized system for stereoscopic view of scientific data have been available in the industry, and proprietary solutions were affordable only to large research institutions. In the last decade, thanks to the GeoWall Consortium, the basics of stereoscopy have been applied for setting up stereoscopic viewers based on off-the shelf hardware products. Geowalls have been spread and are now used by several geo-science research institutes and universities. We are exploring techniques for visualizing planetary subsurface sounding radar data in three dimensions and we are developing a hardware system for rendering it in a stereoscopic vision system. Several Free Open Source Software tools and libraries are being used, as their level of interoperability is typically high and their licensing system offers the opportunity to implement quickly new functionalities to solve specific needs during the progress of the project. Visualization of planetary radar data in three dimensions represents a challenging task, and the exploration of different strategies will bring to the selection of the most appropriate ones for a meaningful extraction of information from the products of these innovative instruments.