Developing Simulations in Multi-User Virtual Environments to Enhance Healthcare Education

ERIC Educational Resources Information Center

Rogers, Luke

2011-01-01

Computer-based clinical simulations are a powerful teaching and learning tool because of their ability to expand healthcare students' clinical experience by providing practice-based learning. Despite the benefits of traditional computer-based clinical simulations, there are significant issues that arise when incorporating them into a flexible,…

Applications of the pipeline environment for visual informatics and genomics computations

PubMed Central

2011-01-01

Background Contemporary informatics and genomics research require efficient, flexible and robust management of large heterogeneous data, advanced computational tools, powerful visualization, reliable hardware infrastructure, interoperability of computational resources, and detailed data and analysis-protocol provenance. The Pipeline is a client-server distributed computational environment that facilitates the visual graphical construction, execution, monitoring, validation and dissemination of advanced data analysis protocols. Results This paper reports on the applications of the LONI Pipeline environment to address two informatics challenges - graphical management of diverse genomics tools, and the interoperability of informatics software. Specifically, this manuscript presents the concrete details of deploying general informatics suites and individual software tools to new hardware infrastructures, the design, validation and execution of new visual analysis protocols via the Pipeline graphical interface, and integration of diverse informatics tools via the Pipeline eXtensible Markup Language syntax. We demonstrate each of these processes using several established informatics packages (e.g., miBLAST, EMBOSS, mrFAST, GWASS, MAQ, SAMtools, Bowtie) for basic local sequence alignment and search, molecular biology data analysis, and genome-wide association studies. These examples demonstrate the power of the Pipeline graphical workflow environment to enable integration of bioinformatics resources which provide a well-defined syntax for dynamic specification of the input/output parameters and the run-time execution controls. Conclusions The LONI Pipeline environment http://pipeline.loni.ucla.edu provides a flexible graphical infrastructure for efficient biomedical computing and distributed informatics research. The interactive Pipeline resource manager enables the utilization and interoperability of diverse types of informatics resources. The Pipeline client-server model provides computational power to a broad spectrum of informatics investigators - experienced developers and novice users, user with or without access to advanced computational-resources (e.g., Grid, data), as well as basic and translational scientists. The open development, validation and dissemination of computational networks (pipeline workflows) facilitates the sharing of knowledge, tools, protocols and best practices, and enables the unbiased validation and replication of scientific findings by the entire community. PMID:21791102

Constraint-based component-modeling for knowledge-based design

NASA Technical Reports Server (NTRS)

Kolb, Mark A.

1992-01-01

The paper describes the application of various advanced programming techniques derived from artificial intelligence research to the development of flexible design tools for conceptual design. Special attention is given to two techniques which appear to be readily applicable to such design tools: the constraint propagation technique and the object-oriented programming. The implementation of these techniques in a prototype computer tool, Rubber Airplane, is described.

Performance Evaluation of the Gravity Probe B Design

NASA Technical Reports Server (NTRS)

Francis, Ronnie; Wells, Eugene M.

1996-01-01

This report documents the simulation of the Lockheed Martin designed Gravity Probe B (GPB) spacecraft developed tool by bd Systems Inc using the TREETOPS simulation. This study quantifies the effects of flexibility and liquid helium slosh on GPB spacecraft control performance. The TREETOPS simulation tool permits the simulation of flexible structures given that a flexible body model of the structure is available. For purposes of this study, a flexible model of the GPB spacecraft was obtained from Lockheed Martin. To model the liquid helium slosh effects, computational fluid dynamics (CFD) results' were obtained, and used to develop a dynamic model of the slosh effects. The flexible body and slosh effects were incorporated separately into the TREETOPS simulation, which places the vehicle in a 650 km circular polar orbit and subjects the spacecraft to realistic environmental disturbances and sensor error quantities. In all of the analysis conducted in this study the spacecraft is pointed at an inertially fixed guide star (GS) and is rotating at a constant rate about this line of sight.

Library Signage: Applications for the Apple Macintosh and MacPaint.

ERIC Educational Resources Information Center

Diskin, Jill A.; FitzGerald, Patricia

1984-01-01

Describes specific applications of the Macintosh computer at Carnegie-Mellon University Libraries, where MacPaint was used as a flexible, easy to use, and powerful tool to produce informational, instructional, and promotional signage. Profiles of system hardware and software, an evaluation of the computer program MacPaint, and MacPaint signage…

PACE 2: Pricing and Cost Estimating Handbook

NASA Technical Reports Server (NTRS)

Stewart, R. D.; Shepherd, T.

1977-01-01

An automatic data processing system to be used for the preparation of industrial engineering type manhour and material cost estimates has been established. This computer system has evolved into a highly versatile and highly flexible tool which significantly reduces computation time, eliminates computational errors, and reduces typing and reproduction time for estimators and pricers since all mathematical and clerical functions are automatic once basic inputs are derived.

A semi-analytical bearing model considering outer race flexibility for model based bearing load monitoring

NASA Astrophysics Data System (ADS)

Kerst, Stijn; Shyrokau, Barys; Holweg, Edward

2018-05-01

This paper proposes a novel semi-analytical bearing model addressing flexibility of the bearing outer race structure. It furthermore presents the application of this model in a bearing load condition monitoring approach. The bearing model is developed as current computational low cost bearing models fail to provide an accurate description of the more and more common flexible size and weight optimized bearing designs due to their assumptions of rigidity. In the proposed bearing model raceway flexibility is described by the use of static deformation shapes. The excitation of the deformation shapes is calculated based on the modelled rolling element loads and a Fourier series based compliance approximation. The resulting model is computational low cost and provides an accurate description of the rolling element loads for flexible outer raceway structures. The latter is validated by a simulation-based comparison study with a well-established bearing simulation software tool. An experimental study finally shows the potential of the proposed model in a bearing load monitoring approach.

Price and cost estimation

NASA Technical Reports Server (NTRS)

Stewart, R. D.

1979-01-01

Price and Cost Estimating Program (PACE II) was developed to prepare man-hour and material cost estimates. Versatile and flexible tool significantly reduces computation time and errors and reduces typing and reproduction time involved in preparation of cost estimates.

MACBenAbim: A Multi-platform Mobile Application for searching keyterms in Computational Biology and Bioinformatics.

PubMed

Oluwagbemi, Olugbenga O; Adewumi, Adewole; Esuruoso, Abimbola

2012-01-01

Computational biology and bioinformatics are gradually gaining grounds in Africa and other developing nations of the world. However, in these countries, some of the challenges of computational biology and bioinformatics education are inadequate infrastructures, and lack of readily-available complementary and motivational tools to support learning as well as research. This has lowered the morale of many promising undergraduates, postgraduates and researchers from aspiring to undertake future study in these fields. In this paper, we developed and described MACBenAbim (Multi-platform Mobile Application for Computational Biology and Bioinformatics), a flexible user-friendly tool to search for, define and describe the meanings of keyterms in computational biology and bioinformatics, thus expanding the frontiers of knowledge of the users. This tool also has the capability of achieving visualization of results on a mobile multi-platform context. MACBenAbim is available from the authors for non-commercial purposes.

Building a Community Infrastructure for Scalable On-Line Performance Analysis Tools around Open|Speedshop

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

Miller, Barton

2014-06-30

Peta-scale computing environments pose significant challenges for both system and application developers and addressing them required more than simply scaling up existing tera-scale solutions. Performance analysis tools play an important role in gaining this understanding, but previous monolithic tools with fixed feature sets have not sufficed. Instead, this project worked on the design, implementation, and evaluation of a general, flexible tool infrastructure supporting the construction of performance tools as “pipelines” of high-quality tool building blocks. These tool building blocks provide common performance tool functionality, and are designed for scalability, lightweight data acquisition and analysis, and interoperability. For this project, wemore » built on Open|SpeedShop, a modular and extensible open source performance analysis tool set. The design and implementation of such a general and reusable infrastructure targeted for petascale systems required us to address several challenging research issues. All components needed to be designed for scale, a task made more difficult by the need to provide general modules. The infrastructure needed to support online data aggregation to cope with the large amounts of performance and debugging data. We needed to be able to map any combination of tool components to each target architecture. And we needed to design interoperable tool APIs and workflows that were concrete enough to support the required functionality, yet provide the necessary flexibility to address a wide range of tools. A major result of this project is the ability to use this scalable infrastructure to quickly create tools that match with a machine architecture and a performance problem that needs to be understood. Another benefit is the ability for application engineers to use the highly scalable, interoperable version of Open|SpeedShop, which are reassembled from the tool building blocks into a flexible, multi-user interface set of tools. This set of tools targeted at Office of Science Leadership Class computer systems and selected Office of Science application codes. We describe the contributions made by the team at the University of Wisconsin. The project built on the efforts in Open|SpeedShop funded by DOE/NNSA and the DOE/NNSA Tri-Lab community, extended Open|Speedshop to the Office of Science Leadership Class Computing Facilities, and addressed new challenges found on these cutting edge systems. Work done under this project at Wisconsin can be divided into two categories, new algorithms and techniques for debugging, and foundation infrastructure work on our Dyninst binary analysis and instrumentation toolkits and MRNet scalability infrastructure.« less

OCCAM: a flexible, multi-purpose and extendable HPC cluster

NASA Astrophysics Data System (ADS)

Aldinucci, M.; Bagnasco, S.; Lusso, S.; Pasteris, P.; Rabellino, S.; Vallero, S.

2017-10-01

The Open Computing Cluster for Advanced data Manipulation (OCCAM) is a multipurpose flexible HPC cluster designed and operated by a collaboration between the University of Torino and the Sezione di Torino of the Istituto Nazionale di Fisica Nucleare. It is aimed at providing a flexible, reconfigurable and extendable infrastructure to cater to a wide range of different scientific computing use cases, including ones from solid-state chemistry, high-energy physics, computer science, big data analytics, computational biology, genomics and many others. Furthermore, it will serve as a platform for R&D activities on computational technologies themselves, with topics ranging from GPU acceleration to Cloud Computing technologies. A heterogeneous and reconfigurable system like this poses a number of challenges related to the frequency at which heterogeneous hardware resources might change their availability and shareability status, which in turn affect methods and means to allocate, manage, optimize, bill, monitor VMs, containers, virtual farms, jobs, interactive bare-metal sessions, etc. This work describes some of the use cases that prompted the design and construction of the HPC cluster, its architecture and resource provisioning model, along with a first characterization of its performance by some synthetic benchmark tools and a few realistic use-case tests.

Software systems for modeling articulated figures

NASA Technical Reports Server (NTRS)

Phillips, Cary B.

1989-01-01

Research in computer animation and simulation of human task performance requires sophisticated geometric modeling and user interface tools. The software for a research environment should present the programmer with a powerful but flexible substrate of facilities for displaying and manipulating geometric objects, yet insure that future tools have a consistent and friendly user interface. Jack is a system which provides a flexible and extensible programmer and user interface for displaying and manipulating complex geometric figures, particularly human figures in a 3D working environment. It is a basic software framework for high-performance Silicon Graphics IRIS workstations for modeling and manipulating geometric objects in a general but powerful way. It provides a consistent and user-friendly interface across various applications in computer animation and simulation of human task performance. Currently, Jack provides input and control for applications including lighting specification and image rendering, anthropometric modeling, figure positioning, inverse kinematics, dynamic simulation, and keyframe animation.

Simulation System for Training in Laparoscopic Surgery

NASA Technical Reports Server (NTRS)

Basdogan, Cagatay; Ho, Chih-Hao

2003-01-01

A computer-based simulation system creates a visual and haptic virtual environment for training a medical practitioner in laparoscopic surgery. Heretofore, it has been common practice to perform training in partial laparoscopic surgical procedures by use of a laparoscopic training box that encloses a pair of laparoscopic tools, objects to be manipulated by the tools, and an endoscopic video camera. However, the surgical procedures simulated by use of a training box are usually poor imitations of the actual ones. The present computer-based system improves training by presenting a more realistic simulated environment to the trainee. The system includes a computer monitor that displays a real-time image of the affected interior region of the patient, showing laparoscopic instruments interacting with organs and tissues, as would be viewed by use of an endoscopic video camera and displayed to a surgeon during a laparoscopic operation. The system also includes laparoscopic tools that the trainee manipulates while observing the image on the computer monitor (see figure). The instrumentation on the tools consists of (1) position and orientation sensors that provide input data for the simulation and (2) actuators that provide force feedback to simulate the contact forces between the tools and tissues. The simulation software includes components that model the geometries of surgical tools, components that model the geometries and physical behaviors of soft tissues, and components that detect collisions between them. Using the measured positions and orientations of the tools, the software detects whether they are in contact with tissues. In the event of contact, the deformations of the tissues and contact forces are computed by use of the geometric and physical models. The image on the computer screen shows tissues deformed accordingly, while the actuators apply the corresponding forces to the distal ends of the tools. For the purpose of demonstration, the system has been set up to simulate the insertion of a flexible catheter in a bile duct. [As thus configured, the system can also be used to simulate other endoscopic procedures (e.g., bronchoscopy and colonoscopy) that include the insertion of flexible tubes into flexible ducts.] A hybrid approach has been followed in developing the software for real-time simulation of the visual and haptic interactions (1) between forceps and the catheter, (2) between the forceps and the duct, and (3) between the catheter and the duct. The deformations of the duct are simulated by finite-element and modalanalysis procedures, using only the most significant vibration modes of the duct for computing deformations and interaction forces. The catheter is modeled as a set of virtual particles uniformly distributed along the center line of the catheter and connected to each other via linear and torsional springs and damping elements. The interactions between the forceps and the duct as well as the catheter are simulated by use of a ray-based haptic-interaction- simulating technique in which the forceps are modeled as connected line segments.

Modeling of Passive Forces of Machine Tool Covers

NASA Astrophysics Data System (ADS)

Kolar, Petr; Hudec, Jan; Sulitka, Matej

The passive forces acting against the drive force are phenomena that influence dynamical properties and precision of linear axes equipped with feed drives. Covers are one of important sources of passive forces in machine tools. The paper describes virtual evaluation of cover passive forces using the cover complex model. The model is able to compute interaction between flexible cover segments and sealing wiper. The result is deformation of cover segments and wipers which is used together with measured friction coefficient for computation of cover total passive force. This resulting passive force is dependent on cover position. Comparison of computational results and measurement on the real cover is presented in the paper.

XS: a FASTQ read simulator.

PubMed

Pratas, Diogo; Pinho, Armando J; Rodrigues, João M O S

2014-01-16

The emerging next-generation sequencing (NGS) is bringing, besides the natural huge amounts of data, an avalanche of new specialized tools (for analysis, compression, alignment, among others) and large public and private network infrastructures. Therefore, a direct necessity of specific simulation tools for testing and benchmarking is rising, such as a flexible and portable FASTQ read simulator, without the need of a reference sequence, yet correctly prepared for producing approximately the same characteristics as real data. We present XS, a skilled FASTQ read simulation tool, flexible, portable (does not need a reference sequence) and tunable in terms of sequence complexity. It has several running modes, depending on the time and memory available, and is aimed at testing computing infrastructures, namely cloud computing of large-scale projects, and testing FASTQ compression algorithms. Moreover, XS offers the possibility of simulating the three main FASTQ components individually (headers, DNA sequences and quality-scores). XS provides an efficient and convenient method for fast simulation of FASTQ files, such as those from Ion Torrent (currently uncovered by other simulators), Roche-454, Illumina and ABI-SOLiD sequencing machines. This tool is publicly available at http://bioinformatics.ua.pt/software/xs/.

Computers in the Classroom: Experiences Teaching with Flexible Tools. Teachers Writing to Teachers Series.

ERIC Educational Resources Information Center

Thompson, Charles, Ed.; Vaughan, Larry, Ed.

First-hand accounts of what teachers have done with students and computers in their classrooms, how students have responded, and what and how teachers have learned from these experiences are discussed in the 19 articles in this book. The articles are presented under these headings: (1) teaching writing with word processors; (2) learning to inquire…

Structural reliability assessment capability in NESSUS

NASA Technical Reports Server (NTRS)

Millwater, H.; Wu, Y.-T.

1992-01-01

The principal capabilities of NESSUS (Numerical Evaluation of Stochastic Structures Under Stress), an advanced computer code developed for probabilistic structural response analysis, are reviewed, and its structural reliability assessed. The code combines flexible structural modeling tools with advanced probabilistic algorithms in order to compute probabilistic structural response and resistance, component reliability and risk, and system reliability and risk. An illustrative numerical example is presented.

Structural reliability assessment capability in NESSUS

NASA Astrophysics Data System (ADS)

Millwater, H.; Wu, Y.-T.

1992-07-01

The principal capabilities of NESSUS (Numerical Evaluation of Stochastic Structures Under Stress), an advanced computer code developed for probabilistic structural response analysis, are reviewed, and its structural reliability assessed. The code combines flexible structural modeling tools with advanced probabilistic algorithms in order to compute probabilistic structural response and resistance, component reliability and risk, and system reliability and risk. An illustrative numerical example is presented.

Agreement Between Face-to-Face and Free Software Video Analysis for Assessing Hamstring Flexibility in Adolescents.

PubMed

Moral-Muñoz, José A; Esteban-Moreno, Bernabé; Arroyo-Morales, Manuel; Cobo, Manuel J; Herrera-Viedma, Enrique

2015-09-01

The objective of this study was to determine the level of agreement between face-to-face hamstring flexibility measurements and free software video analysis in adolescents. Reduced hamstring flexibility is common in adolescents (75% of boys and 35% of girls aged 10). The length of the hamstring muscle has an important role in both the effectiveness and the efficiency of basic human movements, and reduced hamstring flexibility is related to various musculoskeletal conditions. There are various approaches to measuring hamstring flexibility with high reliability; the most commonly used approaches in the scientific literature are the sit-and-reach test, hip joint angle (HJA), and active knee extension. The assessment of hamstring flexibility using video analysis could help with adolescent flexibility follow-up. Fifty-four adolescents from a local school participated in a descriptive study of repeated measures using a crossover design. Active knee extension and HJA were measured with an inclinometer and were simultaneously recorded with a video camera. Each video was downloaded to a computer and subsequently analyzed using Kinovea 0.8.15, a free software application for movement analysis. All outcome measures showed reliability estimates with α > 0.90. The lowest reliability was obtained for HJA (α = 0.91). The preliminary findings support the use of a free software tool for assessing hamstring flexibility, offering health professionals a useful tool for adolescent flexibility follow-up.

Management Tools

NASA Technical Reports Server (NTRS)

1987-01-01

Manugistics, Inc. (formerly AVYX, Inc.) has introduced a new programming language for IBM and IBM compatible computers called TREES-pls. It is a resource management tool originating from the space shuttle, that can be used in such applications as scheduling, resource allocation project control, information management, and artificial intelligence. Manugistics, Inc. was looking for a flexible tool that can be applied to many problems with minimal adaptation. Among the non-government markets are aerospace, other manufacturing, transportation, health care, food and beverage and professional services.

Testing the Use of Implicit Solvent in the Molecular Dynamics Modelling of DNA Flexibility

NASA Astrophysics Data System (ADS)

Mitchell, J.; Harris, S.

DNA flexibility controls packaging, looping and in some cases sequence specific protein binding. Molecular dynamics simulations carried out with a computationally efficient implicit solvent model are potentially a powerful tool for studying larger DNA molecules than can be currently simulated when water and counterions are represented explicitly. In this work we compare DNA flexibility at the base pair step level modelled using an implicit solvent model to that previously determined from explicit solvent simulations and database analysis. Although much of the sequence dependent behaviour is preserved in implicit solvent, the DNA is considerably more flexible when the approximate model is used. In addition we test the ability of the implicit solvent to model stress induced DNA disruptions by simulating a series of DNA minicircle topoisomers which vary in size and superhelical density. When compared with previously run explicit solvent simulations, we find that while the levels of DNA denaturation are similar using both computational methodologies, the specific structural form of the disruptions is different.

Multidisciplinary analysis of actively controlled large flexible spacecraft

NASA Technical Reports Server (NTRS)

Cooper, Paul A.; Young, John W.; Sutter, Thomas R.

1986-01-01

The control of Flexible Structures (COFS) program has supported the development of an analysis capability at the Langley Research Center called the Integrated Multidisciplinary Analysis Tool (IMAT) which provides an efficient data storage and transfer capability among commercial computer codes to aid in the dynamic analysis of actively controlled structures. IMAT is a system of computer programs which transfers Computer-Aided-Design (CAD) configurations, structural finite element models, material property and stress information, structural and rigid-body dynamic model information, and linear system matrices for control law formulation among various commercial applications programs through a common database. Although general in its formulation, IMAT was developed specifically to aid in the evaluation of the structures. A description of the IMAT system and results of an application of the system are given.

Using Open Source Software in Visual Simulation Development

DTIC Science & Technology

2005-09-01

increased the use of the technology in training activities. Using open source/free software tools in the process can expand these possibilities...resulting in even greater cost reduction and allowing the flexibility needed in a training environment. This thesis presents a configuration and architecture...to be used when developing training visual simulations using both personal computers and open source tools. Aspects of the requirements needed in a

The Preliminary Design of a Standardized Spacecraft Bus for Small Tactical Satellites (Volume 2)

DTIC Science & Technology

1996-11-01

this requirement, conditions of the model need to be modified to provide some flexibility to the original solution set. In the business world this...time The mission modules modeled in the Modsat computer model are necessarily "generic" in nature to provide both flexibility in design evaluation and...methods employed during the study, the scope of the problem, the value system used to evaluate alternatives, tradeoff studies performed, modeling tools

Computing tools for implementing standards for single-case designs.

PubMed

Chen, Li-Ting; Peng, Chao-Ying Joanne; Chen, Ming-E

2015-11-01

In the single-case design (SCD) literature, five sets of standards have been formulated and distinguished: design standards, assessment standards, analysis standards, reporting standards, and research synthesis standards. This article reviews computing tools that can assist researchers and practitioners in meeting the analysis standards recommended by the What Works Clearinghouse: Procedures and Standards Handbook-the WWC standards. These tools consist of specialized web-based calculators or downloadable software for SCD data, and algorithms or programs written in Excel, SAS procedures, SPSS commands/Macros, or the R programming language. We aligned these tools with the WWC standards and evaluated them for accuracy and treatment of missing data, using two published data sets. All tools were tested to be accurate. When missing data were present, most tools either gave an error message or conducted analysis based on the available data. Only one program used a single imputation method. This article concludes with suggestions for an inclusive computing tool or environment, additional research on the treatment of missing data, and reasonable and flexible interpretations of the WWC standards. © The Author(s) 2015.

PlantCV v2: Image analysis software for high-throughput plant phenotyping

PubMed Central

Abbasi, Arash; Berry, Jeffrey C.; Callen, Steven T.; Chavez, Leonardo; Doust, Andrew N.; Feldman, Max J.; Gilbert, Kerrigan B.; Hodge, John G.; Hoyer, J. Steen; Lin, Andy; Liu, Suxing; Lizárraga, César; Lorence, Argelia; Miller, Michael; Platon, Eric; Tessman, Monica; Sax, Tony

2017-01-01

Systems for collecting image data in conjunction with computer vision techniques are a powerful tool for increasing the temporal resolution at which plant phenotypes can be measured non-destructively. Computational tools that are flexible and extendable are needed to address the diversity of plant phenotyping problems. We previously described the Plant Computer Vision (PlantCV) software package, which is an image processing toolkit for plant phenotyping analysis. The goal of the PlantCV project is to develop a set of modular, reusable, and repurposable tools for plant image analysis that are open-source and community-developed. Here we present the details and rationale for major developments in the second major release of PlantCV. In addition to overall improvements in the organization of the PlantCV project, new functionality includes a set of new image processing and normalization tools, support for analyzing images that include multiple plants, leaf segmentation, landmark identification tools for morphometrics, and modules for machine learning. PMID:29209576

PlantCV v2: Image analysis software for high-throughput plant phenotyping.

PubMed

Gehan, Malia A; Fahlgren, Noah; Abbasi, Arash; Berry, Jeffrey C; Callen, Steven T; Chavez, Leonardo; Doust, Andrew N; Feldman, Max J; Gilbert, Kerrigan B; Hodge, John G; Hoyer, J Steen; Lin, Andy; Liu, Suxing; Lizárraga, César; Lorence, Argelia; Miller, Michael; Platon, Eric; Tessman, Monica; Sax, Tony

2017-01-01

Systems for collecting image data in conjunction with computer vision techniques are a powerful tool for increasing the temporal resolution at which plant phenotypes can be measured non-destructively. Computational tools that are flexible and extendable are needed to address the diversity of plant phenotyping problems. We previously described the Plant Computer Vision (PlantCV) software package, which is an image processing toolkit for plant phenotyping analysis. The goal of the PlantCV project is to develop a set of modular, reusable, and repurposable tools for plant image analysis that are open-source and community-developed. Here we present the details and rationale for major developments in the second major release of PlantCV. In addition to overall improvements in the organization of the PlantCV project, new functionality includes a set of new image processing and normalization tools, support for analyzing images that include multiple plants, leaf segmentation, landmark identification tools for morphometrics, and modules for machine learning.

PlantCV v2: Image analysis software for high-throughput plant phenotyping

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

Gehan, Malia A.; Fahlgren, Noah; Abbasi, Arash

Systems for collecting image data in conjunction with computer vision techniques are a powerful tool for increasing the temporal resolution at which plant phenotypes can be measured non-destructively. Computational tools that are flexible and extendable are needed to address the diversity of plant phenotyping problems. We previously described the Plant Computer Vision (PlantCV) software package, which is an image processing toolkit for plant phenotyping analysis. The goal of the PlantCV project is to develop a set of modular, reusable, and repurposable tools for plant image analysis that are open-source and community-developed. Here in this paper we present the details andmore » rationale for major developments in the second major release of PlantCV. In addition to overall improvements in the organization of the PlantCV project, new functionality includes a set of new image processing and normalization tools, support for analyzing images that include multiple plants, leaf segmentation, landmark identification tools for morphometrics, and modules for machine learning.« less

PlantCV v2: Image analysis software for high-throughput plant phenotyping

DOE PAGES

Gehan, Malia A.; Fahlgren, Noah; Abbasi, Arash; ...

2017-12-01

Systems for collecting image data in conjunction with computer vision techniques are a powerful tool for increasing the temporal resolution at which plant phenotypes can be measured non-destructively. Computational tools that are flexible and extendable are needed to address the diversity of plant phenotyping problems. We previously described the Plant Computer Vision (PlantCV) software package, which is an image processing toolkit for plant phenotyping analysis. The goal of the PlantCV project is to develop a set of modular, reusable, and repurposable tools for plant image analysis that are open-source and community-developed. Here in this paper we present the details andmore » rationale for major developments in the second major release of PlantCV. In addition to overall improvements in the organization of the PlantCV project, new functionality includes a set of new image processing and normalization tools, support for analyzing images that include multiple plants, leaf segmentation, landmark identification tools for morphometrics, and modules for machine learning.« less

An Efficient Finite Element Framework to Assess Flexibility Performances of SMA Self-Expandable Carotid Artery Stents

PubMed Central

Ferraro, Mauro; Auricchio, Ferdinando; Boatti, Elisa; Scalet, Giulia; Conti, Michele; Morganti, Simone; Reali, Alessandro

2015-01-01

Computer-based simulations are nowadays widely exploited for the prediction of the mechanical behavior of different biomedical devices. In this aspect, structural finite element analyses (FEA) are currently the preferred computational tool to evaluate the stent response under bending. This work aims at developing a computational framework based on linear and higher order FEA to evaluate the flexibility of self-expandable carotid artery stents. In particular, numerical simulations involving large deformations and inelastic shape memory alloy constitutive modeling are performed, and the results suggest that the employment of higher order FEA allows accurately representing the computational domain and getting a better approximation of the solution with a widely-reduced number of degrees of freedom with respect to linear FEA. Moreover, when buckling phenomena occur, higher order FEA presents a superior capability of reproducing the nonlinear local effects related to buckling phenomena. PMID:26184329

Characterization of Protein Flexibility Using Small-Angle X-Ray Scattering and Amplified Collective Motion Simulations

PubMed Central

Wen, Bin; Peng, Junhui; Zuo, Xiaobing; Gong, Qingguo; Zhang, Zhiyong

2014-01-01

Large-scale flexibility within a multidomain protein often plays an important role in its biological function. Despite its inherent low resolution, small-angle x-ray scattering (SAXS) is well suited to investigate protein flexibility and determine, with the help of computational modeling, what kinds of protein conformations would coexist in solution. In this article, we develop a tool that combines SAXS data with a previously developed sampling technique called amplified collective motions (ACM) to elucidate structures of highly dynamic multidomain proteins in solution. We demonstrate the use of this tool in two proteins, bacteriophage T4 lysozyme and tandem WW domains of the formin-binding protein 21. The ACM simulations can sample the conformational space of proteins much more extensively than standard molecular dynamics (MD) simulations. Therefore, conformations generated by ACM are significantly better at reproducing the SAXS data than are those from MD simulations. PMID:25140431

A Wearable Mobile Sensor Platform to Assist Fruit Grading

PubMed Central

Aroca, Rafael V.; Gomes, Rafael B.; Dantas, Rummennigue R.; Calbo, Adonai G.; Gonçalves, Luiz M. G.

2013-01-01

Wearable computing is a form of ubiquitous computing that offers flexible and useful tools for users. Specifically, glove-based systems have been used in the last 30 years in a variety of applications, but mostly focusing on sensing people's attributes, such as finger bending and heart rate. In contrast, we propose in this work a novel flexible and reconfigurable instrumentation platform in the form of a glove, which can be used to analyze and measure attributes of fruits by just pointing or touching them with the proposed glove. An architecture for such a platform is designed and its application for intuitive fruit grading is also presented, including experimental results for several fruits. PMID:23666134

Dynamics of flexible bodies in tree topology - A computer oriented approach

NASA Technical Reports Server (NTRS)

Singh, R. P.; Vandervoort, R. J.; Likins, P. W.

1984-01-01

An approach suited for automatic generation of the equations of motion for large mechanical systems (i.e., large space structures, mechanisms, robots, etc.) is presented. The system topology is restricted to a tree configuration. The tree is defined as an arbitrary set of rigid and flexible bodies connected by hinges characterizing relative translations and rotations of two adjoining bodies. The equations of motion are derived via Kane's method. The resulting equation set is of minimum dimension. Dynamical equations are imbedded in a computer program called TREETOPS. Extensive control simulation capability is built in the TREETOPS program. The simulation is driven by an interactive set-up program resulting in an easy to use analysis tool.

Building Flexible User Interfaces for Solving PDEs

NASA Astrophysics Data System (ADS)

Logg, Anders; Wells, Garth N.

2010-09-01

FEniCS is a collection of software tools for the automated solution of differential equations by finite element methods. In this note, we describe how FEniCS can be used to solve a simple nonlinear model problem with varying levels of automation. At one extreme, FEniCS provides tools for the fully automated and adaptive solution of nonlinear partial differential equations. At the other extreme, FEniCS provides a range of tools that allow the computational scientist to experiment with novel solution algorithms.

Enabling a Scientific Cloud Marketplace: VGL (Invited)

NASA Astrophysics Data System (ADS)

Fraser, R.; Woodcock, R.; Wyborn, L. A.; Vote, J.; Rankine, T.; Cox, S. J.

2013-12-01

The Virtual Geophysics Laboratory (VGL) provides a flexible, web based environment where researchers can browse data and use a variety of scientific software packaged into tool kits that run in the Cloud. Both data and tool kits are published by multiple researchers and registered with the VGL infrastructure forming a data and application marketplace. The VGL provides the basic work flow of Discovery and Access to the disparate data sources and a Library for tool kits and scripting to drive the scientific codes. Computation is then performed on the Research or Commercial Clouds. Provenance information is collected throughout the work flow and can be published alongside the results allowing for experiment comparison and sharing with other researchers. VGL's "mix and match" approach to data, computational resources and scientific codes, enables a dynamic approach to scientific collaboration. VGL allows scientists to publish their specific contribution, be it data, code, compute or work flow, knowing the VGL framework will provide other components needed for a complete application. Other scientists can choose the pieces that suit them best to assemble an experiment. The coarse grain workflow of the VGL framework combined with the flexibility of the scripting library and computational toolkits allows for significant customisation and sharing amongst the community. The VGL utilises the cloud computational and storage resources from the Australian academic research cloud provided by the NeCTAR initiative and a large variety of data accessible from national and state agencies via the Spatial Information Services Stack (SISS - http://siss.auscope.org). VGL v1.2 screenshot - http://vgl.auscope.org

Towards early software reliability prediction for computer forensic tools (case study).

PubMed

Abu Talib, Manar

2016-01-01

Versatility, flexibility and robustness are essential requirements for software forensic tools. Researchers and practitioners need to put more effort into assessing this type of tool. A Markov model is a robust means for analyzing and anticipating the functioning of an advanced component based system. It is used, for instance, to analyze the reliability of the state machines of real time reactive systems. This research extends the architecture-based software reliability prediction model for computer forensic tools, which is based on Markov chains and COSMIC-FFP. Basically, every part of the computer forensic tool is linked to a discrete time Markov chain. If this can be done, then a probabilistic analysis by Markov chains can be performed to analyze the reliability of the components and of the whole tool. The purposes of the proposed reliability assessment method are to evaluate the tool's reliability in the early phases of its development, to improve the reliability assessment process for large computer forensic tools over time, and to compare alternative tool designs. The reliability analysis can assist designers in choosing the most reliable topology for the components, which can maximize the reliability of the tool and meet the expected reliability level specified by the end-user. The approach of assessing component-based tool reliability in the COSMIC-FFP context is illustrated with the Forensic Toolkit Imager case study.

Using Cloud Computing infrastructure with CloudBioLinux, CloudMan and Galaxy

PubMed Central

Afgan, Enis; Chapman, Brad; Jadan, Margita; Franke, Vedran; Taylor, James

2012-01-01

Cloud computing has revolutionized availability and access to computing and storage resources; making it possible to provision a large computational infrastructure with only a few clicks in a web browser. However, those resources are typically provided in the form of low-level infrastructure components that need to be procured and configured before use. In this protocol, we demonstrate how to utilize cloud computing resources to perform open-ended bioinformatics analyses, with fully automated management of the underlying cloud infrastructure. By combining three projects, CloudBioLinux, CloudMan, and Galaxy into a cohesive unit, we have enabled researchers to gain access to more than 100 preconfigured bioinformatics tools and gigabytes of reference genomes on top of the flexible cloud computing infrastructure. The protocol demonstrates how to setup the available infrastructure and how to use the tools via a graphical desktop interface, a parallel command line interface, and the web-based Galaxy interface. PMID:22700313

Using cloud computing infrastructure with CloudBioLinux, CloudMan, and Galaxy.

PubMed

Afgan, Enis; Chapman, Brad; Jadan, Margita; Franke, Vedran; Taylor, James

2012-06-01

Cloud computing has revolutionized availability and access to computing and storage resources, making it possible to provision a large computational infrastructure with only a few clicks in a Web browser. However, those resources are typically provided in the form of low-level infrastructure components that need to be procured and configured before use. In this unit, we demonstrate how to utilize cloud computing resources to perform open-ended bioinformatic analyses, with fully automated management of the underlying cloud infrastructure. By combining three projects, CloudBioLinux, CloudMan, and Galaxy, into a cohesive unit, we have enabled researchers to gain access to more than 100 preconfigured bioinformatics tools and gigabytes of reference genomes on top of the flexible cloud computing infrastructure. The protocol demonstrates how to set up the available infrastructure and how to use the tools via a graphical desktop interface, a parallel command-line interface, and the Web-based Galaxy interface.

WEBnm@ v2.0: Web server and services for comparing protein flexibility.

PubMed

Tiwari, Sandhya P; Fuglebakk, Edvin; Hollup, Siv M; Skjærven, Lars; Cragnolini, Tristan; Grindhaug, Svenn H; Tekle, Kidane M; Reuter, Nathalie

2014-12-30

Normal mode analysis (NMA) using elastic network models is a reliable and cost-effective computational method to characterise protein flexibility and by extension, their dynamics. Further insight into the dynamics-function relationship can be gained by comparing protein motions between protein homologs and functional classifications. This can be achieved by comparing normal modes obtained from sets of evolutionary related proteins. We have developed an automated tool for comparative NMA of a set of pre-aligned protein structures. The user can submit a sequence alignment in the FASTA format and the corresponding coordinate files in the Protein Data Bank (PDB) format. The computed normalised squared atomic fluctuations and atomic deformation energies of the submitted structures can be easily compared on graphs provided by the web user interface. The web server provides pairwise comparison of the dynamics of all proteins included in the submitted set using two measures: the Root Mean Squared Inner Product and the Bhattacharyya Coefficient. The Comparative Analysis has been implemented on our web server for NMA, WEBnm@, which also provides recently upgraded functionality for NMA of single protein structures. This includes new visualisations of protein motion, visualisation of inter-residue correlations and the analysis of conformational change using the overlap analysis. In addition, programmatic access to WEBnm@ is now available through a SOAP-based web service. Webnm@ is available at http://apps.cbu.uib.no/webnma . WEBnm@ v2.0 is an online tool offering unique capability for comparative NMA on multiple protein structures. Along with a convenient web interface, powerful computing resources, and several methods for mode analyses, WEBnm@ facilitates the assessment of protein flexibility within protein families and superfamilies. These analyses can give a good view of how the structures move and how the flexibility is conserved over the different structures.

Validation of an Active Gear, Flexible Aircraft Take-off and Landing analysis (AGFATL)

NASA Technical Reports Server (NTRS)

Mcgehee, J. R.

1984-01-01

The results of an analytical investigation using a computer program for active gear, flexible aircraft take off and landing analysis (AGFATL) are compared with experimental data from shaker tests, drop tests, and simulated landing tests to validate the AGFATL computer program. Comparison of experimental and analytical responses for both passive and active gears indicates good agreement for shaker tests and drop tests. For the simulated landing tests, the passive and active gears were influenced by large strut binding friction forces. The inclusion of these undefined forces in the analytical simulations was difficult, and consequently only fair to good agreement was obtained. An assessment of the results from the investigation indicates that the AGFATL computer program is a valid tool for the study and initial design of series hydraulic active control landing gear systems.

Flexible structure control experiments using a real-time workstation for computer-aided control engineering

NASA Technical Reports Server (NTRS)

Stieber, Michael E.

1989-01-01

A Real-Time Workstation for Computer-Aided Control Engineering has been developed jointly by the Communications Research Centre (CRC) and Ruhr-Universitaet Bochum (RUB), West Germany. The system is presently used for the development and experimental verification of control techniques for large space systems with significant structural flexibility. The Real-Time Workstation essentially is an implementation of RUB's extensive Computer-Aided Control Engineering package KEDDC on an INTEL micro-computer running under the RMS real-time operating system. The portable system supports system identification, analysis, control design and simulation, as well as the immediate implementation and test of control systems. The Real-Time Workstation is currently being used by CRC to study control/structure interaction on a ground-based structure called DAISY, whose design was inspired by a reflector antenna. DAISY emulates the dynamics of a large flexible spacecraft with the following characteristics: rigid body modes, many clustered vibration modes with low frequencies and extremely low damping. The Real-Time Workstation was found to be a very powerful tool for experimental studies, supporting control design and simulation, and conducting and evaluating tests withn one integrated environment.

Airfoil/Wing Flow Control Using Flexible Extended Trailing Edge

DTIC Science & Technology

2009-02-27

and (b) Power spectrums of drag coefficient Figure 4. Mean velocity profiles O Baseline NACA0012. AoA 18 deg c Baseline NACA0012. AoA 20...dynamics, (a) fin amplitude and (b) power spectrum of fin amplitude Development of Computational Tools Simulations of the time-dependent deformation of...combination of experimental, computational and theoretical methods. Compared with Gurney flap and conventional flap, this device enhanced lift at a smaller

CAESY - COMPUTER AIDED ENGINEERING SYSTEM

NASA Technical Reports Server (NTRS)

Wette, M. R.

1994-01-01

Many developers of software and algorithms for control system design have recognized that current tools have limits in both flexibility and efficiency. Many forces drive the development of new tools including the desire to make complex system modeling design and analysis easier and the need for quicker turnaround time in analysis and design. Other considerations include the desire to make use of advanced computer architectures to help in control system design, adopt new methodologies in control, and integrate design processes (e.g., structure, control, optics). CAESY was developed to provide a means to evaluate methods for dealing with user needs in computer-aided control system design. It is an interpreter for performing engineering calculations and incorporates features of both Ada and MATLAB. It is designed to be reasonably flexible and powerful. CAESY includes internally defined functions and procedures, as well as user defined ones. Support for matrix calculations is provided in the same manner as MATLAB. However, the development of CAESY is a research project, and while it provides some features which are not found in commercially sold tools, it does not exhibit the robustness that many commercially developed tools provide. CAESY is written in C-language for use on Sun4 series computers running SunOS 4.1.1 and later. The program is designed to optionally use the LAPACK math library. The LAPACK math routines are available through anonymous ftp from research.att.com. CAESY requires 4Mb of RAM for execution. The standard distribution medium is a .25 inch streaming magnetic tape cartridge (QIC-24) in UNIX tar format. CAESY was developed in 1993 and is a copyrighted work with all copyright vested in NASA.

Hybrid and Electric Advanced Vehicle Systems Simulation

NASA Technical Reports Server (NTRS)

Beach, R. F.; Hammond, R. A.; Mcgehee, R. K.

1985-01-01

Predefined components connected to represent wide variety of propulsion systems. Hybrid and Electric Advanced Vehicle System (HEAVY) computer program is flexible tool for evaluating performance and cost of electric and hybrid vehicle propulsion systems. Allows designer to quickly, conveniently, and economically predict performance of proposed drive train.

Critical Success Factors in a TRIDEM Exchange

ERIC Educational Resources Information Center

Hauck, Mirjam

2007-01-01

Computer-mediated-communication (CMC) tools allowing learners to be in contact with native speakers of their target language in other locations are becoming increasingly flexible, often combining different modes of communication in a single web- and internet-based environment. The literature on telecollaborative exchanges reveals, however, that…

System capacity and economic modeling computer tool for satellite mobile communications systems

NASA Technical Reports Server (NTRS)

Wiedeman, Robert A.; Wen, Doong; Mccracken, Albert G.

1988-01-01

A unique computer modeling tool that combines an engineering tool with a financial analysis program is described. The resulting combination yields a flexible economic model that can predict the cost effectiveness of various mobile systems. Cost modeling is necessary in order to ascertain if a given system with a finite satellite resource is capable of supporting itself financially and to determine what services can be supported. Personal computer techniques using Lotus 123 are used for the model in order to provide as universal an application as possible such that the model can be used and modified to fit many situations and conditions. The output of the engineering portion of the model consists of a channel capacity analysis and link calculations for several qualities of service using up to 16 types of earth terminal configurations. The outputs of the financial model are a revenue analysis, an income statement, and a cost model validation section.

A generic flexible and robust approach for intelligent real-time video-surveillance systems

NASA Astrophysics Data System (ADS)

Desurmont, Xavier; Delaigle, Jean-Francois; Bastide, Arnaud; Macq, Benoit

2004-05-01

In this article we present a generic, flexible and robust approach for an intelligent real-time video-surveillance system. A previous version of the system was presented in [1]. The goal of these advanced tools is to provide help to operators by detecting events of interest in visual scenes and highlighting alarms and compute statistics. The proposed system is a multi-camera platform able to handle different standards of video inputs (composite, IP, IEEE1394 ) and which can basically compress (MPEG4), store and display them. This platform also integrates advanced video analysis tools, such as motion detection, segmentation, tracking and interpretation. The design of the architecture is optimised to playback, display, and process video flows in an efficient way for video-surveillance application. The implementation is distributed on a scalable computer cluster based on Linux and IP network. It relies on POSIX threads for multitasking scheduling. Data flows are transmitted between the different modules using multicast technology and under control of a TCP-based command network (e.g. for bandwidth occupation control). We report here some results and we show the potential use of such a flexible system in third generation video surveillance system. We illustrate the interest of the system in a real case study, which is the indoor surveillance.

vFitness: a web-based computing tool for improving estimation of in vitro HIV-1 fitness experiments

PubMed Central

2010-01-01

Background The replication rate (or fitness) between viral variants has been investigated in vivo and in vitro for human immunodeficiency virus (HIV). HIV fitness plays an important role in the development and persistence of drug resistance. The accurate estimation of viral fitness relies on complicated computations based on statistical methods. This calls for tools that are easy to access and intuitive to use for various experiments of viral fitness. Results Based on a mathematical model and several statistical methods (least-squares approach and measurement error models), a Web-based computing tool has been developed for improving estimation of virus fitness in growth competition assays of human immunodeficiency virus type 1 (HIV-1). Conclusions Unlike the two-point calculation used in previous studies, the estimation here uses linear regression methods with all observed data in the competition experiment to more accurately estimate relative viral fitness parameters. The dilution factor is introduced for making the computational tool more flexible to accommodate various experimental conditions. This Web-based tool is implemented in C# language with Microsoft ASP.NET, and is publicly available on the Web at http://bis.urmc.rochester.edu/vFitness/. PMID:20482791

vFitness: a web-based computing tool for improving estimation of in vitro HIV-1 fitness experiments.

PubMed

Ma, Jingming; Dykes, Carrie; Wu, Tao; Huang, Yangxin; Demeter, Lisa; Wu, Hulin

2010-05-18

The replication rate (or fitness) between viral variants has been investigated in vivo and in vitro for human immunodeficiency virus (HIV). HIV fitness plays an important role in the development and persistence of drug resistance. The accurate estimation of viral fitness relies on complicated computations based on statistical methods. This calls for tools that are easy to access and intuitive to use for various experiments of viral fitness. Based on a mathematical model and several statistical methods (least-squares approach and measurement error models), a Web-based computing tool has been developed for improving estimation of virus fitness in growth competition assays of human immunodeficiency virus type 1 (HIV-1). Unlike the two-point calculation used in previous studies, the estimation here uses linear regression methods with all observed data in the competition experiment to more accurately estimate relative viral fitness parameters. The dilution factor is introduced for making the computational tool more flexible to accommodate various experimental conditions. This Web-based tool is implemented in C# language with Microsoft ASP.NET, and is publicly available on the Web at http://bis.urmc.rochester.edu/vFitness/.

Efficient matrix approach to optical wave propagation and Linear Canonical Transforms.

PubMed

Shakir, Sami A; Fried, David L; Pease, Edwin A; Brennan, Terry J; Dolash, Thomas M

2015-10-05

The Fresnel diffraction integral form of optical wave propagation and the more general Linear Canonical Transforms (LCT) are cast into a matrix transformation form. Taking advantage of recent efficient matrix multiply algorithms, this approach promises an efficient computational and analytical tool that is competitive with FFT based methods but offers better behavior in terms of aliasing, transparent boundary condition, and flexibility in number of sampling points and computational window sizes of the input and output planes being independent. This flexibility makes the method significantly faster than FFT based propagators when only a single point, as in Strehl metrics, or a limited number of points, as in power-in-the-bucket metrics, are needed in the output observation plane.

MODELS-3 INSTALLATION PROCEDURES FOR A PERSONAL COMPUTER WITH A NT OPERATING SYSTEM (MODELS-3 VERSION 4.1)

EPA Science Inventory

Models-3 is a flexible system designed to simplify the development and use of air quality models and other environmental decision support tools. It is designed for applications ranging from regulatory and policy analysis to understanding the complex interactions of atmospheric...

Leveraging Python Interoperability Tools to Improve Sapphire's Usability

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

Gezahegne, A; Love, N S

2007-12-10

The Sapphire project at the Center for Applied Scientific Computing (CASC) develops and applies an extensive set of data mining algorithms for the analysis of large data sets. Sapphire's algorithms are currently available as a set of C++ libraries. However many users prefer higher level scripting languages such as Python for their ease of use and flexibility. In this report, we evaluate four interoperability tools for the purpose of wrapping Sapphire's core functionality with Python. Exposing Sapphire's functionality through a Python interface would increase its usability and connect its algorithms to existing Python tools.

High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis.

PubMed

Simonyan, Vahan; Mazumder, Raja

2014-09-30

The High-performance Integrated Virtual Environment (HIVE) is a high-throughput cloud-based infrastructure developed for the storage and analysis of genomic and associated biological data. HIVE consists of a web-accessible interface for authorized users to deposit, retrieve, share, annotate, compute and visualize Next-generation Sequencing (NGS) data in a scalable and highly efficient fashion. The platform contains a distributed storage library and a distributed computational powerhouse linked seamlessly. Resources available through the interface include algorithms, tools and applications developed exclusively for the HIVE platform, as well as commonly used external tools adapted to operate within the parallel architecture of the system. HIVE is composed of a flexible infrastructure, which allows for simple implementation of new algorithms and tools. Currently, available HIVE tools include sequence alignment and nucleotide variation profiling tools, metagenomic analyzers, phylogenetic tree-building tools using NGS data, clone discovery algorithms, and recombination analysis algorithms. In addition to tools, HIVE also provides knowledgebases that can be used in conjunction with the tools for NGS sequence and metadata analysis.

High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis

PubMed Central

Simonyan, Vahan; Mazumder, Raja

2014-01-01

The High-performance Integrated Virtual Environment (HIVE) is a high-throughput cloud-based infrastructure developed for the storage and analysis of genomic and associated biological data. HIVE consists of a web-accessible interface for authorized users to deposit, retrieve, share, annotate, compute and visualize Next-generation Sequencing (NGS) data in a scalable and highly efficient fashion. The platform contains a distributed storage library and a distributed computational powerhouse linked seamlessly. Resources available through the interface include algorithms, tools and applications developed exclusively for the HIVE platform, as well as commonly used external tools adapted to operate within the parallel architecture of the system. HIVE is composed of a flexible infrastructure, which allows for simple implementation of new algorithms and tools. Currently, available HIVE tools include sequence alignment and nucleotide variation profiling tools, metagenomic analyzers, phylogenetic tree-building tools using NGS data, clone discovery algorithms, and recombination analysis algorithms. In addition to tools, HIVE also provides knowledgebases that can be used in conjunction with the tools for NGS sequence and metadata analysis. PMID:25271953

A non-linear programming approach to the computer-aided design of regulators using a linear-quadratic formulation

NASA Technical Reports Server (NTRS)

Fleming, P.

1985-01-01

A design technique is proposed for linear regulators in which a feedback controller of fixed structure is chosen to minimize an integral quadratic objective function subject to the satisfaction of integral quadratic constraint functions. Application of a non-linear programming algorithm to this mathematically tractable formulation results in an efficient and useful computer-aided design tool. Particular attention is paid to computational efficiency and various recommendations are made. Two design examples illustrate the flexibility of the approach and highlight the special insight afforded to the designer.

Challenges in Reproducibility, Replicability, and Comparability of Computational Models and Tools for Neuronal and Glial Networks, Cells, and Subcellular Structures.

PubMed

Manninen, Tiina; Aćimović, Jugoslava; Havela, Riikka; Teppola, Heidi; Linne, Marja-Leena

2018-01-01

The possibility to replicate and reproduce published research results is one of the biggest challenges in all areas of science. In computational neuroscience, there are thousands of models available. However, it is rarely possible to reimplement the models based on the information in the original publication, let alone rerun the models just because the model implementations have not been made publicly available. We evaluate and discuss the comparability of a versatile choice of simulation tools: tools for biochemical reactions and spiking neuronal networks, and relatively new tools for growth in cell cultures. The replicability and reproducibility issues are considered for computational models that are equally diverse, including the models for intracellular signal transduction of neurons and glial cells, in addition to single glial cells, neuron-glia interactions, and selected examples of spiking neuronal networks. We also address the comparability of the simulation results with one another to comprehend if the studied models can be used to answer similar research questions. In addition to presenting the challenges in reproducibility and replicability of published results in computational neuroscience, we highlight the need for developing recommendations and good practices for publishing simulation tools and computational models. Model validation and flexible model description must be an integral part of the tool used to simulate and develop computational models. Constant improvement on experimental techniques and recording protocols leads to increasing knowledge about the biophysical mechanisms in neural systems. This poses new challenges for computational neuroscience: extended or completely new computational methods and models may be required. Careful evaluation and categorization of the existing models and tools provide a foundation for these future needs, for constructing multiscale models or extending the models to incorporate additional or more detailed biophysical mechanisms. Improving the quality of publications in computational neuroscience, enabling progressive building of advanced computational models and tools, can be achieved only through adopting publishing standards which underline replicability and reproducibility of research results.

Challenges in Reproducibility, Replicability, and Comparability of Computational Models and Tools for Neuronal and Glial Networks, Cells, and Subcellular Structures

PubMed Central

Manninen, Tiina; Aćimović, Jugoslava; Havela, Riikka; Teppola, Heidi; Linne, Marja-Leena

2018-01-01

The possibility to replicate and reproduce published research results is one of the biggest challenges in all areas of science. In computational neuroscience, there are thousands of models available. However, it is rarely possible to reimplement the models based on the information in the original publication, let alone rerun the models just because the model implementations have not been made publicly available. We evaluate and discuss the comparability of a versatile choice of simulation tools: tools for biochemical reactions and spiking neuronal networks, and relatively new tools for growth in cell cultures. The replicability and reproducibility issues are considered for computational models that are equally diverse, including the models for intracellular signal transduction of neurons and glial cells, in addition to single glial cells, neuron-glia interactions, and selected examples of spiking neuronal networks. We also address the comparability of the simulation results with one another to comprehend if the studied models can be used to answer similar research questions. In addition to presenting the challenges in reproducibility and replicability of published results in computational neuroscience, we highlight the need for developing recommendations and good practices for publishing simulation tools and computational models. Model validation and flexible model description must be an integral part of the tool used to simulate and develop computational models. Constant improvement on experimental techniques and recording protocols leads to increasing knowledge about the biophysical mechanisms in neural systems. This poses new challenges for computational neuroscience: extended or completely new computational methods and models may be required. Careful evaluation and categorization of the existing models and tools provide a foundation for these future needs, for constructing multiscale models or extending the models to incorporate additional or more detailed biophysical mechanisms. Improving the quality of publications in computational neuroscience, enabling progressive building of advanced computational models and tools, can be achieved only through adopting publishing standards which underline replicability and reproducibility of research results. PMID:29765315

Protein flexibility in the light of structural alphabets

PubMed Central

Craveur, Pierrick; Joseph, Agnel P.; Esque, Jeremy; Narwani, Tarun J.; Noël, Floriane; Shinada, Nicolas; Goguet, Matthieu; Leonard, Sylvain; Poulain, Pierre; Bertrand, Olivier; Faure, Guilhem; Rebehmed, Joseph; Ghozlane, Amine; Swapna, Lakshmipuram S.; Bhaskara, Ramachandra M.; Barnoud, Jonathan; Téletchéa, Stéphane; Jallu, Vincent; Cerny, Jiri; Schneider, Bohdan; Etchebest, Catherine; Srinivasan, Narayanaswamy; Gelly, Jean-Christophe; de Brevern, Alexandre G.

2015-01-01

Protein structures are valuable tools to understand protein function. Nonetheless, proteins are often considered as rigid macromolecules while their structures exhibit specific flexibility, which is essential to complete their functions. Analyses of protein structures and dynamics are often performed with a simplified three-state description, i.e., the classical secondary structures. More precise and complete description of protein backbone conformation can be obtained using libraries of small protein fragments that are able to approximate every part of protein structures. These libraries, called structural alphabets (SAs), have been widely used in structure analysis field, from definition of ligand binding sites to superimposition of protein structures. SAs are also well suited to analyze the dynamics of protein structures. Here, we review innovative approaches that investigate protein flexibility based on SAs description. Coupled to various sources of experimental data (e.g., B-factor) and computational methodology (e.g., Molecular Dynamic simulation), SAs turn out to be powerful tools to analyze protein dynamics, e.g., to examine allosteric mechanisms in large set of structures in complexes, to identify order/disorder transition. SAs were also shown to be quite efficient to predict protein flexibility from amino-acid sequence. Finally, in this review, we exemplify the interest of SAs for studying flexibility with different cases of proteins implicated in pathologies and diseases. PMID:26075209

An overview of recent applications of computational modelling in neonatology

PubMed Central

Wrobel, Luiz C.; Ginalski, Maciej K.; Nowak, Andrzej J.; Ingham, Derek B.; Fic, Anna M.

2010-01-01

This paper reviews some of our recent applications of computational fluid dynamics (CFD) to model heat and mass transfer problems in neonatology and investigates the major heat and mass-transfer mechanisms taking place in medical devices, such as incubators, radiant warmers and oxygen hoods. It is shown that CFD simulations are very flexible tools that can take into account all modes of heat transfer in assisting neonatal care and improving the design of medical devices. PMID:20439275

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

Grote, D. P.

Forthon generates links between Fortran and Python. Python is a high level, object oriented, interactive and scripting language that allows a flexible and versatile interface to computational tools. The Forthon package generates the necessary wrapping code which allows access to the Fortran database and to the Fortran subroutines and functions. This provides a development package where the computationally intensive parts of a code can be written in efficient Fortran, and the high level controlling code can be written in the much more versatile Python language.

A Flexible Computational Framework Using R and Map-Reduce for Permutation Tests of Massive Genetic Analysis of Complex Traits.

PubMed

Mahjani, Behrang; Toor, Salman; Nettelblad, Carl; Holmgren, Sverker

2017-01-01

In quantitative trait locus (QTL) mapping significance of putative QTL is often determined using permutation testing. The computational needs to calculate the significance level are immense, 10 4 up to 10 8 or even more permutations can be needed. We have previously introduced the PruneDIRECT algorithm for multiple QTL scan with epistatic interactions. This algorithm has specific strengths for permutation testing. Here, we present a flexible, parallel computing framework for identifying multiple interacting QTL using the PruneDIRECT algorithm which uses the map-reduce model as implemented in Hadoop. The framework is implemented in R, a widely used software tool among geneticists. This enables users to rearrange algorithmic steps to adapt genetic models, search algorithms, and parallelization steps to their needs in a flexible way. Our work underlines the maturity of accessing distributed parallel computing for computationally demanding bioinformatics applications through building workflows within existing scientific environments. We investigate the PruneDIRECT algorithm, comparing its performance to exhaustive search and DIRECT algorithm using our framework on a public cloud resource. We find that PruneDIRECT is vastly superior for permutation testing, and perform 2 ×10 5 permutations for a 2D QTL problem in 15 hours, using 100 cloud processes. We show that our framework scales out almost linearly for a 3D QTL search.

Docking ligands into flexible and solvated macromolecules. 7. Impact of protein flexibility and water molecules on docking-based virtual screening accuracy.

PubMed

Therrien, Eric; Weill, Nathanael; Tomberg, Anna; Corbeil, Christopher R; Lee, Devin; Moitessier, Nicolas

2014-11-24

The use of predictive computational methods in the drug discovery process is in a state of continual growth. Over the last two decades, an increasingly large number of docking tools have been developed to identify hits or optimize lead molecules through in-silico screening of chemical libraries to proteins. In recent years, the focus has been on implementing protein flexibility and water molecules. Our efforts led to the development of Fitted first reported in 2007 and further developed since then. In this study, we wished to evaluate the impact of protein flexibility and occurrence of water molecules on the accuracy of the Fitted docking program to discriminate active compounds from inactive compounds in virtual screening (VS) campaigns. For this purpose, a total of 171 proteins cocrystallized with small molecules representing 40 unique enzymes and receptors as well as sets of known ligands and decoys were selected from the Protein Data Bank (PDB) and the Directory of Useful Decoys (DUD), respectively. This study revealed that implementing displaceable crystallographic or computationally placed particle water molecules and protein flexibility can improve the enrichment in active compounds. In addition, an informed decision based on library diversity or research objectives (hit discovery vs lead optimization) on which implementation to use may lead to significant improvements.

Flexible Force Field Parameterization through Fitting on the Ab Initio-Derived Elastic Tensor

PubMed Central

2017-01-01

Constructing functional forms and their corresponding force field parameters for the metal–linker interface of metal–organic frameworks is challenging. We propose fitting these parameters on the elastic tensor, computed from ab initio density functional theory calculations. The advantage of this top-down approach is that it becomes evident if functional forms are missing when components of the elastic tensor are off. As a proof-of-concept, a new flexible force field for MIL-47(V) is derived. Negative thermal expansion is observed and framework flexibility has a negligible effect on adsorption and transport properties for small guest molecules. We believe that this force field parametrization approach can serve as a useful tool for developing accurate flexible force field models that capture the correct mechanical behavior of the full periodic structure. PMID:28661672

Framework for architecture-independent run-time reconfigurable applications

NASA Astrophysics Data System (ADS)

Lehn, David I.; Hudson, Rhett D.; Athanas, Peter M.

2000-10-01

Configurable Computing Machines (CCMs) have emerged as a technology with the computational benefits of custom ASICs as well as the flexibility and reconfigurability of general-purpose microprocessors. Significant effort from the research community has focused on techniques to move this reconfigurability from a rapid application development tool to a run-time tool. This requires the ability to change the hardware design while the application is executing and is known as Run-Time Reconfiguration (RTR). Widespread acceptance of run-time reconfigurable custom computing depends upon the existence of high-level automated design tools. Such tools must reduce the designers effort to port applications between different platforms as the architecture, hardware, and software evolves. A Java implementation of a high-level application framework, called Janus, is presented here. In this environment, developers create Java classes that describe the structural behavior of an application. The framework allows hardware and software modules to be freely mixed and interchanged. A compilation phase of the development process analyzes the structure of the application and adapts it to the target platform. Janus is capable of structuring the run-time behavior of an application to take advantage of the memory and computational resources available.

Robonaut's Flexible Information Technology Infrastructure

NASA Technical Reports Server (NTRS)

Askew, Scott; Bluethmann, William; Alder, Ken; Ambrose, Robert

2003-01-01

Robonaut, NASA's humanoid robot, is designed to work as both an astronaut assistant and, in certain situations, an astronaut surrogate. This highly dexterous robot performs complex tasks under telepresence control that could previously only be carried out directly by humans. Currently with 47 degrees of freedom (DOF), Robonaut is a state-of-the-art human size telemanipulator system. while many of Robonaut's embedded components have been custom designed to meet packaging or environmental requirements, the primary computing systems used in Robonaut are currently commercial-off-the-shelf (COTS) products which have some correlation to flight qualified computer systems. This loose coupling of information technology (IT) resources allows Robonaut to exploit cost effective solutions while floating the technology base to take advantage of the rapid pace of IT advances. These IT systems utilize a software development environment, which is both compatible with COTS hardware as well as flight proven computing systems, preserving the majority of software development for a flight system. The ability to use highly integrated and flexible COTS software development tools improves productivity while minimizing redesign for a space flight system. Further, the flexibility of Robonaut's software and communication architecture has allowed it to become a widely used distributed development testbed for integrating new capabilities and furthering experimental research.

OpenStructure: a flexible software framework for computational structural biology.

PubMed

Biasini, Marco; Mariani, Valerio; Haas, Jürgen; Scheuber, Stefan; Schenk, Andreas D; Schwede, Torsten; Philippsen, Ansgar

2010-10-15

Developers of new methods in computational structural biology are often hampered in their research by incompatible software tools and non-standardized data formats. To address this problem, we have developed OpenStructure as a modular open source platform to provide a powerful, yet flexible general working environment for structural bioinformatics. OpenStructure consists primarily of a set of libraries written in C++ with a cleanly designed application programmer interface. All functionality can be accessed directly in C++ or in a Python layer, meeting both the requirements for high efficiency and ease of use. Powerful selection queries and the notion of entity views to represent these selections greatly facilitate the development and implementation of algorithms on structural data. The modular integration of computational core methods with powerful visualization tools makes OpenStructure an ideal working and development environment. Several applications, such as the latest versions of IPLT and QMean, have been implemented based on OpenStructure-demonstrating its value for the development of next-generation structural biology algorithms. Source code licensed under the GNU lesser general public license and binaries for MacOS X, Linux and Windows are available for download at http://www.openstructure.org. torsten.schwede@unibas.ch Supplementary data are available at Bioinformatics online.

Kinematic synthesis of adjustable robotic mechanisms

NASA Astrophysics Data System (ADS)

Chuenchom, Thatchai

1993-01-01

Conventional hard automation, such as a linkage-based or a cam-driven system, provides high speed capability and repeatability but not the flexibility required in many industrial applications. The conventional mechanisms, that are typically single-degree-of-freedom systems, are being increasingly replaced by multi-degree-of-freedom multi-actuators driven by logic controllers. Although this new trend in sophistication provides greatly enhanced flexibility, there are many instances where the flexibility needs are exaggerated and the associated complexity is unnecessary. Traditional mechanism-based hard automation, on the other hand, neither can fulfill multi-task requirements nor are cost-effective mainly due to lack of methods and tools to design-in flexibility. This dissertation attempts to bridge this technological gap by developing Adjustable Robotic Mechanisms (ARM's) or 'programmable mechanisms' as a middle ground between high speed hard automation and expensive serial jointed-arm robots. This research introduces the concept of adjustable robotic mechanisms towards cost-effective manufacturing automation. A generalized analytical synthesis technique has been developed to support the computational design of ARM's that lays the theoretical foundation for synthesis of adjustable mechanisms. The synthesis method developed in this dissertation, called generalized adjustable dyad and triad synthesis, advances the well-known Burmester theory in kinematics to a new level. While this method provides planar solutions, a novel patented scheme is utilized for converting prescribed three-dimensional motion specifications into sets of planar projections. This provides an analytical and a computational tool for designing adjustable mechanisms that satisfy multiple sets of three-dimensional motion specifications. Several design issues were addressed, including adjustable parameter identification, branching defect, and mechanical errors. An efficient mathematical scheme for identification of adjustable member was also developed. The analytical synthesis techniques developed in this dissertation were successfully implemented in a graphic-intensive user-friendly computer program. A physical prototype of a general purpose adjustable robotic mechanism has been constructed to serve as a proof-of-concept model.

EEGLAB, SIFT, NFT, BCILAB, and ERICA: new tools for advanced EEG processing.

PubMed

Delorme, Arnaud; Mullen, Tim; Kothe, Christian; Akalin Acar, Zeynep; Bigdely-Shamlo, Nima; Vankov, Andrey; Makeig, Scott

2011-01-01

We describe a set of complementary EEG data collection and processing tools recently developed at the Swartz Center for Computational Neuroscience (SCCN) that connect to and extend the EEGLAB software environment, a freely available and readily extensible processing environment running under Matlab. The new tools include (1) a new and flexible EEGLAB STUDY design facility for framing and performing statistical analyses on data from multiple subjects; (2) a neuroelectromagnetic forward head modeling toolbox (NFT) for building realistic electrical head models from available data; (3) a source information flow toolbox (SIFT) for modeling ongoing or event-related effective connectivity between cortical areas; (4) a BCILAB toolbox for building online brain-computer interface (BCI) models from available data, and (5) an experimental real-time interactive control and analysis (ERICA) environment for real-time production and coordination of interactive, multimodal experiments.

Tools for Atmospheric Radiative Transfer: Streamer and FluxNet. Revised

NASA Technical Reports Server (NTRS)

Key, Jeffrey R.; Schweiger, Axel J.

1998-01-01

Two tools for the solution of radiative transfer problems are presented. Streamer is a highly flexible medium spectral resolution radiative transfer model based on the plane-parallel theory of radiative transfer. Capable of computing either fluxes or radiances, it is suitable for studying radiative processes at the surface or within the atmosphere and for the development of remote-sensing algorithms. FluxNet is a fast neural network-based implementation of Streamer for computing surface fluxes. It allows for a sophisticated treatment of radiative processes in the analysis of large data sets and potential integration into geophysical models where computational efficiency is an issue. Documentation and tools for the development of alternative versions of Fluxnet are available. Collectively, Streamer and FluxNet solve a wide variety of problems related to radiative transfer: Streamer provides the detail and sophistication needed to perform basic research on most aspects of complex radiative processes while the efficiency and simplicity of FluxNet make it ideal for operational use.

Using computer-aided drug design and medicinal chemistry strategies in the fight against diabetes.

PubMed

Semighini, Evandro P; Resende, Jonathan A; de Andrade, Peterson; Morais, Pedro A B; Carvalho, Ivone; Taft, Carlton A; Silva, Carlos H T P

2011-04-01

The aim of this work is to present a simple, practical and efficient protocol for drug design, in particular Diabetes, which includes selection of the illness, good choice of a target as well as a bioactive ligand and then usage of various computer aided drug design and medicinal chemistry tools to design novel potential drug candidates in different diseases. We have selected the validated target dipeptidyl peptidase IV (DPP-IV), whose inhibition contributes to reduce glucose levels in type 2 diabetes patients. The most active inhibitor with complex X-ray structure reported was initially extracted from the BindingDB database. By using molecular modification strategies widely used in medicinal chemistry, besides current state-of-the-art tools in drug design (including flexible docking, virtual screening, molecular interaction fields, molecular dynamics, ADME and toxicity predictions), we have proposed 4 novel potential DPP-IV inhibitors with drug properties for Diabetes control, which have been supported and validated by all the computational tools used herewith.

Improving Conceptual Design for Launch Vehicles

NASA Technical Reports Server (NTRS)

Olds, John R.

1998-01-01

This report summarizes activities performed during the second year of a three year cooperative agreement between NASA - Langley Research Center and Georgia Tech. Year 1 of the project resulted in the creation of a new Cost and Business Assessment Model (CABAM) for estimating the economic performance of advanced reusable launch vehicles including non-recurring costs, recurring costs, and revenue. The current year (second year) activities were focused on the evaluation of automated, collaborative design frameworks (computation architectures or computational frameworks) for automating the design process in advanced space vehicle design. Consistent with NASA's new thrust area in developing and understanding Intelligent Synthesis Environments (ISE), the goals of this year's research efforts were to develop and apply computer integration techniques and near-term computational frameworks for conducting advanced space vehicle design. NASA - Langley (VAB) has taken a lead role in developing a web-based computing architectures within which the designer can interact with disciplinary analysis tools through a flexible web interface. The advantages of this approach are, 1) flexible access to the designer interface through a simple web browser (e.g. Netscape Navigator), 2) ability to include existing 'legacy' codes, and 3) ability to include distributed analysis tools running on remote computers. To date, VAB's internal emphasis has been on developing this test system for the planetary entry mission under the joint Integrated Design System (IDS) program with NASA - Ames and JPL. Georgia Tech's complementary goals this year were to: 1) Examine an alternate 'custom' computational architecture for the three-discipline IDS planetary entry problem to assess the advantages and disadvantages relative to the web-based approach.and 2) Develop and examine a web-based interface and framework for a typical launch vehicle design problem.

Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories.

PubMed

Haider, Kamran; Cruz, Anthony; Ramsey, Steven; Gilson, Michael K; Kurtzman, Tom

2018-01-09

We have developed SSTMap, a software package for mapping structural and thermodynamic water properties in molecular dynamics trajectories. The package introduces automated analysis and mapping of local measures of frustration and enhancement of water structure. The thermodynamic calculations are based on Inhomogeneous Fluid Solvation Theory (IST), which is implemented using both site-based and grid-based approaches. The package also extends the applicability of solvation analysis calculations to multiple molecular dynamics (MD) simulation programs by using existing cross-platform tools for parsing MD parameter and trajectory files. SSTMap is implemented in Python and contains both command-line tools and a Python module to facilitate flexibility in setting up calculations and for automated generation of large data sets involving analysis of multiple solutes. Output is generated in formats compatible with popular Python data science packages. This tool will be used by the molecular modeling community for computational analysis of water in problems of biophysical interest such as ligand binding and protein function.

The medical simulation markup language - simplifying the biomechanical modeling workflow.

PubMed

Suwelack, Stefan; Stoll, Markus; Schalck, Sebastian; Schoch, Nicolai; Dillmann, Rüdiger; Bendl, Rolf; Heuveline, Vincent; Speidel, Stefanie

2014-01-01

Modeling and simulation of the human body by means of continuum mechanics has become an important tool in diagnostics, computer-assisted interventions and training. This modeling approach seeks to construct patient-specific biomechanical models from tomographic data. Usually many different tools such as segmentation and meshing algorithms are involved in this workflow. In this paper we present a generalized and flexible description for biomechanical models. The unique feature of the new modeling language is that it not only describes the final biomechanical simulation, but also the workflow how the biomechanical model is constructed from tomographic data. In this way, the MSML can act as a middleware between all tools used in the modeling pipeline. The MSML thus greatly facilitates the prototyping of medical simulation workflows for clinical and research purposes. In this paper, we not only detail the XML-based modeling scheme, but also present a concrete implementation. Different examples highlight the flexibility, robustness and ease-of-use of the approach.

Visualization and Interaction in Research, Teaching, and Scientific Communication

NASA Astrophysics Data System (ADS)

Ammon, C. J.

2017-12-01

Modern computing provides many tools for exploring observations, numerical calculations, and theoretical relationships. The number of options is, in fact, almost overwhelming. But the choices provide those with modest programming skills opportunities to create unique views of scientific information and to develop deeper insights into their data, their computations, and the underlying theoretical data-model relationships. I present simple examples of using animation and human-computer interaction to explore scientific data and scientific-analysis approaches. I illustrate how valuable a little programming ability can free scientists from the constraints of existing tools and can facilitate the development of deeper appreciation data and models. I present examples from a suite of programming languages ranging from C to JavaScript including the Wolfram Language. JavaScript is valuable for sharing tools and insight (hopefully) with others because it is integrated into one of the most powerful communication tools in human history, the web browser. Although too much of that power is often spent on distracting advertisements, the underlying computation and graphics engines are efficient, flexible, and almost universally available in desktop and mobile computing platforms. Many are working to fulfill the browser's potential to become the most effective tool for interactive study. Open-source frameworks for visualizing everything from algorithms to data are available, but advance rapidly. One strategy for dealing with swiftly changing tools is to adopt common, open data formats that are easily adapted (often by framework or tool developers). I illustrate the use of animation and interaction in research and teaching with examples from earthquake seismology.

Taxiing, Take-Off, and Landing Simulation of the High Speed Civil Transport Aircraft

NASA Technical Reports Server (NTRS)

Reaves, Mercedes C.; Horta, Lucas G.

1999-01-01

The aircraft industry jointly with NASA is studying enabling technologies for higher speed, longer range aircraft configurations. Higher speeds, higher temperatures, and aerodynamics are driving these newer aircraft configurations towards long, slender, flexible fuselages. Aircraft response during ground operations, although often overlooked, is a concern due to the increased fuselage flexibility. This paper discusses modeling and simulation of the High Speed Civil Transport aircraft during taxiing, take-off, and landing. Finite element models of the airframe for various configurations are used and combined with nonlinear landing gear models to provide a simulation tool to study responses to different ground input conditions. A commercial computer simulation program is used to numerically integrate the equations of motion and to compute estimates of the responses using an existing runway profile. Results show aircraft responses exceeding safe acceptable human response levels.

Towards a flexible middleware for context-aware pervasive and wearable systems.

PubMed

Muro, Marco; Amoretti, Michele; Zanichelli, Francesco; Conte, Gianni

2012-11-01

Ambient intelligence and wearable computing call for innovative hardware and software technologies, including a highly capable, flexible and efficient middleware, allowing for the reuse of existing pervasive applications when developing new ones. In the considered application domain, middleware should also support self-management, interoperability among different platforms, efficient communications, and context awareness. In the on-going "everything is networked" scenario scalability appears as a very important issue, for which the peer-to-peer (P2P) paradigm emerges as an appealing solution for connecting software components in an overlay network, allowing for efficient and balanced data distribution mechanisms. In this paper, we illustrate how all these concepts can be placed into a theoretical tool, called networked autonomic machine (NAM), implemented into a NAM-based middleware, and evaluated against practical problems of pervasive computing.

Aeroelastic Analysis of a Flexible Wing Wind Tunnel Model with Variable Camber Continuous Trailing Edge Flap Design

NASA Technical Reports Server (NTRS)

Nguyen, Nhan; Ting, Eric; Lebofsky, Sonia

2015-01-01

This paper presents data analysis of a flexible wing wind tunnel model with a variable camber continuous trailing edge flap (VCCTEF) design for drag minimization tested at the University of Washington Aeronautical Laboratory (UWAL). The wind tunnel test was designed to explore the relative merit of the VCCTEF concept for improved cruise efficiency through the use of low-cost aeroelastic model test techniques. The flexible wing model is a 10%-scale model of a typical transport wing and is constructed of woven fabric composites and foam core. The wing structural stiffness in bending is tailored to be half of the stiffness of a Boeing 757-era transport wing while the torsional stiffness is about the same. This stiffness reduction results in a wing tip deflection of about 10% of the wing semi-span. The VCCTEF is a multi-segment flap design having three chordwise camber segments and five spanwise flap sections for a total of 15 individual flap elements. The three chordwise camber segments can be positioned appropriately to create a desired trailing edge camber. Elastomeric material is used to cover the gaps in between the spanwise flap sections, thereby creating a continuous trailing edge. Wind tunnel data analysis conducted previously shows that the VCCTEF can achieve a drag reduction of up to 6.31% and an improvement in the lift-to-drag ratio (L=D) of up to 4.85%. A method for estimating the bending and torsional stiffnesses of the flexible wingUWAL wind tunnel model from static load test data is presented. The resulting estimation indicates that the stiffness of the flexible wing is significantly stiffer in torsion than in bending by as much as 9 to 1. The lift prediction for the flexible wing is computed by a coupled aerodynamic-structural model. The coupled model is developed by coupling a conceptual aerodynamic tool Vorlax with a finite-element model of the flexible wing via an automated geometry deformation tool. Based on the comparison of the lift curve slope, the lift prediction for the rigid wing is in good agreement with the estimated lift coefficients derived from the wind tunnel test data. Due to the movement of the VCCTEF during the wind tunnel test, uncertainty in the lift prediction due to the indicated variations of the VCCTEF deflection is studied. The results show a significant spread in the lift prediction which contradicts the consistency in the aerodynamic measurements, thus suggesting that the indicated variations as measured by the VICON system may not be reliable. The lift prediction of the flexible wing agrees very well with the measured lift curve for the baseline configuration. The computed bending deflection and wash-out twist of the flexible wing also match reasonably well with the aeroelastic deflection measurements. The results demonstrate the validity of the aerodynamic-structural tool for use to analyze aerodynamic performance of flexible wings.

Computer-composite mapping for geologists

USGS Publications Warehouse

van Driel, J.N.

1980-01-01

A computer program for overlaying maps has been tested and evaluated as a means for producing geologic derivative maps. Four maps of the Sugar House Quadrangle, Utah, were combined, using the Multi-Scale Data Analysis and Mapping Program, in a single composite map that shows the relative stability of the land surface during earthquakes. Computer-composite mapping can provide geologists with a powerful analytical tool and a flexible graphic display technique. Digitized map units can be shown singly, grouped with different units from the same map, or combined with units from other source maps to produce composite maps. The mapping program permits the user to assign various values to the map units and to specify symbology for the final map. Because of its flexible storage, easy manipulation, and capabilities of graphic output, the composite-mapping technique can readily be applied to mapping projects in sedimentary and crystalline terranes, as well as to maps showing mineral resource potential. ?? 1980 Springer-Verlag New York Inc.

EggLib: processing, analysis and simulation tools for population genetics and genomics

PubMed Central

2012-01-01

Background With the considerable growth of available nucleotide sequence data over the last decade, integrated and flexible analytical tools have become a necessity. In particular, in the field of population genetics, there is a strong need for automated and reliable procedures to conduct repeatable and rapid polymorphism analyses, coalescent simulations, data manipulation and estimation of demographic parameters under a variety of scenarios. Results In this context, we present EggLib (Evolutionary Genetics and Genomics Library), a flexible and powerful C++/Python software package providing efficient and easy to use computational tools for sequence data management and extensive population genetic analyses on nucleotide sequence data. EggLib is a multifaceted project involving several integrated modules: an underlying computationally efficient C++ library (which can be used independently in pure C++ applications); two C++ programs; a Python package providing, among other features, a high level Python interface to the C++ library; and the egglib script which provides direct access to pre-programmed Python applications. Conclusions EggLib has been designed aiming to be both efficient and easy to use. A wide array of methods are implemented, including file format conversion, sequence alignment edition, coalescent simulations, neutrality tests and estimation of demographic parameters by Approximate Bayesian Computation (ABC). Classes implementing different demographic scenarios for ABC analyses can easily be developed by the user and included to the package. EggLib source code is distributed freely under the GNU General Public License (GPL) from its website http://egglib.sourceforge.net/ where a full documentation and a manual can also be found and downloaded. PMID:22494792

EggLib: processing, analysis and simulation tools for population genetics and genomics.

PubMed

De Mita, Stéphane; Siol, Mathieu

2012-04-11

With the considerable growth of available nucleotide sequence data over the last decade, integrated and flexible analytical tools have become a necessity. In particular, in the field of population genetics, there is a strong need for automated and reliable procedures to conduct repeatable and rapid polymorphism analyses, coalescent simulations, data manipulation and estimation of demographic parameters under a variety of scenarios. In this context, we present EggLib (Evolutionary Genetics and Genomics Library), a flexible and powerful C++/Python software package providing efficient and easy to use computational tools for sequence data management and extensive population genetic analyses on nucleotide sequence data. EggLib is a multifaceted project involving several integrated modules: an underlying computationally efficient C++ library (which can be used independently in pure C++ applications); two C++ programs; a Python package providing, among other features, a high level Python interface to the C++ library; and the egglib script which provides direct access to pre-programmed Python applications. EggLib has been designed aiming to be both efficient and easy to use. A wide array of methods are implemented, including file format conversion, sequence alignment edition, coalescent simulations, neutrality tests and estimation of demographic parameters by Approximate Bayesian Computation (ABC). Classes implementing different demographic scenarios for ABC analyses can easily be developed by the user and included to the package. EggLib source code is distributed freely under the GNU General Public License (GPL) from its website http://egglib.sourceforge.net/ where a full documentation and a manual can also be found and downloaded.

Chimera grids in the simulation of three-dimensional flowfields in turbine-blade-coolant passages

NASA Technical Reports Server (NTRS)

Stephens, M. A.; Rimlinger, M. J.; Shih, T. I.-P.; Civinskas, K. C.

1993-01-01

When computing flows inside geometrically complex turbine-blade coolant passages, the structure of the grid system used can affect significantly the overall time and cost required to obtain solutions. This paper addresses this issue while evaluating and developing computational tools for the design and analysis of coolant-passages, and is divided into two parts. In the first part, the various types of structured and unstructured grids are compared in relation to their ability to provide solutions in a timely and cost-effective manner. This comparison shows that the overlapping structured grids, known as Chimera grids, can rival and in some instances exceed the cost-effectiveness of unstructured grids in terms of both the man hours needed to generate grids and the amount of computer memory and CPU time needed to obtain solutions. In the second part, a computational tool utilizing Chimera grids was used to compute the flow and heat transfer in two different turbine-blade coolant passages that contain baffles and numerous pin fins. These computations showed the versatility and flexibility offered by Chimera grids.

EEGLAB, SIFT, NFT, BCILAB, and ERICA: New Tools for Advanced EEG Processing

PubMed Central

Delorme, Arnaud; Mullen, Tim; Kothe, Christian; Akalin Acar, Zeynep; Bigdely-Shamlo, Nima; Vankov, Andrey; Makeig, Scott

2011-01-01

We describe a set of complementary EEG data collection and processing tools recently developed at the Swartz Center for Computational Neuroscience (SCCN) that connect to and extend the EEGLAB software environment, a freely available and readily extensible processing environment running under Matlab. The new tools include (1) a new and flexible EEGLAB STUDY design facility for framing and performing statistical analyses on data from multiple subjects; (2) a neuroelectromagnetic forward head modeling toolbox (NFT) for building realistic electrical head models from available data; (3) a source information flow toolbox (SIFT) for modeling ongoing or event-related effective connectivity between cortical areas; (4) a BCILAB toolbox for building online brain-computer interface (BCI) models from available data, and (5) an experimental real-time interactive control and analysis (ERICA) environment for real-time production and coordination of interactive, multimodal experiments. PMID:21687590

The Design of Modular Web-Based Collaboration

NASA Astrophysics Data System (ADS)

Intapong, Ploypailin; Settapat, Sittapong; Kaewkamnerdpong, Boonserm; Achalakul, Tiranee

Online collaborative systems are popular communication channels as the systems allow people from various disciplines to interact and collaborate with ease. The systems provide communication tools and services that can be integrated on the web; consequently, the systems are more convenient to use and easier to install. Nevertheless, most of the currently available systems are designed according to some specific requirements and cannot be straightforwardly integrated into various applications. This paper provides the design of a new collaborative platform, which is component-based and re-configurable. The platform is called the Modular Web-based Collaboration (MWC). MWC shares the same concept as computer supported collaborative work (CSCW) and computer-supported collaborative learning (CSCL), but it provides configurable tools for online collaboration. Each tool module can be integrated into users' web applications freely and easily. This makes collaborative system flexible, adaptable and suitable for online collaboration.

Collaboration technology and space science

NASA Technical Reports Server (NTRS)

Leiner, Barry M.; Brown, R. L.; Haines, R. F.

1990-01-01

A summary of available collaboration technologies and their applications to space science is presented as well as investigations into remote coaching paradigms and the role of a specific collaboration tool for distributed task coordination in supporting such teleoperations. The applicability and effectiveness of different communication media and tools in supporting remote coaching are investigated. One investigation concerns a distributed check-list, a computer-based tool that allows a group of people, e.g., onboard crew, ground based investigator, and mission control, to synchronize their actions while providing full flexibility for the flight crew to set the pace and remain on their operational schedule. This autonomy is shown to contribute to morale and productivity.

Numerical analysis of the flexible roll forming of an automotive component from high strength steel

NASA Astrophysics Data System (ADS)

Abeyrathna, B.; Abvabi, A.; Rolfe, B.; Taube, R.; Weiss, M.

2016-11-01

Conventional roll forming is limited to components with uniform cross-section; the recently developed flexible roll forming (FRF) process can be used to form components which vary in both width and depth. It has been suggested that this process can be used to manufacture automotive components from Ultra High Strength Steel (UHSS) which has limited tensile elongation. In the flexible roll forming process, the pre-cut blank is fed through a set of rolls; some rolls are computer-numerically controlled (CNC) to follow the 3D contours of the part and hence parts with a variable cross-section can be produced. This paper introduces a new flexible roll forming technique which can be used to form a complex shape with the minimum tooling requirements. In this method, the pre-cut blank is held between two dies and the whole system moves back and forth past CNC forming rolls. The forming roll changes its angle and position in each pass to incrementally form the part. In this work, the process is simulated using the commercial software package Copra FEA. The distribution of total strain and final part quality are investigated as well as related shape defects observed in the process. Different tooling concepts are used to improve the strain distribution and hence the part quality.

Understanding Glocal Learning Spaces. An Empirical Study of Languaging and Transmigrant Positions in the Virtual Classroom

ERIC Educational Resources Information Center

Messina Dahlberg, Giulia; Bagga-Gupta, Sangeeta

2014-01-01

The use of digital tools like computers and tablets in institutional learning arenas give rise to forms of flexibility where time and space boundaries become diffuse. Online learning sites are understood as being crucial today, especially in large parts of the Global North, where anyone anywhere potentially can become a student and have access to…

Navy Medical Information Storage and Retrieval System: Navy MEDISTARS. TR-1-71-Part 2, Manual of Indexing Terms; First Edition.

ERIC Educational Resources Information Center

Ramsey-Klee, Diane M.

A computer-based information storage and retrieval system was designed and implemented for processing Navy neuropsychiatric case history reports. The system design objectives were to produce a dynamic and flexible medical information processing tool. The system that was designed has been given the name NAVY MEDical Information STorage and…

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

Hagberg, Aric; Swart, Pieter; S Chult, Daniel

NetworkX is a Python language package for exploration and analysis of networks and network algorithms. The core package provides data structures for representing many types of networks, or graphs, including simple graphs, directed graphs, and graphs with parallel edges and self loops. The nodes in NetworkX graphs can be any (hashable) Python object and edges can contain arbitrary data; this flexibility mades NetworkX ideal for representing networks found in many different scientific fields. In addition to the basic data structures many graph algorithms are implemented for calculating network properties and structure measures: shortest paths, betweenness centrality, clustering, and degree distributionmore » and many more. NetworkX can read and write various graph formats for eash exchange with existing data, and provides generators for many classic graphs and popular graph models, such as the Erdoes-Renyi, Small World, and Barabasi-Albert models, are included. The ease-of-use and flexibility of the Python programming language together with connection to the SciPy tools make NetworkX a powerful tool for scientific computations. We discuss some of our recent work studying synchronization of coupled oscillators to demonstrate how NetworkX enables research in the field of computational networks.« less

Kernel methods and flexible inference for complex stochastic dynamics

NASA Astrophysics Data System (ADS)

Capobianco, Enrico

2008-07-01

Approximation theory suggests that series expansions and projections represent standard tools for random process applications from both numerical and statistical standpoints. Such instruments emphasize the role of both sparsity and smoothness for compression purposes, the decorrelation power achieved in the expansion coefficients space compared to the signal space, and the reproducing kernel property when some special conditions are met. We consider these three aspects central to the discussion in this paper, and attempt to analyze the characteristics of some known approximation instruments employed in a complex application domain such as financial market time series. Volatility models are often built ad hoc, parametrically and through very sophisticated methodologies. But they can hardly deal with stochastic processes with regard to non-Gaussianity, covariance non-stationarity or complex dependence without paying a big price in terms of either model mis-specification or computational efficiency. It is thus a good idea to look at other more flexible inference tools; hence the strategy of combining greedy approximation and space dimensionality reduction techniques, which are less dependent on distributional assumptions and more targeted to achieve computationally efficient performances. Advantages and limitations of their use will be evaluated by looking at algorithmic and model building strategies, and by reporting statistical diagnostics.

A Flexible and Non-instrusive Approach for Computing Complex Structural Coverage Metrics

NASA Technical Reports Server (NTRS)

Whalen, Michael W.; Person, Suzette J.; Rungta, Neha; Staats, Matt; Grijincu, Daniela

2015-01-01

Software analysis tools and techniques often leverage structural code coverage information to reason about the dynamic behavior of software. Existing techniques instrument the code with the required structural obligations and then monitor the execution of the compiled code to report coverage. Instrumentation based approaches often incur considerable runtime overhead for complex structural coverage metrics such as Modified Condition/Decision (MC/DC). Code instrumentation, in general, has to be approached with great care to ensure it does not modify the behavior of the original code. Furthermore, instrumented code cannot be used in conjunction with other analyses that reason about the structure and semantics of the code under test. In this work, we introduce a non-intrusive preprocessing approach for computing structural coverage information. It uses a static partial evaluation of the decisions in the source code and a source-to-bytecode mapping to generate the information necessary to efficiently track structural coverage metrics during execution. Our technique is flexible; the results of the preprocessing can be used by a variety of coverage-driven software analysis tasks, including automated analyses that are not possible for instrumented code. Experimental results in the context of symbolic execution show the efficiency and flexibility of our nonintrusive approach for computing code coverage information

Computational Ion Optics Design Evaluations

NASA Technical Reports Server (NTRS)

Malone, Shane P.; Soulas, George C.

2004-01-01

Ion optics computational models are invaluable tools in the design of ion optics systems. In this study a new computational model developed by an outside vendor for use at the NASA Glenn Research Center (GRC) is presented. This computational model is a gun code that has been modified to model the plasma sheaths both upstream and downstream of the ion optics. The model handles multiple species (e.g. singly and doubly-charged ions) and includes a charge-exchange model to support erosion estimations. The model uses commercially developed solid design and meshing software to allow high flexibility in ion optics geometric configurations. The results from this computational model are applied to the NEXT project to investigate the effects of crossover impingement erosion seen during the 2000-hour wear test.

Teleoperation of steerable flexible needles by combining kinesthetic and vibratory feedback.

PubMed

Pacchierotti, Claudio; Abayazid, Momen; Misra, Sarthak; Prattichizzo, Domenico

2014-01-01

Needle insertion in soft-tissue is a minimally invasive surgical procedure that demands high accuracy. In this respect, robotic systems with autonomous control algorithms have been exploited as the main tool to achieve high accuracy and reliability. However, for reasons of safety and responsibility, autonomous robotic control is often not desirable. Therefore, it is necessary to focus also on techniques enabling clinicians to directly control the motion of the surgical tools. In this work, we address that challenge and present a novel teleoperated robotic system able to steer flexible needles. The proposed system tracks the position of the needle using an ultrasound imaging system and computes needle's ideal position and orientation to reach a given target. The master haptic interface then provides the clinician with mixed kinesthetic-vibratory navigation cues to guide the needle toward the computed ideal position and orientation. Twenty participants carried out an experiment of teleoperated needle insertion into a soft-tissue phantom, considering four different experimental conditions. Participants were provided with either mixed kinesthetic-vibratory feedback or mixed kinesthetic-visual feedback. Moreover, we considered two different ways of computing ideal position and orientation of the needle: with or without set-points. Vibratory feedback was found more effective than visual feedback in conveying navigation cues, with a mean targeting error of 0.72 mm when using set-points, and of 1.10 mm without set-points.

A meta-analysis of pedagogical tools used in introductory programming courses

NASA Astrophysics Data System (ADS)

Trees, Frances P.

Programming is recognized as being challenging for teachers to teach and difficult for students to learn. For decades, computer science educators have looked at innovative approaches by creating pedagogical software tools that attempt to facilitate both the teaching of and the learning of programming. This dissertation investigates the motivations for the integration of pedagogical tools in introductory programming courses and the characteristics that are perceived to contribute to the effectiveness of these tools. The study employs three research stages that examine the tool characteristics and their use. The first stage surveys teachers who use pedagogical tools in an introductory programming course. The second interviews teachers to explore the survey results in more detail and to add greater depth into the choice and use of pedagogical tools in the introductory programming class. The third interviews tool developers to provide an explanatory insight of the tool and the motivation for its creation. The results indicate that the pedagogical tools perceived to be effective share common characteristics: They provide an environment that is manageable, flexible and visual; they provide for active engagement in learning activities and support programming in small pieces; they allow for an easy transition to subsequent courses and more robust environments; they provide technical support and resource materials. The results of this study also indicate that recommendations from other computer science educators have a strong impact on a teacher's initial tool choice for an introductory programming course. This study informs present and future tool developers of the characteristics that the teachers perceive to contribute to the effectiveness of a pedagogical tool and how to present their tools to encourage a more efficient and more effective widespread adoption of the tool into the teacher's curriculum. The teachers involved in this study are actively involved in the computer science education community. The results of this study, based on the perceptions of these computer science educators, provide guidance to those educators choosing to introduce a new pedagogical tool into their programming course.

Experimental and analytical investigation of active loads control for aircraft landing gear

NASA Technical Reports Server (NTRS)

Morris, D. L.; Mcgehee, J. R.

1983-01-01

A series hydraulic, active loads control main landing gear from a light, twin-engine civil aircraft was investigated. Tests included landing impact and traversal of simulated runway roughness. It is shown that the active gear is feasible and very effective in reducing the force transmitted to the airframe. Preliminary validation of a multidegree of freedom active gear flexible airframe takeoff and landing analysis computer program, which may be used as a design tool for active gear systems, is accomplished by comparing experimental and computed data for the passive and active gears.

A flexible spatial scan statistic with a restricted likelihood ratio for detecting disease clusters.

PubMed

Tango, Toshiro; Takahashi, Kunihiko

2012-12-30

Spatial scan statistics are widely used tools for detection of disease clusters. Especially, the circular spatial scan statistic proposed by Kulldorff (1997) has been utilized in a wide variety of epidemiological studies and disease surveillance. However, as it cannot detect noncircular, irregularly shaped clusters, many authors have proposed different spatial scan statistics, including the elliptic version of Kulldorff's scan statistic. The flexible spatial scan statistic proposed by Tango and Takahashi (2005) has also been used for detecting irregularly shaped clusters. However, this method sets a feasible limitation of a maximum of 30 nearest neighbors for searching candidate clusters because of heavy computational load. In this paper, we show a flexible spatial scan statistic implemented with a restricted likelihood ratio proposed by Tango (2008) to (1) eliminate the limitation of 30 nearest neighbors and (2) to have surprisingly much less computational time than the original flexible spatial scan statistic. As a side effect, it is shown to be able to detect clusters with any shape reasonably well as the relative risk of the cluster becomes large via Monte Carlo simulation. We illustrate the proposed spatial scan statistic with data on mortality from cerebrovascular disease in the Tokyo Metropolitan area, Japan. Copyright © 2012 John Wiley & Sons, Ltd.

Intelligent Manufacturing of Commercial Optics Final Report CRADA No. TC-0313-92

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

Taylor, J. S.; Pollicove, H.

The project combined the research and development efforts of LLNL and the University of Rochester Center for Manufacturing Optics (COM), to develop a new generation of flexible computer controlled optics· grinding machines. COM's principal near term development effort is to commercialize the OPTICAM-SM, a new prototype spherical grinding machine. A crucial requirement for commercializing the OPTICAM-SM is the development of a predictable and repeatable material removal process ( deterministic micro-grinding) that yields high quality surfaces that minimize non-deterministic polishing. OPTICAM machine tools and the fabrication process development studies are part of COM' s response to the DOD (ARPA) request tomore » implement a modernization strategy for revitalizing the U.S. optics manufacturing base. This project was entered into in order to develop a new generation of :flexible, computer-controlled optics grinding machines.« less

Overview of computational control research at UT Austin

NASA Technical Reports Server (NTRS)

Bong, Wie

1989-01-01

An overview of current research activities at UT Austin is presented to discuss certain technical issues in the following areas: (1) Computer-Aided Nonlinear Control Design: In this project, the describing function method is employed for the nonlinear control analysis and design of a flexible spacecraft equipped with pulse modulated reaction jets. INCA program has been enhanced to allow the numerical calculation of describing functions as well as the nonlinear limit cycle analysis capability in the frequency domain; (2) Robust Linear Quadratic Gaussian (LQG) Compensator Synthesis: Robust control design techniques and software tools are developed for flexible space structures with parameter uncertainty. In particular, an interactive, robust multivariable control design capability is being developed for INCA program; and (3) LQR-Based Autonomous Control System for the Space Station: In this project, real time implementation of LQR-based autonomous control system is investigated for the space station with time-varying inertias and with significant multibody dynamic interactions.

A new DoD initiative: the Computational Research and Engineering Acquisition Tools and Environments (CREATE) program

NASA Astrophysics Data System (ADS)

Arevalo, S.; Atwood, C.; Bell, P.; Blacker, T. D.; Dey, S.; Fisher, D.; Fisher, D. A.; Genalis, P.; Gorski, J.; Harris, A.; Hill, K.; Hurwitz, M.; Kendall, R. P.; Meakin, R. L.; Morton, S.; Moyer, E. T.; Post, D. E.; Strawn, R.; Veldhuizen, D. v.; Votta, L. G.; Wynn, S.; Zelinski, G.

2008-07-01

In FY2008, the U.S. Department of Defense (DoD) initiated the Computational Research and Engineering Acquisition Tools and Environments (CREATE) program, a 360M program with a two-year planning phase and a ten-year execution phase. CREATE will develop and deploy three computational engineering tool sets for DoD acquisition programs to use to design aircraft, ships and radio-frequency antennas. The planning and execution of CREATE are based on the 'lessons learned' from case studies of large-scale computational science and engineering projects. The case studies stress the importance of a stable, close-knit development team; a focus on customer needs and requirements; verification and validation; flexible and agile planning, management, and development processes; risk management; realistic schedules and resource levels; balanced short- and long-term goals and deliverables; and stable, long-term support by the program sponsor. Since it began in FY2008, the CREATE program has built a team and project structure, developed requirements and begun validating them, identified candidate products, established initial connections with the acquisition programs, begun detailed project planning and development, and generated the initial collaboration infrastructure necessary for success by its multi-institutional, multidisciplinary teams.

Variability of the Cyclin-Dependent Kinase 2 Flexibility Without Significant Change in the Initial Conformation of the Protein or Its Environment; a Computational Study.

PubMed

Taghizadeh, Mohammad; Goliaei, Bahram; Madadkar-Sobhani, Armin

2016-06-01

Protein flexibility, which has been referred as a dynamic behavior has various roles in proteins' functions. Furthermore, for some developed tools in bioinformatics, such as protein-protein docking software, considering the protein flexibility, causes a higher degree of accuracy. Through undertaking the present work, we have accomplished the quantification plus analysis of the variations in the human Cyclin Dependent Kinase 2 (hCDK2) protein flexibility without affecting a significant change in its initial environment or the protein per se. The main goal of the present research was to calculate variations in the flexibility for each residue of the hCDK2, analysis of their flexibility variations through clustering, and to investigate the functional aspects of the residues with high flexibility variations. Using Gromacs package (version 4.5.4), three independent molecular dynamics (MD) simulations of the hCDK2 protein (PDB ID: 1HCL) was accomplished with no significant changes in their initial environments, structures, or conformations, followed by Root Mean Square Fluctuations (RMSF) calculation of these MD trajectories. The amount of variations in these three curves of RMSF was calculated using two formulas. More than 50% of the variation in the flexibility (the distance between the maximum and the minimum amount of the RMSF) was found at the region of Val-154. As well, there are other major flexibility fluctuations in other residues. These residues were mostly positioned in the vicinity of the functional residues. The subsequent works were done, as followed by clustering all hCDK2 residues into four groups considering the amount of their variability with respect to flexibility and their position in the RMSF curves. This work has introduced a new class of flexibility aspect of the proteins' residues. It could also help designing and engineering proteins, with introducing a new dynamic aspect of hCDK2, and accordingly, for the other similar globular proteins. In addition, it could provide a better computational calculation of the protein flexibility, which is, especially important in the comparative studies of the proteins' flexibility.

Variability of the Cyclin-Dependent Kinase 2 Flexibility Without Significant Change in the Initial Conformation of the Protein or Its Environment; a Computational Study

PubMed Central

Taghizadeh, Mohammad; Goliaei, Bahram; Madadkar-Sobhani, Armin

2016-01-01

Background Protein flexibility, which has been referred as a dynamic behavior has various roles in proteins’ functions. Furthermore, for some developed tools in bioinformatics, such as protein-protein docking software, considering the protein flexibility, causes a higher degree of accuracy. Through undertaking the present work, we have accomplished the quantification plus analysis of the variations in the human Cyclin Dependent Kinase 2 (hCDK2) protein flexibility without affecting a significant change in its initial environment or the protein per se. Objectives The main goal of the present research was to calculate variations in the flexibility for each residue of the hCDK2, analysis of their flexibility variations through clustering, and to investigate the functional aspects of the residues with high flexibility variations. Materials and Methods Using Gromacs package (version 4.5.4), three independent molecular dynamics (MD) simulations of the hCDK2 protein (PDB ID: 1HCL) was accomplished with no significant changes in their initial environments, structures, or conformations, followed by Root Mean Square Fluctuations (RMSF) calculation of these MD trajectories. The amount of variations in these three curves of RMSF was calculated using two formulas. Results More than 50% of the variation in the flexibility (the distance between the maximum and the minimum amount of the RMSF) was found at the region of Val-154. As well, there are other major flexibility fluctuations in other residues. These residues were mostly positioned in the vicinity of the functional residues. The subsequent works were done, as followed by clustering all hCDK2 residues into four groups considering the amount of their variability with respect to flexibility and their position in the RMSF curves. Conclusions This work has introduced a new class of flexibility aspect of the proteins’ residues. It could also help designing and engineering proteins, with introducing a new dynamic aspect of hCDK2, and accordingly, for the other similar globular proteins. In addition, it could provide a better computational calculation of the protein flexibility, which is, especially important in the comparative studies of the proteins’ flexibility. PMID:28959320

High-order computational fluid dynamics tools for aircraft design

PubMed Central

Wang, Z. J.

2014-01-01

Most forecasts predict an annual airline traffic growth rate between 4.5 and 5% in the foreseeable future. To sustain that growth, the environmental impact of aircraft cannot be ignored. Future aircraft must have much better fuel economy, dramatically less greenhouse gas emissions and noise, in addition to better performance. Many technical breakthroughs must take place to achieve the aggressive environmental goals set up by governments in North America and Europe. One of these breakthroughs will be physics-based, highly accurate and efficient computational fluid dynamics and aeroacoustics tools capable of predicting complex flows over the entire flight envelope and through an aircraft engine, and computing aircraft noise. Some of these flows are dominated by unsteady vortices of disparate scales, often highly turbulent, and they call for higher-order methods. As these tools will be integral components of a multi-disciplinary optimization environment, they must be efficient to impact design. Ultimately, the accuracy, efficiency, robustness, scalability and geometric flexibility will determine which methods will be adopted in the design process. This article explores these aspects and identifies pacing items. PMID:25024419

RGmatch: matching genomic regions to proximal genes in omics data integration.

PubMed

Furió-Tarí, Pedro; Conesa, Ana; Tarazona, Sonia

2016-11-22

The integrative analysis of multiple genomics data often requires that genome coordinates-based signals have to be associated with proximal genes. The relative location of a genomic region with respect to the gene (gene area) is important for functional data interpretation; hence algorithms that match regions to genes should be able to deliver insight into this information. In this work we review the tools that are publicly available for making region-to-gene associations. We also present a novel method, RGmatch, a flexible and easy-to-use Python tool that computes associations either at the gene, transcript, or exon level, applying a set of rules to annotate each region-gene association with the region location within the gene. RGmatch can be applied to any organism as long as genome annotation is available. Furthermore, we qualitatively and quantitatively compare RGmatch to other tools. RGmatch simplifies the association of a genomic region with its closest gene. At the same time, it is a powerful tool because the rules used to annotate these associations are very easy to modify according to the researcher's specific interests. Some important differences between RGmatch and other similar tools already in existence are RGmatch's flexibility, its wide range of user options, compatibility with any annotatable organism, and its comprehensive and user-friendly output.

JPRS Report, Soviet Union, International Affairs.

DTIC Science & Technology

1987-11-27

becoming very relevant in this connection. One direct consequence is the need for closer interaction not only of the technical and production potential... personal computers, systems for numeric programmed control for functional machine tools and flexible produc- tion modules, programmable master... personality of the collective director— his enterprising nature, his ability to work in a new way (or his willing- ness to learn). "Even today many

Building flexible real-time systems using the Flex language

NASA Technical Reports Server (NTRS)

Kenny, Kevin B.; Lin, Kwei-Jay

1991-01-01

The design and implementation of a real-time programming language called Flex, which is a derivative of C++, are presented. It is shown how different types of timing requirements might be expressed and enforced in Flex, how they might be fulfilled in a flexible way using different program models, and how the programming environment can help in making binding and scheduling decisions. The timing constraint primitives in Flex are easy to use yet powerful enough to define both independent and relative timing constraints. Program models like imprecise computation and performance polymorphism can carry out flexible real-time programs. In addition, programmers can use a performance measurement tool that produces statistically correct timing models to predict the expected execution time of a program and to help make binding decisions. A real-time programming environment is also presented.

TethysCluster: A comprehensive approach for harnessing cloud resources for hydrologic modeling

NASA Astrophysics Data System (ADS)

Nelson, J.; Jones, N.; Ames, D. P.

2015-12-01

Advances in water resources modeling are improving the information that can be supplied to support decisions affecting the safety and sustainability of society. However, as water resources models become more sophisticated and data-intensive they require more computational power to run. Purchasing and maintaining the computing facilities needed to support certain modeling tasks has been cost-prohibitive for many organizations. With the advent of the cloud, the computing resources needed to address this challenge are now available and cost-effective, yet there still remains a significant technical barrier to leverage these resources. This barrier inhibits many decision makers and even trained engineers from taking advantage of the best science and tools available. Here we present the Python tools TethysCluster and CondorPy, that have been developed to lower the barrier to model computation in the cloud by providing (1) programmatic access to dynamically scalable computing resources, (2) a batch scheduling system to queue and dispatch the jobs to the computing resources, (3) data management for job inputs and outputs, and (4) the ability to dynamically create, submit, and monitor computing jobs. These Python tools leverage the open source, computing-resource management, and job management software, HTCondor, to offer a flexible and scalable distributed-computing environment. While TethysCluster and CondorPy can be used independently to provision computing resources and perform large modeling tasks, they have also been integrated into Tethys Platform, a development platform for water resources web apps, to enable computing support for modeling workflows and decision-support systems deployed as web apps.

Dynamo: a flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments.

PubMed

Castaño-Díez, Daniel; Kudryashev, Mikhail; Arheit, Marcel; Stahlberg, Henning

2012-05-01

Dynamo is a new software package for subtomogram averaging of cryo Electron Tomography (cryo-ET) data with three main goals: first, Dynamo allows user-transparent adaptation to a variety of high-performance computing platforms such as GPUs or CPU clusters. Second, Dynamo implements user-friendliness through GUI interfaces and scripting resources. Third, Dynamo offers user-flexibility through a plugin API. Besides the alignment and averaging procedures, Dynamo includes native tools for visualization and analysis of results and data, as well as support for third party visualization software, such as Chimera UCSF or EMAN2. As a demonstration of these functionalities, we studied bacterial flagellar motors and showed automatically detected classes with absent and present C-rings. Subtomogram averaging is a common task in current cryo-ET pipelines, which requires extensive computational resources and follows a well-established workflow. However, due to the data diversity, many existing packages offer slight variations of the same algorithm to improve results. One of the main purposes behind Dynamo is to provide explicit tools to allow the user the insertion of custom designed procedures - or plugins - to replace or complement the native algorithms in the different steps of the processing pipeline for subtomogram averaging without the burden of handling parallelization. Custom scripts that implement new approaches devised by the user are integrated into the Dynamo data management system, so that they can be controlled by the GUI or the scripting capacities. Dynamo executables do not require licenses for third party commercial software. Sources, executables and documentation are freely distributed on http://www.dynamo-em.org. Copyright © 2012 Elsevier Inc. All rights reserved.

Mergeomics: a web server for identifying pathological pathways, networks, and key regulators via multidimensional data integration.

PubMed

Arneson, Douglas; Bhattacharya, Anindya; Shu, Le; Mäkinen, Ville-Petteri; Yang, Xia

2016-09-09

Human diseases are commonly the result of multidimensional changes at molecular, cellular, and systemic levels. Recent advances in genomic technologies have enabled an outpour of omics datasets that capture these changes. However, separate analyses of these various data only provide fragmented understanding and do not capture the holistic view of disease mechanisms. To meet the urgent needs for tools that effectively integrate multiple types of omics data to derive biological insights, we have developed Mergeomics, a computational pipeline that integrates multidimensional disease association data with functional genomics and molecular networks to retrieve biological pathways, gene networks, and central regulators critical for disease development. To make the Mergeomics pipeline available to a wider research community, we have implemented an online, user-friendly web server ( http://mergeomics. idre.ucla.edu/ ). The web server features a modular implementation of the Mergeomics pipeline with detailed tutorials. Additionally, it provides curated genomic resources including tissue-specific expression quantitative trait loci, ENCODE functional annotations, biological pathways, and molecular networks, and offers interactive visualization of analytical results. Multiple computational tools including Marker Dependency Filtering (MDF), Marker Set Enrichment Analysis (MSEA), Meta-MSEA, and Weighted Key Driver Analysis (wKDA) can be used separately or in flexible combinations. User-defined summary-level genomic association datasets (e.g., genetic, transcriptomic, epigenomic) related to a particular disease or phenotype can be uploaded and computed real-time to yield biologically interpretable results, which can be viewed online and downloaded for later use. Our Mergeomics web server offers researchers flexible and user-friendly tools to facilitate integration of multidimensional data into holistic views of disease mechanisms in the form of tissue-specific key regulators, biological pathways, and gene networks.

CBRAIN: a web-based, distributed computing platform for collaborative neuroimaging research

PubMed Central

Sherif, Tarek; Rioux, Pierre; Rousseau, Marc-Etienne; Kassis, Nicolas; Beck, Natacha; Adalat, Reza; Das, Samir; Glatard, Tristan; Evans, Alan C.

2014-01-01

The Canadian Brain Imaging Research Platform (CBRAIN) is a web-based collaborative research platform developed in response to the challenges raised by data-heavy, compute-intensive neuroimaging research. CBRAIN offers transparent access to remote data sources, distributed computing sites, and an array of processing and visualization tools within a controlled, secure environment. Its web interface is accessible through any modern browser and uses graphical interface idioms to reduce the technical expertise required to perform large-scale computational analyses. CBRAIN's flexible meta-scheduling has allowed the incorporation of a wide range of heterogeneous computing sites, currently including nine national research High Performance Computing (HPC) centers in Canada, one in Korea, one in Germany, and several local research servers. CBRAIN leverages remote computing cycles and facilitates resource-interoperability in a transparent manner for the end-user. Compared with typical grid solutions available, our architecture was designed to be easily extendable and deployed on existing remote computing sites with no tool modification, administrative intervention, or special software/hardware configuration. As October 2013, CBRAIN serves over 200 users spread across 53 cities in 17 countries. The platform is built as a generic framework that can accept data and analysis tools from any discipline. However, its current focus is primarily on neuroimaging research and studies of neurological diseases such as Autism, Parkinson's and Alzheimer's diseases, Multiple Sclerosis as well as on normal brain structure and development. This technical report presents the CBRAIN Platform, its current deployment and usage and future direction. PMID:24904400

CBRAIN: a web-based, distributed computing platform for collaborative neuroimaging research.

PubMed

Sherif, Tarek; Rioux, Pierre; Rousseau, Marc-Etienne; Kassis, Nicolas; Beck, Natacha; Adalat, Reza; Das, Samir; Glatard, Tristan; Evans, Alan C

2014-01-01

The Canadian Brain Imaging Research Platform (CBRAIN) is a web-based collaborative research platform developed in response to the challenges raised by data-heavy, compute-intensive neuroimaging research. CBRAIN offers transparent access to remote data sources, distributed computing sites, and an array of processing and visualization tools within a controlled, secure environment. Its web interface is accessible through any modern browser and uses graphical interface idioms to reduce the technical expertise required to perform large-scale computational analyses. CBRAIN's flexible meta-scheduling has allowed the incorporation of a wide range of heterogeneous computing sites, currently including nine national research High Performance Computing (HPC) centers in Canada, one in Korea, one in Germany, and several local research servers. CBRAIN leverages remote computing cycles and facilitates resource-interoperability in a transparent manner for the end-user. Compared with typical grid solutions available, our architecture was designed to be easily extendable and deployed on existing remote computing sites with no tool modification, administrative intervention, or special software/hardware configuration. As October 2013, CBRAIN serves over 200 users spread across 53 cities in 17 countries. The platform is built as a generic framework that can accept data and analysis tools from any discipline. However, its current focus is primarily on neuroimaging research and studies of neurological diseases such as Autism, Parkinson's and Alzheimer's diseases, Multiple Sclerosis as well as on normal brain structure and development. This technical report presents the CBRAIN Platform, its current deployment and usage and future direction.

Dynamics modelling and Hybrid Suppression Control of space robots performing cooperative object manipulation

NASA Astrophysics Data System (ADS)

Zarafshan, P.; Moosavian, S. Ali A.

2013-10-01

Dynamics modelling and control of multi-body space robotic systems composed of rigid and flexible elements is elaborated here. Control of such systems is highly complicated due to severe under-actuated condition caused by flexible elements, and an inherent uneven nonlinear dynamics. Therefore, developing a compact dynamics model with the requirement of limited computations is extremely useful for controller design, also to develop simulation studies in support of design improvement, and finally for practical implementations. In this paper, the Rigid-Flexible Interactive dynamics Modelling (RFIM) approach is introduced as a combination of Lagrange and Newton-Euler methods, in which the motion equations of rigid and flexible members are separately developed in an explicit closed form. These equations are then assembled and solved simultaneously at each time step by considering the mutual interaction and constraint forces. The proposed approach yields a compact model rather than common accumulation approach that leads to a massive set of equations in which the dynamics of flexible elements is united with the dynamics equations of rigid members. To reveal such merits of this new approach, a Hybrid Suppression Control (HSC) for a cooperative object manipulation task will be proposed, and applied to usual space systems. A Wheeled Mobile Robotic (WMR) system with flexible appendages as a typical space rover is considered which contains a rigid main body equipped with two manipulating arms and two flexible solar panels, and next a Space Free Flying Robotic system (SFFR) with flexible members is studied. Modelling verification of these complicated systems is vigorously performed using ANSYS and ADAMS programs, while the limited computations of RFIM approach provides an efficient tool for the proposed controller design. Furthermore, it will be shown that the vibrations of the flexible solar panels results in disturbing forces on the base which may produce undesirable errors and perturb the object manipulation task. So, it is shown that these effects can be significantly eliminated by the proposed Hybrid Suppression Control algorithm.

Static Aeroelastic and Longitudinal Trim Model of Flexible Wing Aircraft Using Finite-Element Vortex-Lattice Coupled Solution

NASA Technical Reports Server (NTRS)

Ting, Eric; Nguyen, Nhan; Trinh, Khanh

2014-01-01

This paper presents a static aeroelastic model and longitudinal trim model for the analysis of a flexible wing transport aircraft. The static aeroelastic model is built using a structural model based on finite-element modeling and coupled to an aerodynamic model that uses vortex-lattice solution. An automatic geometry generation tool is used to close the loop between the structural and aerodynamic models. The aeroelastic model is extended for the development of a three degree-of-freedom longitudinal trim model for an aircraft with flexible wings. The resulting flexible aircraft longitudinal trim model is used to simultaneously compute the static aeroelastic shape for the aircraft model and the longitudinal state inputs to maintain an aircraft trim state. The framework is applied to an aircraft model based on the NASA Generic Transport Model (GTM) with wing structures allowed to flexibly deformed referred to as the Elastically Shaped Aircraft Concept (ESAC). The ESAC wing mass and stiffness properties are based on a baseline "stiff" values representative of current generation transport aircraft.

Virtual Sensor for Kinematic Estimation of Flexible Links in Parallel Robots

PubMed Central

Cabanes, Itziar; Mancisidor, Aitziber; Pinto, Charles

2017-01-01

The control of flexible link parallel manipulators is still an open area of research, endpoint trajectory tracking being one of the main challenges in this type of robot. The flexibility and deformations of the limbs make the estimation of the Tool Centre Point (TCP) position a challenging one. Authors have proposed different approaches to estimate this deformation and deduce the location of the TCP. However, most of these approaches require expensive measurement systems or the use of high computational cost integration methods. This work presents a novel approach based on a virtual sensor which can not only precisely estimate the deformation of the flexible links in control applications (less than 2% error), but also its derivatives (less than 6% error in velocity and 13% error in acceleration) according to simulation results. The validity of the proposed Virtual Sensor is tested in a Delta Robot, where the position of the TCP is estimated based on the Virtual Sensor measurements with less than a 0.03% of error in comparison with the flexible approach developed in ADAMS Multibody Software. PMID:28832510

NeuroManager: a workflow analysis based simulation management engine for computational neuroscience

PubMed Central

Stockton, David B.; Santamaria, Fidel

2015-01-01

We developed NeuroManager, an object-oriented simulation management software engine for computational neuroscience. NeuroManager automates the workflow of simulation job submissions when using heterogeneous computational resources, simulators, and simulation tasks. The object-oriented approach (1) provides flexibility to adapt to a variety of neuroscience simulators, (2) simplifies the use of heterogeneous computational resources, from desktops to super computer clusters, and (3) improves tracking of simulator/simulation evolution. We implemented NeuroManager in MATLAB, a widely used engineering and scientific language, for its signal and image processing tools, prevalence in electrophysiology analysis, and increasing use in college Biology education. To design and develop NeuroManager we analyzed the workflow of simulation submission for a variety of simulators, operating systems, and computational resources, including the handling of input parameters, data, models, results, and analyses. This resulted in 22 stages of simulation submission workflow. The software incorporates progress notification, automatic organization, labeling, and time-stamping of data and results, and integrated access to MATLAB's analysis and visualization tools. NeuroManager provides users with the tools to automate daily tasks, and assists principal investigators in tracking and recreating the evolution of research projects performed by multiple people. Overall, NeuroManager provides the infrastructure needed to improve workflow, manage multiple simultaneous simulations, and maintain provenance of the potentially large amounts of data produced during the course of a research project. PMID:26528175

NeuroManager: a workflow analysis based simulation management engine for computational neuroscience.

PubMed

Stockton, David B; Santamaria, Fidel

2015-01-01

We developed NeuroManager, an object-oriented simulation management software engine for computational neuroscience. NeuroManager automates the workflow of simulation job submissions when using heterogeneous computational resources, simulators, and simulation tasks. The object-oriented approach (1) provides flexibility to adapt to a variety of neuroscience simulators, (2) simplifies the use of heterogeneous computational resources, from desktops to super computer clusters, and (3) improves tracking of simulator/simulation evolution. We implemented NeuroManager in MATLAB, a widely used engineering and scientific language, for its signal and image processing tools, prevalence in electrophysiology analysis, and increasing use in college Biology education. To design and develop NeuroManager we analyzed the workflow of simulation submission for a variety of simulators, operating systems, and computational resources, including the handling of input parameters, data, models, results, and analyses. This resulted in 22 stages of simulation submission workflow. The software incorporates progress notification, automatic organization, labeling, and time-stamping of data and results, and integrated access to MATLAB's analysis and visualization tools. NeuroManager provides users with the tools to automate daily tasks, and assists principal investigators in tracking and recreating the evolution of research projects performed by multiple people. Overall, NeuroManager provides the infrastructure needed to improve workflow, manage multiple simultaneous simulations, and maintain provenance of the potentially large amounts of data produced during the course of a research project.

INTELLIGENT COMPUTING SYSTEM FOR RESERVOIR ANALYSIS AND RISK ASSESSMENT OF THE RED RIVER FORMATION

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

Kenneth D. Luff

2002-06-30

Integrated software has been written that comprises the tool kit for the Intelligent Computing System (ICS). Luff Exploration Company is applying these tools for analysis of carbonate reservoirs in the southern Williston Basin. The integrated software programs are designed to be used by small team consisting of an engineer, geologist and geophysicist. The software tools are flexible and robust, allowing application in many environments for hydrocarbon reservoirs. Keystone elements of the software tools include clustering and neural-network techniques. The tools are used to transform seismic attribute data to reservoir characteristics such as storage (phi-h), probable oil-water contacts, structural depths andmore » structural growth history. When these reservoir characteristics are combined with neural network or fuzzy logic solvers, they can provide a more complete description of the reservoir. This leads to better estimates of hydrocarbons in place, areal limits and potential for infill or step-out drilling. These tools were developed and tested using seismic, geologic and well data from the Red River Play in Bowman County, North Dakota and Harding County, South Dakota. The geologic setting for the Red River Formation is shallow-shelf carbonate at a depth from 8000 to 10,000 ft.« less

INTELLIGENT COMPUTING SYSTEM FOR RESERVOIR ANALYSIS AND RISK ASSESSMENT OF THE RED RIVER FORMATION

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

Kenneth D. Luff

2002-09-30

Integrated software has been written that comprises the tool kit for the Intelligent Computing System (ICS). Luff Exploration Company is applying these tools for analysis of carbonate reservoirs in the southern Williston Basin. The integrated software programs are designed to be used by small team consisting of an engineer, geologist and geophysicist. The software tools are flexible and robust, allowing application in many environments for hydrocarbon reservoirs. Keystone elements of the software tools include clustering and neural-network techniques. The tools are used to transform seismic attribute data to reservoir characteristics such as storage (phi-h), probable oil-water contacts, structural depths andmore » structural growth history. When these reservoir characteristics are combined with neural network or fuzzy logic solvers, they can provide a more complete description of the reservoir. This leads to better estimates of hydrocarbons in place, areal limits and potential for infill or step-out drilling. These tools were developed and tested using seismic, geologic and well data from the Red River Play in Bowman County, North Dakota and Harding County, South Dakota. The geologic setting for the Red River Formation is shallow-shelf carbonate at a depth from 8000 to 10,000 ft.« less

Advanced construction management for lunar base construction - Surface operations planner

NASA Technical Reports Server (NTRS)

Kehoe, Robert P.

1992-01-01

The study proposes a conceptual solution and lays the framework for developing a new, sophisticated and intelligent tool for a lunar base construction crew to use. This concept integrates expert systems for critical decision making, virtual reality for training, logistics and laydown optimization, automated productivity measurements, and an advanced scheduling tool to form a unique new planning tool. The concept features extensive use of computers and expert systems software to support the actual work, while allowing the crew to control the project from the lunar surface. Consideration is given to a logistics data base, laydown area management, flexible critical progress scheduler, video simulation of assembly tasks, and assembly information and tracking documentation.

SNAVA-A real-time multi-FPGA multi-model spiking neural network simulation architecture.

PubMed

Sripad, Athul; Sanchez, Giovanny; Zapata, Mireya; Pirrone, Vito; Dorta, Taho; Cambria, Salvatore; Marti, Albert; Krishnamourthy, Karthikeyan; Madrenas, Jordi

2018-01-01

Spiking Neural Networks (SNN) for Versatile Applications (SNAVA) simulation platform is a scalable and programmable parallel architecture that supports real-time, large-scale, multi-model SNN computation. This parallel architecture is implemented in modern Field-Programmable Gate Arrays (FPGAs) devices to provide high performance execution and flexibility to support large-scale SNN models. Flexibility is defined in terms of programmability, which allows easy synapse and neuron implementation. This has been achieved by using a special-purpose Processing Elements (PEs) for computing SNNs, and analyzing and customizing the instruction set according to the processing needs to achieve maximum performance with minimum resources. The parallel architecture is interfaced with customized Graphical User Interfaces (GUIs) to configure the SNN's connectivity, to compile the neuron-synapse model and to monitor SNN's activity. Our contribution intends to provide a tool that allows to prototype SNNs faster than on CPU/GPU architectures but significantly cheaper than fabricating a customized neuromorphic chip. This could be potentially valuable to the computational neuroscience and neuromorphic engineering communities. Copyright © 2017 Elsevier Ltd. All rights reserved.

RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps

PubMed Central

Drory Retwitzer, Matan; Polishchuk, Maya; Churkin, Elena; Kifer, Ilona; Yakhini, Zohar; Barash, Danny

2015-01-01

Searching for RNA sequence-structure patterns is becoming an essential tool for RNA practitioners. Novel discoveries of regulatory non-coding RNAs in targeted organisms and the motivation to find them across a wide range of organisms have prompted the use of computational RNA pattern matching as an enhancement to sequence similarity. State-of-the-art programs differ by the flexibility of patterns allowed as queries and by their simplicity of use. In particular—no existing method is available as a user-friendly web server. A general program that searches for RNA sequence-structure patterns is RNA Structator. However, it is not available as a web server and does not provide the option to allow flexible gap pattern representation with an upper bound of the gap length being specified at any position in the sequence. Here, we introduce RNAPattMatch, a web-based application that is user friendly and makes sequence/structure RNA queries accessible to practitioners of various background and proficiency. It also extends RNA Structator and allows a more flexible variable gaps representation, in addition to analysis of results using energy minimization methods. RNAPattMatch service is available at http://www.cs.bgu.ac.il/rnapattmatch. A standalone version of the search tool is also available to download at the site. PMID:25940619

An efficient representation of spatial information for expert reasoning in robotic vehicles

NASA Technical Reports Server (NTRS)

Scott, Steven; Interrante, Mark

1987-01-01

The previous generation of robotic vehicles and drones was designed for a specific task, with limited flexibility in executing their mission. This limited flexibility arises because the robotic vehicles do not possess the intelligence and knowledge upon which to make significant tactical decisions. Current development of robotic vehicles is toward increased intelligence and capabilities, adapting to a changing environment and altering mission objectives. The latest techniques in artificial intelligence (AI) are being employed to increase the robotic vehicle's intelligent decision-making capabilities. This document describes the design of the SARA spatial database tool, which is composed of request parser, reasoning, computations, and database modules that collectively manage and derive information useful for robotic vehicles.

Managing the CMS Data and Monte Carlo Processing during LHC Run 2

NASA Astrophysics Data System (ADS)

Wissing, C.; CMS Collaboration

2017-10-01

In order to cope with the challenges expected during the LHC Run 2 CMS put in a number of enhancements into the main software packages and the tools used for centrally managed processing. In the presentation we will highlight these improvements that allow CMS to deal with the increased trigger output rate, the increased pileup and the evolution in computing technology. The overall system aims at high flexibility, improved operational flexibility and largely automated procedures. The tight coupling of workflow classes to types of sites has been drastically relaxed. Reliable and high-performing networking between most of the computing sites and the successful deployment of a data-federation allow the execution of workflows using remote data access. That required the development of a largely automatized system to assign workflows and to handle necessary pre-staging of data. Another step towards flexibility has been the introduction of one large global HTCondor Pool for all types of processing workflows and analysis jobs. Besides classical Grid resources also some opportunistic resources as well as Cloud resources have been integrated into that Pool, which gives reach to more than 200k CPU cores.

LOS selective fading and AN/FRC-170(V) radio hybrid computer simulation phase A report

NASA Astrophysics Data System (ADS)

Klukis, M. K.; Lyon, T. I.; Walker, R.

1981-09-01

This report documents results of the first phase of modeling, simulation and study of the dual diversity AN/FRC-170(V) radio and frequency selective fading line of sight channel. Both hybrid computer and circuit technologies were used to develop a fast, accurate and flexible simulation tool to investigate changes and proposed improvements to the design of the AN/FRC-170(V) radio. In addition to the simulation study, a remote hybrid computer terminal was provided to DCEC for interactive study of the modeled radio and channel. Simulated performance of the radio for Rayleigh, line of sight two ray channels, and additive noise are included in the report.

The microcomputer scientific software series 9: user's guide to Geo-CLM: geostatistical interpolation of the historical climatic record in the Lake States.

Treesearch

Margaret R. Holdaway

1994-01-01

Describes Geo-CLM, a computer application (for Mac or DOS) whose primary aim is to perform multiple kriging runs to interpolate the historic climatic record at research plots in the Lake States. It is an exploration and analysis tool. Addition capabilities include climatic databases, a flexible test mode, cross validation, lat/long conversion, English/metric units,...

Proceedings of the Workshop on Computational Aspects in the Control of Flexible Systems, part 1

NASA Technical Reports Server (NTRS)

Taylor, Lawrence W., Jr. (Compiler)

1989-01-01

Control/Structures Integration program software needs, computer aided control engineering for flexible spacecraft, computer aided design, computational efficiency and capability, modeling and parameter estimation, and control synthesis and optimization software for flexible structures and robots are among the topics discussed.

Cloud-Based Computational Tools for Earth Science Applications

NASA Astrophysics Data System (ADS)

Arendt, A. A.; Fatland, R.; Howe, B.

2015-12-01

Earth scientists are increasingly required to think across disciplines and utilize a wide range of datasets in order to solve complex environmental challenges. Although significant progress has been made in distributing data, researchers must still invest heavily in developing computational tools to accommodate their specific domain. Here we document our development of lightweight computational data systems aimed at enabling rapid data distribution, analytics and problem solving tools for Earth science applications. Our goal is for these systems to be easily deployable, scalable and flexible to accommodate new research directions. As an example we describe "Ice2Ocean", a software system aimed at predicting runoff from snow and ice in the Gulf of Alaska region. Our backend components include relational database software to handle tabular and vector datasets, Python tools (NumPy, pandas and xray) for rapid querying of gridded climate data, and an energy and mass balance hydrological simulation model (SnowModel). These components are hosted in a cloud environment for direct access across research teams, and can also be accessed via API web services using a REST interface. This API is a vital component of our system architecture, as it enables quick integration of our analytical tools across disciplines, and can be accessed by any existing data distribution centers. We will showcase several data integration and visualization examples to illustrate how our system has expanded our ability to conduct cross-disciplinary research.

Computer Aided Battery Engineering Consortium

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

Pesaran, Ahmad

A multi-national lab collaborative team was assembled that includes experts from academia and industry to enhance recently developed Computer-Aided Battery Engineering for Electric Drive Vehicles (CAEBAT)-II battery crush modeling tools and to develop microstructure models for electrode design - both computationally efficient. Task 1. The new Multi-Scale Multi-Domain model framework (GH-MSMD) provides 100x to 1,000x computation speed-up in battery electrochemical/thermal simulation while retaining modularity of particles and electrode-, cell-, and pack-level domains. The increased speed enables direct use of the full model in parameter identification. Task 2. Mechanical-electrochemical-thermal (MECT) models for mechanical abuse simulation were simultaneously coupled, enabling simultaneous modelingmore » of electrochemical reactions during the short circuit, when necessary. The interactions between mechanical failure and battery cell performance were studied, and the flexibility of the model for various batteries structures and loading conditions was improved. Model validation is ongoing to compare with test data from Sandia National Laboratories. The ABDT tool was established in ANSYS. Task 3. Microstructural modeling was conducted to enhance next-generation electrode designs. This 3- year project will validate models for a variety of electrodes, complementing Advanced Battery Research programs. Prototype tools have been developed for electrochemical simulation and geometric reconstruction.« less

Real-time 3D radiation risk assessment supporting simulation of work in nuclear environments.

PubMed

Szőke, I; Louka, M N; Bryntesen, T R; Bratteli, J; Edvardsen, S T; RøEitrheim, K K; Bodor, K

2014-06-01

This paper describes the latest developments at the Institute for Energy Technology (IFE) in Norway, in the field of real-time 3D (three-dimensional) radiation risk assessment for the support of work simulation in nuclear environments. 3D computer simulation can greatly facilitate efficient work planning, briefing, and training of workers. It can also support communication within and between work teams, and with advisors, regulators, the media and public, at all the stages of a nuclear installation's lifecycle. Furthermore, it is also a beneficial tool for reviewing current work practices in order to identify possible gaps in procedures, as well as to support the updating of international recommendations, dissemination of experience, and education of the current and future generation of workers.IFE has been involved in research and development into the application of 3D computer simulation and virtual reality (VR) technology to support work in radiological environments in the nuclear sector since the mid 1990s. During this process, two significant software tools have been developed, the VRdose system and the Halden Planner, and a number of publications have been produced to contribute to improving the safety culture in the nuclear industry.This paper describes the radiation risk assessment techniques applied in earlier versions of the VRdose system and the Halden Planner, for visualising radiation fields and calculating dose, and presents new developments towards implementing a flexible and up-to-date dosimetric package in these 3D software tools, based on new developments in the field of radiation protection. The latest versions of these 3D tools are capable of more accurate risk estimation, permit more flexibility via a range of user choices, and are applicable to a wider range of irradiation situations than their predecessors.

CFD Fuel Slosh Modeling of Fluid-Structure Interaction in Spacecraft Propellant Tanks with Diaphragms

NASA Technical Reports Server (NTRS)

Sances, Dillon J.; Gangadharan, Sathya N.; Sudermann, James E.; Marsell, Brandon

2010-01-01

Liquid sloshing within spacecraft propellant tanks causes rapid energy dissipation at resonant modes, which can result in attitude destabilization of the vehicle. Identifying resonant slosh modes currently requires experimental testing and mechanical pendulum analogs to characterize the slosh dynamics. Computational Fluid Dynamics (CFD) techniques have recently been validated as an effective tool for simulating fuel slosh within free-surface propellant tanks. Propellant tanks often incorporate an internal flexible diaphragm to separate ullage and propellant which increases modeling complexity. A coupled fluid-structure CFD model is required to capture the damping effects of a flexible diaphragm on the propellant. ANSYS multidisciplinary engineering software employs a coupled solver for analyzing two-way Fluid Structure Interaction (FSI) cases such as the diaphragm propellant tank system. Slosh models generated by ANSYS software are validated by experimental lateral slosh test results. Accurate data correlation would produce an innovative technique for modeling fuel slosh within diaphragm tanks and provide an accurate and efficient tool for identifying resonant modes and the slosh dynamic response.

Flexible Micro-and Nano-Patterning Tools for Photonics

DTIC Science & Technology

2016-03-10

AFRL-AFOSR-VA-TR-2016-0125 Flexible Micro- and Nano -Patterning Tools for Photonics Henry Smith LUMARRAY INC. 15 WARD ST. SOMERVILLE, MA 21434228 03...14-01-2015 4.  TITLE AND SUBTITLE Flexible Micro- and Nano -Patterning Tools for Photonics - OSD STTR Phase 2 5a.  CONTRACT NUMBER FA9550-12-C-0082 5b...2016https://livelink.ebs.afrl.af.mil/livelink/llisapi.dll DISTRIBUTION A: Distribution approved for public release. FLEXIBLE MICRO- AND NANO - PATTERNING

Proceedings of the NATO-Advanced Study Institute on Computer Aided Analysis of Rigid and Flexible Mechanical Systems. Volume 1: Main lectures

NASA Astrophysics Data System (ADS)

Pereira, Manuel S.; Ambrosio, Jorge A. C.

1993-07-01

During the last few years, major scientific progress has been achieved in fields related to computer aided analysis of multibody systems. In view of this progress and recent developments of computer hardware and general purpose software, there is a need to access the current state of art and results from different schools of thought, with the objective of focussing trends in future research. Going back to 1983 when an important NATO-NSF-ARO Advanced Study Institute on Computer Aided Analysis and Optimization of Mechanical Systems was held at the University of Iowa, one may notice that less then 10 years ago the state of art was mainly dwelling on rigid body dynamics. The interest in the dynamic simulation of mechanical systems has steadily increased in recent years coming mainly from the aerospace and automative industries. The development of multibody system analysis formulations have been more recently motivated with the need to include several features such as: real-time simulation capabilities, highly non-linear control devices, work space path planing, active control of machine flexibilities and reliability and accuracy in the analysis results. The need for accurate and efficient analysis tools for design of large and lightweight mechanical systems has driven many research groups in the challenging problem of flexible systems with an increasing interaction with finite element methodologies. Basic approaches to mechanical systems dynamic analysis have recently been presented in several new text books. These publications demonstrate that both recursive and absolute methods still have their proponents to resolve the redundancy encountered in most mechanical systems.

Fast multipurpose Monte Carlo simulation for proton therapy using multi- and many-core CPU architectures.

PubMed

Souris, Kevin; Lee, John Aldo; Sterpin, Edmond

2016-04-01

Accuracy in proton therapy treatment planning can be improved using Monte Carlo (MC) simulations. However the long computation time of such methods hinders their use in clinical routine. This work aims to develop a fast multipurpose Monte Carlo simulation tool for proton therapy using massively parallel central processing unit (CPU) architectures. A new Monte Carlo, called MCsquare (many-core Monte Carlo), has been designed and optimized for the last generation of Intel Xeon processors and Intel Xeon Phi coprocessors. These massively parallel architectures offer the flexibility and the computational power suitable to MC methods. The class-II condensed history algorithm of MCsquare provides a fast and yet accurate method of simulating heavy charged particles such as protons, deuterons, and alphas inside voxelized geometries. Hard ionizations, with energy losses above a user-specified threshold, are simulated individually while soft events are regrouped in a multiple scattering theory. Elastic and inelastic nuclear interactions are sampled from ICRU 63 differential cross sections, thereby allowing for the computation of prompt gamma emission profiles. MCsquare has been benchmarked with the gate/geant4 Monte Carlo application for homogeneous and heterogeneous geometries. Comparisons with gate/geant4 for various geometries show deviations within 2%-1 mm. In spite of the limited memory bandwidth of the coprocessor simulation time is below 25 s for 10(7) primary 200 MeV protons in average soft tissues using all Xeon Phi and CPU resources embedded in a single desktop unit. MCsquare exploits the flexibility of CPU architectures to provide a multipurpose MC simulation tool. Optimized code enables the use of accurate MC calculation within a reasonable computation time, adequate for clinical practice. MCsquare also simulates prompt gamma emission and can thus be used also for in vivo range verification.

LXtoo: an integrated live Linux distribution for the bioinformatics community

PubMed Central

2012-01-01

Background Recent advances in high-throughput technologies dramatically increase biological data generation. However, many research groups lack computing facilities and specialists. This is an obstacle that remains to be addressed. Here, we present a Linux distribution, LXtoo, to provide a flexible computing platform for bioinformatics analysis. Findings Unlike most of the existing live Linux distributions for bioinformatics limiting their usage to sequence analysis and protein structure prediction, LXtoo incorporates a comprehensive collection of bioinformatics software, including data mining tools for microarray and proteomics, protein-protein interaction analysis, and computationally complex tasks like molecular dynamics. Moreover, most of the programs have been configured and optimized for high performance computing. Conclusions LXtoo aims to provide well-supported computing environment tailored for bioinformatics research, reducing duplication of efforts in building computing infrastructure. LXtoo is distributed as a Live DVD and freely available at http://bioinformatics.jnu.edu.cn/LXtoo. PMID:22813356

LXtoo: an integrated live Linux distribution for the bioinformatics community.

PubMed

Yu, Guangchuang; Wang, Li-Gen; Meng, Xiao-Hua; He, Qing-Yu

2012-07-19

Recent advances in high-throughput technologies dramatically increase biological data generation. However, many research groups lack computing facilities and specialists. This is an obstacle that remains to be addressed. Here, we present a Linux distribution, LXtoo, to provide a flexible computing platform for bioinformatics analysis. Unlike most of the existing live Linux distributions for bioinformatics limiting their usage to sequence analysis and protein structure prediction, LXtoo incorporates a comprehensive collection of bioinformatics software, including data mining tools for microarray and proteomics, protein-protein interaction analysis, and computationally complex tasks like molecular dynamics. Moreover, most of the programs have been configured and optimized for high performance computing. LXtoo aims to provide well-supported computing environment tailored for bioinformatics research, reducing duplication of efforts in building computing infrastructure. LXtoo is distributed as a Live DVD and freely available at http://bioinformatics.jnu.edu.cn/LXtoo.

Introduction to the computational structural mechanics testbed

NASA Technical Reports Server (NTRS)

Lotts, C. G.; Greene, W. H.; Mccleary, S. L.; Knight, N. F., Jr.; Paulson, S. S.; Gillian, R. E.

1987-01-01

The Computational Structural Mechanics (CSM) testbed software system based on the SPAR finite element code and the NICE system is described. This software is denoted NICE/SPAR. NICE was developed at Lockheed Palo Alto Research Laboratory and contains data management utilities, a command language interpreter, and a command language definition for integrating engineering computational modules. SPAR is a system of programs used for finite element structural analysis developed for NASA by Lockheed and Engineering Information Systems, Inc. It includes many complementary structural analysis, thermal analysis, utility functions which communicate through a common database. The work on NICE/SPAR was motivated by requirements for a highly modular and flexible structural analysis system to use as a tool in carrying out research in computational methods and exploring computer hardware. Analysis examples are presented which demonstrate the benefits gained from a combination of the NICE command language with a SPAR computational modules.

FOCuS: a metaheuristic algorithm for computing knockouts from genome-scale models for strain optimization.

PubMed

Mutturi, Sarma

2017-06-27

Although handful tools are available for constraint-based flux analysis to generate knockout strains, most of these are either based on bilevel-MIP or its modifications. However, metaheuristic approaches that are known for their flexibility and scalability have been less studied. Moreover, in the existing tools, sectioning of search space to find optimal knocks has not been considered. Herein, a novel computational procedure, termed as FOCuS (Flower-pOllination coupled Clonal Selection algorithm), was developed to find the optimal reaction knockouts from a metabolic network to maximize the production of specific metabolites. FOCuS derives its benefits from nature-inspired flower pollination algorithm and artificial immune system-inspired clonal selection algorithm to converge to an optimal solution. To evaluate the performance of FOCuS, reported results obtained from both MIP and other metaheuristic-based tools were compared in selected case studies. The results demonstrated the robustness of FOCuS irrespective of the size of metabolic network and number of knockouts. Moreover, sectioning of search space coupled with pooling of priority reactions based on their contribution to objective function for generating smaller search space significantly reduced the computational time.

The GLEaMviz computational tool, a publicly available software to explore realistic epidemic spreading scenarios at the global scale

PubMed Central

2011-01-01

Background Computational models play an increasingly important role in the assessment and control of public health crises, as demonstrated during the 2009 H1N1 influenza pandemic. Much research has been done in recent years in the development of sophisticated data-driven models for realistic computer-based simulations of infectious disease spreading. However, only a few computational tools are presently available for assessing scenarios, predicting epidemic evolutions, and managing health emergencies that can benefit a broad audience of users including policy makers and health institutions. Results We present "GLEaMviz", a publicly available software system that simulates the spread of emerging human-to-human infectious diseases across the world. The GLEaMviz tool comprises three components: the client application, the proxy middleware, and the simulation engine. The latter two components constitute the GLEaMviz server. The simulation engine leverages on the Global Epidemic and Mobility (GLEaM) framework, a stochastic computational scheme that integrates worldwide high-resolution demographic and mobility data to simulate disease spread on the global scale. The GLEaMviz design aims at maximizing flexibility in defining the disease compartmental model and configuring the simulation scenario; it allows the user to set a variety of parameters including: compartment-specific features, transition values, and environmental effects. The output is a dynamic map and a corresponding set of charts that quantitatively describe the geo-temporal evolution of the disease. The software is designed as a client-server system. The multi-platform client, which can be installed on the user's local machine, is used to set up simulations that will be executed on the server, thus avoiding specific requirements for large computational capabilities on the user side. Conclusions The user-friendly graphical interface of the GLEaMviz tool, along with its high level of detail and the realism of its embedded modeling approach, opens up the platform to simulate realistic epidemic scenarios. These features make the GLEaMviz computational tool a convenient teaching/training tool as well as a first step toward the development of a computational tool aimed at facilitating the use and exploitation of computational models for the policy making and scenario analysis of infectious disease outbreaks. PMID:21288355

Building Safer Systems With SpecTRM

NASA Technical Reports Server (NTRS)

2003-01-01

System safety, an integral component in software development, often poses a challenge to engineers designing computer-based systems. While the relaxed constraints on software design allow for increased power and flexibility, this flexibility introduces more possibilities for error. As a result, system engineers must identify the design constraints necessary to maintain safety and ensure that the system and software design enforces them. Safeware Engineering Corporation, of Seattle, Washington, provides the information, tools, and techniques to accomplish this task with its Specification Tools and Requirements Methodology (SpecTRM). NASA assisted in developing this engineering toolset by awarding the company several Small Business Innovation Research (SBIR) contracts with Ames Research Center and Langley Research Center. The technology benefits NASA through its applications for Space Station rendezvous and docking. SpecTRM aids system and software engineers in developing specifications for large, complex safety critical systems. The product enables engineers to find errors early in development so that they can be fixed with the lowest cost and impact on the system design. SpecTRM traces both the requirements and design rationale (including safety constraints) throughout the system design and documentation, allowing engineers to build required system properties into the design from the beginning, rather than emphasizing assessment at the end of the development process when changes are limited and costly.System safety, an integral component in software development, often poses a challenge to engineers designing computer-based systems. While the relaxed constraints on software design allow for increased power and flexibility, this flexibility introduces more possibilities for error. As a result, system engineers must identify the design constraints necessary to maintain safety and ensure that the system and software design enforces them. Safeware Engineering Corporation, of Seattle, Washington, provides the information, tools, and techniques to accomplish this task with its Specification Tools and Requirements Methodology (SpecTRM). NASA assisted in developing this engineering toolset by awarding the company several Small Business Innovation Research (SBIR) contracts with Ames Research Center and Langley Research Center. The technology benefits NASA through its applications for Space Station rendezvous and docking. SpecTRM aids system and software engineers in developing specifications for large, complex safety critical systems. The product enables engineers to find errors early in development so that they can be fixed with the lowest cost and impact on the system design. SpecTRM traces both the requirements and design rationale (including safety constraints) throughout the system design and documentation, allowing engineers to build required system properties into the design from the beginning, rather than emphasizing assessment at the end of the development process when changes are limited and costly.

Vacuum-actuated percutaneous insertion/implantation tool for flexible neural probes and interfaces

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

Sheth, Heeral; Bennett, William J.; Pannu, Satinderpall S.

A flexible device insertion tool including an elongated stiffener with one or more suction ports, and a vacuum connector for interfacing the stiffener to a vacuum source, for attaching the flexible device such as a flexible neural probe to the stiffener during insertion by a suction force exerted through the suction ports to, and to release the flexible device by removing the suction force.

Application of desktop computers in nuclear engineering education

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

Graves, H.W. Jr.

1990-01-01

Utilization of desktop computers in the academic environment is based on the same objectives as in the industrial environment - increased quality and efficiency. Desktop computers can be extremely useful teaching tools in two general areas: classroom demonstrations and homework assignments. Although differences in emphasis exist, tutorial programs share many characteristics with interactive software developed for the industrial environment. In the Reactor Design and Fuel Management course at the University of Maryland, several interactive tutorial programs provided by Energy analysis Software Service have been utilized. These programs have been designed to be sufficiently structured to permit an orderly, disciplined solutionmore » to the problem being solved, and yet be flexible enough to accommodate most problem solution options.« less

Parallel Three-Dimensional Computation of Fluid Dynamics and Fluid-Structure Interactions of Ram-Air Parachutes

NASA Technical Reports Server (NTRS)

Tezduyar, Tayfun E.

1998-01-01

This is a final report as far as our work at University of Minnesota is concerned. The report describes our research progress and accomplishments in development of high performance computing methods and tools for 3D finite element computation of aerodynamic characteristics and fluid-structure interactions (FSI) arising in airdrop systems, namely ram-air parachutes and round parachutes. This class of simulations involves complex geometries, flexible structural components, deforming fluid domains, and unsteady flow patterns. The key components of our simulation toolkit are a stabilized finite element flow solver, a nonlinear structural dynamics solver, an automatic mesh moving scheme, and an interface between the fluid and structural solvers; all of these have been developed within a parallel message-passing paradigm.

Complex Source and Radiation Behaviors of Small Elements of Linear and Matrix Flexible Ultrasonic Phased-Array Transducers

NASA Astrophysics Data System (ADS)

Amory, V.; Lhémery, A.

2008-02-01

Inspection of irregular components is problematical: maladjustment of transducer shoes to surfaces causes aberrations. Flexible phased-arrays (FPAs) designed at CEA LIST to maximize contact are driven by adapted delay laws to compensate for irregularities. Optimizing FPA requires simulation tools. The behavior of one element computed by FEM is observed at the surface and its radiation experimentally validated. Efforts for one element prevent from simulating a FPA by FEM. A model is proposed where each element behaves as nonuniform source of stresses. Exact and asymptotic formulas for Lamb problem are used as convolution kernels for longitudinal, transverse and head waves; the latter is of primary importance for angle-T-beam inspections.

Design and experimental validation of a flutter suppression controller for the active flexible wing

NASA Technical Reports Server (NTRS)

Waszak, Martin R.; Srinathkumar, S.

1992-01-01

The synthesis and experimental validation of an active flutter suppression controller for the Active Flexible Wing wind tunnel model is presented. The design is accomplished with traditional root locus and Nyquist methods using interactive computer graphics tools and extensive simulation based analysis. The design approach uses a fundamental understanding of the flutter mechanism to formulate a simple controller structure to meet stringent design specifications. Experimentally, the flutter suppression controller succeeded in simultaneous suppression of two flutter modes, significantly increasing the flutter dynamic pressure despite modeling errors in predicted flutter dynamic pressure and flutter frequency. The flutter suppression controller was also successfully operated in combination with another controller to perform flutter suppression during rapid rolling maneuvers.

An Overview of Modifications Applied to a Turbulence Response Analysis Method for Flexible Aircraft Configurations

NASA Technical Reports Server (NTRS)

Funk, Christie J.

2013-01-01

A software program and associated methodology to study gust loading on aircraft exists for a classification of geometrically simplified flexible configurations. This program consists of a simple aircraft response model with two rigid and three flexible symmetric degrees of freedom and allows for the calculation of various airplane responses due to a discrete one-minus-cosine gust as well as continuous turbulence. Simplifications, assumptions, and opportunities for potential improvements pertaining to the existing software program are first identified, then a revised version of the original software tool is developed with improved methodology to include more complex geometries, additional excitation cases, and output data so as to provide a more useful and accurate tool for gust load analysis. Revisions are made in the categories of aircraft geometry, computation of aerodynamic forces and moments, and implementation of horizontal tail mode shapes. In order to improve the original software program to enhance usefulness, a wing control surface and horizontal tail control surface is added, an extended application of the discrete one-minus-cosine gust input is employed, a supplemental continuous turbulence spectrum is implemented, and a capability to animate the total vehicle deformation response to gust inputs in included. These revisions and enhancements are implemented and an analysis of the results is used to validate the modifications.

Application of enhanced modern structured analysis techniques to Space Station Freedom electric power system requirements

NASA Technical Reports Server (NTRS)

Biernacki, John; Juhasz, John; Sadler, Gerald

1991-01-01

A team of Space Station Freedom (SSF) system engineers are in the process of extensive analysis of the SSF requirements, particularly those pertaining to the electrical power system (EPS). The objective of this analysis is the development of a comprehensive, computer-based requirements model, using an enhanced modern structured analysis methodology (EMSA). Such a model provides a detailed and consistent representation of the system's requirements. The process outlined in the EMSA methodology is unique in that it allows the graphical modeling of real-time system state transitions, as well as functional requirements and data relationships, to be implemented using modern computer-based tools. These tools permit flexible updating and continuous maintenance of the models. Initial findings resulting from the application of EMSA to the EPS have benefited the space station program by linking requirements to design, providing traceability of requirements, identifying discrepancies, and fostering an understanding of the EPS.

Additive manufacturing of materials: Opportunities and challenges

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

Babu, Sudarsanam Suresh; Love, Lonnie J.; Dehoff, Ryan R.

Additive manufacturing (also known as 3D printing) is considered a disruptive technology for producing components with topologically optimized complex geometries as well as functionalities that are not achievable by traditional methods. The realization of the full potential of 3D printing is stifled by a lack of computational design tools, generic material feedstocks, techniques for monitoring thermomechanical processes under in situ conditions, and especially methods for minimizing anisotropic static and dynamic properties brought about by microstructural heterogeneity. In this paper, we discuss the role of interdisciplinary research involving robotics and automation, process control, multiscale characterization of microstructure and properties, and high-performancemore » computational tools to address each of these challenges. In addition, emerging pathways to scale up additive manufacturing of structural materials to large sizes (>1 m) and higher productivities (5–20 kg/h) while maintaining mechanical performance and geometrical flexibility are also discussed.« less

Additive manufacturing of materials: Opportunities and challenges

DOE PAGES

Babu, Sudarsanam Suresh; Love, Lonnie J.; Dehoff, Ryan R.; ...

2015-11-01

Additive manufacturing (also known as 3D printing) is considered a disruptive technology for producing components with topologically optimized complex geometries as well as functionalities that are not achievable by traditional methods. The realization of the full potential of 3D printing is stifled by a lack of computational design tools, generic material feedstocks, techniques for monitoring thermomechanical processes under in situ conditions, and especially methods for minimizing anisotropic static and dynamic properties brought about by microstructural heterogeneity. In this paper, we discuss the role of interdisciplinary research involving robotics and automation, process control, multiscale characterization of microstructure and properties, and high-performancemore » computational tools to address each of these challenges. In addition, emerging pathways to scale up additive manufacturing of structural materials to large sizes (>1 m) and higher productivities (5–20 kg/h) while maintaining mechanical performance and geometrical flexibility are also discussed.« less

Experimental validation of docking and capture using space robotics testbeds

NASA Technical Reports Server (NTRS)

Spofford, John; Schmitz, Eric; Hoff, William

1991-01-01

This presentation describes the application of robotic and computer vision systems to validate docking and capture operations for space cargo transfer vehicles. Three applications are discussed: (1) air bearing systems in two dimensions that yield high quality free-flying, flexible, and contact dynamics; (2) validation of docking mechanisms with misalignment and target dynamics; and (3) computer vision technology for target location and real-time tracking. All the testbeds are supported by a network of engineering workstations for dynamic and controls analyses. Dynamic simulation of multibody rigid and elastic systems are performed with the TREETOPS code. MATRIXx/System-Build and PRO-MATLAB/Simulab are the tools for control design and analysis using classical and modern techniques such as H-infinity and LQG/LTR. SANDY is a general design tool to optimize numerically a multivariable robust compensator with a user-defined structure. Mathematica and Macsyma are used to derive symbolically dynamic and kinematic equations.

Granular materials interacting with thin flexible rods

NASA Astrophysics Data System (ADS)

Neto, Alfredo Gay; Campello, Eduardo M. B.

2017-04-01

In this work, we develop a computational model for the simulation of problems wherein granular materials interact with thin flexible rods. We treat granular materials as a collection of spherical particles following a discrete element method (DEM) approach, while flexible rods are described by a large deformation finite element (FEM) rod formulation. Grain-to-grain, grain-to-rod, and rod-to-rod contacts are fully permitted and resolved. A simple and efficient strategy is proposed for coupling the motion of the two types (discrete and continuum) of materials within an iterative time-stepping solution scheme. Implementation details are shown and discussed. Validity and applicability of the model are assessed by means of a few numerical examples. We believe that robust, efficiently coupled DEM-FEM schemes can be a useful tool to the simulation of problems wherein granular materials interact with thin flexible rods, such as (but not limited to) bombardment of grains on beam structures, flow of granular materials over surfaces covered by threads of hair in many biological processes, flow of grains through filters and strainers in various industrial segregation processes, and many others.

Shipping Science Worldwide with Open Source Containers

NASA Astrophysics Data System (ADS)

Molineaux, J. P.; McLaughlin, B. D.; Pilone, D.; Plofchan, P. G.; Murphy, K. J.

2014-12-01

Scientific applications often present difficult web-hosting needs. Their compute- and data-intensive nature, as well as an increasing need for high-availability and distribution, combine to create a challenging set of hosting requirements. In the past year, advancements in container-based virtualization and related tooling have offered new lightweight and flexible ways to accommodate diverse applications with all the isolation and portability benefits of traditional virtualization. This session will introduce and demonstrate an open-source, single-interface, Platform-as-a-Serivce (PaaS) that empowers application developers to seamlessly leverage geographically distributed, public and private compute resources to achieve highly-available, performant hosting for scientific applications.

An application of nonlinear programming to the design of regulators of a linear-quadratic formulation

NASA Technical Reports Server (NTRS)

Fleming, P.

1983-01-01

A design technique is proposed for linear regulators in which a feedback controller of fixed structure is chosen to minimize an integral quadratic objective function subject to the satisfaction of integral quadratic constraint functions. Application of a nonlinear programming algorithm to this mathematically tractable formulation results in an efficient and useful computer aided design tool. Particular attention is paid to computational efficiency and various recommendations are made. Two design examples illustrate the flexibility of the approach and highlight the special insight afforded to the designer. One concerns helicopter longitudinal dynamics and the other the flight dynamics of an aerodynamically unstable aircraft.

The Effects of Embedded Generative Learning Strategies and Collaboration on Knowledge Acquisition in a Cognitive Flexibility-Based Computer Learning Environment

DTIC Science & Technology

1998-08-07

cognitive flexibility theory and generative learning theory which focus primarily on the individual student’s cognitive development , collaborative... develop "Handling Transfusion Hazards," a computer program based upon cognitive flexibility theory principles. The Program: Handling Transfusion Hazards...computer program was developed according to cognitive flexibility theory principles. A generative version was then developed by embedding

Computer literacy: Where are nurse educators on the continuum?

PubMed

Hanley, Elizabeth

2006-01-01

Computers are becoming ubiquitous in health and education, and it is expected that nurses from undergraduate nursing programmes are computer literate when they enter the workforce. Similarly nurse educators are expected to be computer literate to model the use of information technology in their workplace. They are expected to use email for communication and a range of computer applications for presentation of course materials and reports. Additionally, as more courses are delivered in flexible mode, educators require more comprehensive computing skills, including confidence and competence in a range of applications. A cohort of nurse educators from one tertiary institution was surveyed to assess their perceived computer literacy and how they attained this. A questionnaire that covered seven domains of computer literacy was used to assess this. The results were illuminating and identified specific training needs for this group. Their perceived lack of skill with Groupwise email and the student database program are of concern as these are essential tools for nurse educators at this polytechnic.

LabVIEW: a software system for data acquisition, data analysis, and instrument control.

PubMed

Kalkman, C J

1995-01-01

Computer-based data acquisition systems play an important role in clinical monitoring and in the development of new monitoring tools. LabVIEW (National Instruments, Austin, TX) is a data acquisition and programming environment that allows flexible acquisition and processing of analog and digital data. The main feature that distinguishes LabVIEW from other data acquisition programs is its highly modular graphical programming language, "G," and a large library of mathematical and statistical functions. The advantage of graphical programming is that the code is flexible, reusable, and self-documenting. Subroutines can be saved in a library and reused without modification in other programs. This dramatically reduces development time and enables researchers to develop or modify their own programs. LabVIEW uses a large amount of processing power and computer memory, thus requiring a powerful computer. A large-screen monitor is desirable when developing larger applications. LabVIEW is excellently suited for testing new monitoring paradigms, analysis algorithms, or user interfaces. The typical LabVIEW user is the researcher who wants to develop a new monitoring technique, a set of new (derived) variables by integrating signals from several existing patient monitors, closed-loop control of a physiological variable, or a physiological simulator.

Automatic Tension Adjuster For Flexible-Shaft Grinder

NASA Technical Reports Server (NTRS)

Burley, Richard K.; Hoult, William S.

1990-01-01

Flexible shaft of grinding tool automatically maintained in tension by air pressure. Probelike tool bent to reach hard-to-reach areas for grinding and polishing. Unless shaft held in tension, however, it rubs against its sheath, overheating and wearing out quickly. By taking up slack in flexible cable, tension adjuster reduces friction and enables tool to operate more efficiently, in addition to lengthening operating life.

Practical experience with graphical user interfaces and object-oriented design in the clinical laboratory.

PubMed

Wells, I G; Cartwright, R Y; Farnan, L P

1993-12-15

The computing strategy in our laboratories evolved from research in Artificial Intelligence, and is based on powerful software tools running on high performance desktop computers with a graphical user interface. This allows most tasks to be regarded as design problems rather than implementation projects, and both rapid prototyping and an object-oriented approach to be employed during the in-house development and enhancement of the laboratory information systems. The practical application of this strategy is discussed, with particular reference to the system designer, the laboratory user and the laboratory customer. Routine operation covers five departments, and the systems are stable, flexible and well accepted by the users. Client-server computing, currently undergoing final trials, is seen as the key to further development, and this approach to Pathology computing has considerable potential for the future.

Performance evaluation of the Engineering Analysis and Data Systems (EADS) 2

NASA Technical Reports Server (NTRS)

Debrunner, Linda S.

1994-01-01

The Engineering Analysis and Data System (EADS)II (1) was installed in March 1993 to provide high performance computing for science and engineering at Marshall Space Flight Center (MSFC). EADS II increased the computing capabilities over the existing EADS facility in the areas of throughput and mass storage. EADS II includes a Vector Processor Compute System (VPCS), a Virtual Memory Compute System (CFS), a Common Output System (COS), as well as Image Processing Station, Mini Super Computers, and Intelligent Workstations. These facilities are interconnected by a sophisticated network system. This work considers only the performance of the VPCS and the CFS. The VPCS is a Cray YMP. The CFS is implemented on an RS 6000 using the UniTree Mass Storage System. To better meet the science and engineering computing requirements, EADS II must be monitored, its performance analyzed, and appropriate modifications for performance improvement made. Implementing this approach requires tool(s) to assist in performance monitoring and analysis. In Spring 1994, PerfStat 2.0 was purchased to meet these needs for the VPCS and the CFS. PerfStat(2) is a set of tools that can be used to analyze both historical and real-time performance data. Its flexible design allows significant user customization. The user identifies what data is collected, how it is classified, and how it is displayed for evaluation. Both graphical and tabular displays are supported. The capability of the PerfStat tool was evaluated, appropriate modifications to EADS II to optimize throughput and enhance productivity were suggested and implemented, and the effects of these modifications on the systems performance were observed. In this paper, the PerfStat tool is described, then its use with EADS II is outlined briefly. Next, the evaluation of the VPCS, as well as the modifications made to the system are described. Finally, conclusions are drawn and recommendations for future worked are outlined.

Planning low-carbon electricity systems under uncertainty considering operational flexibility and smart grid technologies.

PubMed

Moreno, Rodrigo; Street, Alexandre; Arroyo, José M; Mancarella, Pierluigi

2017-08-13

Electricity grid operators and planners need to deal with both the rapidly increasing integration of renewables and an unprecedented level of uncertainty that originates from unknown generation outputs, changing commercial and regulatory frameworks aimed to foster low-carbon technologies, the evolving availability of market information on feasibility and costs of various technologies, etc. In this context, there is a significant risk of locking-in to inefficient investment planning solutions determined by current deterministic engineering practices that neither capture uncertainty nor represent the actual operation of the planned infrastructure under high penetration of renewables. We therefore present an alternative optimization framework to plan electricity grids that deals with uncertain scenarios and represents increased operational details. The presented framework is able to model the effects of an array of flexible, smart grid technologies that can efficiently displace the need for conventional solutions. We then argue, and demonstrate via the proposed framework and an illustrative example, that proper modelling of uncertainty and operational constraints in planning is key to valuing operationally flexible solutions leading to optimal investment in a smart grid context. Finally, we review the most used practices in power system planning under uncertainty, highlight the challenges of incorporating operational aspects and advocate the need for new and computationally effective optimization tools to properly value the benefits of flexible, smart grid solutions in planning. Such tools are essential to accelerate the development of a low-carbon energy system and investment in the most appropriate portfolio of renewable energy sources and complementary enabling smart technologies.This article is part of the themed issue 'Energy management: flexibility, risk and optimization'. © 2017 The Author(s).

Development of a New Data Tool for Computing Launch and Landing Availability with Respect to Surface Weather

NASA Technical Reports Server (NTRS)

Burns, K. Lee; Altino, Karen

2008-01-01

The Marshall Space Flight Center Natural Environments Branch has a long history of expertise in the modeling and computation of statistical launch availabilities with respect to weather conditions. Their existing data analysis product, the Atmospheric Parametric Risk Assessment (APRA) tool, computes launch availability given an input set of vehicle hardware and/or operational weather constraints by calculating the climatological probability of exceeding the specified constraint limits, APRA has been used extensively to provide the Space Shuttle program the ability to estimate impacts that various proposed design modifications would have to overall launch availability. The model accounts for both seasonal and diurnal variability at a single geographic location and provides output probabilities for a single arbitrary launch attempt. Recently, the Shuttle program has shown interest in having additional capabilities added to the APRA model, including analysis of humidity parameters, inclusion of landing site weather to produce landing availability, and concurrent analysis of multiple sites, to assist in operational landing site selection. In addition, the Constellation program has also expressed interest in the APRA tool, and has requested several additional capabilities to address some Constellation-specific issues, both in the specification and verification of design requirements and in the development of operations concepts. The combined scope of the requested capability enhancements suggests an evolution of the model beyond a simple revision process. Development has begun for a new data analysis tool that will satisfy the requests of both programs. This new tool, Probabilities of Atmospheric Conditions and Environmental Risk (PACER), will provide greater flexibility and significantly enhanced functionality compared to the currently existing tool.

Flexible Description Language for HPC based Processing of Remote Sense Data

NASA Astrophysics Data System (ADS)

Nandra, Constantin; Gorgan, Dorian; Bacu, Victor

2016-04-01

When talking about Big Data, the most challenging aspect lays in processing them in order to gain new insight, find new patterns and gain knowledge from them. This problem is likely most apparent in the case of Earth Observation (EO) data. With ever higher numbers of data sources and increasing data acquisition rates, dealing with EO data is indeed a challenge [1]. Geoscientists should address this challenge by using flexible and efficient tools and platforms. To answer this trend, the BigEarth project [2] aims to combine the advantages of high performance computing solutions with flexible processing description methodologies in order to reduce both task execution times and task definition time and effort. As a component of the BigEarth platform, WorDeL (Workflow Description Language) [3] is intended to offer a flexible, compact and modular approach to the task definition process. WorDeL, unlike other description alternatives such as Python or shell scripts, is oriented towards the description topologies, using them as abstractions for the processing programs. This feature is intended to make it an attractive alternative for users lacking in programming experience. By promoting modular designs, WorDeL not only makes the processing descriptions more user-readable and intuitive, but also helps organizing the processing tasks into independent sub-tasks, which can be executed in parallel on multi-processor platforms in order to improve execution times. As a BigEarth platform [4] component, WorDeL represents the means by which the user interacts with the system, describing processing algorithms in terms of existing operators and workflows [5], which are ultimately translated into sets of executable commands. The WorDeL language has been designed to help in the definition of compute-intensive, batch tasks which can be distributed and executed on high-performance, cloud or grid-based architectures in order to improve the processing time. Main references for further information: [1] Gorgan, D., "Flexible and Adaptive Processing of Earth Observation Data over High Performance Computation Architectures", International Conference and Exhibition Satellite 2015, August 17-19, Houston, Texas, USA. [2] Bigearth project - flexible processing of big earth data over high performance computing architectures. http://cgis.utcluj.ro/bigearth, (2014) [3] Nandra, C., Gorgan, D., "Workflow Description Language for Defining Big Earth Data Processing Tasks", Proceedings of the Intelligent Computer Communication and Processing (ICCP), IEEE-Press, pp. 461-468, (2015). [4] Bacu, V., Stefan, T., Gorgan, D., "Adaptive Processing of Earth Observation Data on Cloud Infrastructures Based on Workflow Description", Proceedings of the Intelligent Computer Communication and Processing (ICCP), IEEE-Press, pp.444-454, (2015). [5] Mihon, D., Bacu, V., Colceriu, V., Gorgan, D., "Modeling of Earth Observation Use Cases through the KEOPS System", Proceedings of the Intelligent Computer Communication and Processing (ICCP), IEEE-Press, pp. 455-460, (2015).

LEMON - LHC Era Monitoring for Large-Scale Infrastructures

NASA Astrophysics Data System (ADS)

Marian, Babik; Ivan, Fedorko; Nicholas, Hook; Hector, Lansdale Thomas; Daniel, Lenkes; Miroslav, Siket; Denis, Waldron

2011-12-01

At the present time computer centres are facing a massive rise in virtualization and cloud computing as these solutions bring advantages to service providers and consolidate the computer centre resources. However, as a result the monitoring complexity is increasing. Computer centre management requires not only to monitor servers, network equipment and associated software but also to collect additional environment and facilities data (e.g. temperature, power consumption, cooling efficiency, etc.) to have also a good overview of the infrastructure performance. The LHC Era Monitoring (Lemon) system is addressing these requirements for a very large scale infrastructure. The Lemon agent that collects data on every client and forwards the samples to the central measurement repository provides a flexible interface that allows rapid development of new sensors. The system allows also to report on behalf of remote devices such as switches and power supplies. Online and historical data can be visualized via a web-based interface or retrieved via command-line tools. The Lemon Alarm System component can be used for notifying the operator about error situations. In this article, an overview of the Lemon monitoring is provided together with a description of the CERN LEMON production instance. No direct comparison is made with other monitoring tool.

FITSManager: Management of Personal Astronomical Data

NASA Astrophysics Data System (ADS)

Cui, Chenzhou; Fan, Dongwei; Zhao, Yongheng; Kembhavi, Ajit; He, Boliang; Cao, Zihuang; Li, Jian; Nandrekar, Deoyani

2011-07-01

With the increase of personal storage capacity, it is easy to find hundreds to thousands of FITS files in the personal computer of an astrophysicist. Because Flexible Image Transport System (FITS) is a professional data format initiated by astronomers and used mainly in the small community, data management toolkits for FITS files are very few. Astronomers need a powerful tool to help them manage their local astronomical data. Although Virtual Observatory (VO) is a network oriented astronomical research environment, its applications and related technologies provide useful solutions to enhance the management and utilization of astronomical data hosted in an astronomer's personal computer. FITSManager is such a tool to provide astronomers an efficient management and utilization of their local data, bringing VO to astronomers in a seamless and transparent way. FITSManager provides fruitful functions for FITS file management, like thumbnail, preview, type dependent icons, header keyword indexing and search, collaborated working with other tools and online services, and so on. The development of the FITSManager is an effort to fill the gap between management and analysis of astronomical data.

Techniques and Tools for Estimating Ionospheric Effects in Interferometric and Polarimetric SAR Data

NASA Technical Reports Server (NTRS)

Rosen, P.; Lavalle, M.; Pi, X.; Buckley, S.; Szeliga, W.; Zebker, H.; Gurrola, E.

2011-01-01

The InSAR Scientific Computing Environment (ISCE) is a flexible, extensible software tool designed for the end-to-end processing and analysis of synthetic aperture radar data. ISCE inherits the core of the ROI_PAC interferometric tool, but contains improvements at all levels of the radar processing chain, including a modular and extensible architecture, new focusing approach, better geocoding of the data, handling of multi-polarization data, radiometric calibration, and estimation and correction of ionospheric effects. In this paper we describe the characteristics of ISCE with emphasis on the ionospheric modules. To detect ionospheric anomalies, ISCE implements the Faraday rotation method using quadpolarimetric images, and the split-spectrum technique using interferometric single-, dual- and quad-polarimetric images. The ability to generate co-registered time series of quad-polarimetric images makes ISCE also an ideal tool to be used for polarimetric-interferometric radar applications.

An image processing and analysis tool for identifying and analysing complex plant root systems in 3D soil using non-destructive analysis: Root1.

PubMed

Flavel, Richard J; Guppy, Chris N; Rabbi, Sheikh M R; Young, Iain M

2017-01-01

The objective of this study was to develop a flexible and free image processing and analysis solution, based on the Public Domain ImageJ platform, for the segmentation and analysis of complex biological plant root systems in soil from x-ray tomography 3D images. Contrasting root architectures from wheat, barley and chickpea root systems were grown in soil and scanned using a high resolution micro-tomography system. A macro (Root1) was developed that reliably identified with good to high accuracy complex root systems (10% overestimation for chickpea, 1% underestimation for wheat, 8% underestimation for barley) and provided analysis of root length and angle. In-built flexibility allowed the user interaction to (a) amend any aspect of the macro to account for specific user preferences, and (b) take account of computational limitations of the platform. The platform is free, flexible and accurate in analysing root system metrics.

Blood leakage detection during dialysis therapy based on fog computing with array photocell sensors and heteroassociative memory model

PubMed Central

Wu, Jian-Xing; Huang, Ping-Tzan; Li, Chien-Ming

2018-01-01

Blood leakage and blood loss are serious life-threatening complications occurring during dialysis therapy. These events have been of concerns to both healthcare givers and patients. More than 40% of adult blood volume can be lost in just a few minutes, resulting in morbidities and mortality. The authors intend to propose the design of a warning tool for the detection of blood leakage/blood loss during dialysis therapy based on fog computing with an array of photocell sensors and heteroassociative memory (HAM) model. Photocell sensors are arranged in an array on a flexible substrate to detect blood leakage via the resistance changes with illumination in the visible spectrum of 500–700 nm. The HAM model is implemented to design a virtual alarm unit using electricity changes in an embedded system. The proposed warning tool can indicate the risk level in both end-sensing units and remote monitor devices via a wireless network and fog/cloud computing. The animal experimental results (pig blood) will demonstrate the feasibility. PMID:29515815

Blood leakage detection during dialysis therapy based on fog computing with array photocell sensors and heteroassociative memory model.

PubMed

Wu, Jian-Xing; Huang, Ping-Tzan; Lin, Chia-Hung; Li, Chien-Ming

2018-02-01

Blood leakage and blood loss are serious life-threatening complications occurring during dialysis therapy. These events have been of concerns to both healthcare givers and patients. More than 40% of adult blood volume can be lost in just a few minutes, resulting in morbidities and mortality. The authors intend to propose the design of a warning tool for the detection of blood leakage/blood loss during dialysis therapy based on fog computing with an array of photocell sensors and heteroassociative memory (HAM) model. Photocell sensors are arranged in an array on a flexible substrate to detect blood leakage via the resistance changes with illumination in the visible spectrum of 500-700 nm. The HAM model is implemented to design a virtual alarm unit using electricity changes in an embedded system. The proposed warning tool can indicate the risk level in both end-sensing units and remote monitor devices via a wireless network and fog/cloud computing. The animal experimental results (pig blood) will demonstrate the feasibility.

AEROELASTIC SIMULATION TOOL FOR INFLATABLE BALLUTE AEROCAPTURE

NASA Technical Reports Server (NTRS)

Liever, P. A.; Sheta, E. F.; Habchi, S. D.

2006-01-01

A multidisciplinary analysis tool is under development for predicting the impact of aeroelastic effects on the functionality of inflatable ballute aeroassist vehicles in both the continuum and rarefied flow regimes. High-fidelity modules for continuum and rarefied aerodynamics, structural dynamics, heat transfer, and computational grid deformation are coupled in an integrated multi-physics, multi-disciplinary computing environment. This flexible and extensible approach allows the integration of state-of-the-art, stand-alone NASA and industry leading continuum and rarefied flow solvers and structural analysis codes into a computing environment in which the modules can run concurrently with synchronized data transfer. Coupled fluid-structure continuum flow demonstrations were conducted on a clamped ballute configuration. The feasibility of implementing a DSMC flow solver in the simulation framework was demonstrated, and loosely coupled rarefied flow aeroelastic demonstrations were performed. A NASA and industry technology survey identified CFD, DSMC and structural analysis codes capable of modeling non-linear shape and material response of thin-film inflated aeroshells. The simulation technology will find direct and immediate applications with NASA and industry in ongoing aerocapture technology development programs.

Using computer graphics to enhance astronaut and systems safety

NASA Technical Reports Server (NTRS)

Brown, J. W.

1985-01-01

Computer graphics is being employed at the NASA Johnson Space Center as a tool to perform rapid, efficient and economical analyses for man-machine integration, flight operations development and systems engineering. The Operator Station Design System (OSDS), a computer-based facility featuring a highly flexible and versatile interactive software package, PLAID, is described. This unique evaluation tool, with its expanding data base of Space Shuttle elements, various payloads, experiments, crew equipment and man models, supports a multitude of technical evaluations, including spacecraft and workstation layout, definition of astronaut visual access, flight techniques development, cargo integration and crew training. As OSDS is being applied to the Space Shuttle, Orbiter payloads (including the European Space Agency's Spacelab) and future space vehicles and stations, astronaut and systems safety are being enhanced. Typical OSDS examples are presented. By performing physical and operational evaluations during early conceptual phases. supporting systems verification for flight readiness, and applying its capabilities to real-time mission support, the OSDS provides the wherewithal to satisfy a growing need of the current and future space programs for efficient, economical analyses.

Portfolio Analysis Tool

NASA Technical Reports Server (NTRS)

Barth, Tim; Zapata, Edgar; Benjamin, Perakath; Graul, Mike; Jones, Doug

2005-01-01

Portfolio Analysis Tool (PAT) is a Web-based, client/server computer program that helps managers of multiple projects funded by different customers to make decisions regarding investments in those projects. PAT facilitates analysis on a macroscopic level, without distraction by parochial concerns or tactical details of individual projects, so that managers decisions can reflect the broad strategy of their organization. PAT is accessible via almost any Web-browser software. Experts in specific projects can contribute to a broad database that managers can use in analyzing the costs and benefits of all projects, but do not have access for modifying criteria for analyzing projects: access for modifying criteria is limited to managers according to levels of administrative privilege. PAT affords flexibility for modifying criteria for particular "focus areas" so as to enable standardization of criteria among similar projects, thereby making it possible to improve assessments without need to rewrite computer code or to rehire experts, and thereby further reducing the cost of maintaining and upgrading computer code. Information in the PAT database and results of PAT analyses can be incorporated into a variety of ready-made or customizable tabular or graphical displays.

Flexible Animation Computer Program

NASA Technical Reports Server (NTRS)

Stallcup, Scott S.

1990-01-01

FLEXAN (Flexible Animation), computer program animating structural dynamics on Evans and Sutherland PS300-series graphics workstation with VAX/VMS host computer. Typical application is animation of spacecraft undergoing structural stresses caused by thermal and vibrational effects. Displays distortions in shape of spacecraft. Program displays single natural mode of vibration, mode history, or any general deformation of flexible structure. Written in FORTRAN 77.

Galaxy CloudMan: delivering cloud compute clusters.

PubMed

Afgan, Enis; Baker, Dannon; Coraor, Nate; Chapman, Brad; Nekrutenko, Anton; Taylor, James

2010-12-21

Widespread adoption of high-throughput sequencing has greatly increased the scale and sophistication of computational infrastructure needed to perform genomic research. An alternative to building and maintaining local infrastructure is "cloud computing", which, in principle, offers on demand access to flexible computational infrastructure. However, cloud computing resources are not yet suitable for immediate "as is" use by experimental biologists. We present a cloud resource management system that makes it possible for individual researchers to compose and control an arbitrarily sized compute cluster on Amazon's EC2 cloud infrastructure without any informatics requirements. Within this system, an entire suite of biological tools packaged by the NERC Bio-Linux team (http://nebc.nerc.ac.uk/tools/bio-linux) is available for immediate consumption. The provided solution makes it possible, using only a web browser, to create a completely configured compute cluster ready to perform analysis in less than five minutes. Moreover, we provide an automated method for building custom deployments of cloud resources. This approach promotes reproducibility of results and, if desired, allows individuals and labs to add or customize an otherwise available cloud system to better meet their needs. The expected knowledge and associated effort with deploying a compute cluster in the Amazon EC2 cloud is not trivial. The solution presented in this paper eliminates these barriers, making it possible for researchers to deploy exactly the amount of computing power they need, combined with a wealth of existing analysis software, to handle the ongoing data deluge.

A hybrid approach for integrated healthcare cooperative purchasing and supply chain configuration.

PubMed

Rego, Nazaré; Claro, João; Pinho de Sousa, Jorge

2014-12-01

This paper presents an innovative and flexible approach for recommending the number, size and composition of purchasing groups, for a set of hospitals willing to cooperate, while minimising their shared supply chain costs. This approach makes the financial impact of the various cooperation alternatives transparent to the group and the individual participants, opening way to a negotiation process concerning the allocation of the cooperation costs and gains. The approach was developed around a hybrid Variable Neighbourhood Search (VNS)/Tabu Search metaheuristic, resulting in a flexible tool that can be applied to purchasing groups with different characteristics, namely different operative and market circumstances, and to supply chains with different topologies and atypical cost characteristics. Preliminary computational results show the potential of the approach in solving a broad range of problems.

Flutter suppression for the Active Flexible Wing - Control system design and experimental validation

NASA Technical Reports Server (NTRS)

Waszak, M. R.; Srinathkumar, S.

1992-01-01

The synthesis and experimental validation of a control law for an active flutter suppression system for the Active Flexible Wing wind-tunnel model is presented. The design was accomplished with traditional root locus and Nyquist methods using interactive computer graphics tools and with extensive use of simulation-based analysis. The design approach relied on a fundamental understanding of the flutter mechanism to formulate understanding of the flutter mechanism to formulate a simple control law structure. Experimentally, the flutter suppression controller succeeded in simultaneous suppression of two flutter modes, significantly increasing the flutter dynamic pressure despite errors in the design model. The flutter suppression controller was also successfully operated in combination with a rolling maneuver controller to perform flutter suppression during rapid rolling maneuvers.

A High Performance Computing Approach to the Simulation of Fluid Solid Interaction Problems with Rigid and Flexible Components (Open Access Publisher’s Version)

DTIC Science & Technology

2014-08-01

performance computing, smoothed particle hydrodynamics, rigid body dynamics, flexible body dynamics ARMAN PAZOUKI ∗, RADU SERBAN ∗, DAN NEGRUT ∗ A...HIGH PERFORMANCE COMPUTING APPROACH TO THE SIMULATION OF FLUID-SOLID INTERACTION PROBLEMS WITH RIGID AND FLEXIBLE COMPONENTS This work outlines a unified...are implemented to model rigid and flexible multibody dynamics. The two- way coupling of the fluid and solid phases is supported through use of

Object-oriented design and implementation of CFDLab: a computer-assisted learning tool for fluid dynamics using dual reciprocity boundary element methodology

NASA Astrophysics Data System (ADS)

Friedrich, J.

1999-08-01

As lecturers, our main concern and goal is to develop more attractive and efficient ways of communicating up-to-date scientific knowledge to our students and facilitate an in-depth understanding of physical phenomena. Computer-based instruction is very promising to help both teachers and learners in their difficult task, which involves complex cognitive psychological processes. This complexity is reflected in high demands on the design and implementation methods used to create computer-assisted learning (CAL) programs. Due to their concepts, flexibility, maintainability and extended library resources, object-oriented modeling techniques are very suitable to produce this type of pedagogical tool. Computational fluid dynamics (CFD) enjoys not only a growing importance in today's research, but is also very powerful for teaching and learning fluid dynamics. For this purpose, an educational PC program for university level called 'CFDLab 1.1' for Windows™ was developed with an interactive graphical user interface (GUI) for multitasking and point-and-click operations. It uses the dual reciprocity boundary element method as a versatile numerical scheme, allowing to handle a variety of relevant governing equations in two dimensions on personal computers due to its simple pre- and postprocessing including 2D Laplace, Poisson, diffusion, transient convection-diffusion.

Computational framework to support integration of biomolecular and clinical data within a translational approach.

PubMed

Miyoshi, Newton Shydeo Brandão; Pinheiro, Daniel Guariz; Silva, Wilson Araújo; Felipe, Joaquim Cezar

2013-06-06

The use of the knowledge produced by sciences to promote human health is the main goal of translational medicine. To make it feasible we need computational methods to handle the large amount of information that arises from bench to bedside and to deal with its heterogeneity. A computational challenge that must be faced is to promote the integration of clinical, socio-demographic and biological data. In this effort, ontologies play an essential role as a powerful artifact for knowledge representation. Chado is a modular ontology-oriented database model that gained popularity due to its robustness and flexibility as a generic platform to store biological data; however it lacks supporting representation of clinical and socio-demographic information. We have implemented an extension of Chado - the Clinical Module - to allow the representation of this kind of information. Our approach consists of a framework for data integration through the use of a common reference ontology. The design of this framework has four levels: data level, to store the data; semantic level, to integrate and standardize the data by the use of ontologies; application level, to manage clinical databases, ontologies and data integration process; and web interface level, to allow interaction between the user and the system. The clinical module was built based on the Entity-Attribute-Value (EAV) model. We also proposed a methodology to migrate data from legacy clinical databases to the integrative framework. A Chado instance was initialized using a relational database management system. The Clinical Module was implemented and the framework was loaded using data from a factual clinical research database. Clinical and demographic data as well as biomaterial data were obtained from patients with tumors of head and neck. We implemented the IPTrans tool that is a complete environment for data migration, which comprises: the construction of a model to describe the legacy clinical data, based on an ontology; the Extraction, Transformation and Load (ETL) process to extract the data from the source clinical database and load it in the Clinical Module of Chado; the development of a web tool and a Bridge Layer to adapt the web tool to Chado, as well as other applications. Open-source computational solutions currently available for translational science does not have a model to represent biomolecular information and also are not integrated with the existing bioinformatics tools. On the other hand, existing genomic data models do not represent clinical patient data. A framework was developed to support translational research by integrating biomolecular information coming from different "omics" technologies with patient's clinical and socio-demographic data. This framework should present some features: flexibility, compression and robustness. The experiments accomplished from a use case demonstrated that the proposed system meets requirements of flexibility and robustness, leading to the desired integration. The Clinical Module can be accessed in http://dcm.ffclrp.usp.br/caib/pg=iptrans.

Structural Analysis Computer Programs for Rigid Multicomponent Pavement Structures with Discontinuities--WESLIQID and WESLAYER. Report 1. Program Development and Numerical Presentations.

DTIC Science & Technology

1981-05-01

represented as a Winkler foundation. The program can treat any number of slabs connected by steel bars or other load trans- fer devices at the joints...dimensional finite element method. The inherent flexibility of such an approach permits the analysis of a rigid pavement with steel bars and stabilized...layers and provides an efficient tool for analyzing stress conditions at the joint. Unfor- tunately, such a procedure would require a tremendously

Animation of multi-flexible body systems and its use in control system design

NASA Technical Reports Server (NTRS)

Juengst, Carl; Stahlberg, Ron

1993-01-01

Animation can greatly assist the structural dynamicist and control system analyst with better understanding of how multi-flexible body systems behave. For multi-flexible body systems, the structural characteristics (mode frequencies, mode shapes, and damping) change, sometimes dramatically with large angles of rotation between bodies. With computer animation, the analyst can visualize these changes and how the system responds to active control forces and torques. A characterization of the type of system we wish to animate is presented. The lack of clear understanding of the above effects was a key element leading to the development of a multi-flexible body animation software package. The resulting animation software is described in some detail here, followed by its application to the control system analyst. Other applications of this software can be determined on an individual need basis. A number of software products are currently available that make the high-speed rendering of rigid body mechanical system simulation possible. However, such options are not available for use in rendering flexible body mechanical system simulations. The desire for a high-speed flexible body visualization tool led to the development of the Flexible Or Rigid Mechanical System (FORMS) software. This software was developed at the Center for Simulation and Design Optimization of Mechanical Systems at the University of Iowa. FORMS provides interactive high-speed rendering of flexible and/or rigid body mechanical system simulations, and combines geometry and motion information to produce animated output. FORMS is designed to be both portable and flexible, and supports a number of different user interfaces and graphical display devices. Additional features have been added to FORMS that allow special visualization results related to the nature of the flexible body geometric representations.

Fourth NASA Workshop on Computational Control of Flexible Aerospace Systems, part 2

NASA Technical Reports Server (NTRS)

Taylor, Lawrence W., Jr. (Compiler)

1991-01-01

A collection of papers presented at the Fourth NASA Workshop on Computational Control of Flexible Aerospace Systems is given. The papers address modeling, systems identification, and control of flexible aircraft, spacecraft and robotic systems.

SYSTID - A flexible tool for the analysis of communication systems.

NASA Technical Reports Server (NTRS)

Dawson, C. T.; Tranter, W. H.

1972-01-01

Description of the System Time Domain Simulation (SYSTID) computer-aided analysis program which is specifically structured for communication systems analysis. The SYSTID program is user oriented so that very little knowledge of computer techniques and very little programming ability are required for proper application. The program is designed so that the user can go from a system block diagram to an accurate simulation by simply programming a single English language statement for each block in the system. The mathematical and functional models available in the SYSTID library are presented. An example problem is given which illustrates the ease of modeling communication systems. Examples of the outputs available are presented, and proposed improvements are summarized.

SAMICS Validation. SAMICS Support Study, Phase 3

NASA Technical Reports Server (NTRS)

1979-01-01

SAMICS provides a consistent basis for estimating array costs and compares production technology costs. A review and a validation of the SAMICS model are reported. The review had the following purposes: (1) to test the computational validity of the computer model by comparison with preliminary hand calculations based on conventional cost estimating techniques; (2) to review and improve the accuracy of the cost relationships being used by the model: and (3) to provide an independent verification to users of the model's value in decision making for allocation of research and developement funds and for investment in manufacturing capacity. It is concluded that the SAMICS model is a flexible, accurate, and useful tool for managerial decision making.

Domain decomposition methods in computational fluid dynamics

NASA Technical Reports Server (NTRS)

Gropp, William D.; Keyes, David E.

1991-01-01

The divide-and-conquer paradigm of iterative domain decomposition, or substructuring, has become a practical tool in computational fluid dynamic applications because of its flexibility in accommodating adaptive refinement through locally uniform (or quasi-uniform) grids, its ability to exploit multiple discretizations of the operator equations, and the modular pathway it provides towards parallelism. These features are illustrated on the classic model problem of flow over a backstep using Newton's method as the nonlinear iteration. Multiple discretizations (second-order in the operator and first-order in the preconditioner) and locally uniform mesh refinement pay dividends separately, and they can be combined synergistically. Sample performance results are included from an Intel iPSC/860 hypercube implementation.

The Impact and Promise of Open-Source Computational Material for Physics Teaching

NASA Astrophysics Data System (ADS)

Christian, Wolfgang

2017-01-01

A computer-based modeling approach to teaching must be flexible because students and teachers have different skills and varying levels of preparation. Learning how to run the ``software du jour'' is not the objective for integrating computational physics material into the curriculum. Learning computational thinking, how to use computation and computer-based visualization to communicate ideas, how to design and build models, and how to use ready-to-run models to foster critical thinking is the objective. Our computational modeling approach to teaching is a research-proven pedagogy that predates computers. It attempts to enhance student achievement through the Modeling Cycle. This approach was pioneered by Robert Karplus and the SCIS Project in the 1960s and 70s and later extended by the Modeling Instruction Program led by Jane Jackson and David Hestenes at Arizona State University. This talk describes a no-cost open-source computational approach aligned with a Modeling Cycle pedagogy. Our tools, curricular material, and ready-to-run examples are freely available from the Open Source Physics Collection hosted on the AAPT-ComPADRE digital library. Examples will be presented.

Computational Psychiatry

PubMed Central

Wang, Xiao-Jing; Krystal, John H.

2014-01-01

Psychiatric disorders such as autism and schizophrenia arise from abnormalities in brain systems that underlie cognitive, emotional and social functions. The brain is enormously complex and its abundant feedback loops on multiple scales preclude intuitive explication of circuit functions. In close interplay with experiments, theory and computational modeling are essential for understanding how, precisely, neural circuits generate flexible behaviors and their impairments give rise to psychiatric symptoms. This Perspective highlights recent progress in applying computational neuroscience to the study of mental disorders. We outline basic approaches, including identification of core deficits that cut across disease categories, biologically-realistic modeling bridging cellular and synaptic mechanisms with behavior, model-aided diagnosis. The need for new research strategies in psychiatry is urgent. Computational psychiatry potentially provides powerful tools for elucidating pathophysiology that may inform both diagnosis and treatment. To achieve this promise will require investment in cross-disciplinary training and research in this nascent field. PMID:25442941

ProphTools: general prioritization tools for heterogeneous biological networks.

PubMed

Navarro, Carmen; Martínez, Victor; Blanco, Armando; Cano, Carlos

2017-12-01

Networks have been proven effective representations for the analysis of biological data. As such, there exist multiple methods to extract knowledge from biological networks. However, these approaches usually limit their scope to a single biological entity type of interest or they lack the flexibility to analyze user-defined data. We developed ProphTools, a flexible open-source command-line tool that performs prioritization on a heterogeneous network. ProphTools prioritization combines a Flow Propagation algorithm similar to a Random Walk with Restarts and a weighted propagation method. A flexible model for the representation of a heterogeneous network allows the user to define a prioritization problem involving an arbitrary number of entity types and their interconnections. Furthermore, ProphTools provides functionality to perform cross-validation tests, allowing users to select the best network configuration for a given problem. ProphTools core prioritization methodology has already been proven effective in gene-disease prioritization and drug repositioning. Here we make ProphTools available to the scientific community as flexible, open-source software and perform a new proof-of-concept case study on long noncoding RNAs (lncRNAs) to disease prioritization. ProphTools is robust prioritization software that provides the flexibility not present in other state-of-the-art network analysis approaches, enabling researchers to perform prioritization tasks on any user-defined heterogeneous network. Furthermore, the application to lncRNA-disease prioritization shows that ProphTools can reach the performance levels of ad hoc prioritization tools without losing its generality. © The Authors 2017. Published by Oxford University Press.

Tessera: Open source software for accelerated data science

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

Sego, Landon H.; Hafen, Ryan P.; Director, Hannah M.

2014-06-30

Extracting useful, actionable information from data can be a formidable challenge for the safeguards, nonproliferation, and arms control verification communities. Data scientists are often on the “front-lines” of making sense of complex and large datasets. They require flexible tools that make it easy to rapidly reformat large datasets, interactively explore and visualize data, develop statistical algorithms, and validate their approaches—and they need to perform these activities with minimal lines of code. Existing commercial software solutions often lack extensibility and the flexibility required to address the nuances of the demanding and dynamic environments where data scientists work. To address this need,more » Pacific Northwest National Laboratory developed Tessera, an open source software suite designed to enable data scientists to interactively perform their craft at the terabyte scale. Tessera automatically manages the complicated tasks of distributed storage and computation, empowering data scientists to do what they do best: tackling critical research and mission objectives by deriving insight from data. We illustrate the use of Tessera with an example analysis of computer network data.« less

Charting molecular free-energy landscapes with an atlas of collective variables

NASA Astrophysics Data System (ADS)

Hashemian, Behrooz; Millán, Daniel; Arroyo, Marino

2016-11-01

Collective variables (CVs) are a fundamental tool to understand molecular flexibility, to compute free energy landscapes, and to enhance sampling in molecular dynamics simulations. However, identifying suitable CVs is challenging, and is increasingly addressed with systematic data-driven manifold learning techniques. Here, we provide a flexible framework to model molecular systems in terms of a collection of locally valid and partially overlapping CVs: an atlas of CVs. The specific motivation for such a framework is to enhance the applicability and robustness of CVs based on manifold learning methods, which fail in the presence of periodicities in the underlying conformational manifold. More generally, using an atlas of CVs rather than a single chart may help us better describe different regions of conformational space. We develop the statistical mechanics foundation for our multi-chart description and propose an algorithmic implementation. The resulting atlas of data-based CVs are then used to enhance sampling and compute free energy surfaces in two model systems, alanine dipeptide and β-D-glucopyranose, whose conformational manifolds have toroidal and spherical topologies.

Global flexibility--shop floor flexibility: what's a worker to do?

PubMed

Forrant, R

1999-01-01

For several years new forms of work organization have been introduced by U.S. management to cut labor costs, improve productivity, and increase their shop floor control. Corporations have also invested in computer-controlled machinery in an effort to eliminate large numbers of skilled blue-collar workers and to decrease their reliance on the tacit knowledge of such workers. Once seemingly secure jobs in diverse industries like airplanes, jet engines, machine tools, and computer chips, are no longer so stable. In an effort to expand their global reach and reorganize the workplace, managers are able to capitalize on two conflicted and conflicting attitudes among the workforce: the first, workers most deep-seated fear, the loss of a permanent job; the second, their aspirations to contribute their knowledge and skills in a positive way on the shop floor. In this article the reorganization of work at two western Massachusetts metalworking companies is described. What distinguishes these cases is the central role that the union played in the organized plant and the workers played in both plants to improve production and at least for now preserve jobs.

BeatBox-HPC simulation environment for biophysically and anatomically realistic cardiac electrophysiology.

PubMed

Antonioletti, Mario; Biktashev, Vadim N; Jackson, Adrian; Kharche, Sanjay R; Stary, Tomas; Biktasheva, Irina V

2017-01-01

The BeatBox simulation environment combines flexible script language user interface with the robust computational tools, in order to setup cardiac electrophysiology in-silico experiments without re-coding at low-level, so that cell excitation, tissue/anatomy models, stimulation protocols may be included into a BeatBox script, and simulation run either sequentially or in parallel (MPI) without re-compilation. BeatBox is a free software written in C language to be run on a Unix-based platform. It provides the whole spectrum of multi scale tissue modelling from 0-dimensional individual cell simulation, 1-dimensional fibre, 2-dimensional sheet and 3-dimensional slab of tissue, up to anatomically realistic whole heart simulations, with run time measurements including cardiac re-entry tip/filament tracing, ECG, local/global samples of any variables, etc. BeatBox solvers, cell, and tissue/anatomy models repositories are extended via robust and flexible interfaces, thus providing an open framework for new developments in the field. In this paper we give an overview of the BeatBox current state, together with a description of the main computational methods and MPI parallelisation approaches.

Galaxy CloudMan: delivering cloud compute clusters

PubMed Central

2010-01-01

Background Widespread adoption of high-throughput sequencing has greatly increased the scale and sophistication of computational infrastructure needed to perform genomic research. An alternative to building and maintaining local infrastructure is “cloud computing”, which, in principle, offers on demand access to flexible computational infrastructure. However, cloud computing resources are not yet suitable for immediate “as is” use by experimental biologists. Results We present a cloud resource management system that makes it possible for individual researchers to compose and control an arbitrarily sized compute cluster on Amazon’s EC2 cloud infrastructure without any informatics requirements. Within this system, an entire suite of biological tools packaged by the NERC Bio-Linux team (http://nebc.nerc.ac.uk/tools/bio-linux) is available for immediate consumption. The provided solution makes it possible, using only a web browser, to create a completely configured compute cluster ready to perform analysis in less than five minutes. Moreover, we provide an automated method for building custom deployments of cloud resources. This approach promotes reproducibility of results and, if desired, allows individuals and labs to add or customize an otherwise available cloud system to better meet their needs. Conclusions The expected knowledge and associated effort with deploying a compute cluster in the Amazon EC2 cloud is not trivial. The solution presented in this paper eliminates these barriers, making it possible for researchers to deploy exactly the amount of computing power they need, combined with a wealth of existing analysis software, to handle the ongoing data deluge. PMID:21210983

URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries.

PubMed

Drawert, Brian; Engblom, Stefan; Hellander, Andreas

2012-06-22

Experiments in silico using stochastic reaction-diffusion models have emerged as an important tool in molecular systems biology. Designing computational software for such applications poses several challenges. Firstly, realistic lattice-based modeling for biological applications requires a consistent way of handling complex geometries, including curved inner- and outer boundaries. Secondly, spatiotemporal stochastic simulations are computationally expensive due to the fast time scales of individual reaction- and diffusion events when compared to the biological phenomena of actual interest. We therefore argue that simulation software needs to be both computationally efficient, employing sophisticated algorithms, yet in the same time flexible in order to meet present and future needs of increasingly complex biological modeling. We have developed URDME, a flexible software framework for general stochastic reaction-transport modeling and simulation. URDME uses Unstructured triangular and tetrahedral meshes to resolve general geometries, and relies on the Reaction-Diffusion Master Equation formalism to model the processes under study. An interface to a mature geometry and mesh handling external software (Comsol Multiphysics) provides for a stable and interactive environment for model construction. The core simulation routines are logically separated from the model building interface and written in a low-level language for computational efficiency. The connection to the geometry handling software is realized via a Matlab interface which facilitates script computing, data management, and post-processing. For practitioners, the software therefore behaves much as an interactive Matlab toolbox. At the same time, it is possible to modify and extend URDME with newly developed simulation routines. Since the overall design effectively hides the complexity of managing the geometry and meshes, this means that newly developed methods may be tested in a realistic setting already at an early stage of development. In this paper we demonstrate, in a series of examples with high relevance to the molecular systems biology community, that the proposed software framework is a useful tool for both practitioners and developers of spatial stochastic simulation algorithms. Through the combined efforts of algorithm development and improved modeling accuracy, increasingly complex biological models become feasible to study through computational methods. URDME is freely available at http://www.urdme.org.

Cropland rental tool (CROPRENT) for agricultural producers

USDA-ARS?s Scientific Manuscript database

This article describes the Cropland Rental Tool (CROPRENT), which is an Excel-based decision tool for comparing different cropland lease agreements, including flexible cash rents, for up to five crops and/or management systems. Flexible cash rents allow tenants and landowners to share in the risk as...

Tool for Crimping Flexible Circuit Leads

NASA Technical Reports Server (NTRS)

Hulse, Aaron; Diftler, Myron A.

2009-01-01

A hand tool has been developed for crimping leads in flexible tails that are parts of some electronic circuits -- especially some sensor circuits. The tool is used to cut the tails to desired lengths and attach solder tabs to the leads. For tailoring small numbers of circuits for special applications, this hand tool is a less expensive alternative to a commercially available automated crimping tool. The crimping tool consists of an off-the-shelf hand crimping tool plus a specialized crimping insert designed specifically for the intended application.

The InSAR Scientific Computing Environment

NASA Technical Reports Server (NTRS)

Rosen, Paul A.; Gurrola, Eric; Sacco, Gian Franco; Zebker, Howard

2012-01-01

We have developed a flexible and extensible Interferometric SAR (InSAR) Scientific Computing Environment (ISCE) for geodetic image processing. ISCE was designed from the ground up as a geophysics community tool for generating stacks of interferograms that lend themselves to various forms of time-series analysis, with attention paid to accuracy, extensibility, and modularity. The framework is python-based, with code elements rigorously componentized by separating input/output operations from the processing engines. This allows greater flexibility and extensibility in the data models, and creates algorithmic code that is less susceptible to unnecessary modification when new data types and sensors are available. In addition, the components support provenance and checkpointing to facilitate reprocessing and algorithm exploration. The algorithms, based on legacy processing codes, have been adapted to assume a common reference track approach for all images acquired from nearby orbits, simplifying and systematizing the geometry for time-series analysis. The framework is designed to easily allow user contributions, and is distributed for free use by researchers. ISCE can process data from the ALOS, ERS, EnviSAT, Cosmo-SkyMed, RadarSAT-1, RadarSAT-2, and TerraSAR-X platforms, starting from Level-0 or Level 1 as provided from the data source, and going as far as Level 3 geocoded deformation products. With its flexible design, it can be extended with raw/meta data parsers to enable it to work with radar data from other platforms

EEGNET: An Open Source Tool for Analyzing and Visualizing M/EEG Connectome.

PubMed

Hassan, Mahmoud; Shamas, Mohamad; Khalil, Mohamad; El Falou, Wassim; Wendling, Fabrice

2015-01-01

The brain is a large-scale complex network often referred to as the "connectome". Exploring the dynamic behavior of the connectome is a challenging issue as both excellent time and space resolution is required. In this context Magneto/Electroencephalography (M/EEG) are effective neuroimaging techniques allowing for analysis of the dynamics of functional brain networks at scalp level and/or at reconstructed sources. However, a tool that can cover all the processing steps of identifying brain networks from M/EEG data is still missing. In this paper, we report a novel software package, called EEGNET, running under MATLAB (Math works, inc), and allowing for analysis and visualization of functional brain networks from M/EEG recordings. EEGNET is developed to analyze networks either at the level of scalp electrodes or at the level of reconstructed cortical sources. It includes i) Basic steps in preprocessing M/EEG signals, ii) the solution of the inverse problem to localize / reconstruct the cortical sources, iii) the computation of functional connectivity among signals collected at surface electrodes or/and time courses of reconstructed sources and iv) the computation of the network measures based on graph theory analysis. EEGNET is the unique tool that combines the M/EEG functional connectivity analysis and the computation of network measures derived from the graph theory. The first version of EEGNET is easy to use, flexible and user friendly. EEGNET is an open source tool and can be freely downloaded from this webpage: https://sites.google.com/site/eegnetworks/.

EEGNET: An Open Source Tool for Analyzing and Visualizing M/EEG Connectome

PubMed Central

Hassan, Mahmoud; Shamas, Mohamad; Khalil, Mohamad; El Falou, Wassim; Wendling, Fabrice

2015-01-01

The brain is a large-scale complex network often referred to as the “connectome”. Exploring the dynamic behavior of the connectome is a challenging issue as both excellent time and space resolution is required. In this context Magneto/Electroencephalography (M/EEG) are effective neuroimaging techniques allowing for analysis of the dynamics of functional brain networks at scalp level and/or at reconstructed sources. However, a tool that can cover all the processing steps of identifying brain networks from M/EEG data is still missing. In this paper, we report a novel software package, called EEGNET, running under MATLAB (Math works, inc), and allowing for analysis and visualization of functional brain networks from M/EEG recordings. EEGNET is developed to analyze networks either at the level of scalp electrodes or at the level of reconstructed cortical sources. It includes i) Basic steps in preprocessing M/EEG signals, ii) the solution of the inverse problem to localize / reconstruct the cortical sources, iii) the computation of functional connectivity among signals collected at surface electrodes or/and time courses of reconstructed sources and iv) the computation of the network measures based on graph theory analysis. EEGNET is the unique tool that combines the M/EEG functional connectivity analysis and the computation of network measures derived from the graph theory. The first version of EEGNET is easy to use, flexible and user friendly. EEGNET is an open source tool and can be freely downloaded from this webpage: https://sites.google.com/site/eegnetworks/. PMID:26379232

The structural flexibility of the human copper chaperone Atox1: Insights from combined pulsed EPR studies and computations.

PubMed

Levy, Ariel R; Turgeman, Meital; Gevorkyan-Aiapetov, Lada; Ruthstein, Sharon

2017-08-01

Metallochaperones are responsible for shuttling metal ions to target proteins. Thus, a metallochaperone's structure must be sufficiently flexible both to hold onto its ion while traversing the cytoplasm and to transfer the ion to or from a partner protein. Here, we sought to shed light on the structure of Atox1, a metallochaperone involved in the human copper regulation system. Atox1 shuttles copper ions from the main copper transporter, Ctr1, to the ATP7b transporter in the Golgi apparatus. Conventional biophysical tools such as X-ray or NMR cannot always target the various conformational states of metallochaperones, owing to a requirement for crystallography or low sensitivity and resolution. Electron paramagnetic resonance (EPR) spectroscopy has recently emerged as a powerful tool for resolving biological reactions and mechanisms in solution. When coupled with computational methods, EPR with site-directed spin labeling and nanoscale distance measurements can provide structural information on a protein or protein complex in solution. We use these methods to show that Atox1 can accommodate at least four different conformations in the apo state (unbound to copper), and two different conformations in the holo state (bound to copper). We also demonstrate that the structure of Atox1 in the holo form is more compact than in the apo form. Our data provide insight regarding the structural mechanisms through which Atox1 can fulfill its dual role of copper binding and transfer. © 2017 The Protein Society.

Fast multipurpose Monte Carlo simulation for proton therapy using multi- and many-core CPU architectures

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

Souris, Kevin, E-mail: kevin.souris@uclouvain.be; Lee, John Aldo; Sterpin, Edmond

2016-04-15

Purpose: Accuracy in proton therapy treatment planning can be improved using Monte Carlo (MC) simulations. However the long computation time of such methods hinders their use in clinical routine. This work aims to develop a fast multipurpose Monte Carlo simulation tool for proton therapy using massively parallel central processing unit (CPU) architectures. Methods: A new Monte Carlo, called MCsquare (many-core Monte Carlo), has been designed and optimized for the last generation of Intel Xeon processors and Intel Xeon Phi coprocessors. These massively parallel architectures offer the flexibility and the computational power suitable to MC methods. The class-II condensed history algorithmmore » of MCsquare provides a fast and yet accurate method of simulating heavy charged particles such as protons, deuterons, and alphas inside voxelized geometries. Hard ionizations, with energy losses above a user-specified threshold, are simulated individually while soft events are regrouped in a multiple scattering theory. Elastic and inelastic nuclear interactions are sampled from ICRU 63 differential cross sections, thereby allowing for the computation of prompt gamma emission profiles. MCsquare has been benchmarked with the GATE/GEANT4 Monte Carlo application for homogeneous and heterogeneous geometries. Results: Comparisons with GATE/GEANT4 for various geometries show deviations within 2%–1 mm. In spite of the limited memory bandwidth of the coprocessor simulation time is below 25 s for 10{sup 7} primary 200 MeV protons in average soft tissues using all Xeon Phi and CPU resources embedded in a single desktop unit. Conclusions: MCsquare exploits the flexibility of CPU architectures to provide a multipurpose MC simulation tool. Optimized code enables the use of accurate MC calculation within a reasonable computation time, adequate for clinical practice. MCsquare also simulates prompt gamma emission and can thus be used also for in vivo range verification.« less

r.randomwalk v1.0, a multi-functional conceptual tool for mass movement routing

NASA Astrophysics Data System (ADS)

Mergili, M.; Krenn, J.; Chu, H.-J.

2015-09-01

We introduce r.randomwalk, a flexible and multi-functional open source tool for backward- and forward-analyses of mass movement propagation. r.randomwalk builds on GRASS GIS, the R software for statistical computing and the programming languages Python and C. Using constrained random walks, mass points are routed from defined release pixels of one to many mass movements through a digital elevation model until a defined break criterion is reached. Compared to existing tools, the major innovative features of r.randomwalk are: (i) multiple break criteria can be combined to compute an impact indicator score, (ii) the uncertainties of break criteria can be included by performing multiple parallel computations with randomized parameter settings, resulting in an impact indicator index in the range 0-1, (iii) built-in functions for validation and visualization of the results are provided, (iv) observed landslides can be back-analyzed to derive the density distribution of the observed angles of reach. This distribution can be employed to compute impact probabilities for each pixel. Further, impact indicator scores and probabilities can be combined with release indicator scores or probabilities, and with exposure indicator scores. We demonstrate the key functionalities of r.randomwalk (i) for a single event, the Acheron Rock Avalanche in New Zealand, (ii) for landslides in a 61.5 km2 study area in the Kao Ping Watershed, Taiwan; and (iii) for lake outburst floods in a 2106 km2 area in the Gunt Valley, Tajikistan.

r.randomwalk v1, a multi-functional conceptual tool for mass movement routing

NASA Astrophysics Data System (ADS)

Mergili, M.; Krenn, J.; Chu, H.-J.

2015-12-01

We introduce r.randomwalk, a flexible and multi-functional open-source tool for backward and forward analyses of mass movement propagation. r.randomwalk builds on GRASS GIS (Geographic Resources Analysis Support System - Geographic Information System), the R software for statistical computing and the programming languages Python and C. Using constrained random walks, mass points are routed from defined release pixels of one to many mass movements through a digital elevation model until a defined break criterion is reached. Compared to existing tools, the major innovative features of r.randomwalk are (i) multiple break criteria can be combined to compute an impact indicator score; (ii) the uncertainties of break criteria can be included by performing multiple parallel computations with randomized parameter sets, resulting in an impact indicator index in the range 0-1; (iii) built-in functions for validation and visualization of the results are provided; (iv) observed landslides can be back analysed to derive the density distribution of the observed angles of reach. This distribution can be employed to compute impact probabilities for each pixel. Further, impact indicator scores and probabilities can be combined with release indicator scores or probabilities, and with exposure indicator scores. We demonstrate the key functionalities of r.randomwalk for (i) a single event, the Acheron rock avalanche in New Zealand; (ii) landslides in a 61.5 km2 study area in the Kao Ping Watershed, Taiwan; and (iii) lake outburst floods in a 2106 km2 area in the Gunt Valley, Tajikistan.

Using Palm Technology in Participatory Simulations of Complex Systems: A New Take on Ubiquitous and Accessible Mobile Computing

NASA Astrophysics Data System (ADS)

Klopfer, Eric; Yoon, Susan; Perry, Judy

2005-09-01

This paper reports on teachers' perceptions of the educational affordances of a handheld application called Participatory Simulations. It presents evidence from five cases representing each of the populations who work with these computational tools. Evidence across multiple data sources yield similar results to previous research evaluations of handheld activities with respect to enhancing motivation, engagement and self-directed learning. Three additional themes are discussed that provide insight into understanding curricular applicability of Participatory Simulations that suggest a new take on ubiquitous and accessible mobile computing. These themes generally point to the multiple layers of social and cognitive flexibility intrinsic to their design: ease of adaptation to subject-matter content knowledge and curricular integration; facility in attending to teacher-individualized goals; and encouraging the adoption of learner-centered strategies.

POLLUX: a program for simulated cloning, mutagenesis and database searching of DNA constructs.

PubMed

Dayringer, H E; Sammons, S A

1991-04-01

Computer support for research in biotechnology has developed rapidly and has provided several tools to aid the researcher. This report describes the capabilities of new computer software developed in this laboratory to aid in the documentation and planning of experiments in molecular biology. The program, POLLUX, provides a graphical medium for the entry, edit and manipulation of DNA constructs and a textual format for display and edit of construct descriptive data. Program operation and procedures are designed to mimic the actual laboratory experiments with respect to capability and the order in which they are performed. Flexible control over the content of the computer-generated displays and program facilities is provided by a mouse-driven menu interface. Programmed facilities for mutagenesis, simulated cloning and searching of the database from networked workstations are described.

MOOSE: A parallel computational framework for coupled systems of nonlinear equations.

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

Derek Gaston; Chris Newman; Glen Hansen

Systems of coupled, nonlinear partial differential equations (PDEs) often arise in simulation of nuclear processes. MOOSE: Multiphysics Object Oriented Simulation Environment, a parallel computational framework targeted at the solution of such systems, is presented. As opposed to traditional data-flow oriented computational frameworks, MOOSE is instead founded on the mathematical principle of Jacobian-free Newton-Krylov (JFNK) solution methods. Utilizing the mathematical structure present in JFNK, physics expressions are modularized into `Kernels,'' allowing for rapid production of new simulation tools. In addition, systems are solved implicitly and fully coupled, employing physics based preconditioning, which provides great flexibility even with large variance in timemore » scales. A summary of the mathematics, an overview of the structure of MOOSE, and several representative solutions from applications built on the framework are presented.« less

Holographic imaging and photostimulation of neural activity.

PubMed

Yang, Weijian; Yuste, Rafael

2018-06-01

Optical imaging methods are powerful tools in neuroscience as they can systematically monitor the activity of neuronal populations with high spatiotemporal resolution using calcium or voltage indicators. Moreover, caged compounds and optogenetic actuators enable to optically manipulate neural activity. Among optical methods, computer-generated holography offers an enormous flexibility to sculpt the excitation light in three-dimensions (3D), particularly when combined with two-photon light sources. By projecting holographic light patterns on the sample, the activity of multiple neurons across a 3D brain volume can be simultaneously imaged or optically manipulated with single-cell precision. This flexibility makes two-photon holographic microscopy an ideal all-optical platform to simultaneously read and write activity in neuronal populations in vivo in 3D, a critical ability to dissect the function of neural circuits. Copyright © 2018 Elsevier Ltd. All rights reserved.

Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description.

PubMed

Spyrakis, Francesca; Cavasotto, Claudio N

2015-10-01

Structure-based virtual screening is currently an established tool in drug lead discovery projects. Although in the last years the field saw an impressive progress in terms of algorithm development, computational performance, and retrospective and prospective applications in ligand identification, there are still long-standing challenges where further improvement is needed. In this review, we consider the conceptual frame, state-of-the-art and recent developments of three critical "structural" issues in structure-based drug lead discovery: the use of homology modeling to accurately model the binding site when no experimental structures are available, the necessity of accounting for the dynamics of intrinsically flexible systems as proteins, and the importance of considering active site water molecules in lead identification and optimization campaigns. Copyright © 2015 Elsevier Inc. All rights reserved.

Bio-TDS: bioscience query tool discovery system.

PubMed

Gnimpieba, Etienne Z; VanDiermen, Menno S; Gustafson, Shayla M; Conn, Bill; Lushbough, Carol M

2017-01-04

Bioinformatics and computational biology play a critical role in bioscience and biomedical research. As researchers design their experimental projects, one major challenge is to find the most relevant bioinformatics toolkits that will lead to new knowledge discovery from their data. The Bio-TDS (Bioscience Query Tool Discovery Systems, http://biotds.org/) has been developed to assist researchers in retrieving the most applicable analytic tools by allowing them to formulate their questions as free text. The Bio-TDS is a flexible retrieval system that affords users from multiple bioscience domains (e.g. genomic, proteomic, bio-imaging) the ability to query over 12 000 analytic tool descriptions integrated from well-established, community repositories. One of the primary components of the Bio-TDS is the ontology and natural language processing workflow for annotation, curation, query processing, and evaluation. The Bio-TDS's scientific impact was evaluated using sample questions posed by researchers retrieved from Biostars, a site focusing on BIOLOGICAL DATA ANALYSIS: The Bio-TDS was compared to five similar bioscience analytic tool retrieval systems with the Bio-TDS outperforming the others in terms of relevance and completeness. The Bio-TDS offers researchers the capacity to associate their bioscience question with the most relevant computational toolsets required for the data analysis in their knowledge discovery process. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Distributed environmental control

NASA Technical Reports Server (NTRS)

Cleveland, Gary A.

1992-01-01

We present an architecture of distributed, independent control agents designed to work with the Computer Aided System Engineering and Analysis (CASE/A) simulation tool. CASE/A simulates behavior of Environmental Control and Life Support Systems (ECLSS). We describe a lattice of agents capable of distributed sensing and overcoming certain sensor and effector failures. We address how the architecture can achieve the coordinating functions of a hierarchical command structure while maintaining the robustness and flexibility of independent agents. These agents work between the time steps of the CASE/A simulation tool to arrive at command decisions based on the state variables maintained by CASE/A. Control is evaluated according to both effectiveness (e.g., how well temperature was maintained) and resource utilization (the amount of power and materials used).

Applications of colored petri net and genetic algorithms to cluster tool scheduling

NASA Astrophysics Data System (ADS)

Liu, Tung-Kuan; Kuo, Chih-Jen; Hsiao, Yung-Chin; Tsai, Jinn-Tsong; Chou, Jyh-Horng

2005-12-01

In this paper, we propose a method, which uses Coloured Petri Net (CPN) and genetic algorithm (GA) to obtain an optimal deadlock-free schedule and to solve re-entrant problem for the flexible process of the cluster tool. The process of the cluster tool for producing a wafer usually can be classified into three types: 1) sequential process, 2) parallel process, and 3) sequential parallel process. But these processes are not economical enough to produce a variety of wafers in small volume. Therefore, this paper will propose the flexible process where the operations of fabricating wafers are randomly arranged to achieve the best utilization of the cluster tool. However, the flexible process may have deadlock and re-entrant problems which can be detected by CPN. On the other hand, GAs have been applied to find the optimal schedule for many types of manufacturing processes. Therefore, we successfully integrate CPN and GAs to obtain an optimal schedule with the deadlock and re-entrant problems for the flexible process of the cluster tool.

BCM: toolkit for Bayesian analysis of Computational Models using samplers.

PubMed

Thijssen, Bram; Dijkstra, Tjeerd M H; Heskes, Tom; Wessels, Lodewyk F A

2016-10-21

Computational models in biology are characterized by a large degree of uncertainty. This uncertainty can be analyzed with Bayesian statistics, however, the sampling algorithms that are frequently used for calculating Bayesian statistical estimates are computationally demanding, and each algorithm has unique advantages and disadvantages. It is typically unclear, before starting an analysis, which algorithm will perform well on a given computational model. We present BCM, a toolkit for the Bayesian analysis of Computational Models using samplers. It provides efficient, multithreaded implementations of eleven algorithms for sampling from posterior probability distributions and for calculating marginal likelihoods. BCM includes tools to simplify the process of model specification and scripts for visualizing the results. The flexible architecture allows it to be used on diverse types of biological computational models. In an example inference task using a model of the cell cycle based on ordinary differential equations, BCM is significantly more efficient than existing software packages, allowing more challenging inference problems to be solved. BCM represents an efficient one-stop-shop for computational modelers wishing to use sampler-based Bayesian statistics.

Computer Games as Therapy for Persons with Stroke.

PubMed

Lauterbach, Sarah A; Foreman, Matt H; Engsberg, Jack R

2013-02-01

Stroke affects approximately 800,000 individuals each year, with 65% having residual impairments. Studies have demonstrated that mass practice leads to regaining motor function in affected extremities; however, traditional therapy does not include the repetitions needed for this recovery. Videogames have been shown to be good motivators to complete repetitions. Advances in technology and low-cost hardware bring new opportunities to use computer games during stroke therapy. This study examined the use of the Microsoft (Redmond, WA) Kinect™ and Flexible Action and Articulated Skeleton Toolkit (FAAST) software as a therapy tool to play existing free computer games on the Internet. Three participants attended a 1-hour session where they played two games with upper extremity movements as game controls. Video was taken for analysis of movement repetitions, and questions were answered about participant history and their perceptions of the games. Participants remained engaged through both games; regardless of previous computer use all participants successfully played two games. Five minutes of game play averaged 34 repetitions of the affected extremity. The Intrinsic Motivation Inventory showed a high level of satisfaction in two of the three participants. The Kinect Sensor with the FAAST software has the potential to be an economical tool to be used alongside traditional therapy to increase the number of repetitions completed in a motivating and engaging way for clients.

High-resolution Modeling Assisted Design of Customized and Individualized Transcranial Direct Current Stimulation Protocols

PubMed Central

Bikson, Marom; Rahman, Asif; Datta, Abhishek; Fregni, Felipe; Merabet, Lotfi

2012-01-01

Objectives Transcranial direct current stimulation (tDCS) is a neuromodulatory technique that delivers low-intensity currents facilitating or inhibiting spontaneous neuronal activity. tDCS is attractive since dose is readily adjustable by simply changing electrode number, position, size, shape, and current. In the recent past, computational models have been developed with increased precision with the goal to help customize tDCS dose. The aim of this review is to discuss the incorporation of high-resolution patient-specific computer modeling to guide and optimize tDCS. Methods In this review, we discuss the following topics: (i) The clinical motivation and rationale for models of transcranial stimulation is considered pivotal in order to leverage the flexibility of neuromodulation; (ii) The protocols and the workflow for developing high-resolution models; (iii) The technical challenges and limitations of interpreting modeling predictions, and (iv) Real cases merging modeling and clinical data illustrating the impact of computational models on the rational design of rehabilitative electrotherapy. Conclusions Though modeling for non-invasive brain stimulation is still in its development phase, it is predicted that with increased validation, dissemination, simplification and democratization of modeling tools, computational forward models of neuromodulation will become useful tools to guide the optimization of clinical electrotherapy. PMID:22780230

Identifying Key Features, Cutting Edge Cloud Resources, and Artificial Intelligence Tools to Achieve User-Friendly Water Science in the Cloud

NASA Astrophysics Data System (ADS)

Pierce, S. A.

2017-12-01

Decision making for groundwater systems is becoming increasingly important, as shifting water demands increasingly impact aquifers. As buffer systems, aquifers provide room for resilient responses and augment the actual timeframe for hydrological response. Yet the pace impacts, climate shifts, and degradation of water resources is accelerating. To meet these new drivers, groundwater science is transitioning toward the emerging field of Integrated Water Resources Management, or IWRM. IWRM incorporates a broad array of dimensions, methods, and tools to address problems that tend to be complex. Computational tools and accessible cyberinfrastructure (CI) are needed to cross the chasm between science and society. Fortunately cloud computing environments, such as the new Jetstream system, are evolving rapidly. While still targeting scientific user groups systems such as, Jetstream, offer configurable cyberinfrastructure to enable interactive computing and data analysis resources on demand. The web-based interfaces allow researchers to rapidly customize virtual machines, modify computing architecture and increase the usability and access for broader audiences to advanced compute environments. The result enables dexterous configurations and opening up opportunities for IWRM modelers to expand the reach of analyses, number of case studies, and quality of engagement with stakeholders and decision makers. The acute need to identify improved IWRM solutions paired with advanced computational resources refocuses the attention of IWRM researchers on applications, workflows, and intelligent systems that are capable of accelerating progress. IWRM must address key drivers of community concern, implement transdisciplinary methodologies, adapt and apply decision support tools in order to effectively support decisions about groundwater resource management. This presentation will provide an overview of advanced computing services in the cloud using integrated groundwater management case studies to highlight how Cloud CI streamlines the process for setting up an interactive decision support system. Moreover, advances in artificial intelligence offer new techniques for old problems from integrating data to adaptive sensing or from interactive dashboards to optimizing multi-attribute problems. The combination of scientific expertise, flexible cloud computing solutions, and intelligent systems opens new research horizons.

NOTE: MMCTP: a radiotherapy research environment for Monte Carlo and patient-specific treatment planning

NASA Astrophysics Data System (ADS)

Alexander, A.; DeBlois, F.; Stroian, G.; Al-Yahya, K.; Heath, E.; Seuntjens, J.

2007-07-01

Radiotherapy research lacks a flexible computational research environment for Monte Carlo (MC) and patient-specific treatment planning. The purpose of this study was to develop a flexible software package on low-cost hardware with the aim of integrating new patient-specific treatment planning with MC dose calculations suitable for large-scale prospective and retrospective treatment planning studies. We designed the software package 'McGill Monte Carlo treatment planning' (MMCTP) for the research development of MC and patient-specific treatment planning. The MMCTP design consists of a graphical user interface (GUI), which runs on a simple workstation connected through standard secure-shell protocol to a cluster for lengthy MC calculations. Treatment planning information (e.g., images, structures, beam geometry properties and dose distributions) is converted into a convenient MMCTP local file storage format designated, the McGill RT format. MMCTP features include (a) DICOM_RT, RTOG and CADPlan CART format imports; (b) 2D and 3D visualization views for images, structure contours, and dose distributions; (c) contouring tools; (d) DVH analysis, and dose matrix comparison tools; (e) external beam editing; (f) MC transport calculation from beam source to patient geometry for photon and electron beams. The MC input files, which are prepared from the beam geometry properties and patient information (e.g., images and structure contours), are uploaded and run on a cluster using shell commands controlled from the MMCTP GUI. The visualization, dose matrix operation and DVH tools offer extensive options for plan analysis and comparison between MC plans and plans imported from commercial treatment planning systems. The MMCTP GUI provides a flexible research platform for the development of patient-specific MC treatment planning for photon and electron external beam radiation therapy. The impact of this tool lies in the fact that it allows for systematic, platform-independent, large-scale MC treatment planning for different treatment sites. Patient recalculations were performed to validate the software and ensure proper functionality.

Independent Metrics for Protein Backbone and Side-Chain Flexibility: Time Scales and Effects of Ligand Binding.

PubMed

Fuchs, Julian E; Waldner, Birgit J; Huber, Roland G; von Grafenstein, Susanne; Kramer, Christian; Liedl, Klaus R

2015-03-10

Conformational dynamics are central for understanding biomolecular structure and function, since biological macromolecules are inherently flexible at room temperature and in solution. Computational methods are nowadays capable of providing valuable information on the conformational ensembles of biomolecules. However, analysis tools and intuitive metrics that capture dynamic information from in silico generated structural ensembles are limited. In standard work-flows, flexibility in a conformational ensemble is represented through residue-wise root-mean-square fluctuations or B-factors following a global alignment. Consequently, these approaches relying on global alignments discard valuable information on local dynamics. Results inherently depend on global flexibility, residue size, and connectivity. In this study we present a novel approach for capturing positional fluctuations based on multiple local alignments instead of one single global alignment. The method captures local dynamics within a structural ensemble independent of residue type by splitting individual local and global degrees of freedom of protein backbone and side-chains. Dependence on residue type and size in the side-chains is removed via normalization with the B-factors of the isolated residue. As a test case, we demonstrate its application to a molecular dynamics simulation of bovine pancreatic trypsin inhibitor (BPTI) on the millisecond time scale. This allows for illustrating different time scales of backbone and side-chain flexibility. Additionally, we demonstrate the effects of ligand binding on side-chain flexibility of three serine proteases. We expect our new methodology for quantifying local flexibility to be helpful in unraveling local changes in biomolecular dynamics.

High-Fidelity Multidisciplinary Design Optimization of Aircraft Configurations

NASA Technical Reports Server (NTRS)

Martins, Joaquim R. R. A.; Kenway, Gaetan K. W.; Burdette, David; Jonsson, Eirikur; Kennedy, Graeme J.

2017-01-01

To evaluate new airframe technologies we need design tools based on high-fidelity models that consider multidisciplinary interactions early in the design process. The overarching goal of this NRA is to develop tools that enable high-fidelity multidisciplinary design optimization of aircraft configurations, and to apply these tools to the design of high aspect ratio flexible wings. We develop a geometry engine that is capable of quickly generating conventional and unconventional aircraft configurations including the internal structure. This geometry engine features adjoint derivative computation for efficient gradient-based optimization. We also added overset capability to a computational fluid dynamics solver, complete with an adjoint implementation and semiautomatic mesh generation. We also developed an approach to constraining buffet and started the development of an approach for constraining utter. On the applications side, we developed a new common high-fidelity model for aeroelastic studies of high aspect ratio wings. We performed optimal design trade-o s between fuel burn and aircraft weight for metal, conventional composite, and carbon nanotube composite wings. We also assessed a continuous morphing trailing edge technology applied to high aspect ratio wings. This research resulted in the publication of 26 manuscripts so far, and the developed methodologies were used in two other NRAs. 1

Extension of least squares spectral resolution algorithm to high-resolution lipidomics data.

PubMed

Zeng, Ying-Xu; Mjøs, Svein Are; David, Fabrice P A; Schmid, Adrien W

2016-03-31

Lipidomics, which focuses on the global study of molecular lipids in biological systems, has been driven tremendously by technical advances in mass spectrometry (MS) instrumentation, particularly high-resolution MS. This requires powerful computational tools that handle the high-throughput lipidomics data analysis. To address this issue, a novel computational tool has been developed for the analysis of high-resolution MS data, including the data pretreatment, visualization, automated identification, deconvolution and quantification of lipid species. The algorithm features the customized generation of a lipid compound library and mass spectral library, which covers the major lipid classes such as glycerolipids, glycerophospholipids and sphingolipids. Next, the algorithm performs least squares resolution of spectra and chromatograms based on the theoretical isotope distribution of molecular ions, which enables automated identification and quantification of molecular lipid species. Currently, this methodology supports analysis of both high and low resolution MS as well as liquid chromatography-MS (LC-MS) lipidomics data. The flexibility of the methodology allows it to be expanded to support more lipid classes and more data interpretation functions, making it a promising tool in lipidomic data analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

Proposed algorithm to improve job shop production scheduling using ant colony optimization method

NASA Astrophysics Data System (ADS)

Pakpahan, Eka KA; Kristina, Sonna; Setiawan, Ari

2017-12-01

This paper deals with the determination of job shop production schedule on an automatic environment. On this particular environment, machines and material handling system are integrated and controlled by a computer center where schedule were created and then used to dictate the movement of parts and the operations at each machine. This setting is usually designed to have an unmanned production process for a specified interval time. We consider here parts with various operations requirement. Each operation requires specific cutting tools. These parts are to be scheduled on machines each having identical capability, meaning that each machine is equipped with a similar set of cutting tools therefore is capable of processing any operation. The availability of a particular machine to process a particular operation is determined by the remaining life time of its cutting tools. We proposed an algorithm based on the ant colony optimization method and embedded them on matlab software to generate production schedule which minimize the total processing time of the parts (makespan). We test the algorithm on data provided by real industry and the process shows a very short computation time. This contributes a lot to the flexibility and timelines targeted on an automatic environment.

TNSPackage: A Fortran2003 library designed for tensor network state methods

NASA Astrophysics Data System (ADS)

Dong, Shao-Jun; Liu, Wen-Yuan; Wang, Chao; Han, Yongjian; Guo, G.-C.; He, Lixin

2018-07-01

Recently, the tensor network states (TNS) methods have proven to be very powerful tools to investigate the strongly correlated many-particle physics in one and two dimensions. The implementation of TNS methods depends heavily on the operations of tensors, including contraction, permutation, reshaping tensors, SVD and so on. Unfortunately, the most popular computer languages for scientific computation, such as Fortran and C/C++ do not have a standard library for such operations, and therefore make the coding of TNS very tedious. We develop a Fortran2003 package that includes all kinds of basic tensor operations designed for TNS. It is user-friendly and flexible for different forms of TNS, and therefore greatly simplifies the coding work for the TNS methods.

Building a computer-aided design capability using a standard time share operating system

NASA Technical Reports Server (NTRS)

Sobieszczanski, J.

1975-01-01

The paper describes how an integrated system of engineering computer programs can be built using a standard commercially available operating system. The discussion opens with an outline of the auxiliary functions that an operating system can perform for a team of engineers involved in a large and complex task. An example of a specific integrated system is provided to explain how the standard operating system features can be used to organize the programs into a simple and inexpensive but effective system. Applications to an aircraft structural design study are discussed to illustrate the use of an integrated system as a flexible and efficient engineering tool. The discussion concludes with an engineer's assessment of an operating system's capabilities and desirable improvements.

A High-Availability, Distributed Hardware Control System Using Java

NASA Technical Reports Server (NTRS)

Niessner, Albert F.

2011-01-01

Two independent coronagraph experiments that require 24/7 availability with different optical layouts and different motion control requirements are commanded and controlled with the same Java software system executing on many geographically scattered computer systems interconnected via TCP/IP. High availability of a distributed system requires that the computers have a robust communication messaging system making the mix of TCP/IP (a robust transport), and XML (a robust message) a natural choice. XML also adds the configuration flexibility. Java then adds object-oriented paradigms, exception handling, heavily tested libraries, and many third party tools for implementation robustness. The result is a software system that provides users 24/7 access to two diverse experiments with XML files defining the differences

PopSc: Computing Toolkit for Basic Statistics of Molecular Population Genetics Simultaneously Implemented in Web-Based Calculator, Python and R

PubMed Central

Huang, Ying; Li, Cao; Liu, Linhai; Jia, Xianbo; Lai, Song-Jia

2016-01-01

Although various computer tools have been elaborately developed to calculate a series of statistics in molecular population genetics for both small- and large-scale DNA data, there is no efficient and easy-to-use toolkit available yet for exclusively focusing on the steps of mathematical calculation. Here, we present PopSc, a bioinformatic toolkit for calculating 45 basic statistics in molecular population genetics, which could be categorized into three classes, including (i) genetic diversity of DNA sequences, (ii) statistical tests for neutral evolution, and (iii) measures of genetic differentiation among populations. In contrast to the existing computer tools, PopSc was designed to directly accept the intermediate metadata, such as allele frequencies, rather than the raw DNA sequences or genotyping results. PopSc is first implemented as the web-based calculator with user-friendly interface, which greatly facilitates the teaching of population genetics in class and also promotes the convenient and straightforward calculation of statistics in research. Additionally, we also provide the Python library and R package of PopSc, which can be flexibly integrated into other advanced bioinformatic packages of population genetics analysis. PMID:27792763

Verifying Stability of Dynamic Soft-Computing Systems

NASA Technical Reports Server (NTRS)

Wen, Wu; Napolitano, Marcello; Callahan, John

1997-01-01

Soft computing is a general term for algorithms that learn from human knowledge and mimic human skills. Example of such algorithms are fuzzy inference systems and neural networks. Many applications, especially in control engineering, have demonstrated their appropriateness in building intelligent systems that are flexible and robust. Although recent research have shown that certain class of neuro-fuzzy controllers can be proven bounded and stable, they are implementation dependent and difficult to apply to the design and validation process. Many practitioners adopt the trial and error approach for system validation or resort to exhaustive testing using prototypes. In this paper, we describe our on-going research towards establishing necessary theoretic foundation as well as building practical tools for the verification and validation of soft-computing systems. A unified model for general neuro-fuzzy system is adopted. Classic non-linear system control theory and recent results of its applications to neuro-fuzzy systems are incorporated and applied to the unified model. It is hoped that general tools can be developed to help the designer to visualize and manipulate the regions of stability and boundedness, much the same way Bode plots and Root locus plots have helped conventional control design and validation.

PopSc: Computing Toolkit for Basic Statistics of Molecular Population Genetics Simultaneously Implemented in Web-Based Calculator, Python and R.

PubMed

Chen, Shi-Yi; Deng, Feilong; Huang, Ying; Li, Cao; Liu, Linhai; Jia, Xianbo; Lai, Song-Jia

2016-01-01

Although various computer tools have been elaborately developed to calculate a series of statistics in molecular population genetics for both small- and large-scale DNA data, there is no efficient and easy-to-use toolkit available yet for exclusively focusing on the steps of mathematical calculation. Here, we present PopSc, a bioinformatic toolkit for calculating 45 basic statistics in molecular population genetics, which could be categorized into three classes, including (i) genetic diversity of DNA sequences, (ii) statistical tests for neutral evolution, and (iii) measures of genetic differentiation among populations. In contrast to the existing computer tools, PopSc was designed to directly accept the intermediate metadata, such as allele frequencies, rather than the raw DNA sequences or genotyping results. PopSc is first implemented as the web-based calculator with user-friendly interface, which greatly facilitates the teaching of population genetics in class and also promotes the convenient and straightforward calculation of statistics in research. Additionally, we also provide the Python library and R package of PopSc, which can be flexibly integrated into other advanced bioinformatic packages of population genetics analysis.

Development of methodology for horizontal axis wind turbine dynamic analysis

NASA Technical Reports Server (NTRS)

Dugundji, J.

1982-01-01

Horizontal axis wind turbine dynamics were studied. The following findings are summarized: (1) review of the MOSTAS computer programs for dynamic analysis of horizontal axis wind turbines; (2) review of various analysis methods for rotating systems with periodic coefficients; (3) review of structural dynamics analysis tools for large wind turbine; (4) experiments for yaw characteristics of a rotating rotor; (5) development of a finite element model for rotors; (6) development of simple models for aeroelastics; and (7) development of simple models for stability and response of wind turbines on flexible towers.

An object oriented Python interface for atomistic simulations

NASA Astrophysics Data System (ADS)

Hynninen, T.; Himanen, L.; Parkkinen, V.; Musso, T.; Corander, J.; Foster, A. S.

2016-01-01

Programmable simulation environments allow one to monitor and control calculations efficiently and automatically before, during, and after runtime. Environments directly accessible in a programming environment can be interfaced with powerful external analysis tools and extensions to enhance the functionality of the core program, and by incorporating a flexible object based structure, the environments make building and analysing computational setups intuitive. In this work, we present a classical atomistic force field with an interface written in Python language. The program is an extension for an existing object based atomistic simulation environment.

Computational tools for multi-linked flexible structures

NASA Technical Reports Server (NTRS)

Lee, Gordon K. F.; Brubaker, Thomas A.; Shults, James R.

1990-01-01

A software module which designs and tests controllers and filters in Kalman Estimator form, based on a polynomial state-space model is discussed. The user-friendly program employs an interactive graphics approach to simplify the design process. A variety of input methods are provided to test the effectiveness of the estimator. Utilities are provided which address important issues in filter design such as graphical analysis, statistical analysis, and calculation time. The program also provides the user with the ability to save filter parameters, inputs, and outputs for future use.

Designing a training tool for imaging mental models

NASA Technical Reports Server (NTRS)

Dede, Christopher J.; Jayaram, Geetha

1990-01-01

The training process can be conceptualized as the student acquiring an evolutionary sequence of classification-problem solving mental models. For example a physician learns (1) classification systems for patient symptoms, diagnostic procedures, diseases, and therapeutic interventions and (2) interrelationships among these classifications (e.g., how to use diagnostic procedures to collect data about a patient's symptoms in order to identify the disease so that therapeutic measures can be taken. This project developed functional specifications for a computer-based tool, Mental Link, that allows the evaluative imaging of such mental models. The fundamental design approach underlying this representational medium is traversal of virtual cognition space. Typically intangible cognitive entities and links among them are visible as a three-dimensional web that represents a knowledge structure. The tool has a high degree of flexibility and customizability to allow extension to other types of uses, such a front-end to an intelligent tutoring system, knowledge base, hypermedia system, or semantic network.

Designing a Software Tool for Fuzzy Logic Programming

NASA Astrophysics Data System (ADS)

Abietar, José M.; Morcillo, Pedro J.; Moreno, Ginés

2007-12-01

Fuzzy Logic Programming is an interesting and still growing research area that agglutinates the efforts for introducing fuzzy logic into logic programming (LP), in order to incorporate more expressive resources on such languages for dealing with uncertainty and approximated reasoning. The multi-adjoint logic programming approach is a recent and extremely flexible fuzzy logic paradigm for which, unfortunately, we have not found practical tools implemented so far. In this work, we describe a prototype system which is able to directly translate fuzzy logic programs into Prolog code in order to safely execute these residual programs inside any standard Prolog interpreter in a completely transparent way for the final user. We think that the development of such fuzzy languages and programing tools might play an important role in the design of advanced software applications for computational physics, chemistry, mathematics, medicine, industrial control and so on.

R-based Tool for a Pairwise Structure-activity Relationship Analysis.

PubMed

Klimenko, Kyrylo

2018-04-01

The Structure-Activity Relationship analysis is a complex process that can be enhanced by computational techniques. This article describes a simple tool for SAR analysis that has a graphic user interface and a flexible approach towards the input of molecular data. The application allows calculating molecular similarity represented by Tanimoto index & Euclid distance, as well as, determining activity cliffs by means of Structure-Activity Landscape Index. The calculation is performed in a pairwise manner either for the reference compound and other compounds or for all possible pairs in the data set. The results of SAR analysis are visualized using two types of plot. The application capability is demonstrated by the analysis of a set of COX2 inhibitors with respect to Isoxicam. This tool is available online: it includes manual and input file examples. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Strategic Flexibility in Computational Estimation for Chinese- and Canadian-Educated Adults

ERIC Educational Resources Information Center

Xu, Chang; Wells, Emma; LeFevre, Jo-Anne; Imbo, Ineke

2014-01-01

The purpose of the present study was to examine factors that influence strategic flexibility in computational estimation for Chinese- and Canadian-educated adults. Strategic flexibility was operationalized as the percentage of trials on which participants chose the problem-based procedure that best balanced proximity to the correct answer with…

Rigidity controllable polishing tool based on magnetorheological effect

NASA Astrophysics Data System (ADS)

Wang, Jia; Wan, Yongjian; Shi, Chunyan

2012-10-01

A stable and predictable material removal function (MRF) plays a crucial role in computer controlled optical surfacing (CCOS). For physical contact polishing case, the stability of MRF depends on intimate contact between polishing interface and workpiece. Rigid laps maintain this function in polishing spherical surfaces, whose curvature has no variation with the position on the surface. Such rigid laps provide smoothing effect for mid-spatial frequency errors, but can't be used in aspherical surfaces for they will destroy the surface figure. Flexible tools such as magnetorheological fluid or air bonnet conform to the surface [1]. They lack rigidity and provide little natural smoothing effect. We present a rigidity controllable polishing tool that uses a kind of magnetorheological elastomers (MRE) medium [2]. It provides the ability of both conforming to the aspheric surface and maintaining natural smoothing effect. What's more, its rigidity can be controlled by the magnetic field. This paper will present the design, analysis, and stiffness variation mechanism model of such polishing tool [3].

Fragment informatics and computational fragment-based drug design: an overview and update.

PubMed

Sheng, Chunquan; Zhang, Wannian

2013-05-01

Fragment-based drug design (FBDD) is a promising approach for the discovery and optimization of lead compounds. Despite its successes, FBDD also faces some internal limitations and challenges. FBDD requires a high quality of target protein and good solubility of fragments. Biophysical techniques for fragment screening necessitate expensive detection equipment and the strategies for evolving fragment hits to leads remain to be improved. Regardless, FBDD is necessary for investigating larger chemical space and can be applied to challenging biological targets. In this scenario, cheminformatics and computational chemistry can be used as alternative approaches that can significantly improve the efficiency and success rate of lead discovery and optimization. Cheminformatics and computational tools assist FBDD in a very flexible manner. Computational FBDD can be used independently or in parallel with experimental FBDD for efficiently generating and optimizing leads. Computational FBDD can also be integrated into each step of experimental FBDD and help to play a synergistic role by maximizing its performance. This review will provide critical analysis of the complementarity between computational and experimental FBDD and highlight recent advances in new algorithms and successful examples of their applications. In particular, fragment-based cheminformatics tools, high-throughput fragment docking, and fragment-based de novo drug design will provide the focus of this review. We will also discuss the advantages and limitations of different methods and the trends in new developments that should inspire future research. © 2012 Wiley Periodicals, Inc.

HTAPP: High-Throughput Autonomous Proteomic Pipeline

PubMed Central

Yu, Kebing; Salomon, Arthur R.

2011-01-01

Recent advances in the speed and sensitivity of mass spectrometers and in analytical methods, the exponential acceleration of computer processing speeds, and the availability of genomic databases from an array of species and protein information databases have led to a deluge of proteomic data. The development of a lab-based automated proteomic software platform for the automated collection, processing, storage, and visualization of expansive proteomic datasets is critically important. The high-throughput autonomous proteomic pipeline (HTAPP) described here is designed from the ground up to provide critically important flexibility for diverse proteomic workflows and to streamline the total analysis of a complex proteomic sample. This tool is comprised of software that controls the acquisition of mass spectral data along with automation of post-acquisition tasks such as peptide quantification, clustered MS/MS spectral database searching, statistical validation, and data exploration within a user-configurable lab-based relational database. The software design of HTAPP focuses on accommodating diverse workflows and providing missing software functionality to a wide range of proteomic researchers to accelerate the extraction of biological meaning from immense proteomic data sets. Although individual software modules in our integrated technology platform may have some similarities to existing tools, the true novelty of the approach described here is in the synergistic and flexible combination of these tools to provide an integrated and efficient analysis of proteomic samples. PMID:20336676

Can enzyme engineering benefit from the modulation of protein motions? Lessons learned from NMR relaxation dispersion experiments.

PubMed

Doucet, Nicolas

2011-04-01

Despite impressive progress in protein engineering and design, our ability to create new and efficient enzyme activities remains a laborious and time-consuming endeavor. In the past few years, intricate combinations of rational mutagenesis, directed evolution and computational methods have paved the way to exciting engineering examples and are now offering a new perspective on the structural requirements of enzyme activity. However, these structure-function analyses are usually guided by the time-averaged static models offered by enzyme crystal structures, which often fail to describe the functionally relevant 'invisible states' adopted by proteins in space and time. To alleviate such limitations, NMR relaxation dispersion experiments coupled to mutagenesis studies have recently been applied to the study of enzyme catalysis, effectively complementing 'structure-function' analyses with 'flexibility-function' investigations. In addition to offering quantitative, site-specific information to help characterize residue motion, these NMR methods are now being applied to enzyme engineering purposes, providing a powerful tool to help characterize the effects of controlling long-range networks of flexible residues affecting enzyme function. Recent advancements in this emerging field are presented here, with particular attention to mutagenesis reports highlighting the relevance of NMR relaxation dispersion tools in enzyme engineering.

Online, offline, realtime: recent developments in industrial photogrammetry

NASA Astrophysics Data System (ADS)

Boesemann, Werner

2003-01-01

In recent years industrial photogrammetry has emerged from a highly specialized niche technology to a well established tool in industrial coordinate measurement applications with numerous installations in a significantly growing market of flexible and portable optical measurement systems. This is due to the development of powerful, but affordable video and computer technology. The increasing industrial requirements for accuracy, speed, robustness and ease of use of these systems together with a demand for the highest possible degree of automation have forced universities and system manufacturer to develop hard- and software solutions to meet these requirements. The presentation will show the latest trends in hardware development, especially new generation digital and/or intelligent cameras, aspects of image engineering like use of controlled illumination or projection technologies, and algorithmic and software aspects like automation strategies or new camera models. The basic qualities of digital photogrammetry- like portability and flexibility on one hand and fully automated quality control on the other - sometimes lead to certain conflicts in the design of measurement systems for different online, offline, or real-time solutions. The presentation will further show, how these tools and methods are combined in different configurations to be able to cover the still growing demands of the industrial end-users.

Photogrammetry in the line: recent developments in industrial photogrammetry

NASA Astrophysics Data System (ADS)

Boesemann, Werner

2003-05-01

In recent years industrial photogrammetry has emerged from a highly specialized niche technology to a well established tool in industrial coordinate measurement applications with numerous installations in a significantly growing market of flexible and portable optical measurement systems. This is due to the development of powerful, but affordable video and computer technology. The increasing industrial requirements for accuracy, speed, robustness and ease of use of these systems together with a demand for the highest possible degree of automation have forced universities and system manufacturers to develop hard- and software solutions to meet these requirements. The presentation will show the latest trends in hardware development, especially new generation digital and/or intelligent cameras, aspects of image engineering like use of controlled illumination or projection technologies,and algorithmic and software aspects like automation strategies or new camera models. The basic qualities of digital photogrammetry-like portability and flexibility on one hand and fully automated quality control on the other -- sometimes lead to certain conflicts in the design of measurement systems for different online, offline or real-time solutions. The presentation will further show, how these tools and methods are combined in different configurations to be able to cover the still growing demands of the industrial end-users.

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.

An investigation of constraint-based component-modeling for knowledge representation in computer-aided conceptual design

NASA Technical Reports Server (NTRS)

Kolb, Mark A.

1990-01-01

Originally, computer programs for engineering design focused on detailed geometric design. Later, computer programs for algorithmically performing the preliminary design of specific well-defined classes of objects became commonplace. However, due to the need for extreme flexibility, it appears unlikely that conventional programming techniques will prove fruitful in developing computer aids for engineering conceptual design. The use of symbolic processing techniques, such as object-oriented programming and constraint propagation, facilitate such flexibility. Object-oriented programming allows programs to be organized around the objects and behavior to be simulated, rather than around fixed sequences of function- and subroutine-calls. Constraint propagation allows declarative statements to be understood as designating multi-directional mathematical relationships among all the variables of an equation, rather than as unidirectional assignments to the variable on the left-hand side of the equation, as in conventional computer programs. The research has concentrated on applying these two techniques to the development of a general-purpose computer aid for engineering conceptual design. Object-oriented programming techniques are utilized to implement a user-extensible database of design components. The mathematical relationships which model both geometry and physics of these components are managed via constraint propagation. In addition, to this component-based hierarchy, special-purpose data structures are provided for describing component interactions and supporting state-dependent parameters. In order to investigate the utility of this approach, a number of sample design problems from the field of aerospace engineering were implemented using the prototype design tool, Rubber Airplane. The additional level of organizational structure obtained by representing design knowledge in terms of components is observed to provide greater convenience to the program user, and to result in a database of engineering information which is easier both to maintain and to extend.

Static aeroelastic analysis and tailoring of a single-element racing car wing

NASA Astrophysics Data System (ADS)

Sadd, Christopher James

This thesis presents the research from an Engineering Doctorate research programme in collaboration with Reynard Motorsport Ltd, a manufacturer of racing cars. Racing car wing design has traditionally considered structures to be rigid. However, structures are never perfectly rigid and the interaction between aerodynamic loading and structural flexibility has a direct impact on aerodynamic performance. This interaction is often referred to as static aeroelasticity and the focus of this research has been the development of a computational static aeroelastic analysis method to improve the design of a single-element racing car wing. A static aeroelastic analysis method has been developed by coupling a Reynolds-Averaged Navier-Stokes CFD analysis method with a Finite Element structural analysis method using an iterative scheme. Development of this method has included assessment of CFD and Finite Element analysis methods and development of data transfer and mesh deflection methods. Experimental testing was also completed to further assess the computational analyses. The computational and experimental results show a good correlation and these studies have also shown that a Navier-Stokes static aeroelastic analysis of an isolated wing can be performed at an acceptable computational cost. The static aeroelastic analysis tool was used to assess methods of tailoring the structural flexibility of the wing to increase its aerodynamic performance. These tailoring methods were then used to produce two final wing designs to increase downforce and reduce drag respectively. At the average operating dynamic pressure of the racing car, the computational analysis predicts that the downforce-increasing wing has a downforce of C[1]=-1.377 in comparison to C[1]=-1.265 for the original wing. The computational analysis predicts that the drag-reducing wing has a drag of C[d]=0.115 in comparison to C[d]=0.143 for the original wing.

Bayesian networks of age estimation and classification based on dental evidence: A study on the third molar mineralization.

PubMed

Sironi, Emanuele; Pinchi, Vilma; Pradella, Francesco; Focardi, Martina; Bozza, Silvia; Taroni, Franco

2018-04-01

Not only does the Bayesian approach offer a rational and logical environment for evidence evaluation in a forensic framework, but it also allows scientists to coherently deal with uncertainty related to a collection of multiple items of evidence, due to its flexible nature. Such flexibility might come at the expense of elevated computational complexity, which can be handled by using specific probabilistic graphical tools, namely Bayesian networks. In the current work, such probabilistic tools are used for evaluating dental evidence related to the development of third molars. A set of relevant properties characterizing the graphical models are discussed and Bayesian networks are implemented to deal with the inferential process laying beyond the estimation procedure, as well as to provide age estimates. Such properties include operationality, flexibility, coherence, transparence and sensitivity. A data sample composed of Italian subjects was employed for the analysis; results were in agreement with previous studies in terms of point estimate and age classification. The influence of the prior probability elicitation in terms of Bayesian estimate and classifies was also analyzed. Findings also supported the opportunity to take into consideration multiple teeth in the evaluative procedure, since it can be shown this results in an increased robustness towards the prior probability elicitation process, as well as in more favorable outcomes from a forensic perspective. Copyright © 2018 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

Loci-STREAM Version 0.9

NASA Technical Reports Server (NTRS)

Wright, Jeffrey; Thakur, Siddharth

2006-01-01

Loci-STREAM is an evolving computational fluid dynamics (CFD) software tool for simulating possibly chemically reacting, possibly unsteady flows in diverse settings, including rocket engines, turbomachines, oil refineries, etc. Loci-STREAM implements a pressure- based flow-solving algorithm that utilizes unstructured grids. (The benefit of low memory usage by pressure-based algorithms is well recognized by experts in the field.) The algorithm is robust for flows at all speeds from zero to hypersonic. The flexibility of arbitrary polyhedral grids enables accurate, efficient simulation of flows in complex geometries, including those of plume-impingement problems. The present version - Loci-STREAM version 0.9 - includes an interface with the Portable, Extensible Toolkit for Scientific Computation (PETSc) library for access to enhanced linear-equation-solving programs therein that accelerate convergence toward a solution. The name "Loci" reflects the creation of this software within the Loci computational framework, which was developed at Mississippi State University for the primary purpose of simplifying the writing of complex multidisciplinary application programs to run in distributed-memory computing environments including clusters of personal computers. Loci has been designed to relieve application programmers of the details of programming for distributed-memory computers.

Dynamic analysis of flexible mechanical systems using LATDYN

NASA Technical Reports Server (NTRS)

Wu, Shih-Chin; Chang, Che-Wei; Housner, Jerrold M.

1989-01-01

A 3-D, finite element based simulation tool for flexible multibody systems is presented. Hinge degrees-of-freedom is built into equations of motion to reduce geometric constraints. The approach avoids the difficulty in selecting deformation modes for flexible components by using assumed mode method. The tool is applied to simulate a practical space structure deployment problem. Results of examples demonstrate the capability of the code and approach.

Simultaneous Aerodynamic Analysis and Design Optimization (SAADO) for a 3-D Flexible Wing

NASA Technical Reports Server (NTRS)

Gumbert, Clyde R.; Hou, Gene J.-W.

2001-01-01

The formulation and implementation of an optimization method called Simultaneous Aerodynamic Analysis and Design Optimization (SAADO) are extended from single discipline analysis (aerodynamics only) to multidisciplinary analysis - in this case, static aero-structural analysis - and applied to a simple 3-D wing problem. The method aims to reduce the computational expense incurred in performing shape optimization using state-of-the-art Computational Fluid Dynamics (CFD) flow analysis, Finite Element Method (FEM) structural analysis and sensitivity analysis tools. Results for this small problem show that the method reaches the same local optimum as conventional optimization. However, unlike its application to the win,, (single discipline analysis), the method. as I implemented here, may not show significant reduction in the computational cost. Similar reductions were seen in the two-design-variable (DV) problem results but not in the 8-DV results given here.

Computer-assisted concept mapping: Visual aids for knowledge construction

PubMed Central

Mammen, Jennifer R.

2016-01-01

Background Concept mapping is a visual representation of ideas that facilitates critical thinking and is applicable to many areas of nursing education. Computer-Assisted Concept Maps are more flexible and less constrained than traditional paper methods, allowing for analysis and synthesis of complex topics and larger amounts of data. Ability to iteratively revise and collaboratively create computerized maps can contribute to enhanced interpersonal learning. However, there is limited awareness of free software that can support these types of applications. Discussion This educational brief examines affordances and limitations of Computer-Assisted Concept Maps and reviews free software for development of complex, collaborative malleable maps. Free software such as VUE, Xmind, MindMaple, and others can substantially contribute to utility of concept-mapping for nursing education. Conclusions Computerized concept-mapping is an important tool for nursing and is likely to hold greater benefit for students and faculty than traditional pen and paper methods alone. PMID:27351610

Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline.

PubMed

Reid, Jeffrey G; Carroll, Andrew; Veeraraghavan, Narayanan; Dahdouli, Mahmoud; Sundquist, Andreas; English, Adam; Bainbridge, Matthew; White, Simon; Salerno, William; Buhay, Christian; Yu, Fuli; Muzny, Donna; Daly, Richard; Duyk, Geoff; Gibbs, Richard A; Boerwinkle, Eric

2014-01-29

Massively parallel DNA sequencing generates staggering amounts of data. Decreasing cost, increasing throughput, and improved annotation have expanded the diversity of genomics applications in research and clinical practice. This expanding scale creates analytical challenges: accommodating peak compute demand, coordinating secure access for multiple analysts, and sharing validated tools and results. To address these challenges, we have developed the Mercury analysis pipeline and deployed it in local hardware and the Amazon Web Services cloud via the DNAnexus platform. Mercury is an automated, flexible, and extensible analysis workflow that provides accurate and reproducible genomic results at scales ranging from individuals to large cohorts. By taking advantage of cloud computing and with Mercury implemented on the DNAnexus platform, we have demonstrated a powerful combination of a robust and fully validated software pipeline and a scalable computational resource that, to date, we have applied to more than 10,000 whole genome and whole exome samples.

Large scale rigidity-based flexibility analysis of biomolecules

PubMed Central

Streinu, Ileana

2016-01-01

KINematics And RIgidity (KINARI) is an on-going project for in silico flexibility analysis of proteins. The new version of the software, Kinari-2, extends the functionality of our free web server KinariWeb, incorporates advanced web technologies, emphasizes the reproducibility of its experiments, and makes substantially improved tools available to the user. It is designed specifically for large scale experiments, in particular, for (a) very large molecules, including bioassemblies with high degree of symmetry such as viruses and crystals, (b) large collections of related biomolecules, such as those obtained through simulated dilutions, mutations, or conformational changes from various types of dynamics simulations, and (c) is intended to work as seemlessly as possible on the large, idiosyncratic, publicly available repository of biomolecules, the Protein Data Bank. We describe the system design, along with the main data processing, computational, mathematical, and validation challenges underlying this phase of the KINARI project. PMID:26958583

Rule-based optimization and multicriteria decision support for packaging a truck chassis

NASA Astrophysics Data System (ADS)

Berger, Martin; Lindroth, Peter; Welke, Richard

2017-06-01

Trucks are highly individualized products where exchangeable parts are flexibly combined to suit different customer requirements, this leading to a great complexity in product development. Therefore, an optimization approach based on constraint programming is proposed for automatically packaging parts of a truck chassis by following packaging rules expressed as constraints. A multicriteria decision support system is developed where a database of truck layouts is computed, among which interactive navigation then can be performed. The work has been performed in cooperation with Volvo Group Trucks Technology (GTT), from which specific rules have been used. Several scenarios are described where the methods developed can be successfully applied and lead to less time-consuming manual work, fewer mistakes, and greater flexibility in configuring trucks. A numerical evaluation is also presented showing the efficiency and practical relevance of the methods, which are implemented in a software tool.

DOT2: Macromolecular Docking With Improved Biophysical Models

PubMed Central

Roberts, Victoria A.; Thompson, Elaine E.; Pique, Michael E.; Perez, Martin S.; Eyck, Lynn Ten

2015-01-01

Computational docking is a useful tool for predicting macromolecular complexes, which are often difficult to determine experimentally. Here we present the DOT2 software suite, an updated version of the DOT intermolecular docking program. DOT2 provides straightforward, automated construction of improved biophysical models based on molecular coordinates, offering checkpoints that guide the user to include critical features. DOT has been updated to run more quickly, allow flexibility in grid size and spacing, and generate a complete list of favorable candidate configu-rations. Output can be filtered by experimental data and rescored by the sum of electrostatic and atomic desolvation energies. We show that this rescoring method improves the ranking of correct complexes for a wide range of macromolecular interactions, and demonstrate that biologically relevant models are essential for biologically relevant results. The flexibility and versatility of DOT2 accommodate realistic models of complex biological systems, improving the likelihood of a successful docking outcome. PMID:23695987

CAST: a new program package for the accurate characterization of large and flexible molecular systems.

PubMed

Grebner, Christoph; Becker, Johannes; Weber, Daniel; Bellinger, Daniel; Tafipolski, Maxim; Brückner, Charlotte; Engels, Bernd

2014-09-15

The presented program package, Conformational Analysis and Search Tool (CAST) allows the accurate treatment of large and flexible (macro) molecular systems. For the determination of thermally accessible minima CAST offers the newly developed TabuSearch algorithm, but algorithms such as Monte Carlo (MC), MC with minimization, and molecular dynamics are implemented as well. For the determination of reaction paths, CAST provides the PathOpt, the Nudge Elastic band, and the umbrella sampling approach. Access to free energies is possible through the free energy perturbation approach. Along with a number of standard force fields, a newly developed symmetry-adapted perturbation theory-based force field is included. Semiempirical computations are possible through DFTB+ and MOPAC interfaces. For calculations based on density functional theory, a Message Passing Interface (MPI) interface to the Graphics Processing Unit (GPU)-accelerated TeraChem program is available. The program is available on request. Copyright © 2014 Wiley Periodicals, Inc.

Bending induced electrical response variations in ultra-thin flexible chips and device modeling

NASA Astrophysics Data System (ADS)

Heidari, Hadi; Wacker, Nicoleta; Dahiya, Ravinder

2017-09-01

Electronics that conform to 3D surfaces are attracting wider attention from both academia and industry. The research in the field has, thus far, focused primarily on showcasing the efficacy of various materials and fabrication methods for electronic/sensing devices on flexible substrates. As the device response changes are bound to change with stresses induced by bending, the next step will be to develop the capacity to predict the response of flexible systems under various bending conditions. This paper comprehensively reviews the effects of bending on the response of devices on ultra-thin chips in terms of variations in electrical parameters such as mobility, threshold voltage, and device performance (static and dynamic). The discussion also includes variations in the device response due to crystal orientation, applied mechanics, band structure, and fabrication processes. Further, strategies for compensating or minimizing these bending-induced variations have been presented. Following the in-depth analysis, this paper proposes new mathematical relations to simulate and predict the device response under various bending conditions. These mathematical relations have also been used to develop new compact models that have been verified by comparing simulation results with the experimental values reported in the recent literature. These advances will enable next generation computer-aided-design tools to meet the future design needs in flexible electronics.

Fluid-structure coupling for wind turbine blade analysis using OpenFOAM

NASA Astrophysics Data System (ADS)

Dose, Bastian; Herraez, Ivan; Peinke, Joachim

2015-11-01

Modern wind turbine rotor blades are designed increasingly large and flexible. This structural flexibility represents a problem for the field of Computational Fluid Dynamics (CFD), which is used for accurate load calculations and detailed investigations of rotor aerodynamics. As the blade geometries within CFD simulations are considered stiff, the effect of blade deformation caused by aerodynamic loads cannot be captured by the common CFD approach. Coupling the flow solver with a structural solver can overcome this restriction and enables the investigation of flexible wind turbine blades. For this purpose, a new Finite Element (FE) solver was implemented into the open source CFD code OpenFOAM. Using a beam element formulation based on the Geometrically Exact Beam Theory (GEBT), the structural model can capture geometric non-linearities such as large deformations. Coupled with CFD solvers of the OpenFOAM package, the new framework represents a powerful tool for aerodynamic investigations. In this work, we investigated the aerodynamic performance of a state of the art wind turbine. For different wind speeds, aerodynamic key parameters are evaluated and compared for both, rigid and flexible blade geometries. The present work is funded within the framework of the joint project Smart Blades (0325601D) by the German Federal Ministry for Economic Affairs and Energy (BMWi) under decision of the German Federal Parliament.

Vivaldi: A Domain-Specific Language for Volume Processing and Visualization on Distributed Heterogeneous Systems.

PubMed

Choi, Hyungsuk; Choi, Woohyuk; Quan, Tran Minh; Hildebrand, David G C; Pfister, Hanspeter; Jeong, Won-Ki

2014-12-01

As the size of image data from microscopes and telescopes increases, the need for high-throughput processing and visualization of large volumetric data has become more pressing. At the same time, many-core processors and GPU accelerators are commonplace, making high-performance distributed heterogeneous computing systems affordable. However, effectively utilizing GPU clusters is difficult for novice programmers, and even experienced programmers often fail to fully leverage the computing power of new parallel architectures due to their steep learning curve and programming complexity. In this paper, we propose Vivaldi, a new domain-specific language for volume processing and visualization on distributed heterogeneous computing systems. Vivaldi's Python-like grammar and parallel processing abstractions provide flexible programming tools for non-experts to easily write high-performance parallel computing code. Vivaldi provides commonly used functions and numerical operators for customized visualization and high-throughput image processing applications. We demonstrate the performance and usability of Vivaldi on several examples ranging from volume rendering to image segmentation.

Integrating Reconfigurable Hardware-Based Grid for High Performance Computing

PubMed Central

Dondo Gazzano, Julio; Sanchez Molina, Francisco; Rincon, Fernando; López, Juan Carlos

2015-01-01

FPGAs have shown several characteristics that make them very attractive for high performance computing (HPC). The impressive speed-up factors that they are able to achieve, the reduced power consumption, and the easiness and flexibility of the design process with fast iterations between consecutive versions are examples of benefits obtained with their use. However, there are still some difficulties when using reconfigurable platforms as accelerator that need to be addressed: the need of an in-depth application study to identify potential acceleration, the lack of tools for the deployment of computational problems in distributed hardware platforms, and the low portability of components, among others. This work proposes a complete grid infrastructure for distributed high performance computing based on dynamically reconfigurable FPGAs. Besides, a set of services designed to facilitate the application deployment is described. An example application and a comparison with other hardware and software implementations are shown. Experimental results show that the proposed architecture offers encouraging advantages for deployment of high performance distributed applications simplifying development process. PMID:25874241

NASA Tech Briefs, November 2005

NASA Technical Reports Server (NTRS)

2005-01-01

Topics covered include: Laser System for Precise, Unambiguous Range Measurements; Flexible Cryogenic Temperature and Liquid-Level Probes; Precision Cryogenic Dilatometer; Stroboscopic Interferometer for Measuring Mirror Vibrations; Some Improvements in H-PDLCs; Multiple-Bit Differential Detection of OQPSK; Absolute Position Encoders With Vertical Image Binning; Flexible, Carbon-Based Ohmic Contacts for Organic Transistors; GaAs QWIP Array Containing More Than a Million Pixels; AutoChem; Virtual Machine Language; Two-Dimensional Ffowcs Williams/Hawkings Equation Solver; Full Multigrid Flow Solver; Doclet To Synthesize UML; Computing Thermal Effects of Cavitation in Cryogenic Liquids; GUI for Computational Simulation of a Propellant Mixer; Control Program for an Optical-Calibration Robot; SQL-RAMS; Distributing Data from Desktop to Hand-Held Computers; Best-Fit Conic Approximation of Spacecraft Trajectory; Improved Charge-Transfer Fluorescent Dyes; Stability-Augmentation Devices for Miniature Aircraft; Tool Measures Depths of Defects on a Case Tang Joint; Two Heat-Transfer Improvements for Gas Liquefiers; Controlling Force and Depth in Friction Stir Welding; Spill-Resistant Alkali-Metal-Vapor Dispenser; A Methodology for Quantifying Certain Design Requirements During the Design Phase; Measuring Two Key Parameters of H3 Color Centers in Diamond; Improved Compression of Wavelet-Transformed Images; NASA Interactive Forms Type Interface - NIFTI; Predicting Numbers of Problems in Development of Software; Hot-Electron Photon Counters for Detecting Terahertz Photons; Magnetic Variations Associated With Solar Flares; and Artificial Intelligence for Controlling Robotic Aircraft.

BMPOS: a Flexible and User-Friendly Tool Sets for Microbiome Studies.

PubMed

Pylro, Victor S; Morais, Daniel K; de Oliveira, Francislon S; Dos Santos, Fausto G; Lemos, Leandro N; Oliveira, Guilherme; Roesch, Luiz F W

2016-08-01

Recent advances in science and technology are leading to a revision and re-orientation of methodologies, addressing old and current issues under a new perspective. Advances in next generation sequencing (NGS) are allowing comparative analysis of the abundance and diversity of whole microbial communities, generating a large amount of data and findings at a systems level. The current limitation for biologists has been the increasing demand for computational power and training required for processing of NGS data. Here, we describe the deployment of the Brazilian Microbiome Project Operating System (BMPOS), a flexible and user-friendly Linux distribution dedicated to microbiome studies. The Brazilian Microbiome Project (BMP) has developed data analyses pipelines for metagenomic studies (phylogenetic marker genes), conducted using the two main high-throughput sequencing platforms (Ion Torrent and Illumina MiSeq). The BMPOS is freely available and possesses the entire requirement of bioinformatics packages and databases to perform all the pipelines suggested by the BMP team. The BMPOS may be used as a bootable live USB stick or installed in any computer with at least 1 GHz CPU and 512 MB RAM, independent of the operating system previously installed. The BMPOS has proved to be effective for sequences processing, sequences clustering, alignment, taxonomic annotation, statistical analysis, and plotting of metagenomic data. The BMPOS has been used during several metagenomic analyses courses, being valuable as a tool for training, and an excellent starting point to anyone interested in performing metagenomic studies. The BMPOS and its documentation are available at http://www.brmicrobiome.org .

Artificial neural network prediction of aircraft aeroelastic behavior

NASA Astrophysics Data System (ADS)

Pesonen, Urpo Juhani

An Artificial Neural Network that predicts aeroelastic behavior of aircraft is presented. The neural net was designed to predict the shape of a flexible wing in static flight conditions using results from a structural analysis and an aerodynamic analysis performed with traditional computational tools. To generate reliable training and testing data for the network, an aeroelastic analysis code using these tools as components was designed and validated. To demonstrate the advantages and reliability of Artificial Neural Networks, a network was also designed and trained to predict airfoil maximum lift at low Reynolds numbers where wind tunnel data was used for the training. Finally, a neural net was designed and trained to predict the static aeroelastic behavior of a wing without the need to iterate between the structural and aerodynamic solvers.

Improving usability and accessibility of cheminformatics tools for chemists through cyberinfrastructure and education.

PubMed

Guha, Rajarshi; Wiggins, Gary D; Wild, David J; Baik, Mu-Hyun; Pierce And, Marlon E; Fox, Geoffrey C

Some of the latest trends in cheminformatics, computation, and the world wide web are reviewed with predictions of how these are likely to impact the field of cheminformatics in the next five years. The vision and some of the work of the Chemical Informatics and Cyberinfrastructure Collaboratory at Indiana University are described, which we base around the core concepts of e-Science and cyberinfrastructure that have proven successful in other fields. Our chemical informatics cyberinfrastructure is realized by building a flexible, generic infrastructure for cheminformatics tools and databases, exporting "best of breed" methods as easily-accessible web APIs for cheminformaticians, scientists, and researchers in other disciplines, and hosting a unique chemical informatics education program aimed at scientists and cheminformatics practitioners in academia and industry.

Online Tools for Astronomy and Cosmochemistry

NASA Technical Reports Server (NTRS)

Meyer, B. S.

2005-01-01

Over the past year, the Webnucleo Group at Clemson University has been developing a web site with a number of interactive online tools for astronomy and cosmochemistry applications. The site uses SHP (Simplified Hypertext Preprocessor), which, because of its flexibility, allows us to embed almost any computer language into our web pages. For a description of SHP, please see http://www.joeldenny.com/ At our web site, an internet user may mine large and complex data sets, such as our stellar evolution models, and make graphs or tables of the results. The user may also run some of our detailed nuclear physics and astrophysics codes, such as our nuclear statistical equilibrium code, which is written in fortran and C. Again, the user may make graphs and tables and download the results.

FESetup: Automating Setup for Alchemical Free Energy Simulations.

PubMed

Loeffler, Hannes H; Michel, Julien; Woods, Christopher

2015-12-28

FESetup is a new pipeline tool which can be used flexibly within larger workflows. The tool aims to support fast and easy setup of alchemical free energy simulations for molecular simulation packages such as AMBER, GROMACS, Sire, or NAMD. Post-processing methods like MM-PBSA and LIE can be set up as well. Ligands are automatically parametrized with AM1-BCC, and atom mappings for a single topology description are computed with a maximum common substructure search (MCSS) algorithm. An abstract molecular dynamics (MD) engine can be used for equilibration prior to free energy setup or standalone. Currently, all modern AMBER force fields are supported. Ease of use, robustness of the code, and automation where it is feasible are the main development goals. The project follows an open development model, and we welcome contributions.

LiPISC: A Lightweight and Flexible Method for Privacy-Aware Intersection Set Computation

PubMed Central

Huang, Shiyong; Ren, Yi; Choo, Kim-Kwang Raymond

2016-01-01

Privacy-aware intersection set computation (PISC) can be modeled as secure multi-party computation. The basic idea is to compute the intersection of input sets without leaking privacy. Furthermore, PISC should be sufficiently flexible to recommend approximate intersection items. In this paper, we reveal two previously unpublished attacks against PISC, which can be used to reveal and link one input set to another input set, resulting in privacy leakage. We coin these as Set Linkage Attack and Set Reveal Attack. We then present a lightweight and flexible PISC scheme (LiPISC) and prove its security (including against Set Linkage Attack and Set Reveal Attack). PMID:27326763

LiPISC: A Lightweight and Flexible Method for Privacy-Aware Intersection Set Computation.

PubMed

Ren, Wei; Huang, Shiyong; Ren, Yi; Choo, Kim-Kwang Raymond

2016-01-01

Privacy-aware intersection set computation (PISC) can be modeled as secure multi-party computation. The basic idea is to compute the intersection of input sets without leaking privacy. Furthermore, PISC should be sufficiently flexible to recommend approximate intersection items. In this paper, we reveal two previously unpublished attacks against PISC, which can be used to reveal and link one input set to another input set, resulting in privacy leakage. We coin these as Set Linkage Attack and Set Reveal Attack. We then present a lightweight and flexible PISC scheme (LiPISC) and prove its security (including against Set Linkage Attack and Set Reveal Attack).

Integrated flexible manufacturing program for manufacturing automation and rapid prototyping

NASA Technical Reports Server (NTRS)

Brooks, S. L.; Brown, C. W.; King, M. S.; Simons, W. R.; Zimmerman, J. J.

1993-01-01

The Kansas City Division of Allied Signal Inc., as part of the Integrated Flexible Manufacturing Program (IFMP), is developing an integrated manufacturing environment. Several systems are being developed to produce standards and automation tools for specific activities within the manufacturing environment. The Advanced Manufacturing Development System (AMDS) is concentrating on information standards (STEP) and product data transfer; the Expert Cut Planner system (XCUT) is concentrating on machining operation process planning standards and automation capabilities; the Advanced Numerical Control system (ANC) is concentrating on NC data preparation standards and NC data generation tools; the Inspection Planning and Programming Expert system (IPPEX) is concentrating on inspection process planning, coordinate measuring machine (CMM) inspection standards and CMM part program generation tools; and the Intelligent Scheduling and Planning System (ISAPS) is concentrating on planning and scheduling tools for a flexible manufacturing system environment. All of these projects are working together to address information exchange, standardization, and information sharing to support rapid prototyping in a Flexible Manufacturing System (FMS) environment.

NCI's High Performance Computing (HPC) and High Performance Data (HPD) Computing Platform for Environmental and Earth System Data Science

NASA Astrophysics Data System (ADS)

Evans, Ben; Allen, Chris; Antony, Joseph; Bastrakova, Irina; Gohar, Kashif; Porter, David; Pugh, Tim; Santana, Fabiana; Smillie, Jon; Trenham, Claire; Wang, Jingbo; Wyborn, Lesley

2015-04-01

The National Computational Infrastructure (NCI) has established a powerful and flexible in-situ petascale computational environment to enable both high performance computing and Data-intensive Science across a wide spectrum of national environmental and earth science data collections - in particular climate, observational data and geoscientific assets. This paper examines 1) the computational environments that supports the modelling and data processing pipelines, 2) the analysis environments and methods to support data analysis, and 3) the progress so far to harmonise the underlying data collections for future interdisciplinary research across these large volume data collections. NCI has established 10+ PBytes of major national and international data collections from both the government and research sectors based on six themes: 1) weather, climate, and earth system science model simulations, 2) marine and earth observations, 3) geosciences, 4) terrestrial ecosystems, 5) water and hydrology, and 6) astronomy, social and biosciences. Collectively they span the lithosphere, crust, biosphere, hydrosphere, troposphere, and stratosphere. The data is largely sourced from NCI's partners (which include the custodians of many of the major Australian national-scale scientific collections), leading research communities, and collaborating overseas organisations. New infrastructures created at NCI mean the data collections are now accessible within an integrated High Performance Computing and Data (HPC-HPD) environment - a 1.2 PFlop supercomputer (Raijin), a HPC class 3000 core OpenStack cloud system and several highly connected large-scale high-bandwidth Lustre filesystems. The hardware was designed at inception to ensure that it would allow the layered software environment to flexibly accommodate the advancement of future data science. New approaches to software technology and data models have also had to be developed to enable access to these large and exponentially increasing data volumes at NCI. Traditional HPC and data environments are still made available in a way that flexibly provides the tools, services and supporting software systems on these new petascale infrastructures. But to enable the research to take place at this scale, the data, metadata and software now need to evolve together - creating a new integrated high performance infrastructure. The new infrastructure at NCI currently supports a catalogue of integrated, reusable software and workflows from earth system and ecosystem modelling, weather research, satellite and other observed data processing and analysis. One of the challenges for NCI has been to support existing techniques and methods, while carefully preparing the underlying infrastructure for the transition needed for the next class of Data-intensive Science. In doing so, a flexible range of techniques and software can be made available for application across the corpus of data collections available, and to provide a new infrastructure for future interdisciplinary research.

Clinical Bioinformatics: challenges and opportunities

PubMed Central

2012-01-01

Background Network Tools and Applications in Biology (NETTAB) Workshops are a series of meetings focused on the most promising and innovative ICT tools and to their usefulness in Bioinformatics. The NETTAB 2011 workshop, held in Pavia, Italy, in October 2011 was aimed at presenting some of the most relevant methods, tools and infrastructures that are nowadays available for Clinical Bioinformatics (CBI), the research field that deals with clinical applications of bioinformatics. Methods In this editorial, the viewpoints and opinions of three world CBI leaders, who have been invited to participate in a panel discussion of the NETTAB workshop on the next challenges and future opportunities of this field, are reported. These include the development of data warehouses and ICT infrastructures for data sharing, the definition of standards for sharing phenotypic data and the implementation of novel tools to implement efficient search computing solutions. Results Some of the most important design features of a CBI-ICT infrastructure are presented, including data warehousing, modularity and flexibility, open-source development, semantic interoperability, integrated search and retrieval of -omics information. Conclusions Clinical Bioinformatics goals are ambitious. Many factors, including the availability of high-throughput "-omics" technologies and equipment, the widespread availability of clinical data warehouses and the noteworthy increase in data storage and computational power of the most recent ICT systems, justify research and efforts in this domain, which promises to be a crucial leveraging factor for biomedical research. PMID:23095472

BP-Dock: A Flexible Docking Scheme for Exploring Protein–Ligand Interactions Based on Unbound Structures

PubMed Central

Bolia, Ashini; Gerek, Z. Nevin; Ozkan, S. Banu

2016-01-01

Molecular docking serves as an important tool in modeling protein–ligand interactions. However, it is still challenging to incorporate overall receptor flexibility, especially backbone flexibility, in docking due to the large conformational space that needs to be sampled. To overcome this problem, we developed a novel flexible docking approach, BP-Dock (Backbone Perturbation-Dock) that can integrate both backbone and side chain conformational changes induced by ligand binding through a multi-scale approach. In the BP-Dock method, we mimic the nature of binding-induced events as a first-order approximation by perturbing the residues along the protein chain with a small Brownian kick one at a time. The response fluctuation profile of the chain upon these perturbations is computed using the perturbation response scanning method. These response fluctuation profiles are then used to generate binding-induced multiple receptor conformations for ensemble docking. To evaluate the performance of BP-Dock, we applied our approach on a large and diverse data set using unbound structures as receptors. We also compared the BP-Dock results with bound and unbound docking, where overall receptor flexibility was not taken into account. Our results highlight the importance of modeling backbone flexibility in docking for recapitulating the experimental binding affinities, especially when an unbound structure is used. With BP-Dock, we can generate a wide range of binding site conformations realized in nature even in the absence of a ligand that can help us to improve the accuracy of unbound docking. We expect that our fast and efficient flexible docking approach may further aid in our understanding of protein–ligand interactions as well as virtual screening of novel targets for rational drug design. PMID:24380381

Utilization of a CRT display light pen in the design of feedback control systems

NASA Technical Reports Server (NTRS)

Thompson, J. G.; Young, K. R.

1972-01-01

A hierarchical structure of the interlinked programs was developed to provide a flexible computer-aided design tool. A graphical input technique and a data structure are considered which provide the capability of entering the control system model description into the computer in block diagram form. An information storage and retrieval system was developed to keep track of the system description, and analysis and simulation results, and to provide them to the correct routines for further manipulation or display. Error analysis and diagnostic capabilities are discussed, and a technique was developed to reduce a transfer function to a set of nested integrals suitable for digital simulation. A general, automated block diagram reduction procedure was set up to prepare the system description for the analysis routines.

Research into display sharing techniques for distributed computing environments

NASA Technical Reports Server (NTRS)

Hugg, Steven B.; Fitzgerald, Paul F., Jr.; Rosson, Nina Y.; Johns, Stephen R.

1990-01-01

The X-based Display Sharing solution for distributed computing environments is described. The Display Sharing prototype includes the base functionality for telecast and display copy requirements. Since the prototype implementation is modular and the system design provided flexibility for the Mission Control Center Upgrade (MCCU) operational consideration, the prototype implementation can be the baseline for a production Display Sharing implementation. To facilitate the process the following discussions are presented: Theory of operation; System of architecture; Using the prototype; Software description; Research tools; Prototype evaluation; and Outstanding issues. The prototype is based on the concept of a dedicated central host performing the majority of the Display Sharing processing, allowing minimal impact on each individual workstation. Each workstation participating in Display Sharing hosts programs to facilitate the user's access to Display Sharing as host machine.

[The Durkheim Test. Remarks on Susan Leigh Star's Boundary Objects].

PubMed

Gießmann, Sebastian

2015-09-01

The article reconstructs Susan Leigh Star's conceptual work on the notion of 'boundary objects'. It traces the emergence of the concept, beginning with her PhD thesis and its publication as Regions of the Mind in 1989. 'Boundary objects' attempt to represent the distributed, multifold nature of scientific work and its mediations between different 'social worlds'. Being addressed to several 'communities of practice', the term responded to questions from Distributed Artificial Intelligence in Computer Science, Workplace Studies and Computer Supported Cooperative Work (CSCW), and microhistorical approaches inside the growing Science and Technology Studies. Yet the interdisciplinary character and interpretive flexibility of Star’s invention has rarely been noticed as a conceptual tool for media theory. I therefore propose to reconsider Star's 'Durkheim test' for sociotechnical media practices.

The Python Spectral Analysis Tool (PySAT) for Powerful, Flexible, and Easy Preprocessing and Machine Learning with Point Spectral Data

NASA Astrophysics Data System (ADS)

Anderson, R. B.; Finch, N.; Clegg, S. M.; Graff, T.; Morris, R. V.; Laura, J.

2018-04-01

The PySAT point spectra tool provides a flexible graphical interface, enabling scientists to apply a wide variety of preprocessing and machine learning methods to point spectral data, with an emphasis on multivariate regression.

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

Gross, D.; Eisert, J.; Schuch, N.

We introduce schemes for quantum computing based on local measurements on entangled resource states. This work elaborates on the framework established in Gross and Eisert [Phys. Rev. Lett. 98, 220503 (2007); quant-ph/0609149]. Our method makes use of tools from many-body physics--matrix product states, finitely correlated states, or projected entangled pairs states--to show how measurements on entangled states can be viewed as processing quantum information. This work hence constitutes an instance where a quantum information problem--how to realize quantum computation--was approached using tools from many-body theory and not vice versa. We give a more detailed description of the setting and presentmore » a large number of examples. We find computational schemes, which differ from the original one-way computer, for example, in the way the randomness of measurement outcomes is handled. Also, schemes are presented where the logical qubits are no longer strictly localized on the resource state. Notably, we find a great flexibility in the properties of the universal resource states: They may, for example, exhibit nonvanishing long-range correlation functions or be locally arbitrarily close to a pure state. We discuss variants of Kitaev's toric code states as universal resources, and contrast this with situations where they can be efficiently classically simulated. This framework opens up a way of thinking of tailoring resource states to specific physical systems, such as cold atoms in optical lattices or linear optical systems.« less

Flexible Bronchoscopy.

PubMed

Miller, Russell J; Casal, Roberto F; Lazarus, Donald R; Ost, David E; Eapen, George A

2018-03-01

Flexible bronchoscopy has changed the course of pulmonary medicine. As technology advances, the role of the flexible bronchoscope for both diagnostic and therapeutic indications is continually expanding. This article reviews the historical development of the flexible bronchoscopy, fundamental uses of the flexible bronchoscope as a tool to examine the central airways and obtain diagnostic tissue, and the indications, complications, and contraindications to flexible bronchoscopy. Copyright © 2017 Elsevier Inc. All rights reserved.

A dynamic scheduling algorithm for singe-arm two-cluster tools with flexible processing times

NASA Astrophysics Data System (ADS)

Li, Xin; Fung, Richard Y. K.

2018-02-01

This article presents a dynamic algorithm for job scheduling in two-cluster tools producing multi-type wafers with flexible processing times. Flexible processing times mean that the actual times for processing wafers should be within given time intervals. The objective of the work is to minimize the completion time of the newly inserted wafer. To deal with this issue, a two-cluster tool is decomposed into three reduced single-cluster tools (RCTs) in a series based on a decomposition approach proposed in this article. For each single-cluster tool, a dynamic scheduling algorithm based on temporal constraints is developed to schedule the newly inserted wafer. Three experiments have been carried out to test the dynamic scheduling algorithm proposed, comparing with the results the 'earliest starting time' heuristic (EST) adopted in previous literature. The results show that the dynamic algorithm proposed in this article is effective and practical.

Conversion of IVA Human Computer Model to EVA Use and Evaluation and Comparison of the Result to Existing EVA Models

NASA Technical Reports Server (NTRS)

Hamilton, George S.; Williams, Jermaine C.

1998-01-01

This paper describes the methods, rationale, and comparative results of the conversion of an intravehicular (IVA) 3D human computer model (HCM) to extravehicular (EVA) use and compares the converted model to an existing model on another computer platform. The task of accurately modeling a spacesuited human figure in software is daunting: the suit restricts the human's joint range of motion (ROM) and does not have joints collocated with human joints. The modeling of the variety of materials needed to construct a space suit (e. g. metal bearings, rigid fiberglass torso, flexible cloth limbs and rubber coated gloves) attached to a human figure is currently out of reach of desktop computer hardware and software. Therefore a simplified approach was taken. The HCM's body parts were enlarged and the joint ROM was restricted to match the existing spacesuit model. This basic approach could be used to model other restrictive environments in industry such as chemical or fire protective clothing. In summary, the approach provides a moderate fidelity, usable tool which will run on current notebook computers.

Development and preliminary validation of an index for indicating the risks of the design of working hours to health and wellbeing.

PubMed

Schomann, Carsten; Giebel, Ole; Nachreiner, Friedhelm

2006-01-01

BASS 4, a computer program for the design and evaluation of workings hours, is an example of an ergonomics-based software tool that can be used by safety practitioners at the shop floor with regard to legal, ergonomic, and economic criteria. Based on experiences with this computer program, a less sophisticated Working-Hours-Risk Index for assessing the quality of work schedules (including flexible work hours) to indicate risks to health and wellbeing has been developed to provide a quick and easy applicable tool for legally required risk assessments. The results of a validation study show that this risk index seems to be a promising indicator for predicting risks of health complaints and wellbeing. The purpose of the Risk Index is to simplify the evaluation process at the shop floor and provide some more general information about the quality of a work schedule that can be used for triggering preventive interventions. Such a risk index complies with practitioners' expectations and requests for easy, useful, and valid instruments.

A computational procedure for multibody systems including flexible beam dynamics

NASA Technical Reports Server (NTRS)

Downer, J. D.; Park, K. C.; Chiou, J. C.

1990-01-01

A computational procedure suitable for the solution of equations of motions for flexible multibody systems has been developed. A fully nonlinear continuum approach capable of accounting for both finite rotations and large deformations has been used to model a flexible beam component. The beam kinematics are referred directly to an inertial reference frame such that the degrees of freedom embody both the rigid and flexible deformation motions. As such, the beam inertia expression is identical to that of rigid body dynamics. The nonlinear coupling between gross body motion and elastic deformation is contained in the internal force expression. Numerical solution procedures for the integration of spatial kinematic systems can be directily applied to the generalized coordinates of both the rigid and flexible components. An accurate computation of the internal force term which is invariant to rigid motions is incorporated into the general solution procedure.

eShadow: A tool for comparing closely related sequences

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

Ovcharenko, Ivan; Boffelli, Dario; Loots, Gabriela G.

2004-01-15

Primate sequence comparisons are difficult to interpret due to the high degree of sequence similarity shared between such closely related species. Recently, a novel method, phylogenetic shadowing, has been pioneered for predicting functional elements in the human genome through the analysis of multiple primate sequence alignments. We have expanded this theoretical approach to create a computational tool, eShadow, for the identification of elements under selective pressure in multiple sequence alignments of closely related genomes, such as in comparisons of human to primate or mouse to rat DNA. This tool integrates two different statistical methods and allows for the dynamic visualizationmore » of the resulting conservation profile. eShadow also includes a versatile optimization module capable of training the underlying Hidden Markov Model to differentially predict functional sequences. This module grants the tool high flexibility in the analysis of multiple sequence alignments and in comparing sequences with different divergence rates. Here, we describe the eShadow comparative tool and its potential uses for analyzing both multiple nucleotide and protein alignments to predict putative functional elements. The eShadow tool is publicly available at http://eshadow.dcode.org/« less

Flexibility of Bricard's linkages and other structures via resultants and computer algebra.

PubMed

Lewis, Robert H; Coutsias, Evangelos A

2016-07-01

Flexibility of structures is extremely important for chemistry and robotics. Following our earlier work, we study flexibility using polynomial equations, resultants, and a symbolic algorithm of our creation that analyzes the resultant. We show that the software solves a classic arrangement of quadrilaterals in the plane due to Bricard. We fill in several gaps in Bricard's work and discover new flexible arrangements that he was apparently unaware of. This provides strong evidence for the maturity of the software, and is a wonderful example of mathematical discovery via computer assisted experiment.

Nonlinear ordinary difference equations

NASA Technical Reports Server (NTRS)

Caughey, T. K.

1979-01-01

Future space vehicles will be relatively large and flexible, and active control will be necessary to maintain geometrical configuration. While the stresses and strains in these space vehicles are not expected to be excessively large, their cumulative effects will cause significant geometrical nonlinearities to appear in the equations of motion, in addition to the nonlinearities caused by material properties. Since the only effective tool for the analysis of such large complex structures is the digital computer, it will be necessary to gain a better understanding of the nonlinear ordinary difference equations which result from the time discretization of the semidiscrete equations of motion for such structures.

Spectral Factorization and Homogenization Methods for Modeling and Control of Flexible Structures.

DTIC Science & Technology

1986-12-15

to the computation of hybrid, state-space modeling of an integrated space platform . Throughout this effort we have focused on the potential for...models can provide an effective tool for analysis of dynamics of vibrations and their effect on small angle motions for complex space platforms . In this... WIX 1 v .41(Ac 0 0o4 1 2.. 9 2% - L .0U V)V14IC Ma a * 9L 0 a soe - a a.. x m c 4. i.! 0~~~I W ** PMiscellaneous Routines• Power Series Expansion

Fitting ERGMs on big networks.

PubMed

An, Weihua

2016-09-01

The exponential random graph model (ERGM) has become a valuable tool for modeling social networks. In particular, ERGM provides great flexibility to account for both covariates effects on tie formations and endogenous network formation processes. However, there are both conceptual and computational issues for fitting ERGMs on big networks. This paper describes a framework and a series of methods (based on existent algorithms) to address these issues. It also outlines the advantages and disadvantages of the methods and the conditions to which they are most applicable. Selected methods are illustrated through examples. Copyright © 2016 Elsevier Inc. All rights reserved.

Mikado: A graphic program

NASA Astrophysics Data System (ADS)

Secretan, Y.

A discussion of the modular program Mikado is presented. Mikado was developed with the goal of creating a flexible graphic tool to display and help analyze the results of finite element fluid flow computations. Mikado works on unstructured meshes, with elements of mixed geometric type, but also offers the possibility of using structured meshes. The program can be operated by both menu and mouse (interactive), or by command file (batch). Mikado is written in FORTRAN, except for a few system dependent subroutines which are in C. It runs presently on Silicon Graphics' workstations and could be easily ported to the IBM-RISC System/6000 family of workstations.

KERNELHR: A program for estimating animal home ranges

USGS Publications Warehouse

Seaman, D.E.; Griffith, B.; Powell, R.A.

1998-01-01

Kernel methods are state of the art for estimating animal home-range area and utilization distribution (UD). The KERNELHR program was developed to provide researchers and managers a tool to implement this extremely flexible set of methods with many variants. KERNELHR runs interactively or from the command line on any personal computer (PC) running DOS. KERNELHR provides output of fixed and adaptive kernel home-range estimates, as well as density values in a format suitable for in-depth statistical and spatial analyses. An additional package of programs creates contour files for plotting in geographic information systems (GIS) and estimates core areas of ranges.

3D printed microfluidic mixer for point-of-care diagnosis of anemia.

PubMed

Plevniak, Kimberly; Campbell, Matthew; Mei He

2016-08-01

3D printing has been an emerging fabrication tool in prototyping and manufacturing. We demonstrated a 3D microfluidic simulation guided computer design and 3D printer prototyping for quick turnaround development of microfluidic 3D mixers, which allows fast self-mixing of reagents with blood through capillary force. Combined with smartphone, the point-of-care diagnosis of anemia from finger-prick blood has been successfully implemented and showed consistent results with clinical measurements. Capable of 3D fabrication flexibility and smartphone compatibility, this work presents a novel diagnostic strategy for advancing personalized medicine and mobile healthcare.

Satellite -Based Networks for U-Health & U-Learning

NASA Astrophysics Data System (ADS)

Graschew, G.; Roelofs, T. A.; Rakowsky, S.; Schlag, P. M.

2008-08-01

The use of modern Information and Communication Technologies (ICT) as enabling tools for healthcare services (eHealth) introduces new ways of creating ubiquitous access to high-level medical care for all, anytime and anywhere (uHealth). Satellite communication constitutes one of the most flexible methods of broadband communication offering high reliability and cost-effectiveness of connections meeting telemedicine communication requirements. Global networks and the use of computers for educational purposes stimulate and support the development of virtual universities for e-learning. Especially real-time interactive applications can play an important role in tailored and personalised services.

Flexible rotor dynamics analysis

NASA Technical Reports Server (NTRS)

Shen, F. A.

1973-01-01

A digital computer program was developed to analyze the general nonaxisymmetric and nonsynchronous transient and steady-state rotor dynamic performance of a bending- and shear-wise flexible rotor-bearing system under various operating conditions. The effects of rotor material mechanical hysteresis, rotor torsion flexibility, transverse effects of rotor axial and torsional loading and the anisotropic, in-phase and out-of-phase bearing stiffness and damping force and moment coefficients were included in the program to broaden its capability. An optimum solution method was found and incorporated in the computer program. Computer simulation of experimental data was made and qualitative agreements observed. The mathematical formulations, computer program verification, test data simulation, and user instruction was presented and discussed.

Proceedings of the Workshop on Computational Aspects in the Control of Flexible Systems, part 2

NASA Technical Reports Server (NTRS)

Taylor, Lawrence W., Jr. (Compiler)

1989-01-01

The Control/Structures Integration Program, a survey of available software for control of flexible structures, computational efficiency and capability, modeling and parameter estimation, and control synthesis and optimization software are discussed.

Addition and Removal Energies via the In-Medium Similarity Renormalization Group Method

NASA Astrophysics Data System (ADS)

Yuan, Fei

The in-medium similarity renormalization group (IM-SRG) is an ab initio many-body method suitable for systems with moderate numbers of particles due to its polynomial scaling in computational cost. The formalism is highly flexible and admits a variety of modifications that extend its utility beyond the original goal of computing ground state energies of closed-shell systems. In this work, we present an extension of IM-SRG through quasidegenerate perturbation theory (QDPT) to compute addition and removal energies (single particle energies) near the Fermi level at low computational cost. This expands the range of systems that can be studied from closed-shell ones to nearby systems that differ by one particle. The method is applied to circular quantum dot systems and nuclei, and compared against other methods including equations-of-motion (EOM) IM-SRG and EOM coupled-cluster (CC) theory. The results are in good agreement for most cases. As part of this work, we present an open-source implementation of our flexible and easy-to-use J-scheme framework as well as the HF, IM-SRG, and QDPT codes built upon this framework. We include an overview of the overall structure, the implementation details, and strategies for maintaining high code quality and efficiency. Lastly, we also present a graphical application for manipulation of angular momentum coupling coefficients through a diagrammatic notation for angular momenta (Jucys diagrams). The tool enables rapid derivations of equations involving angular momentum coupling--such as in J-scheme--and significantly reduces the risk of human errors.

Metabolic flexibility of mitochondrial respiratory chain disorders predicted by computer modelling.

PubMed

Zieliński, Łukasz P; Smith, Anthony C; Smith, Alexander G; Robinson, Alan J

2016-11-01

Mitochondrial respiratory chain dysfunction causes a variety of life-threatening diseases affecting about 1 in 4300 adults. These diseases are genetically heterogeneous, but have the same outcome; reduced activity of mitochondrial respiratory chain complexes causing decreased ATP production and potentially toxic accumulation of metabolites. Severity and tissue specificity of these effects varies between patients by unknown mechanisms and treatment options are limited. So far most research has focused on the complexes themselves, and the impact on overall cellular metabolism is largely unclear. To illustrate how computer modelling can be used to better understand the potential impact of these disorders and inspire new research directions and treatments, we simulated them using a computer model of human cardiomyocyte mitochondrial metabolism containing over 300 characterised reactions and transport steps with experimental parameters taken from the literature. Overall, simulations were consistent with patient symptoms, supporting their biological and medical significance. These simulations predicted: complex I deficiencies could be compensated using multiple pathways; complex II deficiencies had less metabolic flexibility due to impacting both the TCA cycle and the respiratory chain; and complex III and IV deficiencies caused greatest decreases in ATP production with metabolic consequences that parallel hypoxia. Our study demonstrates how results from computer models can be compared to a clinical phenotype and used as a tool for hypothesis generation for subsequent experimental testing. These simulations can enhance understanding of dysfunctional mitochondrial metabolism and suggest new avenues for research into treatment of mitochondrial disease and other areas of mitochondrial dysfunction. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Implications of recent new concepts on the future of mainstream laser processing

NASA Astrophysics Data System (ADS)

La Rocca, Aldo V.

2000-07-01

According to one of today's most accepted visualizations of the first viable realizations of The Computer Integrated Manufacturing Plant, C.I.M.P., the manufacturing systems herein discussed tend to be multiprocessing, and tend to incorporate the lasers to take advantage of the unique capacities of the laser as a processing tool. Finally also the present laser sources, while having been for a long time more than sufficient, inevitably tend also to new generations. Said visualizations stand in the belief that the first realizations of the C I M P most likely will use flexible multiprocessing machines, which, for flexibility requirements, grow in multi-station cells, in their aggregation in isles and finally in complete manufacturing centers. To constitute the CIMP all partaking elements must be the most easily amenable to Computer Aided Design, CAD, and Computer Aided Manufacturing, CAM. Another basic requirement is that all elements constituting the CIMP must possess the highest System Efficiency and Energy Efficiency at the level of the single element and of its aggregations throughout the various combinations at each and every operating level of said aggregations, up to that of the CIMP. The mastering of the CIMP design constitute a New Discipline that presents very formidable but necessary tasks. Of these the first examples were those related to the early flexible manufacturing system Design Programs. For what concerns the laser processing machines and their integration in manufacturing systems, attention must be given to not repeat the events that hindered their diffusion in the production field keeping it at a level much lower than the expectations and their true potential. Said events stemmed from the confusion between System Efficiency and Energy Efficiency, which persisted for too long and is still common. This has taken place at the levels of introduction of a single element into the combination of the several elements constituting a linear arrangement such as a Transfer Production Line. It because greater and with graver consequences in the case of arrangements possessing more than one degree of product routings, arrangements, as previously mentioned, which evolved in the Flexible Manufacturing Centers.

Flexible Learning in Teacher Education: Myths, Muddles and Models

ERIC Educational Resources Information Center

Bigum, Chris; Rowan, Leonie

2004-01-01

While there has been widespread take-up of the concept 'flexible learning' within various educational environments--and equally frequent references to the flexible 'natures' of the computer and communication technologies that often underpin flexible learning initiatives--the relationship between technologies and flexibility is not a simple one. In…

Multi-agent systems in epidemiology: a first step for computational biology in the study of vector-borne disease transmission.

PubMed

Roche, Benjamin; Guégan, Jean-François; Bousquet, François

2008-10-15

Computational biology is often associated with genetic or genomic studies only. However, thanks to the increase of computational resources, computational models are appreciated as useful tools in many other scientific fields. Such modeling systems are particularly relevant for the study of complex systems, like the epidemiology of emerging infectious diseases. So far, mathematical models remain the main tool for the epidemiological and ecological analysis of infectious diseases, with SIR models could be seen as an implicit standard in epidemiology. Unfortunately, these models are based on differential equations and, therefore, can become very rapidly unmanageable due to the too many parameters which need to be taken into consideration. For instance, in the case of zoonotic and vector-borne diseases in wildlife many different potential host species could be involved in the life-cycle of disease transmission, and SIR models might not be the most suitable tool to truly capture the overall disease circulation within that environment. This limitation underlines the necessity to develop a standard spatial model that can cope with the transmission of disease in realistic ecosystems. Computational biology may prove to be flexible enough to take into account the natural complexity observed in both natural and man-made ecosystems. In this paper, we propose a new computational model to study the transmission of infectious diseases in a spatially explicit context. We developed a multi-agent system model for vector-borne disease transmission in a realistic spatial environment. Here we describe in detail the general behavior of this model that we hope will become a standard reference for the study of vector-borne disease transmission in wildlife. To conclude, we show how this simple model could be easily adapted and modified to be used as a common framework for further research developments in this field.

Stereoscopic vascular models of the head and neck: A computed tomography angiography visualization.

PubMed

Cui, Dongmei; Lynch, James C; Smith, Andrew D; Wilson, Timothy D; Lehman, Michael N

2016-01-01

Computer-assisted 3D models are used in some medical and allied health science schools; however, they are often limited to online use and 2D flat screen-based imaging. Few schools take advantage of 3D stereoscopic learning tools in anatomy education and clinically relevant anatomical variations when teaching anatomy. A new approach to teaching anatomy includes use of computed tomography angiography (CTA) images of the head and neck to create clinically relevant 3D stereoscopic virtual models. These high resolution images of the arteries can be used in unique and innovative ways to create 3D virtual models of the vasculature as a tool for teaching anatomy. Blood vessel 3D models are presented stereoscopically in a virtual reality environment, can be rotated 360° in all axes, and magnified according to need. In addition, flexible views of internal structures are possible. Images are displayed in a stereoscopic mode, and students view images in a small theater-like classroom while wearing polarized 3D glasses. Reconstructed 3D models enable students to visualize vascular structures with clinically relevant anatomical variations in the head and neck and appreciate spatial relationships among the blood vessels, the skull and the skin. © 2015 American Association of Anatomists.

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

Sauter, Nicholas K., E-mail: nksauter@lbl.gov; Hattne, Johan; Grosse-Kunstleve, Ralf W.

The Computational Crystallography Toolbox (cctbx) is a flexible software platform that has been used to develop high-throughput crystal-screening tools for both synchrotron sources and X-ray free-electron lasers. Plans for data-processing and visualization applications are discussed, and the benefits and limitations of using graphics-processing units are evaluated. Current pixel-array detectors produce diffraction images at extreme data rates (of up to 2 TB h{sup −1}) that make severe demands on computational resources. New multiprocessing frameworks are required to achieve rapid data analysis, as it is important to be able to inspect the data quickly in order to guide the experiment in realmore » time. By utilizing readily available web-serving tools that interact with the Python scripting language, it was possible to implement a high-throughput Bragg-spot analyzer (cctbx.spotfinder) that is presently in use at numerous synchrotron-radiation beamlines. Similarly, Python interoperability enabled the production of a new data-reduction package (cctbx.xfel) for serial femtosecond crystallography experiments at the Linac Coherent Light Source (LCLS). Future data-reduction efforts will need to focus on specialized problems such as the treatment of diffraction spots on interleaved lattices arising from multi-crystal specimens. In these challenging cases, accurate modeling of close-lying Bragg spots could benefit from the high-performance computing capabilities of graphics-processing units.« less

BGFit: management and automated fitting of biological growth curves.

PubMed

Veríssimo, André; Paixão, Laura; Neves, Ana Rute; Vinga, Susana

2013-09-25

Existing tools to model cell growth curves do not offer a flexible integrative approach to manage large datasets and automatically estimate parameters. Due to the increase of experimental time-series from microbiology and oncology, the need for a software that allows researchers to easily organize experimental data and simultaneously extract relevant parameters in an efficient way is crucial. BGFit provides a web-based unified platform, where a rich set of dynamic models can be fitted to experimental time-series data, further allowing to efficiently manage the results in a structured and hierarchical way. The data managing system allows to organize projects, experiments and measurements data and also to define teams with different editing and viewing permission. Several dynamic and algebraic models are already implemented, such as polynomial regression, Gompertz, Baranyi, Logistic and Live Cell Fraction models and the user can add easily new models thus expanding current ones. BGFit allows users to easily manage their data and models in an integrated way, even if they are not familiar with databases or existing computational tools for parameter estimation. BGFit is designed with a flexible architecture that focus on extensibility and leverages free software with existing tools and methods, allowing to compare and evaluate different data modeling techniques. The application is described in the context of bacterial and tumor cells growth data fitting, but it is also applicable to any type of two-dimensional data, e.g. physical chemistry and macroeconomic time series, being fully scalable to high number of projects, data and model complexity.

A powerful graphical pulse sequence programming tool for magnetic resonance imaging.

PubMed

Jie, Shen; Ying, Liu; Jianqi, Li; Gengying, Li

2005-12-01

A powerful graphical pulse sequence programming tool has been designed for creating magnetic resonance imaging (MRI) applications. It allows rapid development of pulse sequences in graphical mode (allowing for the visualization of sequences), and consists of three modules which include a graphical sequence editor, a parameter management module and a sequence compiler. Its key features are ease to use, flexibility and hardware independence. When graphic elements are combined with a certain text expressions, the graphical pulse sequence programming is as flexible as text-based programming tool. In addition, a hardware-independent design is implemented by using the strategy of two step compilations. To demonstrate the flexibility and the capability of this graphical sequence programming tool, a multi-slice fast spin echo experiment is performed on our home-made 0.3 T permanent magnet MRI system.

DKIST Adaptive Optics System: Simulation Results

NASA Astrophysics Data System (ADS)

Marino, Jose; Schmidt, Dirk

2016-05-01

The 4 m class Daniel K. Inouye Solar Telescope (DKIST), currently under construction, will be equipped with an ultra high order solar adaptive optics (AO) system. The requirements and capabilities of such a solar AO system are beyond those of any other solar AO system currently in operation. We must rely on solar AO simulations to estimate and quantify its performance.We present performance estimation results of the DKIST AO system obtained with a new solar AO simulation tool. This simulation tool is a flexible and fast end-to-end solar AO simulator which produces accurate solar AO simulations while taking advantage of current multi-core computer technology. It relies on full imaging simulations of the extended field Shack-Hartmann wavefront sensor (WFS), which directly includes important secondary effects such as field dependent distortions and varying contrast of the WFS sub-aperture images.

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories.

PubMed

McGibbon, Robert T; Beauchamp, Kyle A; Harrigan, Matthew P; Klein, Christoph; Swails, Jason M; Hernández, Carlos X; Schwantes, Christian R; Wang, Lee-Ping; Lane, Thomas J; Pande, Vijay S

2015-10-20

As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. MDTraj is a powerful and user-friendly software package that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

PubMed Central

McGibbon, Robert T.; Beauchamp, Kyle A.; Harrigan, Matthew P.; Klein, Christoph; Swails, Jason M.; Hernández, Carlos X.; Schwantes, Christian R.; Wang, Lee-Ping; Lane, Thomas J.; Pande, Vijay S.

2015-01-01

As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. MDTraj is a powerful and user-friendly software package that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python. PMID:26488642

Great apes select tools on the basis of their rigidity.

PubMed

Manrique, Héctor Marín; Gross, Alexandra Nam-Mi; Call, Josep

2010-10-01

Wild chimpanzees select tools according to their rigidity. However, little is known about whether choices are solely based on familiarity with the materials or knowledge about tool properties. Furthermore, it is unclear whether tool manipulation is required prior to selection or whether observation alone can suffice. We investigated whether chimpanzees (Pan troglodytes) (n = 9), bonobos (Pan paniscus) (n = 4), orangutans (Pongo pygmaeus) (n = 6), and gorillas (Gorilla gorilla) (n = 2) selected new tools on the basis of their rigidity. Subjects faced an out-of-reach reward and a choice of three tools differing in color, diameter, material, and rigidity. We used 10 different 3-tool sets (1 rigid, 2 flexible). Subjects were unfamiliar with the tools and needed to select and use the rigid tool to retrieve the reward. Experiment 1 showed that subjects chose the rigid tool from the first trial with a 90% success rate. Experiments 2a and 2b addressed the role of manipulation and observation in tool selection. Subjects performed equally well in conditions in which they could manipulate the tools themselves or saw the experimenter manipulate the tools but decreased their performance if they could only visually inspect the tools. Experiment 3 showed that subjects could select flexible tools (as opposed to rigid ones) to meet new task demands. We conclude that great apes spontaneously selected unfamiliar rigid or flexible tools even after gathering minimal observational information. 2010 APA, all rights reserved

A WPS Based Architecture for Climate Data Analytic Services (CDAS) at NASA

NASA Astrophysics Data System (ADS)

Maxwell, T. P.; McInerney, M.; Duffy, D.; Carriere, L.; Potter, G. L.; Doutriaux, C.

2015-12-01

Faced with unprecedented growth in the Big Data domain of climate science, NASA has developed the Climate Data Analytic Services (CDAS) framework. This framework enables scientists to execute trusted and tested analysis operations in a high performance environment close to the massive data stores at NASA. The data is accessed in standard (NetCDF, HDF, etc.) formats in a POSIX file system and processed using trusted climate data analysis tools (ESMF, CDAT, NCO, etc.). The framework is structured as a set of interacting modules allowing maximal flexibility in deployment choices. The current set of module managers include: Staging Manager: Runs the computation locally on the WPS server or remotely using tools such as celery or SLURM. Compute Engine Manager: Runs the computation serially or distributed over nodes using a parallelization framework such as celery or spark. Decomposition Manger: Manages strategies for distributing the data over nodes. Data Manager: Handles the import of domain data from long term storage and manages the in-memory and disk-based caching architectures. Kernel manager: A kernel is an encapsulated computational unit which executes a processor's compute task. Each kernel is implemented in python exploiting existing analysis packages (e.g. CDAT) and is compatible with all CDAS compute engines and decompositions. CDAS services are accessed via a WPS API being developed in collaboration with the ESGF Compute Working Team to support server-side analytics for ESGF. The API can be executed using either direct web service calls, a python script or application, or a javascript-based web application. Client packages in python or javascript contain everything needed to make CDAS requests. The CDAS architecture brings together the tools, data storage, and high-performance computing required for timely analysis of large-scale data sets, where the data resides, to ultimately produce societal benefits. It is is currently deployed at NASA in support of the Collaborative REAnalysis Technical Environment (CREATE) project, which centralizes numerous global reanalysis datasets onto a single advanced data analytics platform. This service permits decision makers to investigate climate changes around the globe, inspect model trends, compare multiple reanalysis datasets, and variability.

Accessing and distributing EMBL data using CORBA (common object request broker architecture).

PubMed

Wang, L; Rodriguez-Tomé, P; Redaschi, N; McNeil, P; Robinson, A; Lijnzaad, P

2000-01-01

The EMBL Nucleotide Sequence Database is a comprehensive database of DNA and RNA sequences and related information traditionally made available in flat-file format. Queries through tools such as SRS (Sequence Retrieval System) also return data in flat-file format. Flat files have a number of shortcomings, however, and the resources therefore currently lack a flexible environment to meet individual researchers' needs. The Object Management Group's common object request broker architecture (CORBA) is an industry standard that provides platform-independent programming interfaces and models for portable distributed object-oriented computing applications. Its independence from programming languages, computing platforms and network protocols makes it attractive for developing new applications for querying and distributing biological data. A CORBA infrastructure developed by EMBL-EBI provides an efficient means of accessing and distributing EMBL data. The EMBL object model is defined such that it provides a basis for specifying interfaces in interface definition language (IDL) and thus for developing the CORBA servers. The mapping from the object model to the relational schema in the underlying Oracle database uses the facilities provided by PersistenceTM, an object/relational tool. The techniques of developing loaders and 'live object caching' with persistent objects achieve a smart live object cache where objects are created on demand. The objects are managed by an evictor pattern mechanism. The CORBA interfaces to the EMBL database address some of the problems of traditional flat-file formats and provide an efficient means for accessing and distributing EMBL data. CORBA also provides a flexible environment for users to develop their applications by building clients to our CORBA servers, which can be integrated into existing systems.

Accessing and distributing EMBL data using CORBA (common object request broker architecture)

PubMed Central

Wang, Lichun; Rodriguez-Tomé, Patricia; Redaschi, Nicole; McNeil, Phil; Robinson, Alan; Lijnzaad, Philip

2000-01-01

Background: The EMBL Nucleotide Sequence Database is a comprehensive database of DNA and RNA sequences and related information traditionally made available in flat-file format. Queries through tools such as SRS (Sequence Retrieval System) also return data in flat-file format. Flat files have a number of shortcomings, however, and the resources therefore currently lack a flexible environment to meet individual researchers' needs. The Object Management Group's common object request broker architecture (CORBA) is an industry standard that provides platform-independent programming interfaces and models for portable distributed object-oriented computing applications. Its independence from programming languages, computing platforms and network protocols makes it attractive for developing new applications for querying and distributing biological data. Results: A CORBA infrastructure developed by EMBL-EBI provides an efficient means of accessing and distributing EMBL data. The EMBL object model is defined such that it provides a basis for specifying interfaces in interface definition language (IDL) and thus for developing the CORBA servers. The mapping from the object model to the relational schema in the underlying Oracle database uses the facilities provided by PersistenceTM, an object/relational tool. The techniques of developing loaders and 'live object caching' with persistent objects achieve a smart live object cache where objects are created on demand. The objects are managed by an evictor pattern mechanism. Conclusions: The CORBA interfaces to the EMBL database address some of the problems of traditional flat-file formats and provide an efficient means for accessing and distributing EMBL data. CORBA also provides a flexible environment for users to develop their applications by building clients to our CORBA servers, which can be integrated into existing systems. PMID:11178259

HEPMath 1.4: A mathematica package for semi-automatic computations in high energy physics

NASA Astrophysics Data System (ADS)

Wiebusch, Martin

2015-10-01

This article introduces the Mathematica package HEPMath which provides a number of utilities and algorithms for High Energy Physics computations in Mathematica. Its functionality is similar to packages like FormCalc or FeynCalc, but it takes a more complete and extensible approach to implementing common High Energy Physics notations in the Mathematica language, in particular those related to tensors and index contractions. It also provides a more flexible method for the generation of numerical code which is based on new features for C code generation in Mathematica. In particular it can automatically generate Python extension modules which make the compiled functions callable from Python, thus eliminating the need to write any code in a low-level language like C or Fortran. It also contains seamless interfaces to LHAPDF, FeynArts, and LoopTools.

The PAWS and STEM reliability analysis programs

NASA Technical Reports Server (NTRS)

Butler, Ricky W.; Stevenson, Philip H.

1988-01-01

The PAWS and STEM programs are new design/validation tools. These programs provide a flexible, user-friendly, language-based interface for the input of Markov models describing the behavior of fault-tolerant computer systems. These programs produce exact solutions of the probability of system failure and provide a conservative estimate of the number of significant digits in the solution. PAWS uses a Pade approximation as a solution technique; STEM uses a Taylor series as a solution technique. Both programs have the capability to solve numerically stiff models. PAWS and STEM possess complementary properties with regard to their input space; and, an additional strength of these programs is that they accept input compatible with the SURE program. If used in conjunction with SURE, PAWS and STEM provide a powerful suite of programs to analyze the reliability of fault-tolerant computer systems.

Space shuttle rendezous, radiation and reentry analysis code

NASA Technical Reports Server (NTRS)

Mcglathery, D. M.

1973-01-01

A preliminary space shuttle mission design and analysis tool is reported emphasizing versatility, flexibility, and user interaction through the use of a relatively small computer (IBM-7044). The Space Shuttle Rendezvous, Radiation and Reentry Analysis Code is used to perform mission and space radiation environmental analyses for four typical space shuttle missions. Included also is a version of the proposed Apollo/Soyuz rendezvous and docking test mission. Tangential steering circle to circle low-thrust tug orbit raising and the effects of the trapped radiation environment on trajectory shaping due to solar electric power losses are also features of this mission analysis code. The computational results include a parametric study on single impulse versus double impulse deorbiting for relatively low space shuttle orbits as well as some definitive data on the magnetically trapped protons and electrons encountered on a particular mission.

HGML: a hypertext guideline markup language.

PubMed Central

Hagerty, C. G.; Pickens, D.; Kulikowski, C.; Sonnenberg, F.

2000-01-01

Existing text-based clinical practice guidelines can be difficult to put into practice. While a growing number of such documents have gained acceptance in the medical community and contain a wealth of valuable information, the time required to digest them is substantial. Yet the expressive power, subtlety and flexibility of natural language pose challenges when designing computer tools that will help in their application. At the same time, formal computer languages typically lack such expressiveness and the effort required to translate existing documents into these languages may be costly. We propose a method based on the mark-up concept for converting text-based clinical guidelines into a machine-operable form. This allows existing guidelines to be manipulated by machine, and viewed in different formats at various levels of detail according to the needs of the practitioner, while preserving their originally published form. PMID:11079898

Computational Toxicology as Implemented by the US EPA ...

EPA Pesticide Factsheets

Computational toxicology is the application of mathematical and computer models to help assess chemical hazards and risks to human health and the environment. Supported by advances in informatics, high-throughput screening (HTS) technologies, and systems biology, the U.S. Environmental Protection Agency EPA is developing robust and flexible computational tools that can be applied to the thousands of chemicals in commerce, and contaminant mixtures found in air, water, and hazardous-waste sites. The Office of Research and Development (ORD) Computational Toxicology Research Program (CTRP) is composed of three main elements. The largest component is the National Center for Computational Toxicology (NCCT), which was established in 2005 to coordinate research on chemical screening and prioritization, informatics, and systems modeling. The second element consists of related activities in the National Health and Environmental Effects Research Laboratory (NHEERL) and the National Exposure Research Laboratory (NERL). The third and final component consists of academic centers working on various aspects of computational toxicology and funded by the U.S. EPA Science to Achieve Results (STAR) program. Together these elements form the key components in the implementation of both the initial strategy, A Framework for a Computational Toxicology Research Program (U.S. EPA, 2003), and the newly released The U.S. Environmental Protection Agency's Strategic Plan for Evaluating the T

Cloud computing approaches to accelerate drug discovery value chain.

PubMed

Garg, Vibhav; Arora, Suchir; Gupta, Chitra

2011-12-01

Continued advancements in the area of technology have helped high throughput screening (HTS) evolve from a linear to parallel approach by performing system level screening. Advanced experimental methods used for HTS at various steps of drug discovery (i.e. target identification, target validation, lead identification and lead validation) can generate data of the order of terabytes. As a consequence, there is pressing need to store, manage, mine and analyze this data to identify informational tags. This need is again posing challenges to computer scientists to offer the matching hardware and software infrastructure, while managing the varying degree of desired computational power. Therefore, the potential of "On-Demand Hardware" and "Software as a Service (SAAS)" delivery mechanisms cannot be denied. This on-demand computing, largely referred to as Cloud Computing, is now transforming the drug discovery research. Also, integration of Cloud computing with parallel computing is certainly expanding its footprint in the life sciences community. The speed, efficiency and cost effectiveness have made cloud computing a 'good to have tool' for researchers, providing them significant flexibility, allowing them to focus on the 'what' of science and not the 'how'. Once reached to its maturity, Discovery-Cloud would fit best to manage drug discovery and clinical development data, generated using advanced HTS techniques, hence supporting the vision of personalized medicine.

Vibration and stability of cracked hollow-sectional beams

NASA Astrophysics Data System (ADS)

Zheng, D. Y.; Fan, S. C.

2003-10-01

This paper presents simple tools for the vibration and stability analysis of cracked hollow-sectional beams. It comprises two parts. In the first, the influences of sectional cracks are expressed in terms of flexibility induced. Each crack is assigned with a local flexibility coefficient, which is derived by virtue of theories of fracture mechanics. The flexibility coefficient is a function of the depth of a crack. The general formulae are derived and expressed in integral form. It is then transformed to explicit form through 128-point Gauss quadrature. According to the depth of the crack, the formulae are derived under two scenarios. The first is for shallow cracks, of which the penetration depth is contained within the top solid-sectional region. The second is for deeper penetration, in which the crack goes into the middle hollow-sectional region. The explicit formulae are best-fitted equations generated by the least-squares method. The best-fitted curves are presented. From the curves, the flexibility coefficients can be read out easily, while the explicit expressions facilitate easy implementation in computer analysis. In the second part, the flexibility coefficients are employed in the vibration and stability analysis of hollow-sectional beams. The cracked beam is treated as an assembly of sub-segments linked up by rotational springs. Division of segments are made coincident with the location of cracks or any abrupt change of sectional property. The crack's flexibility coefficient then serves as that of the rotational spring. Application of the Hamilton's principle leads to the governing equations, which are subsequently solved through employment of a simple technique. It is a kind of modified Fourier series, which is able to represent any order of continuity of the vibration/buckling modes. Illustrative numerical examples are included.

Challenges to Computational Aerothermodynamic Simulation and Validation for Planetary Entry Vehicle Analysis

NASA Technical Reports Server (NTRS)

Gnoffo, Peter A.; Johnston, Christopher O.; Kleb, Bil

2010-01-01

Challenges to computational aerothermodynamic (CA) simulation and validation of hypersonic flow over planetary entry vehicles are discussed. Entry, descent, and landing (EDL) of high mass to Mars is a significant driver of new simulation requirements. These requirements include simulation of large deployable, flexible structures and interactions with reaction control system (RCS) and retro-thruster jets. Simulation of radiation and ablation coupled to the flow solver continues to be a high priority for planetary entry analyses, especially for return to Earth and outer planet missions. Three research areas addressing these challenges are emphasized. The first addresses the need to obtain accurate heating on unstructured tetrahedral grid systems to take advantage of flexibility in grid generation and grid adaptation. A multi-dimensional inviscid flux reconstruction algorithm is defined that is oriented with local flow topology as opposed to grid. The second addresses coupling of radiation and ablation to the hypersonic flow solver - flight- and ground-based data are used to provide limited validation of these multi-physics simulations. The third addresses the challenges of retro-propulsion simulation and the criticality of grid adaptation in this application. The evolution of CA to become a tool for innovation of EDL systems requires a successful resolution of these challenges.

qtcm 0.1.2: A Python Implementation of the Neelin-Zeng Quasi-Equilibrium Tropical Circulation model

NASA Astrophysics Data System (ADS)

Lin, J. W.-B.

2008-10-01

Historically, climate models have been developed incrementally and in compiled languages like Fortran. While the use of legacy compiled languages results in fast, time-tested code, the resulting model is limited in its modularity and cannot take advantage of functionality available with modern computer languages. Here we describe an effort at using the open-source, object-oriented language Python to create more flexible climate models: the package qtcm, a Python implementation of the intermediate-level Neelin-Zeng Quasi-Equilibrium Tropical Circulation model (QTCM1) of the atmosphere. The qtcm package retains the core numerics of QTCM1, written in Fortran to optimize model performance, but uses Python structures and utilities to wrap the QTCM1 Fortran routines and manage model execution. The resulting "mixed language" modeling package allows order and choice of subroutine execution to be altered at run time, and model analysis and visualization to be integrated in interactively with model execution at run time. This flexibility facilitates more complex scientific analysis using less complex code than would be possible using traditional languages alone, and provides tools to transform the traditional "formulate hypothesis → write and test code → run model → analyze results" sequence into a feedback loop that can be executed automatically by the computer.

qtcm 0.1.2: a Python implementation of the Neelin-Zeng Quasi-Equilibrium Tropical Circulation Model

NASA Astrophysics Data System (ADS)

Lin, J. W.-B.

2009-02-01

Historically, climate models have been developed incrementally and in compiled languages like Fortran. While the use of legacy compiled languages results in fast, time-tested code, the resulting model is limited in its modularity and cannot take advantage of functionality available with modern computer languages. Here we describe an effort at using the open-source, object-oriented language Python to create more flexible climate models: the package qtcm, a Python implementation of the intermediate-level Neelin-Zeng Quasi-Equilibrium Tropical Circulation model (QTCM1) of the atmosphere. The qtcm package retains the core numerics of QTCM1, written in Fortran to optimize model performance, but uses Python structures and utilities to wrap the QTCM1 Fortran routines and manage model execution. The resulting "mixed language" modeling package allows order and choice of subroutine execution to be altered at run time, and model analysis and visualization to be integrated in interactively with model execution at run time. This flexibility facilitates more complex scientific analysis using less complex code than would be possible using traditional languages alone, and provides tools to transform the traditional "formulate hypothesis → write and test code → run model → analyze results" sequence into a feedback loop that can be executed automatically by the computer.

A Python Implementation of an Intermediate-Level Tropical Circulation Model and Implications for How Modeling Science is Done

NASA Astrophysics Data System (ADS)

Lin, J. W. B.

2015-12-01

Historically, climate models have been developed incrementally and in compiled languages like Fortran. While the use of legacy compiledlanguages results in fast, time-tested code, the resulting model is limited in its modularity and cannot take advantage of functionalityavailable with modern computer languages. Here we describe an effort at using the open-source, object-oriented language Pythonto create more flexible climate models: the package qtcm, a Python implementation of the intermediate-level Neelin-Zeng Quasi-Equilibrium Tropical Circulation model (QTCM1) of the atmosphere. The qtcm package retains the core numerics of QTCM1, written in Fortran, to optimize model performance but uses Python structures and utilities to wrap the QTCM1 Fortran routines and manage model execution. The resulting "mixed language" modeling package allows order and choice of subroutine execution to be altered at run time, and model analysis and visualization to be integrated in interactively with model execution at run time. This flexibility facilitates more complex scientific analysis using less complex code than would be possible using traditional languages alone and provides tools to transform the traditional "formulate hypothesis → write and test code → run model → analyze results" sequence into a feedback loop that can be executed automatically by the computer.

ReportingTools: an automated result processing and presentation toolkit for high-throughput genomic analyses.

PubMed

Huntley, Melanie A; Larson, Jessica L; Chaivorapol, Christina; Becker, Gabriel; Lawrence, Michael; Hackney, Jason A; Kaminker, Joshua S

2013-12-15

It is common for computational analyses to generate large amounts of complex data that are difficult to process and share with collaborators. Standard methods are needed to transform such data into a more useful and intuitive format. We present ReportingTools, a Bioconductor package, that automatically recognizes and transforms the output of many common Bioconductor packages into rich, interactive, HTML-based reports. Reports are not generic, but have been individually designed to reflect content specific to the result type detected. Tabular output included in reports is sortable, filterable and searchable and contains context-relevant hyperlinks to external databases. Additionally, in-line graphics have been developed for specific analysis types and are embedded by default within table rows, providing a useful visual summary of underlying raw data. ReportingTools is highly flexible and reports can be easily customized for specific applications using the well-defined API. The ReportingTools package is implemented in R and available from Bioconductor (version ≥ 2.11) at the URL: http://bioconductor.org/packages/release/bioc/html/ReportingTools.html. Installation instructions and usage documentation can also be found at the above URL.

An Architecture Combining IMS-LD and Web Services for Flexible Data-Transfer in CSCL

ERIC Educational Resources Information Center

Magnisalis, Ioannis; Demetriadis, Stavros

2017-01-01

This article presents evaluation data regarding the MAPIS3 architecture which is proposed as a solution for the data-transfer among various tools to promote flexible collaborative learning designs. We describe the problem that this architecture deals with as "tool orchestration" in collaborative learning settings. This term refers to a…

Temperature and Material Flow Prediction in Friction-Stir Spot Welding of Advanced High-Strength Steel

NASA Astrophysics Data System (ADS)

Miles, M.; Karki, U.; Hovanski, Y.

2014-10-01

Friction-stir spot welding (FSSW) has been shown to be capable of joining advanced high-strength steel, with its flexibility in controlling the heat of welding and the resulting microstructure of the joint. This makes FSSW a potential alternative to resistance spot welding if tool life is sufficiently high, and if machine spindle loads are sufficiently low that the process can be implemented on an industrial robot. Robots for spot welding can typically sustain vertical loads of about 8 kN, but FSSW at tool speeds of less than 3000 rpm cause loads that are too high, in the range of 11-14 kN. Therefore, in the current work, tool speeds of 5000 rpm were employed to generate heat more quickly and to reduce welding loads to acceptable levels. Si3N4 tools were used for the welding experiments on 1.2-mm DP 980 steel. The FSSW process was modeled with a finite element approach using the Forge® software. An updated Lagrangian scheme with explicit time integration was employed to predict the flow of the sheet material, subjected to boundary conditions of a rotating tool and a fixed backing plate. Material flow was calculated from a velocity field that is two-dimensional, but heat generated by friction was computed by a novel approach, where the rotational velocity component imparted to the sheet by the tool surface was included in the thermal boundary conditions. An isotropic, viscoplastic Norton-Hoff law was used to compute the material flow stress as a function of strain, strain rate, and temperature. The model predicted welding temperatures to within 4%, and the position of the joint interface to within 10%, of the experimental results.

Temperature and Material Flow Prediction in Friction-Stir Spot Welding of Advanced High-Strength Steel

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

Miles, Michael; Karki, U.; Hovanski, Yuri

Friction-stir spot welding (FSSW) has been shown to be capable of joining advanced high-strength steel, with its flexibility in controlling the heat of welding and the resulting microstructure of the joint. This makes FSSW a potential alternative to resistance spot welding if tool life is sufficiently high, and if machine spindle loads are sufficiently low that the process can be implemented on an industrial robot. Robots for spot welding can typically sustain vertical loads of about 8 kN, but FSSW at tool speeds of less than 3000 rpm cause loads that are too high, in the range of 11–14 kN.more » Therefore, in the current work, tool speeds of 5000 rpm were employed to generate heat more quickly and to reduce welding loads to acceptable levels. Si3N4 tools were used for the welding experiments on 1.2-mm DP 980 steel. The FSSW process was modeled with a finite element approach using the Forge* software. An updated Lagrangian scheme with explicit time integration was employed to predict the flow of the sheet material, subjected to boundary conditions of a rotating tool and a fixed backing plate. Material flow was calculated from a velocity field that is two-dimensional, but heat generated by friction was computed by a novel approach, where the rotational velocity component imparted to the sheet by the tool surface was included in the thermal boundary conditions. An isotropic, viscoplastic Norton-Hoff law was used to compute the material flow stress as a function of strain, strain rate, and temperature. The model predicted welding temperatures to within percent, and the position of the joint interface to within 10 percent, of the experimental results.« less

Using a cloud to replenish parched groundwater modeling efforts.

PubMed

Hunt, Randall J; Luchette, Joseph; Schreuder, Willem A; Rumbaugh, James O; Doherty, John; Tonkin, Matthew J; Rumbaugh, Douglas B

2010-01-01

Groundwater models can be improved by introduction of additional parameter flexibility and simultaneous use of soft-knowledge. However, these sophisticated approaches have high computational requirements. Cloud computing provides unprecedented access to computing power via the Internet to facilitate the use of these techniques. A modeler can create, launch, and terminate "virtual" computers as needed, paying by the hour, and save machine images for future use. Such cost-effective and flexible computing power empowers groundwater modelers to routinely perform model calibration and uncertainty analysis in ways not previously possible.

Using a cloud to replenish parched groundwater modeling efforts

USGS Publications Warehouse

Hunt, Randall J.; Luchette, Joseph; Schreuder, Willem A.; Rumbaugh, James O.; Doherty, John; Tonkin, Matthew J.; Rumbaugh, Douglas B.

2010-01-01

Groundwater models can be improved by introduction of additional parameter flexibility and simultaneous use of soft-knowledge. However, these sophisticated approaches have high computational requirements. Cloud computing provides unprecedented access to computing power via the Internet to facilitate the use of these techniques. A modeler can create, launch, and terminate “virtual” computers as needed, paying by the hour, and save machine images for future use. Such cost-effective and flexible computing power empowers groundwater modelers to routinely perform model calibration and uncertainty analysis in ways not previously possible.

Investigation of the effects of process and geometrical parameters on formability in tube hydroforming using a modular hydroforming tool

NASA Astrophysics Data System (ADS)

Joghan, Hamed Dardaei; Staupendahl, Daniel; Hassan, Hamad ul; Henke, Andreas; Keesser, Thorsten; Legat, Francois; Tekkaya, A. Erman

2018-05-01

Tube hydroforming is one of the most important manufacturing processes for the production of exhaust systems. Tube hydroforming allows generating parts with highly complex geometries with the forming accuracies needed in the automotive sector. This is possible due to the form-closed nature of the production process. One of the main cost drivers is tool manufacturing, which is expensive and time consuming, especially when forming large parts. To cope with the design trend of individuality, which is gaining more and more importance and leads to a high number of product variants, a new flexible tool design was developed. The designed tool offers a high flexibility in manufacturing different shapes and geometries of tubes with just local alterations and relocation of tool segments. The tolerancing problems that segmented tools from the state of the art have are overcome by an innovative and flexible die holder design. The break-even point of this initially more expensive tool design is already overcome when forming more than 4 different tube shapes. Together with an additionally designed rotary hydraulic tube feeding system, a highly adaptable forming setup is generated. To investigate the performance of the developed tool setup, a study on geometrical and process parameters during forming of a spherical dome was done. Austenitic stainless steel (grade 1.4301) tube with a diameter of 40 mm and a thickness of 1.5 mm was used for the investigations. The experimental analyses were supported by finite element simulations and statistical analyses. The results show that the flexible tool setup can efficiently be used to analyze the interaction of the inner pressure, friction, and the location of the spherical dome and demonstrate the high influence of the feeding rate on the formed part.

[Application of virtual instrumentation technique in toxicological studies].

PubMed

Moczko, Jerzy A

2005-01-01

Research investigations require frequently direct connection of measuring equipment to the computer. Virtual instrumentation technique considerably facilitates programming of sophisticated acquisition-and-analysis procedures. In standard approach these two steps are performed subsequently with separate software tools. The acquired data are transfered with export / import procedures of particular program to the another one which executes next step of analysis. The described procedure is cumbersome, time consuming and may be potential source of the errors. In 1987 National Instruments Corporation introduced LabVIEW language based on the concept of graphical programming. Contrary to conventional textual languages it allows the researcher to concentrate on the resolved problem and omit all syntactical rules. Programs developed in LabVIEW are called as virtual instruments (VI) and are portable among different computer platforms as PCs, Macintoshes, Sun SPARCstations, Concurrent PowerMAX stations, HP PA/RISK workstations. This flexibility warrants that the programs prepared for one particular platform would be also appropriate to another one. In presented paper basic principles of connection of research equipment to computer systems were described.

Computer-Assisted Concept Mapping: Visual Aids for Knowledge Construction.

PubMed

Mammen, Jennifer R

2016-07-01

Concept mapping is a visual representation of ideas that facilitates critical thinking and is applicable to many areas of nursing education. Computer-assisted concept maps are more flexible and less constrained than traditional paper methods, allowing for analysis and synthesis of complex topics and larger amounts of data. Ability to iteratively revise and collaboratively create computerized maps can contribute to enhanced interpersonal learning. However, there is limited awareness of free software that can support these types of applications. This educational brief examines affordances and limitations of computer-assisted concept maps and reviews free software for development of complex, collaborative malleable maps. Free software, such as VUE, XMind, MindMaple, and others, can substantially contribute to the utility of concept mapping for nursing education. Computerized concept-mapping is an important tool for nursing and is likely to hold greater benefit for students and faculty than traditional pen-and-paper methods alone. [J Nurs Educ. 2016;55(7):403-406.]. Copyright 2016, SLACK Incorporated.

Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline

PubMed Central

2014-01-01

Background Massively parallel DNA sequencing generates staggering amounts of data. Decreasing cost, increasing throughput, and improved annotation have expanded the diversity of genomics applications in research and clinical practice. This expanding scale creates analytical challenges: accommodating peak compute demand, coordinating secure access for multiple analysts, and sharing validated tools and results. Results To address these challenges, we have developed the Mercury analysis pipeline and deployed it in local hardware and the Amazon Web Services cloud via the DNAnexus platform. Mercury is an automated, flexible, and extensible analysis workflow that provides accurate and reproducible genomic results at scales ranging from individuals to large cohorts. Conclusions By taking advantage of cloud computing and with Mercury implemented on the DNAnexus platform, we have demonstrated a powerful combination of a robust and fully validated software pipeline and a scalable computational resource that, to date, we have applied to more than 10,000 whole genome and whole exome samples. PMID:24475911

Development of innovative computer software to facilitate the setup and computation of water quality index.

PubMed

Nabizadeh, Ramin; Valadi Amin, Maryam; Alimohammadi, Mahmood; Naddafi, Kazem; Mahvi, Amir Hossein; Yousefzadeh, Samira

2013-04-26

Developing a water quality index which is used to convert the water quality dataset into a single number is the most important task of most water quality monitoring programmes. As the water quality index setup is based on different local obstacles, it is not feasible to introduce a definite water quality index to reveal the water quality level. In this study, an innovative software application, the Iranian Water Quality Index Software (IWQIS), is presented in order to facilitate calculation of a water quality index based on dynamic weight factors, which will help users to compute the water quality index in cases where some parameters are missing from the datasets. A dataset containing 735 water samples of drinking water quality in different parts of the country was used to show the performance of this software using different criteria parameters. The software proved to be an efficient tool to facilitate the setup of water quality indices based on flexible use of variables and water quality databases.

Global Static Indexing for Real-Time Exploration of Very Large Regular Grids

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

Pascucci, V; Frank, R

2001-07-23

In this paper we introduce a new indexing scheme for progressive traversal and visualization of large regular grids. We demonstrate the potential of our approach by providing a tool that displays at interactive rates planar slices of scalar field data with very modest computing resources. We obtain unprecedented results both in terms of absolute performance and, more importantly, in terms of scalability. On a laptop computer we provide real time interaction with a 2048{sup 3} grid (8 Giga-nodes) using only 20MB of memory. On an SGI Onyx we slice interactively an 8192{sup 3} grid (1/2 tera-nodes) using only 60MB ofmore » memory. The scheme relies simply on the determination of an appropriate reordering of the rectilinear grid data and a progressive construction of the output slice. The reordering minimizes the amount of I/O performed during the out-of-core computation. The progressive and asynchronous computation of the output provides flexible quality/speed tradeoffs and a time-critical and interruptible user interface.« less

Computational design of RNAs with complex energy landscapes.

PubMed

Höner zu Siederdissen, Christian; Hammer, Stefan; Abfalter, Ingrid; Hofacker, Ivo L; Flamm, Christoph; Stadler, Peter F

2013-12-01

RNA has become an integral building material in synthetic biology. Dominated by their secondary structures, which can be computed efficiently, RNA molecules are amenable not only to in vitro and in vivo selection, but also to rational, computation-based design. While the inverse folding problem of constructing an RNA sequence with a prescribed ground-state structure has received considerable attention for nearly two decades, there have been few efforts to design RNAs that can switch between distinct prescribed conformations. We introduce a user-friendly tool for designing RNA sequences that fold into multiple target structures. The underlying algorithm makes use of a combination of graph coloring and heuristic local optimization to find sequences whose energy landscapes are dominated by the prescribed conformations. A flexible interface allows the specification of a wide range of design goals. We demonstrate that bi- and tri-stable "switches" can be designed easily with moderate computational effort for the vast majority of compatible combinations of desired target structures. RNAdesign is freely available under the GPL-v3 license. Copyright © 2013 Wiley Periodicals, Inc.

FMS: The New Wave of Manufacturing Technology.

ERIC Educational Resources Information Center

Industrial Education, 1986

1986-01-01

Flexible manufacturing systems (FMS) are described as a marriage of all of the latest technologies--robotics, numerical control, CAD/CAM (computer-assisted design/computer-assisted manufacturing), etc.--into a cost-efficient, optimized production process yielding the greatest flexibility in making various parts. A typical curriculum to teach FMS…

Building a Generic Virtual Research Environment Framework for Multiple Earth and Space Science Domains and a Diversity of Users.

NASA Astrophysics Data System (ADS)

Wyborn, L. A.; Fraser, R.; Evans, B. J. K.; Friedrich, C.; Klump, J. F.; Lescinsky, D. T.

2017-12-01

Virtual Research Environments (VREs) are now part of academic infrastructures. Online research workflows can be orchestrated whereby data can be accessed from multiple external repositories with processing taking place on public or private clouds, and centralised supercomputers using a mixture of user codes, and well-used community software and libraries. VREs enable distributed members of research teams to actively work together to share data, models, tools, software, workflows, best practices, infrastructures, etc. These environments and their components are increasingly able to support the needs of undergraduate teaching. External to the research sector, they can also be reused by citizen scientists, and be repurposed for industry users to help accelerate the diffusion and hence enable the translation of research innovations. The Virtual Geophysics Laboratory (VGL) in Australia was started in 2012, built using a collaboration between CSIRO, the National Computational Infrastructure (NCI) and Geoscience Australia, with support funding from the Australian Government Department of Education. VGL comprises three main modules that provide an interface to enable users to first select their required data; to choose a tool to process that data; and then access compute infrastructure for execution. VGL was initially built to enable a specific set of researchers in government agencies access to specific data sets and a limited number of tools. Over the years it has evolved into a multi-purpose Earth science platform with access to an increased variety of data (e.g., Natural Hazards, Geochemistry), a broader range of software packages, and an increasing diversity of compute infrastructures. This expansion has been possible because of the approach to loosely couple data, tools and compute resources via interfaces that are built on international standards and accessed as network-enabled services wherever possible. Built originally for researchers that were not fussy about general usability, increasing emphasis on User Interfaces (UIs) and stability will lead to increased uptake in the education and industry sectors. Simultaneously, improvements are being added to facilitate access to data and tools by experienced researchers who want direct access to both data and flexible workflows.

Grant programs : design features shape flexibility, accountability, and performance information

DOT National Transportation Integrated Search

1998-06-01

Flexible grants--block grants and similar programs that give state or local governments the flexibility to adapt funded activities to fit the state or local context--are an adaptable policy tool and are found in fields from urban transit to community...

Open-Source Python Tools for Deploying Interactive GIS Dashboards for a Billion Datapoints on a Laptop

NASA Astrophysics Data System (ADS)

Steinberg, P. D.; Bednar, J. A.; Rudiger, P.; Stevens, J. L. R.; Ball, C. E.; Christensen, S. D.; Pothina, D.

2017-12-01

The rich variety of software libraries available in the Python scientific ecosystem provides a flexible and powerful alternative to traditional integrated GIS (geographic information system) programs. Each such library focuses on doing a certain set of general-purpose tasks well, and Python makes it relatively simple to glue the libraries together to solve a wide range of complex, open-ended problems in Earth science. However, choosing an appropriate set of libraries can be challenging, and it is difficult to predict how much "glue code" will be needed for any particular combination of libraries and tasks. Here we present a set of libraries that have been designed to work well together to build interactive analyses and visualizations of large geographic datasets, in standard web browsers. The resulting workflows run on ordinary laptops even for billions of data points, and easily scale up to larger compute clusters when available. The declarative top-level interface used in these libraries means that even complex, fully interactive applications can be built and deployed as web services using only a few dozen lines of code, making it simple to create and share custom interactive applications even for datasets too large for most traditional GIS systems. The libraries we will cover include GeoViews (HoloViews extended for geographic applications) for declaring visualizable/plottable objects, Bokeh for building visual web applications from GeoViews objects, Datashader for rendering arbitrarily large datasets faithfully as fixed-size images, Param for specifying user-modifiable parameters that model your domain, Xarray for computing with n-dimensional array data, Dask for flexibly dispatching computational tasks across processors, and Numba for compiling array-based Python code down to fast machine code. We will show how to use the resulting workflow with static datasets and with simulators such as GSSHA or AdH, allowing you to deploy flexible, high-performance web-based dashboards for your GIS data or simulations without needing major investments in code development or maintenance.

Generating optimal control simulations of musculoskeletal movement using OpenSim and MATLAB.

PubMed

Lee, Leng-Feng; Umberger, Brian R

2016-01-01

Computer modeling, simulation and optimization are powerful tools that have seen increased use in biomechanics research. Dynamic optimizations can be categorized as either data-tracking or predictive problems. The data-tracking approach has been used extensively to address human movement problems of clinical relevance. The predictive approach also holds great promise, but has seen limited use in clinical applications. Enhanced software tools would facilitate the application of predictive musculoskeletal simulations to clinically-relevant research. The open-source software OpenSim provides tools for generating tracking simulations but not predictive simulations. However, OpenSim includes an extensive application programming interface that permits extending its capabilities with scripting languages such as MATLAB. In the work presented here, we combine the computational tools provided by MATLAB with the musculoskeletal modeling capabilities of OpenSim to create a framework for generating predictive simulations of musculoskeletal movement based on direct collocation optimal control techniques. In many cases, the direct collocation approach can be used to solve optimal control problems considerably faster than traditional shooting methods. Cyclical and discrete movement problems were solved using a simple 1 degree of freedom musculoskeletal model and a model of the human lower limb, respectively. The problems could be solved in reasonable amounts of time (several seconds to 1-2 hours) using the open-source IPOPT solver. The problems could also be solved using the fmincon solver that is included with MATLAB, but the computation times were excessively long for all but the smallest of problems. The performance advantage for IPOPT was derived primarily by exploiting sparsity in the constraints Jacobian. The framework presented here provides a powerful and flexible approach for generating optimal control simulations of musculoskeletal movement using OpenSim and MATLAB. This should allow researchers to more readily use predictive simulation as a tool to address clinical conditions that limit human mobility.

Generating optimal control simulations of musculoskeletal movement using OpenSim and MATLAB

PubMed Central

Lee, Leng-Feng

2016-01-01

Computer modeling, simulation and optimization are powerful tools that have seen increased use in biomechanics research. Dynamic optimizations can be categorized as either data-tracking or predictive problems. The data-tracking approach has been used extensively to address human movement problems of clinical relevance. The predictive approach also holds great promise, but has seen limited use in clinical applications. Enhanced software tools would facilitate the application of predictive musculoskeletal simulations to clinically-relevant research. The open-source software OpenSim provides tools for generating tracking simulations but not predictive simulations. However, OpenSim includes an extensive application programming interface that permits extending its capabilities with scripting languages such as MATLAB. In the work presented here, we combine the computational tools provided by MATLAB with the musculoskeletal modeling capabilities of OpenSim to create a framework for generating predictive simulations of musculoskeletal movement based on direct collocation optimal control techniques. In many cases, the direct collocation approach can be used to solve optimal control problems considerably faster than traditional shooting methods. Cyclical and discrete movement problems were solved using a simple 1 degree of freedom musculoskeletal model and a model of the human lower limb, respectively. The problems could be solved in reasonable amounts of time (several seconds to 1–2 hours) using the open-source IPOPT solver. The problems could also be solved using the fmincon solver that is included with MATLAB, but the computation times were excessively long for all but the smallest of problems. The performance advantage for IPOPT was derived primarily by exploiting sparsity in the constraints Jacobian. The framework presented here provides a powerful and flexible approach for generating optimal control simulations of musculoskeletal movement using OpenSim and MATLAB. This should allow researchers to more readily use predictive simulation as a tool to address clinical conditions that limit human mobility. PMID:26835184

Modelling of human-machine interaction in equipment design of manufacturing cells

NASA Astrophysics Data System (ADS)

Cochran, David S.; Arinez, Jorge F.; Collins, Micah T.; Bi, Zhuming

2017-08-01

This paper proposes a systematic approach to model human-machine interactions (HMIs) in supervisory control of machining operations; it characterises the coexistence of machines and humans for an enterprise to balance the goals of automation/productivity and flexibility/agility. In the proposed HMI model, an operator is associated with a set of behavioural roles as a supervisor for multiple, semi-automated manufacturing processes. The model is innovative in the sense that (1) it represents an HMI based on its functions for process control but provides the flexibility for ongoing improvements in the execution of manufacturing processes; (2) it provides a computational tool to define functional requirements for an operator in HMIs. The proposed model can be used to design production systems at different levels of an enterprise architecture, particularly at the machine level in a production system where operators interact with semi-automation to accomplish the goal of 'autonomation' - automation that augments the capabilities of human beings.

Biological knowledge bases using Wikis: combining the flexibility of Wikis with the structure of databases.

PubMed

Brohée, Sylvain; Barriot, Roland; Moreau, Yves

2010-09-01

In recent years, the number of knowledge bases developed using Wiki technology has exploded. Unfortunately, next to their numerous advantages, classical Wikis present a critical limitation: the invaluable knowledge they gather is represented as free text, which hinders their computational exploitation. This is in sharp contrast with the current practice for biological databases where the data is made available in a structured way. Here, we present WikiOpener an extension for the classical MediaWiki engine that augments Wiki pages by allowing on-the-fly querying and formatting resources external to the Wiki. Those resources may provide data extracted from databases or DAS tracks, or even results returned by local or remote bioinformatics analysis tools. This also implies that structured data can be edited via dedicated forms. Hence, this generic resource combines the structure of biological databases with the flexibility of collaborative Wikis. The source code and its documentation are freely available on the MediaWiki website: http://www.mediawiki.org/wiki/Extension:WikiOpener.

The Virtual Mission Operations Center

NASA Technical Reports Server (NTRS)

Moore, Mike; Fox, Jeffrey

1994-01-01

Spacecraft management is becoming more human intensive as spacecraft become more complex and as operations costs are growing accordingly. Several automation approaches have been proposed to lower these costs. However, most of these approaches are not flexible enough in the operations processes and levels of automation that they support. This paper presents a concept called the Virtual Mission Operations Center (VMOC) that provides highly flexible support for dynamic spacecraft management processes and automation. In a VMOC, operations personnel can be shared among missions, the operations team can change personnel and their locations, and automation can be added and removed as appropriate. The VMOC employs a form of on-demand supervisory control called management by exception to free operators from having to actively monitor their system. The VMOC extends management by exception, however, so that distributed, dynamic teams can work together. The VMOC uses work-group computing concepts and groupware tools to provide a team infrastructure, and it employs user agents to allow operators to define and control system automation.

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.

A multiblock multigrid three-dimensional Euler equation solver

NASA Technical Reports Server (NTRS)

Cannizzaro, Frank E.; Elmiligui, Alaa; Melson, N. Duane; Vonlavante, E.

1990-01-01

Current aerodynamic designs are often quite complex (geometrically). Flexible computational tools are needed for the analysis of a wide range of configurations with both internal and external flows. In the past, geometrically dissimilar configurations required different analysis codes with different grid topologies in each. The duplicity of codes can be avoided with the use of a general multiblock formulation which can handle any grid topology. Rather than hard wiring the grid topology into the program, it is instead dictated by input to the program. In this work, the compressible Euler equations, written in a body-fitted finite-volume formulation, are solved using a pseudo-time-marching approach. Two upwind methods (van Leer's flux-vector-splitting and Roe's flux-differencing) were investigated. Two types of explicit solvers (a two-step predictor-corrector and a modified multistage Runge-Kutta) were used with multigrid acceleration to enhance convergence. A multiblock strategy is used to allow greater geometric flexibility. A report on simple explicit upwind schemes for solving compressible flows is included.

A Foldable Lithium-Sulfur Battery.

PubMed

Li, Lu; Wu, Zi Ping; Sun, Hao; Chen, Deming; Gao, Jian; Suresh, Shravan; Chow, Philippe; Singh, Chandra Veer; Koratkar, Nikhil

2015-11-24

The next generation of deformable and shape-conformable electronics devices will need to be powered by batteries that are not only flexible but also foldable. Here we report a foldable lithium-sulfur (Li-S) rechargeable battery, with the highest areal capacity (∼3 mAh cm(-2)) reported to date among all types of foldable energy-storage devices. The key to this result lies in the use of fully foldable and superelastic carbon nanotube current-collector films and impregnation of the active materials (S and Li) into the current-collectors in a checkerboard pattern, enabling the battery to be folded along two mutually orthogonal directions. The carbon nanotube films also serve as the sulfur entrapment layer in the Li-S battery. The foldable battery showed <12% loss in specific capacity over 100 continuous folding and unfolding cycles. Such shape-conformable Li-S batteries with significantly greater energy density than traditional lithium-ion batteries could power the flexible and foldable devices of the future including laptops, cell phones, tablet computers, surgical tools, and implantable biomedical devices.

Cellulose Nanofiber Composite Substrates for Flexible Electronics

Treesearch

Ronald Sabo; Jung-Hun Seo; Zhenqiang Ma

2012-01-01

Flexible electronics have a large number of potential applications including malleable displays and wearable computers. The current research into high-speed, flexible electronic substrates employs the use of plastics for the flexible substrate, but these plastics typically have drawbacks, such as high thermal expansion coefficients. Transparent films made from...

Chapter 2.3 Cellulose Nanofibril Composite Substrates for Flexible Electronics

Treesearch

Ronald Sabo; Jung-Hun Seo; Zhenqiang Ma

2013-01-01

Flexible electronics have a large number of potential applications, including malleable displays and wearable computers. Current research into high-speed, flexible electronic substrates uses plastics for the flexible substrate, but these plastics typically have drawbacks, such as high thermal expansion coefficients. Transparent films made from cellulose...

Computational prediction of hinge axes in proteins

PubMed Central

2014-01-01

Background A protein's function is determined by the wide range of motions exhibited by its 3D structure. However, current experimental techniques are not able to reliably provide the level of detail required for elucidating the exact mechanisms of protein motion essential for effective drug screening and design. Computational tools are instrumental in the study of the underlying structure-function relationship. We focus on a special type of proteins called "hinge proteins" which exhibit a motion that can be interpreted as a rotation of one domain relative to another. Results This work proposes a computational approach that uses the geometric structure of a single conformation to predict the feasible motions of the protein and is founded in recent work from rigidity theory, an area of mathematics that studies flexibility properties of general structures. Given a single conformational state, our analysis predicts a relative axis of motion between two specified domains. We analyze a dataset of 19 structures known to exhibit this hinge-like behavior. For 15, the predicted axis is consistent with a motion to a second, known conformation. We present a detailed case study for three proteins whose dynamics have been well-studied in the literature: calmodulin, the LAO binding protein and the Bence-Jones protein. Conclusions Our results show that incorporating rigidity-theoretic analyses can lead to effective computational methods for understanding hinge motions in macromolecules. This initial investigation is the first step towards a new tool for probing the structure-dynamics relationship in proteins. PMID:25080829

Advanced Free Flight Planner and Dispatcher's Workstation: Preliminary Design Specification

NASA Technical Reports Server (NTRS)

Wilson, J.; Wright, C.; Couluris, G. J.

1997-01-01

The National Aeronautics and Space Administration (NASA) has implemented the Advanced Air Transportation Technology (AATT) program to investigate future improvements to the national and international air traffic management systems. This research, as part of the AATT program, developed preliminary design requirements for an advanced Airline Operations Control (AOC) dispatcher's workstation, with emphasis on flight planning. This design will support the implementation of an experimental workstation in NASA laboratories that would emulate AOC dispatch operations. The work developed an airline flight plan data base and specified requirements for: a computer tool for generation and evaluation of free flight, user preferred trajectories (UPT); the kernel of an advanced flight planning system to be incorporated into the UPT-generation tool; and an AOC workstation to house the UPT-generation tool and to provide a real-time testing environment. A prototype for the advanced flight plan optimization kernel was developed and demonstrated. The flight planner uses dynamic programming to search a four-dimensional wind and temperature grid to identify the optimal route, altitude and speed for successive segments of a flight. An iterative process is employed in which a series of trajectories are successively refined until the LTPT is identified. The flight planner is designed to function in the current operational environment as well as in free flight. The free flight environment would enable greater flexibility in UPT selection based on alleviation of current procedural constraints. The prototype also takes advantage of advanced computer processing capabilities to implement more powerful optimization routines than would be possible with older computer systems.

Cloud computing for comparative genomics

PubMed Central

2010-01-01

Background Large comparative genomics studies and tools are becoming increasingly more compute-expensive as the number of available genome sequences continues to rise. The capacity and cost of local computing infrastructures are likely to become prohibitive with the increase, especially as the breadth of questions continues to rise. Alternative computing architectures, in particular cloud computing environments, may help alleviate this increasing pressure and enable fast, large-scale, and cost-effective comparative genomics strategies going forward. To test this, we redesigned a typical comparative genomics algorithm, the reciprocal smallest distance algorithm (RSD), to run within Amazon's Elastic Computing Cloud (EC2). We then employed the RSD-cloud for ortholog calculations across a wide selection of fully sequenced genomes. Results We ran more than 300,000 RSD-cloud processes within the EC2. These jobs were farmed simultaneously to 100 high capacity compute nodes using the Amazon Web Service Elastic Map Reduce and included a wide mix of large and small genomes. The total computation time took just under 70 hours and cost a total of $6,302 USD. Conclusions The effort to transform existing comparative genomics algorithms from local compute infrastructures is not trivial. However, the speed and flexibility of cloud computing environments provides a substantial boost with manageable cost. The procedure designed to transform the RSD algorithm into a cloud-ready application is readily adaptable to similar comparative genomics problems. PMID:20482786

Cloud computing for comparative genomics.

PubMed

Wall, Dennis P; Kudtarkar, Parul; Fusaro, Vincent A; Pivovarov, Rimma; Patil, Prasad; Tonellato, Peter J

2010-05-18

Large comparative genomics studies and tools are becoming increasingly more compute-expensive as the number of available genome sequences continues to rise. The capacity and cost of local computing infrastructures are likely to become prohibitive with the increase, especially as the breadth of questions continues to rise. Alternative computing architectures, in particular cloud computing environments, may help alleviate this increasing pressure and enable fast, large-scale, and cost-effective comparative genomics strategies going forward. To test this, we redesigned a typical comparative genomics algorithm, the reciprocal smallest distance algorithm (RSD), to run within Amazon's Elastic Computing Cloud (EC2). We then employed the RSD-cloud for ortholog calculations across a wide selection of fully sequenced genomes. We ran more than 300,000 RSD-cloud processes within the EC2. These jobs were farmed simultaneously to 100 high capacity compute nodes using the Amazon Web Service Elastic Map Reduce and included a wide mix of large and small genomes. The total computation time took just under 70 hours and cost a total of $6,302 USD. The effort to transform existing comparative genomics algorithms from local compute infrastructures is not trivial. However, the speed and flexibility of cloud computing environments provides a substantial boost with manageable cost. The procedure designed to transform the RSD algorithm into a cloud-ready application is readily adaptable to similar comparative genomics problems.

Developing and Applying Smartphone Apps in Online Courses

ERIC Educational Resources Information Center

Yan, Gongjun; Rawat, Danda B.; Shi, Hui; Alnusair, Awny

2014-01-01

Online courses provide students flexible access to class at anytime and anywhere. Most online courses currently rely on computer-based delivery. However, computers still burden instructors and students with limited mobility and flexibility. To provide more convenient access to online courses, smartphones have been increasingly adopted as a mobile…

Molgenis-impute: imputation pipeline in a box.

PubMed

Kanterakis, Alexandros; Deelen, Patrick; van Dijk, Freerk; Byelas, Heorhiy; Dijkstra, Martijn; Swertz, Morris A

2015-08-19

Genotype imputation is an important procedure in current genomic analysis such as genome-wide association studies, meta-analyses and fine mapping. Although high quality tools are available that perform the steps of this process, considerable effort and expertise is required to set up and run a best practice imputation pipeline, particularly for larger genotype datasets, where imputation has to scale out in parallel on computer clusters. Here we present MOLGENIS-impute, an 'imputation in a box' solution that seamlessly and transparently automates the set up and running of all the steps of the imputation process. These steps include genome build liftover (liftovering), genotype phasing with SHAPEIT2, quality control, sample and chromosomal chunking/merging, and imputation with IMPUTE2. MOLGENIS-impute builds on MOLGENIS-compute, a simple pipeline management platform for submission and monitoring of bioinformatics tasks in High Performance Computing (HPC) environments like local/cloud servers, clusters and grids. All the required tools, data and scripts are downloaded and installed in a single step. Researchers with diverse backgrounds and expertise have tested MOLGENIS-impute on different locations and imputed over 30,000 samples so far using the 1,000 Genomes Project and new Genome of the Netherlands data as the imputation reference. The tests have been performed on PBS/SGE clusters, cloud VMs and in a grid HPC environment. MOLGENIS-impute gives priority to the ease of setting up, configuring and running an imputation. It has minimal dependencies and wraps the pipeline in a simple command line interface, without sacrificing flexibility to adapt or limiting the options of underlying imputation tools. It does not require knowledge of a workflow system or programming, and is targeted at researchers who just want to apply best practices in imputation via simple commands. It is built on the MOLGENIS compute workflow framework to enable customization with additional computational steps or it can be included in other bioinformatics pipelines. It is available as open source from: https://github.com/molgenis/molgenis-imputation.

P43-S Computational Biology Applications Suite for High-Performance Computing (BioHPC.net)

PubMed Central

Pillardy, J.

2007-01-01

One of the challenges of high-performance computing (HPC) is user accessibility. At the Cornell University Computational Biology Service Unit, which is also a Microsoft HPC institute, we have developed a computational biology application suite that allows researchers from biological laboratories to submit their jobs to the parallel cluster through an easy-to-use Web interface. Through this system, we are providing users with popular bioinformatics tools including BLAST, HMMER, InterproScan, and MrBayes. The system is flexible and can be easily customized to include other software. It is also scalable; the installation on our servers currently processes approximately 8500 job submissions per year, many of them requiring massively parallel computations. It also has a built-in user management system, which can limit software and/or database access to specified users. TAIR, the major database of the plant model organism Arabidopsis, and SGN, the international tomato genome database, are both using our system for storage and data analysis. The system consists of a Web server running the interface (ASP.NET C#), Microsoft SQL server (ADO.NET), compute cluster running Microsoft Windows, ftp server, and file server. Users can interact with their jobs and data via a Web browser, ftp, or e-mail. The interface is accessible at http://cbsuapps.tc.cornell.edu/.

Computer Simulations to Support Science Instruction and Learning: A critical review of the literature

NASA Astrophysics Data System (ADS)

Smetana, Lara Kathleen; Bell, Randy L.

2012-06-01

Researchers have explored the effectiveness of computer simulations for supporting science teaching and learning during the past four decades. The purpose of this paper is to provide a comprehensive, critical review of the literature on the impact of computer simulations on science teaching and learning, with the goal of summarizing what is currently known and providing guidance for future research. We report on the outcomes of 61 empirical studies dealing with the efficacy of, and implications for, computer simulations in science instruction. The overall findings suggest that simulations can be as effective, and in many ways more effective, than traditional (i.e. lecture-based, textbook-based and/or physical hands-on) instructional practices in promoting science content knowledge, developing process skills, and facilitating conceptual change. As with any other educational tool, the effectiveness of computer simulations is dependent upon the ways in which they are used. Thus, we outline specific research-based guidelines for best practice. Computer simulations are most effective when they (a) are used as supplements; (b) incorporate high-quality support structures; (c) encourage student reflection; and (d) promote cognitive dissonance. Used appropriately, computer simulations involve students in inquiry-based, authentic science explorations. Additionally, as educational technologies continue to evolve, advantages such as flexibility, safety, and efficiency deserve attention.

Computational Toxicology at the US EPA | Science Inventory ...

EPA Pesticide Factsheets

Computational toxicology is the application of mathematical and computer models to help assess chemical hazards and risks to human health and the environment. Supported by advances in informatics, high-throughput screening (HTS) technologies, and systems biology, EPA is developing robust and flexible computational tools that can be applied to the thousands of chemicals in commerce, and contaminant mixtures found in America’s air, water, and hazardous-waste sites. The ORD Computational Toxicology Research Program (CTRP) is composed of three main elements. The largest component is the National Center for Computational Toxicology (NCCT), which was established in 2005 to coordinate research on chemical screening and prioritization, informatics, and systems modeling. The second element consists of related activities in the National Health and Environmental Effects Research Laboratory (NHEERL) and the National Exposure Research Laboratory (NERL). The third and final component consists of academic centers working on various aspects of computational toxicology and funded by the EPA Science to Achieve Results (STAR) program. Key intramural projects of the CTRP include digitizing legacy toxicity testing information toxicity reference database (ToxRefDB), predicting toxicity (ToxCast™) and exposure (ExpoCast™), and creating virtual liver (v-Liver™) and virtual embryo (v-Embryo™) systems models. The models and underlying data are being made publicly available t

The Dynamo package for tomography and subtomogram averaging: components for MATLAB, GPU computing and EC2 Amazon Web Services

PubMed Central

Castaño-Díez, Daniel

2017-01-01

Dynamo is a package for the processing of tomographic data. As a tool for subtomogram averaging, it includes different alignment and classification strategies. Furthermore, its data-management module allows experiments to be organized in groups of tomograms, while offering specialized three-dimensional tomographic browsers that facilitate visualization, location of regions of interest, modelling and particle extraction in complex geometries. Here, a technical description of the package is presented, focusing on its diverse strategies for optimizing computing performance. Dynamo is built upon mbtools (middle layer toolbox), a general-purpose MATLAB library for object-oriented scientific programming specifically developed to underpin Dynamo but usable as an independent tool. Its structure intertwines a flexible MATLAB codebase with precompiled C++ functions that carry the burden of numerically intensive operations. The package can be delivered as a precompiled standalone ready for execution without a MATLAB license. Multicore parallelization on a single node is directly inherited from the high-level parallelization engine provided for MATLAB, automatically imparting a balanced workload among the threads in computationally intense tasks such as alignment and classification, but also in logistic-oriented tasks such as tomogram binning and particle extraction. Dynamo supports the use of graphical processing units (GPUs), yielding considerable speedup factors both for native Dynamo procedures (such as the numerically intensive subtomogram alignment) and procedures defined by the user through its MATLAB-based GPU library for three-dimensional operations. Cloud-based virtual computing environments supplied with a pre-installed version of Dynamo can be publicly accessed through the Amazon Elastic Compute Cloud (EC2), enabling users to rent GPU computing time on a pay-as-you-go basis, thus avoiding upfront investments in hardware and longterm software maintenance. PMID:28580909

The Dynamo package for tomography and subtomogram averaging: components for MATLAB, GPU computing and EC2 Amazon Web Services.

PubMed

Castaño-Díez, Daniel

2017-06-01

Dynamo is a package for the processing of tomographic data. As a tool for subtomogram averaging, it includes different alignment and classification strategies. Furthermore, its data-management module allows experiments to be organized in groups of tomograms, while offering specialized three-dimensional tomographic browsers that facilitate visualization, location of regions of interest, modelling and particle extraction in complex geometries. Here, a technical description of the package is presented, focusing on its diverse strategies for optimizing computing performance. Dynamo is built upon mbtools (middle layer toolbox), a general-purpose MATLAB library for object-oriented scientific programming specifically developed to underpin Dynamo but usable as an independent tool. Its structure intertwines a flexible MATLAB codebase with precompiled C++ functions that carry the burden of numerically intensive operations. The package can be delivered as a precompiled standalone ready for execution without a MATLAB license. Multicore parallelization on a single node is directly inherited from the high-level parallelization engine provided for MATLAB, automatically imparting a balanced workload among the threads in computationally intense tasks such as alignment and classification, but also in logistic-oriented tasks such as tomogram binning and particle extraction. Dynamo supports the use of graphical processing units (GPUs), yielding considerable speedup factors both for native Dynamo procedures (such as the numerically intensive subtomogram alignment) and procedures defined by the user through its MATLAB-based GPU library for three-dimensional operations. Cloud-based virtual computing environments supplied with a pre-installed version of Dynamo can be publicly accessed through the Amazon Elastic Compute Cloud (EC2), enabling users to rent GPU computing time on a pay-as-you-go basis, thus avoiding upfront investments in hardware and longterm software maintenance.

Handheld juggernaut.

PubMed

Hagland, Mark

2010-08-01

Not only are hospital, health system, and medical group ClOs and clinical informaticists deploying handheld mobile devices across their enterprises as clinical computing tools; clinicians, especially physicians, are increasingly bringing their own BlackBerrys, iPhones, iPads, Android devices, and other handhelds, into patient care organizations for their personal clinical use. Not surprisingly, the challenges--as well as the opportunities--are multilayered and complex, and include the strategic planning, infrastructure, clinician preference, clinician workflow, and security issues involved in the emerging mobile handheld revolution. The diversity of approaches among ClOs and other healthcare IT leaders on such issues is striking, and underscores the need for flexibility and nimbleness going forward.

Flight test trajectory control analysis

NASA Technical Reports Server (NTRS)

Walker, R.; Gupta, N.

1983-01-01

Recent extensions to optimal control theory applied to meaningful linear models with sufficiently flexible software tools provide powerful techniques for designing flight test trajectory controllers (FTTCs). This report describes the principal steps for systematic development of flight trajectory controllers, which can be summarized as planning, modeling, designing, and validating a trajectory controller. The techniques have been kept as general as possible and should apply to a wide range of problems where quantities must be computed and displayed to a pilot to improve pilot effectiveness and to reduce workload and fatigue. To illustrate the approach, a detailed trajectory guidance law is developed and demonstrated for the F-15 aircraft flying the zoom-and-pushover maneuver.

Chemical Computer Man: Chemical Agent Response Simulation (CARS). Technical report, January 1983-September 1985

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

Davis, E.G.; Mioduszewski, R.J.

The Chemical Computer Man: Chemical Agent Response Simulation (CARS) is a computer model and simulation program for estimating the dynamic changes in human physiological dysfunction resulting from exposures to chemical-threat nerve agents. The newly developed CARS methodology simulates agent exposure effects on the following five indices of human physiological function: mental, vision, cardio-respiratory, visceral, and limbs. Mathematical models and the application of basic pharmacokinetic principles were incorporated into the simulation so that for each chemical exposure, the relationship between exposure dosage, absorbed dosage (agent blood plasma concentration), and level of physiological response are computed as a function of time. CARS,more » as a simulation tool, is designed for the users with little or no computer-related experience. The model combines maximum flexibility with a comprehensive user-friendly interactive menu-driven system. Users define an exposure problem and obtain immediate results displayed in tabular, graphical, and image formats. CARS has broad scientific and engineering applications, not only in technology for the soldier in the area of Chemical Defense, but also in minimizing animal testing in biomedical and toxicological research and the development of a modeling system for human exposure to hazardous-waste chemicals.« less

The portable UNIX programming system (PUPS) and CANTOR: a computational environment for dynamical representation and analysis of complex neurobiological data.

PubMed

O'Neill, M A; Hilgetag, C C

2001-08-29

Many problems in analytical biology, such as the classification of organisms, the modelling of macromolecules, or the structural analysis of metabolic or neural networks, involve complex relational data. Here, we describe a software environment, the portable UNIX programming system (PUPS), which has been developed to allow efficient computational representation and analysis of such data. The system can also be used as a general development tool for database and classification applications. As the complexity of analytical biology problems may lead to computation times of several days or weeks even on powerful computer hardware, the PUPS environment gives support for persistent computations by providing mechanisms for dynamic interaction and homeostatic protection of processes. Biological objects and their interrelations are also represented in a homeostatic way in PUPS. Object relationships are maintained and updated by the objects themselves, thus providing a flexible, scalable and current data representation. Based on the PUPS environment, we have developed an optimization package, CANTOR, which can be applied to a wide range of relational data and which has been employed in different analyses of neuroanatomical connectivity. The CANTOR package makes use of the PUPS system features by modifying candidate arrangements of objects within the system's database. This restructuring is carried out via optimization algorithms that are based on user-defined cost functions, thus providing flexible and powerful tools for the structural analysis of the database content. The use of stochastic optimization also enables the CANTOR system to deal effectively with incomplete and inconsistent data. Prototypical forms of PUPS and CANTOR have been coded and used successfully in the analysis of anatomical and functional mammalian brain connectivity, involving complex and inconsistent experimental data. In addition, PUPS has been used for solving multivariate engineering optimization problems and to implement the digital identification system (DAISY), a system for the automated classification of biological objects. PUPS is implemented in ANSI-C under the POSIX.1 standard and is to a great extent architecture- and operating-system independent. The software is supported by systems libraries that allow multi-threading (the concurrent processing of several database operations), as well as the distribution of the dynamic data objects and library operations over clusters of computers. These attributes make the system easily scalable, and in principle allow the representation and analysis of arbitrarily large sets of relational data. PUPS and CANTOR are freely distributed (http://www.pups.org.uk) as open-source software under the GNU license agreement.

The portable UNIX programming system (PUPS) and CANTOR: a computational environment for dynamical representation and analysis of complex neurobiological data.

PubMed Central

O'Neill, M A; Hilgetag, C C

2001-01-01

Many problems in analytical biology, such as the classification of organisms, the modelling of macromolecules, or the structural analysis of metabolic or neural networks, involve complex relational data. Here, we describe a software environment, the portable UNIX programming system (PUPS), which has been developed to allow efficient computational representation and analysis of such data. The system can also be used as a general development tool for database and classification applications. As the complexity of analytical biology problems may lead to computation times of several days or weeks even on powerful computer hardware, the PUPS environment gives support for persistent computations by providing mechanisms for dynamic interaction and homeostatic protection of processes. Biological objects and their interrelations are also represented in a homeostatic way in PUPS. Object relationships are maintained and updated by the objects themselves, thus providing a flexible, scalable and current data representation. Based on the PUPS environment, we have developed an optimization package, CANTOR, which can be applied to a wide range of relational data and which has been employed in different analyses of neuroanatomical connectivity. The CANTOR package makes use of the PUPS system features by modifying candidate arrangements of objects within the system's database. This restructuring is carried out via optimization algorithms that are based on user-defined cost functions, thus providing flexible and powerful tools for the structural analysis of the database content. The use of stochastic optimization also enables the CANTOR system to deal effectively with incomplete and inconsistent data. Prototypical forms of PUPS and CANTOR have been coded and used successfully in the analysis of anatomical and functional mammalian brain connectivity, involving complex and inconsistent experimental data. In addition, PUPS has been used for solving multivariate engineering optimization problems and to implement the digital identification system (DAISY), a system for the automated classification of biological objects. PUPS is implemented in ANSI-C under the POSIX.1 standard and is to a great extent architecture- and operating-system independent. The software is supported by systems libraries that allow multi-threading (the concurrent processing of several database operations), as well as the distribution of the dynamic data objects and library operations over clusters of computers. These attributes make the system easily scalable, and in principle allow the representation and analysis of arbitrarily large sets of relational data. PUPS and CANTOR are freely distributed (http://www.pups.org.uk) as open-source software under the GNU license agreement. PMID:11545702

Flight Operations Analysis Tool

NASA Technical Reports Server (NTRS)

Easter, Robert; Herrell, Linda; Pomphrey, Richard; Chase, James; Wertz Chen, Julie; Smith, Jeffrey; Carter, Rebecca

2006-01-01

Flight Operations Analysis Tool (FLOAT) is a computer program that partly automates the process of assessing the benefits of planning spacecraft missions to incorporate various combinations of launch vehicles and payloads. Designed primarily for use by an experienced systems engineer, FLOAT makes it possible to perform a preliminary analysis of trade-offs and costs of a proposed mission in days, whereas previously, such an analysis typically lasted months. FLOAT surveys a variety of prior missions by querying data from authoritative NASA sources pertaining to 20 to 30 mission and interface parameters that define space missions. FLOAT provides automated, flexible means for comparing the parameters to determine compatibility or the lack thereof among payloads, spacecraft, and launch vehicles, and for displaying the results of such comparisons. Sparseness, typical of the data available for analysis, does not confound this software. FLOAT effects an iterative process that identifies modifications of parameters that could render compatible an otherwise incompatible mission set.

Aeroelastic Optimization Study Based on X-56A Model

NASA Technical Reports Server (NTRS)

Li, Wesley; Pak, Chan-Gi

2014-01-01

A design process which incorporates the object-oriented multidisciplinary design, analysis, and optimization (MDAO) tool and the aeroelastic effects of high fidelity finite element models to characterize the design space was successfully developed and established. Two multidisciplinary design optimization studies using an object-oriented MDAO tool developed at NASA Armstrong Flight Research Center were presented. The first study demonstrates the use of aeroelastic tailoring concepts to minimize the structural weight while meeting the design requirements including strength, buckling, and flutter. A hybrid and discretization optimization approach was implemented to improve accuracy and computational efficiency of a global optimization algorithm. The second study presents a flutter mass balancing optimization study. The results provide guidance to modify the fabricated flexible wing design and move the design flutter speeds back into the flight envelope so that the original objective of X-56A flight test can be accomplished.

AMP: a science-driven web-based application for the TeraGrid

NASA Astrophysics Data System (ADS)

Woitaszek, M.; Metcalfe, T.; Shorrock, I.

The Asteroseismic Modeling Portal (AMP) provides a web-based interface for astronomers to run and view simulations that derive the properties of Sun-like stars from observations of their pulsation frequencies. In this paper, we describe the architecture and implementation of AMP, highlighting the lightweight design principles and tools used to produce a functional fully-custom web-based science application in less than a year. Targeted as a TeraGrid science gateway, AMP's architecture and implementation are intended to simplify its orchestration of TeraGrid computational resources. AMP's web-based interface was developed as a traditional standalone database-backed web application using the Python-based Django web development framework, allowing us to leverage the Django framework's capabilities while cleanly separating the user interface development from the grid interface development. We have found this combination of tools flexible and effective for rapid gateway development and deployment.

Adaptive Control Strategies for Flexible Robotic Arm

NASA Technical Reports Server (NTRS)

Bialasiewicz, Jan T.

1996-01-01

The control problem of a flexible robotic arm has been investigated. The control strategies that have been developed have a wide application in approaching the general control problem of flexible space structures. The following control strategies have been developed and evaluated: neural self-tuning control algorithm, neural-network-based fuzzy logic control algorithm, and adaptive pole assignment algorithm. All of the above algorithms have been tested through computer simulation. In addition, the hardware implementation of a computer control system that controls the tip position of a flexible arm clamped on a rigid hub mounted directly on the vertical shaft of a dc motor, has been developed. An adaptive pole assignment algorithm has been applied to suppress vibrations of the described physical model of flexible robotic arm and has been successfully tested using this testbed.

UltraForm Finishing (UFF) a 5-axis computer controlled precision optical component grinding and polishing system

NASA Astrophysics Data System (ADS)

Bechtold, Michael; Mohring, David; Fess, Edward

2007-05-01

OptiPro Systems has developed a new finishing process for the manufacturing of precision optical components. UltraForm Finishing (UFF) has evolved from a tire shaped tool with polishing material on its periphery, to its newest design, which incorporates a precision rubber wheel wrapped with a band of polishing material passing over it. Through our research we have developed a user friendly graphical interface giving the optician a deterministic path for finishing precision optical components. Complex UFF Algorithms combine the removal function and desired depth of removal into a motion controlled tool path which minimizes surface roughness and form errors. The UFF process includes 5 axes of computer controlled motion, (3 linear and 2 rotary) which provide the flexibility for finishing a variety of shapes including spheres, aspheres, and freeform optics. The long arm extension, along with a range of diameters for the "UltraWheel" provides a unique solution for the finishing of steep concave shapes such as ogives and domes. The UltraForm process utilizes, fixed and loose abrasives, in combination with our proprietary "UltraBelts" made of a range of materials such as polyurethane, felt, resin, diamond and others.

NASA Tech Briefs, August 2005

NASA Technical Reports Server (NTRS)

2005-01-01

Topics include: Hidden Identification on Parts: Magnetic Machine-Readable Matrix Symbols; System for Processing Coded OFDM Under Doppler and Fading; Multipurpose Hyperspectral Imaging System; Magnetic-Flux-Compensated Voltage Divider; High-Performance Satellite/Terrestrial-Network Gateway; Internet-Based System for Voice Communication With the ISS; Stripline/Microstrip Transition in Multilayer Circuit Board; Dual-Band Feed for a Microwave Reflector Antenna; Quadratic Programming for Allocating Control Effort; Range Process Simulation Tool; Simulator of Space Communication Networks; Computing Q-D Relationships for Storage of Rocket Fuels; Contour Error Map Algorithm; Portfolio Analysis Tool; Glass Frit Filters for Collecting Metal Oxide Nanoparticles; Anhydrous Proton-Conducting Membranes for Fuel Cells; Portable Electron-Beam Free-Form Fabrication System; Miniature Laboratory for Detecting Sparse Biomolecules; Multicompartment Liquid-Cooling/Warming Protective Garments; Laser Metrology for an Optical-Path-Length Modulator; PCM Passive Cooling System Containing Active Subsystems; Automated Electrostatics Environmental Chamber; Estimating Aeroheating of a 3D Body Using a 2D Flow Solver; Artificial Immune System for Recognizing Patterns; Computing the Thermodynamic State of a Cryogenic Fluid; Safety and Mission Assurance Performance Metric; Magnetic Control of Concentration Gradient in Microgravity; Avionics for a Small Robotic Inspection Spacecraft; and Simulation of Dynamics of a Flexible Miniature Airplane.

PTMscape: an open source tool to predict generic post-translational modifications and map modification crosstalk in protein domains and biological processes.

PubMed

Li, Ginny X H; Vogel, Christine; Choi, Hyungwon

2018-06-07

While tandem mass spectrometry can detect post-translational modifications (PTM) at the proteome scale, reported PTM sites are often incomplete and include false positives. Computational approaches can complement these datasets by additional predictions, but most available tools use prediction models pre-trained for single PTM type by the developers and it remains a difficult task to perform large-scale batch prediction for multiple PTMs with flexible user control, including the choice of training data. We developed an R package called PTMscape which predicts PTM sites across the proteome based on a unified and comprehensive set of descriptors of the physico-chemical microenvironment of modified sites, with additional downstream analysis modules to test enrichment of individual or pairs of PTMs in protein domains. PTMscape is flexible in the ability to process any major modifications, such as phosphorylation and ubiquitination, while achieving the sensitivity and specificity comparable to single-PTM methods and outperforming other multi-PTM tools. Applying this framework, we expanded proteome-wide coverage of five major PTMs affecting different residues by prediction, especially for lysine and arginine modifications. Using a combination of experimentally acquired sites (PSP) and newly predicted sites, we discovered that the crosstalk among multiple PTMs occur more frequently than by random chance in key protein domains such as histone, protein kinase, and RNA recognition motifs, spanning various biological processes such as RNA processing, DNA damage response, signal transduction, and regulation of cell cycle. These results provide a proteome-scale analysis of crosstalk among major PTMs and can be easily extended to other types of PTM.

The GlycanBuilder: a fast, intuitive and flexible software tool for building and displaying glycan structures.

PubMed

Ceroni, Alessio; Dell, Anne; Haslam, Stuart M

2007-08-07

Carbohydrates play a critical role in human diseases and their potential utility as biomarkers for pathological conditions is a major driver for characterization of the glycome. However, the additional complexity of glycans compared to proteins and nucleic acids has slowed the advancement of glycomics in comparison to genomics and proteomics. The branched nature of carbohydrates, the great diversity of their constituents and the numerous alternative symbolic notations, make the input and display of glycans not as straightforward as for example the amino-acid sequence of a protein. Every glycoinformatic tool providing a user interface would benefit from a fast, intuitive, appealing mechanism for input and output of glycan structures in a computer readable format. A software tool for building and displaying glycan structures using a chosen symbolic notation is described here. The "GlycanBuilder" uses an automatic rendering algorithm to draw the saccharide symbols and to place them on the drawing board. The information about the symbolic notation is derived from a configurable graphical model as a set of rules governing the aspect and placement of residues and linkages. The algorithm is able to represent a structure using only few traversals of the tree and is inherently fast. The tool uses an XML format for import and export of encoded structures. The rendering algorithm described here is able to produce high-quality representations of glycan structures in a chosen symbolic notation. The automated rendering process enables the "GlycanBuilder" to be used both as a user-independent component for displaying glycans and as an easy-to-use drawing tool. The "GlycanBuilder" can be integrated in web pages as a Java applet for the visual editing of glycans. The same component is available as a web service to render an encoded structure into a graphical format. Finally, the "GlycanBuilder" can be integrated into other applications to create intuitive and appealing user interfaces: an example is the "GlycoWorkbench", a software tool for assisted annotation of glycan mass spectra. The "GlycanBuilder" represent a flexible, reliable and efficient solution to the problem of input and output of glycan structures in any glycomic tool or database.

Prediction of Solution Properties of Flexible-Chain Polymers: A Computer Simulation Undergraduate Experiment

ERIC Educational Resources Information Center

de la Torre, Jose Garcia; Cifre, Jose G. Hernandez; Martinez, M. Carmen Lopez

2008-01-01

This paper describes a computational exercise at undergraduate level that demonstrates the employment of Monte Carlo simulation to study the conformational statistics of flexible polymer chains, and to predict solution properties. Three simple chain models, including excluded volume interactions, have been implemented in a public-domain computer…

Incorporating Flexibility in the Design of Repairable Systems - Design of Microgrids

DTIC Science & Technology

2014-01-01

MICROGRIDS Vijitashwa Pandey1 Annette Skowronska1,2...optimization of complex systems such as a microgrid is however, computationally intensive. The problem is exacerbated if we must incorporate...flexibility in terms of allowing the microgrid architecture and its running protocol to change with time. To reduce the computational effort, this paper

Diagnostic flexible pharyngo-laryngoscopy: development of a procedure specific assessment tool using a Delphi methodology.

PubMed

Melchiors, Jacob; Henriksen, Mikael Johannes Vuokko; Dikkers, Frederik G; Gavilán, Javier; Noordzij, J Pieter; Fried, Marvin P; Novakovic, Daniel; Fagan, Johannes; Charabi, Birgitte W; Konge, Lars; von Buchwald, Christian

2018-05-01

Proper training and assessment of skill in flexible pharyngo-laryngoscopy are central in the education of otorhinolaryngologists. To facilitate an evidence-based approach to curriculum development in this field, a structured analysis of what constitutes flexible pharyngo-laryngoscopy is necessary. Our aim was to develop an assessment tool based on this analysis. We conducted an international Delphi study involving experts from twelve countries in five continents. Utilizing reiterative assessment, the panel defined the procedure and reached consensus (defined as 80% agreement) on the phrasing of an assessment tool. FIFTY PANELISTS COMPLETED THE DELPHI PROCESS. THE MEDIAN AGE OF THE PANELISTS WAS 44 YEARS (RANGE 33-64 YEARS). MEDIAN EXPERIENCE IN OTORHINOLARYNGOLOGY WAS 15 YEARS (RANGE 6-35 YEARS). TWENTY-FIVE WERE SPECIALIZED IN LARYNGOLOGY, 16 WERE HEAD AND NECK SURGEONS, AND NINE WERE GENERAL OTORHINOLARYNGOLOGISTS. AN ASSESSMENT TOOL WAS CREATED CONSISTING OF TWELVE DISTINCT ITEMS.: Conclusion The gathering of validity evidence for assessment of core procedural skills within Otorhinolaryngology is central to the development of a competence-based education. The use of an international Delphi panel allows for the creation of an assessment tool which is widely applicable and valid. This work allows for an informed approach to technical skills training for flexible pharyngo-laryngoscopy and as further validity evidence is gathered allows for a valid assessment of clinical performance within this important skillset.

Computational Analysis of Dynamic SPK(S8)-JP8 Fueled Combustor-Sector Performance

NASA Technical Reports Server (NTRS)

Ryder, R.; Hendricks, Roberts C.; Huber, M. L.; Shouse, D. T.

2010-01-01

Civil and military flight tests using blends of synthetic and biomass fueling with jet fuel up to 50:50 are currently considered as "drop-in" fuels. They are fully compatible with aircraft performance, emissions and fueling systems, yet the design and operations of such fueling systems and combustors must be capable of running fuels from a range of feedstock sources. This paper provides Smart Combustor or Fuel Flexible Combustor designers with computational tools, preliminary performance, emissions and particulates combustor sector data. The baseline fuel is kerosene-JP-8+100 (military) or Jet A (civil). Results for synthetic paraffinic kerosene (SPK) fuel blends show little change with respect to baseline performance, yet do show lower emissions. The evolution of a validated combustor design procedure is fundamental to the development of dynamic fueling of combustor systems for gas turbine engines that comply with multiple feedstock sources satisfying both new and legacy systems.

Computer-aided design of biological circuits using TinkerCell

PubMed Central

Bergmann, Frank T; Sauro, Herbert M

2010-01-01

Synthetic biology is an engineering discipline that builds on modeling practices from systems biology and wet-lab techniques from genetic engineering. As synthetic biology advances, efficient procedures will be developed that will allow a synthetic biologist to design, analyze and build biological networks. In this idealized pipeline, computer-aided design (CAD) is a necessary component. The role of a CAD application would be to allow efficient transition from a general design to a final product. TinkerCell is a design tool for serving this purpose in synthetic biology. In TinkerCell, users build biological networks using biological parts and modules. The network can be analyzed using one of several functions provided by TinkerCell or custom programs from third-party sources. Since best practices for modeling and constructing synthetic biology networks have not yet been established, TinkerCell is designed as a flexible and extensible application that can adjust itself to changes in the field. PMID:21327060

Averaging business cycles vs. myopia: Do we need a long term vision when developing IRP?

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

McDonald, C.; Gupta, P.C.

1995-05-01

Utility demand forecasting is inherently imprecise due to the number of uncertainties resulting from business cycles, policy making, technology breakthroughs, national and international political upheavals and the limitations of the forecasting tools. This implies that revisions based primarily on recent experience could lead to unstable forecasts. Moreover, new planning tools are required that provide an explicit consideration of uncertainty and lead to flexible and robust planning tools are required that provide an explicit consideration of uncertainty and lead to flexible and robust planning decisions.

Predicting Protein-protein Association Rates using Coarse-grained Simulation and Machine Learning

NASA Astrophysics Data System (ADS)

Xie, Zhong-Ru; Chen, Jiawen; Wu, Yinghao

2017-04-01

Protein-protein interactions dominate all major biological processes in living cells. We have developed a new Monte Carlo-based simulation algorithm to study the kinetic process of protein association. We tested our method on a previously used large benchmark set of 49 protein complexes. The predicted rate was overestimated in the benchmark test compared to the experimental results for a group of protein complexes. We hypothesized that this resulted from molecular flexibility at the interface regions of the interacting proteins. After applying a machine learning algorithm with input variables that accounted for both the conformational flexibility and the energetic factor of binding, we successfully identified most of the protein complexes with overestimated association rates and improved our final prediction by using a cross-validation test. This method was then applied to a new independent test set and resulted in a similar prediction accuracy to that obtained using the training set. It has been thought that diffusion-limited protein association is dominated by long-range interactions. Our results provide strong evidence that the conformational flexibility also plays an important role in regulating protein association. Our studies provide new insights into the mechanism of protein association and offer a computationally efficient tool for predicting its rate.

Predicting Protein–protein Association Rates using Coarse-grained Simulation and Machine Learning

PubMed Central

Xie, Zhong-Ru; Chen, Jiawen; Wu, Yinghao

2017-01-01

Protein–protein interactions dominate all major biological processes in living cells. We have developed a new Monte Carlo-based simulation algorithm to study the kinetic process of protein association. We tested our method on a previously used large benchmark set of 49 protein complexes. The predicted rate was overestimated in the benchmark test compared to the experimental results for a group of protein complexes. We hypothesized that this resulted from molecular flexibility at the interface regions of the interacting proteins. After applying a machine learning algorithm with input variables that accounted for both the conformational flexibility and the energetic factor of binding, we successfully identified most of the protein complexes with overestimated association rates and improved our final prediction by using a cross-validation test. This method was then applied to a new independent test set and resulted in a similar prediction accuracy to that obtained using the training set. It has been thought that diffusion-limited protein association is dominated by long-range interactions. Our results provide strong evidence that the conformational flexibility also plays an important role in regulating protein association. Our studies provide new insights into the mechanism of protein association and offer a computationally efficient tool for predicting its rate. PMID:28418043

Predicting Protein-protein Association Rates using Coarse-grained Simulation and Machine Learning.

PubMed

Xie, Zhong-Ru; Chen, Jiawen; Wu, Yinghao

2017-04-18

Protein-protein interactions dominate all major biological processes in living cells. We have developed a new Monte Carlo-based simulation algorithm to study the kinetic process of protein association. We tested our method on a previously used large benchmark set of 49 protein complexes. The predicted rate was overestimated in the benchmark test compared to the experimental results for a group of protein complexes. We hypothesized that this resulted from molecular flexibility at the interface regions of the interacting proteins. After applying a machine learning algorithm with input variables that accounted for both the conformational flexibility and the energetic factor of binding, we successfully identified most of the protein complexes with overestimated association rates and improved our final prediction by using a cross-validation test. This method was then applied to a new independent test set and resulted in a similar prediction accuracy to that obtained using the training set. It has been thought that diffusion-limited protein association is dominated by long-range interactions. Our results provide strong evidence that the conformational flexibility also plays an important role in regulating protein association. Our studies provide new insights into the mechanism of protein association and offer a computationally efficient tool for predicting its rate.

Structural adaptation of cold-active RTX lipase from Pseudomonas sp. strain AMS8 revealed via homology and molecular dynamics simulation approaches.

PubMed

Mohamad Ali, Mohd Shukuri; Mohd Fuzi, Siti Farhanie; Ganasen, Menega; Abdul Rahman, Raja Noor Zaliha Raja; Basri, Mahiran; Salleh, Abu Bakar

2013-01-01

The psychrophilic enzyme is an interesting subject to study due to its special ability to adapt to extreme temperatures, unlike typical enzymes. Utilizing computer-aided software, the predicted structure and function of the enzyme lipase AMS8 (LipAMS8) (isolated from the psychrophilic Pseudomonas sp., obtained from the Antarctic soil) are studied. The enzyme shows significant sequence similarities with lipases from Pseudomonas sp. MIS38 and Serratia marcescens. These similarities aid in the prediction of the 3D molecular structure of the enzyme. In this study, 12 ns MD simulation is performed at different temperatures for structural flexibility and stability analysis. The results show that the enzyme is most stable at 0°C and 5°C. In terms of stability and flexibility, the catalytic domain (N-terminus) maintained its stability more than the noncatalytic domain (C-terminus), but the non-catalytic domain showed higher flexibility than the catalytic domain. The analysis of the structure and function of LipAMS8 provides new insights into the structural adaptation of this protein at low temperatures. The information obtained could be a useful tool for low temperature industrial applications and molecular engineering purposes, in the near future.

EMAAS: An extensible grid-based Rich Internet Application for microarray data analysis and management

PubMed Central

Barton, G; Abbott, J; Chiba, N; Huang, DW; Huang, Y; Krznaric, M; Mack-Smith, J; Saleem, A; Sherman, BT; Tiwari, B; Tomlinson, C; Aitman, T; Darlington, J; Game, L; Sternberg, MJE; Butcher, SA

2008-01-01

Background Microarray experimentation requires the application of complex analysis methods as well as the use of non-trivial computer technologies to manage the resultant large data sets. This, together with the proliferation of tools and techniques for microarray data analysis, makes it very challenging for a laboratory scientist to keep up-to-date with the latest developments in this field. Our aim was to develop a distributed e-support system for microarray data analysis and management. Results EMAAS (Extensible MicroArray Analysis System) is a multi-user rich internet application (RIA) providing simple, robust access to up-to-date resources for microarray data storage and analysis, combined with integrated tools to optimise real time user support and training. The system leverages the power of distributed computing to perform microarray analyses, and provides seamless access to resources located at various remote facilities. The EMAAS framework allows users to import microarray data from several sources to an underlying database, to pre-process, quality assess and analyse the data, to perform functional analyses, and to track data analysis steps, all through a single easy to use web portal. This interface offers distance support to users both in the form of video tutorials and via live screen feeds using the web conferencing tool EVO. A number of analysis packages, including R-Bioconductor and Affymetrix Power Tools have been integrated on the server side and are available programmatically through the Postgres-PLR library or on grid compute clusters. Integrated distributed resources include the functional annotation tool DAVID, GeneCards and the microarray data repositories GEO, CELSIUS and MiMiR. EMAAS currently supports analysis of Affymetrix 3' and Exon expression arrays, and the system is extensible to cater for other microarray and transcriptomic platforms. Conclusion EMAAS enables users to track and perform microarray data management and analysis tasks through a single easy-to-use web application. The system architecture is flexible and scalable to allow new array types, analysis algorithms and tools to be added with relative ease and to cope with large increases in data volume. PMID:19032776

Three-dimensional surgical simulation.

PubMed

Cevidanes, Lucia H C; Tucker, Scott; Styner, Martin; Kim, Hyungmin; Chapuis, Jonas; Reyes, Mauricio; Proffit, William; Turvey, Timothy; Jaskolka, Michael

2010-09-01

In this article, we discuss the development of methods for computer-aided jaw surgery, which allows us to incorporate the high level of precision necessary for transferring virtual plans into the operating room. We also present a complete computer-aided surgery system developed in close collaboration with surgeons. Surgery planning and simulation include construction of 3-dimensional surface models from cone-beam computed tomography, dynamic cephalometry, semiautomatic mirroring, interactive cutting of bone, and bony segment repositioning. A virtual setup can be used to manufacture positioning splints for intraoperative guidance. The system provides further intraoperative assistance with a computer display showing jaw positions and 3-dimensional positioning guides updated in real time during the surgical procedure. The computer-aided surgery system aids in dealing with complex cases with benefits for the patient, with surgical practice, and for orthodontic finishing. Advanced software tools for diagnosis and treatment planning allow preparation of detailed operative plans, osteotomy repositioning, bone reconstructions, surgical resident training, and assessing the difficulties of the surgical procedures before the surgery. Computer-aided surgery can make the elaboration of the surgical plan a more flexible process, increase the level of detail and accuracy of the plan, yield higher operative precision and control, and enhance documentation of cases. 2010 American Association of Orthodontists. Published by Mosby, Inc. All rights reserved.

Continuous Security and Configuration Monitoring of HPC Clusters

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

Garcia-Lomeli, H. D.; Bertsch, A. D.; Fox, D. M.

Continuous security and configuration monitoring of information systems has been a time consuming and laborious task for system administrators at the High Performance Computing (HPC) center. Prior to this project, system administrators had to manually check the settings of thousands of nodes, which required a significant number of hours rendering the old process ineffective and inefficient. This paper explains the application of Splunk Enterprise, a software agent, and a reporting tool in the development of a user application interface to track and report on critical system updates and security compliance status of HPC Clusters. In conjunction with other configuration managementmore » systems, the reporting tool is to provide continuous situational awareness to system administrators of the compliance state of information systems. Our approach consisted of the development, testing, and deployment of an agent to collect any arbitrary information across a massively distributed computing center, and organize that information into a human-readable format. Using Splunk Enterprise, this raw data was then gathered into a central repository and indexed for search, analysis, and correlation. Following acquisition and accumulation, the reporting tool generated and presented actionable information by filtering the data according to command line parameters passed at run time. Preliminary data showed results for over six thousand nodes. Further research and expansion of this tool could lead to the development of a series of agents to gather and report critical system parameters. However, in order to make use of the flexibility and resourcefulness of the reporting tool the agent must conform to specifications set forth in this paper. This project has simplified the way system administrators gather, analyze, and report on the configuration and security state of HPC clusters, maintaining ongoing situational awareness. Rather than querying each cluster independently, compliance checking can be managed from one central location.« less

The subsea deployment and installation of flexible pipe catenaries for the Enserch Garden Banks 388 Freestanding Production Riser

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

Herman, R.J.

1997-07-01

This narrative addresses the development of the subsea flexible pipe catenary handling tools and procedures as used in the Gulf of Mexico on the Enserch Garden Banks 388 Freestanding Production Riser. The philosophy that was invoked for the development of the tools and procedures was targeted on long term utilization and field maintenance capability with minimum vessel relocation requirements and minimum production interruptions. The initial emphasis for the required tools and procedures was to develop worker safe, environmentally friendly and cost effective equipment. These tools are for the deployment and installation of 3-inch Production and Annulus flexible pipe catenaries frommore » the Enserch Garden Banks 388 Floating Production Vessel to the system`s Freestanding Production Riser. The Pull In Jib system is common to the handling of all the catenaries. The Pull In Jib system has been designed to support the greater loads of the 8-inch and 12-inch export line catenaries.« less

Application of PSAT to Load Flow Analysis with STATCOM under Load Increase Scenario and Line Contingencies

NASA Astrophysics Data System (ADS)

Telang, Aparna S.; Bedekar, P. P.

2017-09-01

Load flow analysis is the initial and essential step for any power system computation. It is required for choosing better options for power system expansion to meet with ever increasing load demand. Implementation of Flexible AC Transmission System (FACTS) device like STATCOM, in the load flow, which is having fast and very flexible control, is one of the important tasks for power system researchers. This paper presents a simple and systematic approach for steady state power flow calculations with FACTS controller, static synchronous compensator (STATCOM) using command line usage of MATLAB tool-power system analysis toolbox (PSAT). The complexity of MATLAB language programming increases due to incorporation of STATCOM in an existing Newton-Raphson load flow algorithm. Thus, the main contribution of this paper is to show how command line usage of user friendly MATLAB tool, PSAT, can extensively be used for quicker and wider interpretation of the results of load flow with STATCOM. The novelty of this paper lies in the method of applying the load increase pattern, where the active and reactive loads have been changed simultaneously at all the load buses under consideration for creating stressed conditions for load flow analysis with STATCOM. The performance have been evaluated on many standard IEEE test systems and the results for standard IEEE-30 bus system, IEEE-57 bus system, and IEEE-118 bus system are presented.

Exploring the potential of a structural alphabet-based tool for mining multiple target conformations and target flexibility insight

PubMed Central

Chéron, Jean-Baptiste; Triki, Dhoha; Senac, Caroline; Flatters, Delphine; Camproux, Anne-Claude

2017-01-01

Protein flexibility is often implied in binding with different partners and is essential for protein function. The growing number of macromolecular structures in the Protein Data Bank entries and their redundancy has become a major source of structural knowledge of the protein universe. The analysis of structural variability through available redundant structures of a target, called multiple target conformations (MTC), obtained using experimental or modeling methods and under different biological conditions or different sources is one way to explore protein flexibility. This analysis is essential to improve the understanding of various mechanisms associated with protein target function and flexibility. In this study, we explored structural variability of three biological targets by analyzing different MTC sets associated with these targets. To facilitate the study of these MTC sets, we have developed an efficient tool, SA-conf, dedicated to capturing and linking the amino acid and local structure variability and analyzing the target structural variability space. The advantage of SA-conf is that it could be applied to divers sets composed of MTCs available in the PDB obtained using NMR and crystallography or homology models. This tool could also be applied to analyze MTC sets obtained by dynamics approaches. Our results showed that SA-conf tool is effective to quantify the structural variability of a MTC set and to localize the structural variable positions and regions of the target. By selecting adapted MTC subsets and comparing their variability detected by SA-conf, we highlighted different sources of target flexibility such as induced by binding partner, by mutation and intrinsic flexibility. Our results support the interest to mine available structures associated with a target using to offer valuable insight into target flexibility and interaction mechanisms. The SA-conf executable script, with a set of pre-compiled binaries are available at http://www.mti.univ-paris-diderot.fr/recherche/plateformes/logiciels. PMID:28817602

Exploring the potential of a structural alphabet-based tool for mining multiple target conformations and target flexibility insight.

PubMed

Regad, Leslie; Chéron, Jean-Baptiste; Triki, Dhoha; Senac, Caroline; Flatters, Delphine; Camproux, Anne-Claude

2017-01-01

Protein flexibility is often implied in binding with different partners and is essential for protein function. The growing number of macromolecular structures in the Protein Data Bank entries and their redundancy has become a major source of structural knowledge of the protein universe. The analysis of structural variability through available redundant structures of a target, called multiple target conformations (MTC), obtained using experimental or modeling methods and under different biological conditions or different sources is one way to explore protein flexibility. This analysis is essential to improve the understanding of various mechanisms associated with protein target function and flexibility. In this study, we explored structural variability of three biological targets by analyzing different MTC sets associated with these targets. To facilitate the study of these MTC sets, we have developed an efficient tool, SA-conf, dedicated to capturing and linking the amino acid and local structure variability and analyzing the target structural variability space. The advantage of SA-conf is that it could be applied to divers sets composed of MTCs available in the PDB obtained using NMR and crystallography or homology models. This tool could also be applied to analyze MTC sets obtained by dynamics approaches. Our results showed that SA-conf tool is effective to quantify the structural variability of a MTC set and to localize the structural variable positions and regions of the target. By selecting adapted MTC subsets and comparing their variability detected by SA-conf, we highlighted different sources of target flexibility such as induced by binding partner, by mutation and intrinsic flexibility. Our results support the interest to mine available structures associated with a target using to offer valuable insight into target flexibility and interaction mechanisms. The SA-conf executable script, with a set of pre-compiled binaries are available at http://www.mti.univ-paris-diderot.fr/recherche/plateformes/logiciels.

CFD Based Computations of Flexible Helicopter Blades for Stability Analysis

NASA Technical Reports Server (NTRS)

Guruswamy, Guru P.

2011-01-01

As a collaborative effort among government aerospace research laboratories an advanced version of a widely used computational fluid dynamics code, OVERFLOW, was recently released. This latest version includes additions to model flexible rotating multiple blades. In this paper, the OVERFLOW code is applied to improve the accuracy of airload computations from the linear lifting line theory that uses displacements from beam model. Data transfers required at every revolution are managed through a Unix based script that runs jobs on large super-cluster computers. Results are demonstrated for the 4-bladed UH-60A helicopter. Deviations of computed data from flight data are evaluated. Fourier analysis post-processing that is suitable for aeroelastic stability computations are performed.

Flexible and Secure Computer-Based Assessment Using a Single Zip Disk

ERIC Educational Resources Information Center

Ko, C. C.; Cheng, C. D.

2008-01-01

Electronic examination systems, which include Internet-based system, require extremely complicated installation, configuration and maintenance of software as well as hardware. In this paper, we present the design and development of a flexible, easy-to-use and secure examination system (e-Test), in which any commonly used computer can be used as a…

A computational procedure for multibody systems including flexible beam dynamics

NASA Technical Reports Server (NTRS)

Downer, J. D.; Park, K. C.; Chiou, J. C.

1990-01-01

A computational procedure suitable for the solution of equations of motions for flexible multibody systems has been developed. The flexible beams are modeled using a fully nonlinear theory which accounts for both finite rotations and large deformations. The present formulation incorporates physical measures of conjugate Cauchy stress and covariant strain increments. As a consequence, the beam model can easily be interfaced with real-time strain measurements and feedback control systems. A distinct feature of the present work is the computational preservation of total energy for undamped systems; this is obtained via an objective strain increment/stress update procedure combined with an energy-conserving time integration algorithm which contains an accurate update of angular orientations. The procedure is demonstrated via several example problems.

Improvements in musculoskeletal health and computing behaviors: Effects of a macroergonomics office workplace and training intervention.

PubMed

Robertson, Michelle M; Huang, Yueng Hsiang; Lee, Jin

2017-07-01

Computer use and its association with musculoskeletal and visual symptoms is an escalating concern. Organizations are shifting to a more proactive injury prevention perspective. Accordingly, a macroergonomics intervention consisting of flexible workplace design and office ergonomics training was designed to examine the effects on worker's computing behaviors, postures, and musculoskeletal discomfort, and their relationship to psychosocial factors. Participants were assigned to either group: 1) no-intervention control 2) flexible Workplace-only (WP-only), and 3) flexible Workplace + Training (WP+T). Observational findings indicate both intervention groups experienced positive, significant changes in improved workstation arrangements and computing postures, with the WP+T intervention group exhibiting a higher, significant change of behavioral translation. Also, significant, positive relationships between observed postures and musculoskeletal discomfort/pain were found. The intervention effect was stronger when management was responsive to workers' ergonomics needs. This study suggests that a macroergonomics intervention can produce beneficial effects for office and computer workers and organizations. Copyright © 2017 Elsevier Ltd. All rights reserved.

A mesh generation and machine learning framework for Drosophila gene expression pattern image analysis

PubMed Central

2013-01-01

Background Multicellular organisms consist of cells of many different types that are established during development. Each type of cell is characterized by the unique combination of expressed gene products as a result of spatiotemporal gene regulation. Currently, a fundamental challenge in regulatory biology is to elucidate the gene expression controls that generate the complex body plans during development. Recent advances in high-throughput biotechnologies have generated spatiotemporal expression patterns for thousands of genes in the model organism fruit fly Drosophila melanogaster. Existing qualitative methods enhanced by a quantitative analysis based on computational tools we present in this paper would provide promising ways for addressing key scientific questions. Results We develop a set of computational methods and open source tools for identifying co-expressed embryonic domains and the associated genes simultaneously. To map the expression patterns of many genes into the same coordinate space and account for the embryonic shape variations, we develop a mesh generation method to deform a meshed generic ellipse to each individual embryo. We then develop a co-clustering formulation to cluster the genes and the mesh elements, thereby identifying co-expressed embryonic domains and the associated genes simultaneously. Experimental results indicate that the gene and mesh co-clusters can be correlated to key developmental events during the stages of embryogenesis we study. The open source software tool has been made available at http://compbio.cs.odu.edu/fly/. Conclusions Our mesh generation and machine learning methods and tools improve upon the flexibility, ease-of-use and accuracy of existing methods. PMID:24373308

"You are free to set your own hours": governing worker productivity and health through flexibility and resilience.

PubMed

MacEachen, Ellen; Polzer, Jessica; Clarke, Judy

2008-03-01

Flexible work is now endemic in modern economies. A growing literature both praises work flexibility for accommodating employees' needs and criticizes it for fueling contingency and job insecurity. Although studies have identified varied effects of flexible work, questions remain about the workplace dimensions of flexibility and how occupational workplace health is managed in these workplaces. This paper presents findings from a qualitative study of how managers in the computer software industry situate workplace flexibility and approach worker health. In-depth interviews were conducted with managers (and some workers) at 30 firms in Ontario, Canada. Using a critical discourse analysis approach, we examine managers' optimistic descriptions of flexibility which emphasize how flexible work contributes to workers' life balance. We then contrast this with managers' depictions of flexibility work practices as intense and inescapable. We suggest that the discourse of flexibility, and the work practices they foster, make possible and reinforce an increased intensity of work that is driven by the demands of technological pace and change that characterize the global information technology and computer software industries. Finally, we propose that flexible knowledge work has led to a re-framing of occupational health management involving a focus on what we call "strategies of resilience" that aim to buttress workers' capacities to withstand intensive and uncertain working conditions.

An Experimental Comparison Between Flexible and Rigid Airfoils at Low Reynolds Numbers

NASA Astrophysics Data System (ADS)

Uzodinma, Jaylon; Macphee, David

2017-11-01

This study uses experimental and computational research methods to compare the aerodynamic performance of rigid and flexible airfoils at a low Reynolds number throughout varying angles of attack. This research can be used to improve the design of small wind turbines, micro-aerial vehicles, and any other devices that operate at low Reynolds numbers. Experimental testing was conducted in the University of Alabama's low-speed wind tunnel, and computational testing was conducted using the open-source CFD code OpenFOAM. For experimental testing, polyurethane-based (rigid) airfoils and silicone-based (flexible) airfoils were constructed using acrylic molds for NACA 0012 and NACA 2412 airfoil profiles. Computer models of the previously-specified airfoils were also created for a computational analysis. Both experimental and computational data were analyzed to examine the critical angles of attack, the lift and drag coefficients, and the occurrence of laminar boundary separation for each airfoil. Moreover, the computational simulations were used to examine the resulting flow fields, in order to provide possible explanations for the aerodynamic performances of each airfoil type. EEC 1659710.

Lessons in molecular recognition: the effects of ligand and protein flexibility on molecular docking accuracy.

PubMed

Erickson, Jon A; Jalaie, Mehran; Robertson, Daniel H; Lewis, Richard A; Vieth, Michal

2004-01-01

The key to success for computational tools used in structure-based drug design is the ability to accurately place or "dock" a ligand in the binding pocket of the target of interest. In this report we examine the effect of several factors on docking accuracy, including ligand and protein flexibility. To examine ligand flexibility in an unbiased fashion, a test set of 41 ligand-protein cocomplex X-ray structures were assembled that represent a diversity of size, flexibility, and polarity with respect to the ligands. Four docking algorithms, DOCK, FlexX, GOLD, and CDOCKER, were applied to the test set, and the results were examined in terms of the ability to reproduce X-ray ligand positions within 2.0A heavy atom root-mean-square deviation. Overall, each method performed well (>50% accuracy) but for all methods it was found that docking accuracy decreased substantially for ligands with eight or more rotatable bonds. Only CDOCKER was able to accurately dock most of those ligands with eight or more rotatable bonds (71% accuracy rate). A second test set of structures was gathered to examine how protein flexibility influences docking accuracy. CDOCKER was applied to X-ray structures of trypsin, thrombin, and HIV-1-protease, using protein structures bound to several ligands and also the unbound (apo) form. Docking experiments of each ligand to one "average" structure and to the apo form were carried out, and the results were compared to docking each ligand back to its originating structure. The results show that docking accuracy falls off dramatically if one uses an average or apo structure. In fact, it is shown that the drop in docking accuracy mirrors the degree to which the protein moves upon ligand binding.

How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications

PubMed Central

Khomtchouk, Bohdan B; Weitz, Edmund; Karp, Peter D; Wahlestedt, Claes

2018-01-01

Abstract We present a rationale for expanding the presence of the Lisp family of programming languages in bioinformatics and computational biology research. Put simply, Lisp-family languages enable programmers to more quickly write programs that run faster than in other languages. Languages such as Common Lisp, Scheme and Clojure facilitate the creation of powerful and flexible software that is required for complex and rapidly evolving domains like biology. We will point out several important key features that distinguish languages of the Lisp family from other programming languages, and we will explain how these features can aid researchers in becoming more productive and creating better code. We will also show how these features make these languages ideal tools for artificial intelligence and machine learning applications. We will specifically stress the advantages of domain-specific languages (DSLs): languages that are specialized to a particular area, and thus not only facilitate easier research problem formulation, but also aid in the establishment of standards and best programming practices as applied to the specific research field at hand. DSLs are particularly easy to build in Common Lisp, the most comprehensive Lisp dialect, which is commonly referred to as the ‘programmable programming language’. We are convinced that Lisp grants programmers unprecedented power to build increasingly sophisticated artificial intelligence systems that may ultimately transform machine learning and artificial intelligence research in bioinformatics and computational biology. PMID:28040748

How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications.

PubMed

Khomtchouk, Bohdan B; Weitz, Edmund; Karp, Peter D; Wahlestedt, Claes

2018-05-01

We present a rationale for expanding the presence of the Lisp family of programming languages in bioinformatics and computational biology research. Put simply, Lisp-family languages enable programmers to more quickly write programs that run faster than in other languages. Languages such as Common Lisp, Scheme and Clojure facilitate the creation of powerful and flexible software that is required for complex and rapidly evolving domains like biology. We will point out several important key features that distinguish languages of the Lisp family from other programming languages, and we will explain how these features can aid researchers in becoming more productive and creating better code. We will also show how these features make these languages ideal tools for artificial intelligence and machine learning applications. We will specifically stress the advantages of domain-specific languages (DSLs): languages that are specialized to a particular area, and thus not only facilitate easier research problem formulation, but also aid in the establishment of standards and best programming practices as applied to the specific research field at hand. DSLs are particularly easy to build in Common Lisp, the most comprehensive Lisp dialect, which is commonly referred to as the 'programmable programming language'. We are convinced that Lisp grants programmers unprecedented power to build increasingly sophisticated artificial intelligence systems that may ultimately transform machine learning and artificial intelligence research in bioinformatics and computational biology.

PseKNC: a flexible web server for generating pseudo K-tuple nucleotide composition.

PubMed

Chen, Wei; Lei, Tian-Yu; Jin, Dian-Chuan; Lin, Hao; Chou, Kuo-Chen

2014-07-01

The pseudo oligonucleotide composition, or pseudo K-tuple nucleotide composition (PseKNC), can be used to represent a DNA or RNA sequence with a discrete model or vector yet still keep considerable sequence order information, particularly the global or long-range sequence order information, via the physicochemical properties of its constituent oligonucleotides. Therefore, the PseKNC approach may hold very high potential for enhancing the power in dealing with many problems in computational genomics and genome sequence analysis. However, dealing with different DNA or RNA problems may need different kinds of PseKNC. Here, we present a flexible and user-friendly web server for PseKNC (at http://lin.uestc.edu.cn/pseknc/default.aspx) by which users can easily generate many different modes of PseKNC according to their need by selecting various parameters and physicochemical properties. Furthermore, for the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the current web server to generate their desired PseKNC without the need to follow the complicated mathematical equations, which are presented in this article just for the integrity of PseKNC formulation and its development. It is anticipated that the PseKNC web server will become a very useful tool in computational genomics and genome sequence analysis. Copyright © 2014 Elsevier Inc. All rights reserved.

Plaster core washout tool

NASA Technical Reports Server (NTRS)

Heisman, R. M.; Keir, A. R.; Teramura, K.

1977-01-01

Tool powered by pressurized water or air removes water soluble plaster lining from Kevlar/epoxy duct. Rotating plastic cutterhead with sealed end fitting connects flexible shaft that allows tool to be used with curved ducts.

The ISO 50001 Impact Estimator Tool (IET 50001 V1.1.4) - User Guide and Introduction to the ISO 50001 Impacts Methodology

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

Therkelsen, Peter L.; Rao, Prakash; Aghajanzadeh, Arian

ISO 50001-Energy management systems – Requirements with guidance for use, is an internationally developed standard that provides organizations with a flexible framework for implementing an energy management system (EnMS) with the goal of continual energy performance improvement. The ISO 50001 standard was first published in 2011 and has since seen growth in the number of certificates issued around the world, primarily in the industrial (agriculture, manufacturing, and mining) and service (commercial) sectors. Policy makers in many regions and countries are looking to or are already using ISO 50001 as a basis for energy efficiency, carbon reduction, and other energy performancemore » improvement schemes. The Impact Estimator Tool 50001 (IET 50001 Tool) is a computational model developed to assist researchers and policy makers determine the potential impact of ISO 50001 implementation in the industrial and service (commercial) sectors for a given region or country. The IET 50001 Tool is based upon a methodology initially developed by the Lawrence Berkeley National Laboratory that has been improved upon and vetted by a group of international researchers. By using a commonly accepted and transparent methodology, users of the IET 50001 Tool can easily and clearly communicate the potential impact of ISO 50001 for a region or country.« less

Addition of flexible body option to the TOLA computer program. Part 2: User and programmer documentation

NASA Technical Reports Server (NTRS)

Dick, J. W.; Benda, B. J.

1975-01-01

User and programmer oriented documentation for the flexible body option of the Takeoff and Landing Analysis (TOLA) computer program are provided. The user information provides sufficient knowledge of the development and use of the option to enable the engineering user to successfully operate the modified program and understand the results. The programmer's information describes the option structure and logic enabling a programmer to make major revisions to this part of the TOLA computer program.

An automated and reproducible workflow for running and analyzing neural simulations using Lancet and IPython Notebook

PubMed Central

Stevens, Jean-Luc R.; Elver, Marco; Bednar, James A.

2013-01-01

Lancet is a new, simulator-independent Python utility for succinctly specifying, launching, and collating results from large batches of interrelated computationally demanding program runs. This paper demonstrates how to combine Lancet with IPython Notebook to provide a flexible, lightweight, and agile workflow for fully reproducible scientific research. This informal and pragmatic approach uses IPython Notebook to capture the steps in a scientific computation as it is gradually automated and made ready for publication, without mandating the use of any separate application that can constrain scientific exploration and innovation. The resulting notebook concisely records each step involved in even very complex computational processes that led to a particular figure or numerical result, allowing the complete chain of events to be replicated automatically. Lancet was originally designed to help solve problems in computational neuroscience, such as analyzing the sensitivity of a complex simulation to various parameters, or collecting the results from multiple runs with different random starting points. However, because it is never possible to know in advance what tools might be required in future tasks, Lancet has been designed to be completely general, supporting any type of program as long as it can be launched as a process and can return output in the form of files. For instance, Lancet is also heavily used by one of the authors in a separate research group for launching batches of microprocessor simulations. This general design will allow Lancet to continue supporting a given research project even as the underlying approaches and tools change. PMID:24416014

A flexible tool for hydraulic and water quality performance analysis of green infrastructure

NASA Astrophysics Data System (ADS)

Massoudieh, A.; Alikhani, J.

2017-12-01

Models that allow for design considerations of green infrastructure (GI) practices to control stormwater runoff and associated contaminants have received considerable attention in recent years. To be used to evaluate the effect design configurations on the long-term performance of GIs, models should be able to consider processes within GIs with good fidelity. In this presentation, a sophisticated, yet flexible tool for hydraulic and water quality assessment of GIs will be introduced. The tool can be used by design engineers and researchers to capture and explore the effect of design factors and properties of the media employed in the performance of GI systems at a relatively small scale. We deemed it essential to have a flexible GI modeling tool that is capable of simulating GI system components and specific biogeochemical processes affecting contaminants such as evapotranspiration, plant uptake, reactions, and particle-associated transport accurately while maintaining a high degree of flexibility to account for the myriad of GI alternatives. The mathematical framework for a stand-alone GI performance assessment tool has been developed and will be demonstrated. The process-based model framework developed here can be used to model a diverse range of GI practices such as stormwater ponds, green roofs, retention ponds, bioretention systems, infiltration trench, permeable pavement and other custom-designed combinatory systems. An example of the application of the system to evaluate the performance of a rain-garden system will be demonstrated.

Reach a New Threshold of Freedom and Control with Dell's Flexible Computing Solution: On-Demand Desktop Streaming

ERIC Educational Resources Information Center

Technology & Learning, 2008

2008-01-01

When it comes to IT, there has always been an important link between data center control and client flexibility. As computing power increases, so do the potentially crippling threats to security, productivity and financial stability. This article talks about Dell's On-Demand Desktop Streaming solution which is designed to centralize complete…

A Set of Free Cross-Platform Authoring Programs for Flexible Web-Based CALL Exercises

ERIC Educational Resources Information Center

O'Brien, Myles

2012-01-01

The Mango Suite is a set of three freely downloadable cross-platform authoring programs for flexible network-based CALL exercises. They are Adobe Air applications, so they can be used on Windows, Macintosh, or Linux computers, provided the freely-available Adobe Air has been installed on the computer. The exercises which the programs generate are…

Using the NASTRAN Thermal Analyzer to simulate a flight scientific instrument package

NASA Technical Reports Server (NTRS)

Lee, H.-P.; Jackson, C. E., Jr.

1974-01-01

The NASTRAN Thermal Analyzer has proven to be a unique and useful tool for thermal analyses involving large and complex structures where small, thermally induced deformations are critical. Among its major advantages are direct grid point-to-grid point compatibility with large structural models; plots of the model that may be generated for both conduction and boundary elements; versatility of applying transient thermal loads especially to repeat orbital cycles; on-line printer plotting of temperatures and rate of temperature changes as a function of time; and direct matrix input to solve linear differential equations on-line. These features provide a flexibility far beyond that available in most finite-difference thermal analysis computer programs.

PIFEX: An advanced programmable pipelined-image processor

NASA Technical Reports Server (NTRS)

Gennery, D. B.; Wilcox, B.

1985-01-01

PIFEX is a pipelined-image processor being built in the JPL Robotics Lab. It will operate on digitized raster-scanned images (at 60 frames per second for images up to about 300 by 400 and at lesser rates for larger images), performing a variety of operations simultaneously under program control. It thus is a powerful, flexible tool for image processing and low-level computer vision. It also has applications in other two-dimensional problems such as route planning for obstacle avoidance and the numerical solution of two-dimensional partial differential equations (although its low numerical precision limits its use in the latter field). The concept and design of PIFEX are described herein, and some examples of its use are given.

Statistical, economic and other tools for assessing natural aggregate

USGS Publications Warehouse

Bliss, J.D.; Moyle, P.R.; Bolm, K.S.

2003-01-01

Quantitative aggregate resource assessment provides resource estimates useful for explorationists, land managers and those who make decisions about land allocation, which may have long-term implications concerning cost and the availability of aggregate resources. Aggregate assessment needs to be systematic and consistent, yet flexible enough to allow updating without invalidating other parts of the assessment. Evaluators need to use standard or consistent aggregate classification and statistic distributions or, in other words, models with geological, geotechnical and economic variables or interrelationships between these variables. These models can be used with subjective estimates, if needed, to estimate how much aggregate may be present in a region or country using distributions generated by Monte Carlo computer simulations.

PSYCHE: An Object-Oriented Approach to Simulating Medical Education

PubMed Central

Mullen, Jamie A.

1990-01-01

Traditional approaches to computer-assisted instruction (CAI) do not provide realistic simulations of medical education, in part because they do not utilize heterogeneous knowledge bases for their source of domain knowledge. PSYCHE, a CAI program designed to teach hypothetico-deductive psychiatric decision-making to medical students, uses an object-oriented implementation of an intelligent tutoring system (ITS) to model the student, domain expert, and tutor. It models the transactions between the participants in complex transaction chains, and uses heterogeneous knowledge bases to represent both domain and procedural knowledge in clinical medicine. This object-oriented approach is a flexible and dynamic approach to modeling, and represents a potentially valuable tool for the investigation of medical education and decision-making.

Prototyping Instruments for Chemical Laboratory Using Inexpensive Electronic Modules.

PubMed

Urban, Pawel L

2018-05-15

Open-source electronics and programming can augment chemical and biomedical research. Currently, chemists can choose from a broad range of low-cost universal electronic modules (microcontroller boards and single-board computers) and use them to assemble working prototypes of scientific tools to address specific experimental problems and to support daily research work. The learning time can be as short as a few hours, and the required budget is often as low as 50 USD. Prototyping instruments using low-cost electronic modules gives chemists enormous flexibility to design and construct customized instrumentation, which can reduce the delays caused by limited access to high-end commercial platforms. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Characteristics of a semi-custom library development system

NASA Technical Reports Server (NTRS)

Yancey, M.; Cannon, R.

1990-01-01

Standard cell and gate array macro libraries are in common use with workstation computer aided design (CAD) tools for application specific integrated circuit (ASIC) semi-custom application and have resulted in significant improvements in the overall design efficiencies as contrasted with custom design methodologies. Similar design methodology enhancements in providing for the efficient development of the library cells is an important factor in responding to the need for continuous technology improvement. The characteristics of a library development system that provides design flexibility and productivity enhancements for the library development engineer as he provides libraries in the state-of-the-art process technologies are presented. An overview of Gould's library development system ('Accolade') is also presented.

PyNEST: A Convenient Interface to the NEST Simulator.

PubMed

Eppler, Jochen Martin; Helias, Moritz; Muller, Eilif; Diesmann, Markus; Gewaltig, Marc-Oliver

2008-01-01

The neural simulation tool NEST (http://www.nest-initiative.org) is a simulator for heterogeneous networks of point neurons or neurons with a small number of compartments. It aims at simulations of large neural systems with more than 10(4) neurons and 10(7) to 10(9) synapses. NEST is implemented in C++ and can be used on a large range of architectures from single-core laptops over multi-core desktop computers to super-computers with thousands of processor cores. Python (http://www.python.org) is a modern programming language that has recently received considerable attention in Computational Neuroscience. Python is easy to learn and has many extension modules for scientific computing (e.g. http://www.scipy.org). In this contribution we describe PyNEST, the new user interface to NEST. PyNEST combines NEST's efficient simulation kernel with the simplicity and flexibility of Python. Compared to NEST's native simulation language SLI, PyNEST makes it easier to set up simulations, generate stimuli, and analyze simulation results. We describe how PyNEST connects NEST and Python and how it is implemented. With a number of examples, we illustrate how it is used.

A scientific workflow framework for (13)C metabolic flux analysis.

PubMed

Dalman, Tolga; Wiechert, Wolfgang; Nöh, Katharina

2016-08-20

Metabolic flux analysis (MFA) with (13)C labeling data is a high-precision technique to quantify intracellular reaction rates (fluxes). One of the major challenges of (13)C MFA is the interactivity of the computational workflow according to which the fluxes are determined from the input data (metabolic network model, labeling data, and physiological rates). Here, the workflow assembly is inevitably determined by the scientist who has to consider interacting biological, experimental, and computational aspects. Decision-making is context dependent and requires expertise, rendering an automated evaluation process hardly possible. Here, we present a scientific workflow framework (SWF) for creating, executing, and controlling on demand (13)C MFA workflows. (13)C MFA-specific tools and libraries, such as the high-performance simulation toolbox 13CFLUX2, are wrapped as web services and thereby integrated into a service-oriented architecture. Besides workflow steering, the SWF features transparent provenance collection and enables full flexibility for ad hoc scripting solutions. To handle compute-intensive tasks, cloud computing is supported. We demonstrate how the challenges posed by (13)C MFA workflows can be solved with our approach on the basis of two proof-of-concept use cases. Copyright © 2015 Elsevier B.V. All rights reserved.

PyNEST: A Convenient Interface to the NEST Simulator

PubMed Central

Eppler, Jochen Martin; Helias, Moritz; Muller, Eilif; Diesmann, Markus; Gewaltig, Marc-Oliver

2008-01-01

The neural simulation tool NEST (http://www.nest-initiative.org) is a simulator for heterogeneous networks of point neurons or neurons with a small number of compartments. It aims at simulations of large neural systems with more than 104 neurons and 107 to 109 synapses. NEST is implemented in C++ and can be used on a large range of architectures from single-core laptops over multi-core desktop computers to super-computers with thousands of processor cores. Python (http://www.python.org) is a modern programming language that has recently received considerable attention in Computational Neuroscience. Python is easy to learn and has many extension modules for scientific computing (e.g. http://www.scipy.org). In this contribution we describe PyNEST, the new user interface to NEST. PyNEST combines NEST's efficient simulation kernel with the simplicity and flexibility of Python. Compared to NEST's native simulation language SLI, PyNEST makes it easier to set up simulations, generate stimuli, and analyze simulation results. We describe how PyNEST connects NEST and Python and how it is implemented. With a number of examples, we illustrate how it is used. PMID:19198667

A user view of office automation or the integrated workstation

NASA Technical Reports Server (NTRS)

Schmerling, E. R.

1984-01-01

Central data bases are useful only if they are kept up to date and easily accessible in an interactive (query) mode rather than in monthly reports that may be out of date and must be searched by hand. The concepts of automatic data capture, data base management and query languages require good communications and readily available work stations to be useful. The minimal necessary work station is a personal computer which can be an important office tool if connected into other office machines and properly integrated into an office system. It has a great deal of flexibility and can often be tailored to suit the tastes, work habits and requirements of the user. Unlike dumb terminals, there is less tendency to saturate a central computer, since its free standing capabilities are available after down loading a selection of data. The PC also permits the sharing of many other facilities, like larger computing power, sophisticated graphics programs, laser printers and communications. It can provide rapid access to common data bases able to provide more up to date information than printed reports. Portable computers can access the same familiar office facilities from anywhere in the world where a telephone connection can be made.

Tool Enlarges Hard-to-Reach Holes

NASA Technical Reports Server (NTRS)

Geddes, J. P.

1984-01-01

Tool centers itself and cuts precise depth. Tool consists of crosscut carbide bur; sleeve that serves as depth stop and pilot; length of flexible, strong piano wire; and standard drive socket. Parts brazed together. Piano wire transmits torque and axial force to cutting tool.

Addition of flexible body option to the TOLA computer program, part 1

NASA Technical Reports Server (NTRS)

Dick, J. W.; Benda, B. J.

1975-01-01

This report describes a flexible body option that was developed and added to the Takeoff and Landing Analysis (TOLA) computer program. The addition of the flexible body option to TOLA allows it to be used to study essentially any conventional type airplane in the ground operating environment. It provides the capability to predict the total motion of selected points on the analytical methods incorporated in the program and operating instructions for the option are described. A program listing is included along with several example problems to aid in interpretation of the operating instructions and to illustrate program usage.

Simulation of flexible appendage interactions with Mariner Venus/Mercury attitude control and science platform pointing

NASA Technical Reports Server (NTRS)

Fleischer, G. E.

1973-01-01

A new computer subroutine, which solves the attitude equations of motion for any vehicle idealized as a topological tree of hinge-connected rigid bodies, is used to simulate and analyze science instrument pointing control interaction with a flexible Mariner Venus/Mercury (MVM) spacecraft. The subroutine's user options include linearized or partially linearized hinge-connected models whose computational advantages are demonstrated for the MVM problem. Results of the pointing control/flexible vehicle interaction simulations, including imaging experiment pointing accuracy predictions and implications for MVM science sequence planning, are described in detail.

Applications of NMR and computational methodologies to study protein dynamics.

PubMed

Narayanan, Chitra; Bafna, Khushboo; Roux, Louise D; Agarwal, Pratul K; Doucet, Nicolas

2017-08-15

Overwhelming evidence now illustrates the defining role of atomic-scale protein flexibility in biological events such as allostery, cell signaling, and enzyme catalysis. Over the years, spin relaxation nuclear magnetic resonance (NMR) has provided significant insights on the structural motions occurring on multiple time frames over the course of a protein life span. The present review article aims to illustrate to the broader community how this technique continues to shape many areas of protein science and engineering, in addition to being an indispensable tool for studying atomic-scale motions and functional characterization. Continuing developments in underlying NMR technology alongside software and hardware developments for complementary computational approaches now enable methodologies to routinely provide spatial directionality and structural representations traditionally harder to achieve solely using NMR spectroscopy. In addition to its well-established role in structural elucidation, we present recent examples that illustrate the combined power of selective isotope labeling, relaxation dispersion experiments, chemical shift analyses, and computational approaches for the characterization of conformational sub-states in proteins and enzymes. Copyright © 2017 Elsevier Inc. All rights reserved.

Computational Cosmology at the Bleeding Edge

NASA Astrophysics Data System (ADS)

Habib, Salman

2013-04-01

Large-area sky surveys are providing a wealth of cosmological information to address the mysteries of dark energy and dark matter. Observational probes based on tracking the formation of cosmic structure are essential to this effort, and rely crucially on N-body simulations that solve the Vlasov-Poisson equation in an expanding Universe. As statistical errors from survey observations continue to shrink, and cosmological probes increase in number and complexity, simulations are entering a new regime in their use as tools for scientific inference. Changes in supercomputer architectures provide another rationale for developing new parallel simulation and analysis capabilities that can scale to computational concurrency levels measured in the millions to billions. In this talk I will outline the motivations behind the development of the HACC (Hardware/Hybrid Accelerated Cosmology Code) extreme-scale cosmological simulation framework and describe its essential features. By exploiting a novel algorithmic structure that allows flexible tuning across diverse computer architectures, including accelerated and many-core systems, HACC has attained a performance of 14 PFlops on the IBM BG/Q Sequoia system at 69% of peak, using more than 1.5 million cores.

Development of innovative computer software to facilitate the setup and computation of water quality index

PubMed Central

2013-01-01

Background Developing a water quality index which is used to convert the water quality dataset into a single number is the most important task of most water quality monitoring programmes. As the water quality index setup is based on different local obstacles, it is not feasible to introduce a definite water quality index to reveal the water quality level. Findings In this study, an innovative software application, the Iranian Water Quality Index Software (IWQIS), is presented in order to facilitate calculation of a water quality index based on dynamic weight factors, which will help users to compute the water quality index in cases where some parameters are missing from the datasets. Conclusion A dataset containing 735 water samples of drinking water quality in different parts of the country was used to show the performance of this software using different criteria parameters. The software proved to be an efficient tool to facilitate the setup of water quality indices based on flexible use of variables and water quality databases. PMID:24499556

Uncertainty Quantification and Certification Prediction of Low-Boom Supersonic Aircraft Configurations

NASA Technical Reports Server (NTRS)

West, Thomas K., IV; Reuter, Bryan W.; Walker, Eric L.; Kleb, Bil; Park, Michael A.

2014-01-01

The primary objective of this work was to develop and demonstrate a process for accurate and efficient uncertainty quantification and certification prediction of low-boom, supersonic, transport aircraft. High-fidelity computational fluid dynamics models of multiple low-boom configurations were investigated including the Lockheed Martin SEEB-ALR body of revolution, the NASA 69 Delta Wing, and the Lockheed Martin 1021-01 configuration. A nonintrusive polynomial chaos surrogate modeling approach was used for reduced computational cost of propagating mixed, inherent (aleatory) and model-form (epistemic) uncertainty from both the computation fluid dynamics model and the near-field to ground level propagation model. A methodology has also been introduced to quantify the plausibility of a design to pass a certification under uncertainty. Results of this study include the analysis of each of the three configurations of interest under inviscid and fully turbulent flow assumptions. A comparison of the uncertainty outputs and sensitivity analyses between the configurations is also given. The results of this study illustrate the flexibility and robustness of the developed framework as a tool for uncertainty quantification and certification prediction of low-boom, supersonic aircraft.

Intrusion Prevention and Detection in Grid Computing - The ALICE Case

NASA Astrophysics Data System (ADS)

Gomez, Andres; Lara, Camilo; Kebschull, Udo

2015-12-01

Grids allow users flexible on-demand usage of computing resources through remote communication networks. A remarkable example of a Grid in High Energy Physics (HEP) research is used in the ALICE experiment at European Organization for Nuclear Research CERN. Physicists can submit jobs used to process the huge amount of particle collision data produced by the Large Hadron Collider (LHC). Grids face complex security challenges. They are interesting targets for attackers seeking for huge computational resources. Since users can execute arbitrary code in the worker nodes on the Grid sites, special care should be put in this environment. Automatic tools to harden and monitor this scenario are required. Currently, there is no integrated solution for such requirement. This paper describes a new security framework to allow execution of job payloads in a sandboxed context. It also allows process behavior monitoring to detect intrusions, even when new attack methods or zero day vulnerabilities are exploited, by a Machine Learning approach. We plan to implement the proposed framework as a software prototype that will be tested as a component of the ALICE Grid middleware.

Multimodal computational microscopy based on transport of intensity equation

NASA Astrophysics Data System (ADS)

Li, Jiaji; Chen, Qian; Sun, Jiasong; Zhang, Jialin; Zuo, Chao

2016-12-01

Transport of intensity equation (TIE) is a powerful tool for phase retrieval and quantitative phase imaging, which requires intensity measurements only at axially closely spaced planes without a separate reference beam. It does not require coherent illumination and works well on conventional bright-field microscopes. The quantitative phase reconstructed by TIE gives valuable information that has been encoded in the complex wave field by passage through a sample of interest. Such information may provide tremendous flexibility to emulate various microscopy modalities computationally without requiring specialized hardware components. We develop a requisite theory to describe such a hybrid computational multimodal imaging system, which yields quantitative phase, Zernike phase contrast, differential interference contrast, and light field moment imaging, simultaneously. It makes the various observations for biomedical samples easy. Then we give the experimental demonstration of these ideas by time-lapse imaging of live HeLa cell mitosis. Experimental results verify that a tunable lens-based TIE system, combined with the appropriate postprocessing algorithm, can achieve a variety of promising imaging modalities in parallel with the quantitative phase images for the dynamic study of cellular processes.

Clustering molecular dynamics trajectories for optimizing docking experiments.

PubMed

De Paris, Renata; Quevedo, Christian V; Ruiz, Duncan D; Norberto de Souza, Osmar; Barros, Rodrigo C

2015-01-01

Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we develop a novel methodology for clustering entire trajectories using structural features from the substrate-binding cavity of the receptor in order to optimize docking experiments on a cloud-based environment. The resulting partition was selected based on three clustering validity criteria, and it was further validated by analyzing the interactions between 20 ligands and a fully flexible receptor (FFR) model containing a 20 ns molecular dynamics simulation trajectory. Our proposed methodology shows that taking into account features of the substrate-binding cavity as input for the k-means algorithm is a promising technique for accurately selecting ensembles of representative structures tailored to a specific ligand.

Behavioral Flexibility and Response Selection Are Impaired after Limited Exposure to Oxycodone

ERIC Educational Resources Information Center

Seip-Cammack, Katharine M.; Shapiro, Matthew L.

2014-01-01

Behavioral flexibility allows individuals to adapt to situations in which rewards and goals change. Potentially addictive drugs may impair flexible decision-making by altering brain mechanisms that compute reward expectancies, thereby facilitating maladaptive drug use. To investigate this hypothesis, we tested the effects of oxycodone exposure on…

EWB: The Environment WorkBench Version 4.0

NASA Technical Reports Server (NTRS)

1995-01-01

The Environment WorkBench EWB is a desktop integrated analysis tool for studying a spacecraft's interactions with its environment. Over 100 environment and analysis models are integrated into the menu-based tool. EWB, which was developed for and under the guidance of the NASA Lewis Research Center, is built atop the Module Integrator and Rule-based Intelligent Analytic Database (MIRIAD) architecture. This allows every module in EWB to communicate information to other modules in a transparent manner from the user's point of view. It removes the tedious and error-prone steps of entering data by hand from one model to another. EWB runs under UNIX operating systems (SGI and SUN workstations) and under MS Windows (3.x, 95, and NT) operating systems. MIRIAD, the unique software that makes up the core of EWB, provides the flexibility to easily modify old models and incorporate new ones as user needs change. The MIRIAD approach separates the computer assisted engineering (CAE) tool into three distinct units: 1) A modern graphical user interface to present information; 2) A data dictionary interpreter to coordinate analysis; and 3) A database for storing system designs and analysis results. The user interface is externally programmable through ASCII data files, which contain the location and type of information to be displayed on the screen. This approach provides great flexibility in tailoring the look and feel of the code to individual user needs. MIRIADbased applications, such as EWB, have utilities for viewing tabulated parametric study data, XY line plots, contour plots, and three-dimensional plots of contour data and system geometries. In addition, a Monte Carlo facility is provided to allow statistical assessments (including uncertainties) in models or data.

A highly articulated robotic surgical system for minimally invasive surgery.

PubMed

Ota, Takeyoshi; Degani, Amir; Schwartzman, David; Zubiate, Brett; McGarvey, Jeremy; Choset, Howie; Zenati, Marco A

2009-04-01

We developed a novel, highly articulated robotic surgical system (CardioARM) to enable minimally invasive intrapericardial therapeutic delivery through a subxiphoid approach. We performed preliminary proof of concept studies in a porcine preparation by performing epicardial ablation. CardioARM is a robotic surgical system having an articulated design to provide unlimited but controllable flexibility. The CardioARM consists of serially connected, rigid cyclindrical links housing flexible working ports through which catheter-based tools for therapy and imaging can be advanced. The CardioARM is controlled by a computer-driven, user interface, which is operated outside the operative field. In six experimental subjects, the CardioARM was introduced percutaneously through a subxiphoid access. A commercial 5-French radiofrequency ablation catheter was introduced through the working port, which was then used to guide deployment. In all subjects, regional ("linear") left atrial ablation was successfully achieved without complications. Based on these preliminary studies, we believe that the CardioARM promises to enable deployment of a number of epicardium-based therapies. Improvements in imaging techniques will likely facilitate increasingly complex procedures.

In silico quantitative structure-toxicity relationship study of aromatic nitro compounds.

PubMed

Pasha, Farhan Ahmad; Neaz, Mohammad Morshed; Cho, Seung Joo; Ansari, Mohiuddin; Mishra, Sunil Kumar; Tiwari, Sharvan

2009-05-01

Small molecules often have toxicities that are a function of molecular structural features. Minor variations in structural features can make large difference in such toxicity. Consequently, in silico techniques may be used to correlate such molecular toxicities with their structural features. Relative to nine different sets of aromatic nitro compounds having known observed toxicities against different targets, we developed ligand-based 2D quantitative structure-toxicity relationship models using 20 selected topological descriptors. The topological descriptors have several advantages such as conformational independency, facile and less time-consuming computation to yield good results. Multiple linear regression analysis was used to correlate variations of toxicity with molecular properties. The information index on molecular size, lopping centric index and Kier flexibility index were identified as fundamental descriptors for different kinds of toxicity, and further showed that molecular size, branching and molecular flexibility might be particularly important factors in quantitative structure-toxicity relationship analysis. This study revealed that topological descriptor-guided quantitative structure-toxicity relationship provided a very useful, cost and time-efficient, in silico tool for describing small-molecule toxicities.

Robust retention and transfer of tool construction techniques in chimpanzees (Pan troglodytes).

PubMed

Vale, Gill L; Flynn, Emma G; Pender, Lydia; Price, Elizabeth; Whiten, Andrew; Lambeth, Susan P; Schapiro, Steven J; Kendal, Rachel L

2016-02-01

Long-term memory can be critical to a species' survival in environments with seasonal and even longer-term cycles of resource availability. The present, longitudinal study investigated whether complex tool behaviors used to gain an out-of-reach reward, following a hiatus of about 3 years and 7 months since initial experiences with a tool use task, were retained and subsequently executed more quickly by experienced than by naïve chimpanzees. Ten of the 11 retested chimpanzees displayed impressive long-term procedural memory, creating elongated tools using the same methods employed years previously, either combining 2 tools or extending a single tool. The complex tool behaviors were also transferred to a different task context, showing behavioral flexibility. This represents some of the first evidence for appreciable long-term procedural memory, and improvements in the utility of complex tool manufacture in chimpanzees. Such long-term procedural memory and behavioral flexibility have important implications for the longevity and transmission of behavioral traditions. (c) 2016 APA, all rights reserved).

Differential Tuning of Ventral and Dorsal Streams during the Generation of Common and Uncommon Tool Uses.

PubMed

Matheson, Heath E; Buxbaum, Laurel J; Thompson-Schill, Sharon L

2017-11-01

Our use of tools is situated in different contexts. Prior evidence suggests that diverse regions within the ventral and dorsal streams represent information supporting common tool use. However, given the flexibility of object concepts, these regions may be tuned to different types of information when generating novel or uncommon uses of tools. To investigate this, we collected fMRI data from participants who reported common or uncommon tool uses in response to visually presented familiar objects. We performed a pattern dissimilarity analysis in which we correlated cortical patterns with behavioral measures of visual, action, and category information. The results showed that evoked cortical patterns within the dorsal tool use network reflected action and visual information to a greater extent in the uncommon use group, whereas evoked neural patterns within the ventral tool use network reflected categorical information more strongly in the common use group. These results reveal the flexibility of cortical representations of tool use and the situated nature of cortical representations more generally.

Robust Retention and Transfer of Tool Construction Techniques in Chimpanzees (Pan troglodytes)

PubMed Central

Vale, Gill L.; Flynn, Emma G.; Pender, Lydia; Price, Elizabeth; Whiten, Andrew; Lambeth, Susan P.; Schapiro, Steven J.; Kendal, Rachel L.

2016-01-01

Long-term memory can be critical to a species’ survival in environments with seasonal and even longer-term cycles of resource availability. The present, longitudinal study investigated whether complex tool behaviors used to gain an out-of-reach reward, following a hiatus of about 3 years and 7 months since initial experiences with a tool use task, were retained and subsequently executed more quickly by experienced than by naïve chimpanzees. Ten of the 11 retested chimpanzees displayed impressive long-term procedural memory, creating elongated tools using the same methods employed years previously, either combining 2 tools or extending a single tool. The complex tool behaviors were also transferred to a different task context, showing behavioral flexibility. This represents some of the first evidence for appreciable long-term procedural memory, and improvements in the utility of complex tool manufacture in chimpanzees. Such long-term procedural memory and behavioral flexibility have important implications for the longevity and transmission of behavioral traditions. PMID:26881941

Refining Pathways: A Model Comparison Approach

PubMed Central

Moffa, Giusi; Erdmann, Gerrit; Voloshanenko, Oksana; Hundsrucker, Christian; Sadeh, Mohammad J.; Boutros, Michael; Spang, Rainer

2016-01-01

Cellular signalling pathways consolidate multiple molecular interactions into working models of signal propagation, amplification, and modulation. They are described and visualized as networks. Adjusting network topologies to experimental data is a key goal of systems biology. While network reconstruction algorithms like nested effects models are well established tools of computational biology, their data requirements can be prohibitive for their practical use. In this paper we suggest focussing on well defined aspects of a pathway and develop the computational tools to do so. We adapt the framework of nested effect models to focus on a specific aspect of activated Wnt signalling in HCT116 colon cancer cells: Does the activation of Wnt target genes depend on the secretion of Wnt ligands or do mutations in the signalling molecule β-catenin make this activation independent from them? We framed this question into two competing classes of models: Models that depend on Wnt ligands secretion versus those that do not. The model classes translate into restrictions of the pathways in the network topology. Wnt dependent models are more flexible than Wnt independent models. Bayes factors are the standard Bayesian tool to compare different models fairly on the data evidence. In our analysis, the Bayes factors depend on the number of potential Wnt signalling target genes included in the models. Stability analysis with respect to this number showed that the data strongly favours Wnt ligands dependent models for all realistic numbers of target genes. PMID:27248690

MAGMA: Generalized Gene-Set Analysis of GWAS Data

PubMed Central

de Leeuw, Christiaan A.; Mooij, Joris M.; Heskes, Tom; Posthuma, Danielle

2015-01-01

By aggregating data for complex traits in a biologically meaningful way, gene and gene-set analysis constitute a valuable addition to single-marker analysis. However, although various methods for gene and gene-set analysis currently exist, they generally suffer from a number of issues. Statistical power for most methods is strongly affected by linkage disequilibrium between markers, multi-marker associations are often hard to detect, and the reliance on permutation to compute p-values tends to make the analysis computationally very expensive. To address these issues we have developed MAGMA, a novel tool for gene and gene-set analysis. The gene analysis is based on a multiple regression model, to provide better statistical performance. The gene-set analysis is built as a separate layer around the gene analysis for additional flexibility. This gene-set analysis also uses a regression structure to allow generalization to analysis of continuous properties of genes and simultaneous analysis of multiple gene sets and other gene properties. Simulations and an analysis of Crohn’s Disease data are used to evaluate the performance of MAGMA and to compare it to a number of other gene and gene-set analysis tools. The results show that MAGMA has significantly more power than other tools for both the gene and the gene-set analysis, identifying more genes and gene sets associated with Crohn’s Disease while maintaining a correct type 1 error rate. Moreover, the MAGMA analysis of the Crohn’s Disease data was found to be considerably faster as well. PMID:25885710

MAGMA: generalized gene-set analysis of GWAS data.

PubMed

de Leeuw, Christiaan A; Mooij, Joris M; Heskes, Tom; Posthuma, Danielle

2015-04-01

By aggregating data for complex traits in a biologically meaningful way, gene and gene-set analysis constitute a valuable addition to single-marker analysis. However, although various methods for gene and gene-set analysis currently exist, they generally suffer from a number of issues. Statistical power for most methods is strongly affected by linkage disequilibrium between markers, multi-marker associations are often hard to detect, and the reliance on permutation to compute p-values tends to make the analysis computationally very expensive. To address these issues we have developed MAGMA, a novel tool for gene and gene-set analysis. The gene analysis is based on a multiple regression model, to provide better statistical performance. The gene-set analysis is built as a separate layer around the gene analysis for additional flexibility. This gene-set analysis also uses a regression structure to allow generalization to analysis of continuous properties of genes and simultaneous analysis of multiple gene sets and other gene properties. Simulations and an analysis of Crohn's Disease data are used to evaluate the performance of MAGMA and to compare it to a number of other gene and gene-set analysis tools. The results show that MAGMA has significantly more power than other tools for both the gene and the gene-set analysis, identifying more genes and gene sets associated with Crohn's Disease while maintaining a correct type 1 error rate. Moreover, the MAGMA analysis of the Crohn's Disease data was found to be considerably faster as well.

Leveraging Modeling Approaches: Reaction Networks and Rules

PubMed Central

Blinov, Michael L.; Moraru, Ion I.

2012-01-01

We have witnessed an explosive growth in research involving mathematical models and computer simulations of intracellular molecular interactions, ranging from metabolic pathways to signaling and gene regulatory networks. Many software tools have been developed to aid in the study of such biological systems, some of which have a wealth of features for model building and visualization, and powerful capabilities for simulation and data analysis. Novel high resolution and/or high throughput experimental techniques have led to an abundance of qualitative and quantitative data related to the spatio-temporal distribution of molecules and complexes, their interactions kinetics, and functional modifications. Based on this information, computational biology researchers are attempting to build larger and more detailed models. However, this has proved to be a major challenge. Traditionally, modeling tools require the explicit specification of all molecular species and interactions in a model, which can quickly become a major limitation in the case of complex networks – the number of ways biomolecules can combine to form multimolecular complexes can be combinatorially large. Recently, a new breed of software tools has been created to address the problems faced when building models marked by combinatorial complexity. These have a different approach for model specification, using reaction rules and species patterns. Here we compare the traditional modeling approach with the new rule-based methods. We make a case for combining the capabilities of conventional simulation software with the unique features and flexibility of a rule-based approach in a single software platform for building models of molecular interaction networks. PMID:22161349

Leveraging modeling approaches: reaction networks and rules.

PubMed

Blinov, Michael L; Moraru, Ion I

2012-01-01

We have witnessed an explosive growth in research involving mathematical models and computer simulations of intracellular molecular interactions, ranging from metabolic pathways to signaling and gene regulatory networks. Many software tools have been developed to aid in the study of such biological systems, some of which have a wealth of features for model building and visualization, and powerful capabilities for simulation and data analysis. Novel high-resolution and/or high-throughput experimental techniques have led to an abundance of qualitative and quantitative data related to the spatiotemporal distribution of molecules and complexes, their interactions kinetics, and functional modifications. Based on this information, computational biology researchers are attempting to build larger and more detailed models. However, this has proved to be a major challenge. Traditionally, modeling tools require the explicit specification of all molecular species and interactions in a model, which can quickly become a major limitation in the case of complex networks - the number of ways biomolecules can combine to form multimolecular complexes can be combinatorially large. Recently, a new breed of software tools has been created to address the problems faced when building models marked by combinatorial complexity. These have a different approach for model specification, using reaction rules and species patterns. Here we compare the traditional modeling approach with the new rule-based methods. We make a case for combining the capabilities of conventional simulation software with the unique features and flexibility of a rule-based approach in a single software platform for building models of molecular interaction networks.

Pressure distribution under flexible polishing tools. I - Conventional aspheric optics

NASA Astrophysics Data System (ADS)

Mehta, Pravin K.; Hufnagel, Robert E.

1990-10-01

The paper presents a mathematical model, based on Kirchoff's thin flat plate theory, developed to determine polishing pressure distribution for a flexible polishing tool. A two-layered tool in which bending and compressive stiffnesses are equal is developed, which is formulated as a plate on a linearly elastic foundation. An equivalent eigenvalue problem and solution for a free-free plate are created from the plate formulation. For aspheric, anamorphic optical surfaces, the tool misfit is derived; it is defined as the result of movement from the initial perfect fit on the optic to any other position. The Polisher Design (POD) software for circular tools on aspheric optics is introduced. NASTRAN-based finite element analysis results are compared with the POD software, showing high correlation. By employing existing free-free eigenvalues and eigenfunctions, the work may be extended to rectangular polishing tools as well.

An Ibm PC/AT-Based Image Acquisition And Processing System For Quantitative Image Analysis

NASA Astrophysics Data System (ADS)

Kim, Yongmin; Alexander, Thomas

1986-06-01

In recent years, a large number of applications have been developed for image processing systems in the area of biological imaging. We have already finished the development of a dedicated microcomputer-based image processing and analysis system for quantitative microscopy. The system's primary function has been to facilitate and ultimately automate quantitative image analysis tasks such as the measurement of cellular DNA contents. We have recognized from this development experience, and interaction with system users, biologists and technicians, that the increasingly widespread use of image processing systems, and the development and application of new techniques for utilizing the capabilities of such systems, would generate a need for some kind of inexpensive general purpose image acquisition and processing system specially tailored for the needs of the medical community. We are currently engaged in the development and testing of hardware and software for a fairly high-performance image processing computer system based on a popular personal computer. In this paper, we describe the design and development of this system. Biological image processing computer systems have now reached a level of hardware and software refinement where they could become convenient image analysis tools for biologists. The development of a general purpose image processing system for quantitative image analysis that is inexpensive, flexible, and easy-to-use represents a significant step towards making the microscopic digital image processing techniques more widely applicable not only in a research environment as a biologist's workstation, but also in clinical environments as a diagnostic tool.

Quantification of rectifications for the Northwestern University Flexible Sub-Ischial Vacuum Socket.

PubMed

Fatone, Stefania; Johnson, William Brett; Tran, Lilly; Tucker, Kerice; Mowrer, Christofer; Caldwell, Ryan

2017-06-01

The fit and function of a prosthetic socket depend on the prosthetist's ability to design the socket's shape to distribute load comfortably over the residual limb. We recently developed a sub-ischial socket for persons with transfemoral amputation: the Northwestern University Flexible Sub-Ischial Vacuum Socket. This study aimed to quantify the rectifications required to fit the Northwestern University Flexible Sub-Ischial Vacuum Socket to teach the technique to prosthetists as well as provide a computer-aided design-computer-aided manufacturing option. Development project. A program was used to align scans of unrectified and rectified negative molds and calculate shape change as a result of rectification. Averaged rectifications were used to create a socket template, which was shared with a central fabrication facility engaged in provision of Northwestern University Flexible Sub-Ischial Vacuum Sockets to early clinical adopters. Feedback regarding quality of fitting was obtained. Rectification maps created from 30 cast pairs of successfully fit Northwestern University Flexible Sub-Ischial Vacuum Sockets confirmed that material was primarily removed from the positive mold in the proximal-lateral and posterior regions. The template was used to fabricate check sockets for 15 persons with transfemoral amputation. Feedback suggested that the template provided a reasonable initial fit with only minor adjustments. Rectification maps and template were used to facilitate teaching and central fabrication of the Northwestern University Flexible Sub-Ischial Vacuum Socket. Minor issues with quality of initial fit achieved with the template may be due to inability to adjust the template to patient characteristics (e.g. tissue type, limb shape) and/or the degree to which it represented a fully mature version of the technique. Clinical relevance Rectification maps help communicate an important step in the fabrication of the Northwestern University Flexible Sub-Ischial Vacuum Socket facilitating dissemination of the technique, while the average template provides an alternative fabrication option via computer-aided design-computer-aided manufacturing and central fabrication.

Constraint Network Analysis (CNA): a Python software package for efficiently linking biomacromolecular structure, flexibility, (thermo-)stability, and function.

PubMed

Pfleger, Christopher; Rathi, Prakash Chandra; Klein, Doris L; Radestock, Sebastian; Gohlke, Holger

2013-04-22

For deriving maximal advantage from information on biomacromolecular flexibility and rigidity, results from rigidity analyses must be linked to biologically relevant characteristics of a structure. Here, we describe the Python-based software package Constraint Network Analysis (CNA) developed for this task. CNA functions as a front- and backend to the graph-based rigidity analysis software FIRST. CNA goes beyond the mere identification of flexible and rigid regions in a biomacromolecule in that it (I) provides a refined modeling of thermal unfolding simulations that also considers the temperature-dependence of hydrophobic tethers, (II) allows performing rigidity analyses on ensembles of network topologies, either generated from structural ensembles or by using the concept of fuzzy noncovalent constraints, and (III) computes a set of global and local indices for quantifying biomacromolecular stability. This leads to more robust results from rigidity analyses and extends the application domain of rigidity analyses in that phase transition points ("melting points") and unfolding nuclei ("structural weak spots") are determined automatically. Furthermore, CNA robustly handles small-molecule ligands in general. Such advancements are important for applying rigidity analysis to data-driven protein engineering and for estimating the influence of ligand molecules on biomacromolecular stability. CNA maintains the efficiency of FIRST such that the analysis of a single protein structure takes a few seconds for systems of several hundred residues on a single core. These features make CNA an interesting tool for linking biomacromolecular structure, flexibility, (thermo-)stability, and function. CNA is available from http://cpclab.uni-duesseldorf.de/software for nonprofit organizations.

GenomeCAT: a versatile tool for the analysis and integrative visualization of DNA copy number variants.

PubMed

Tebel, Katrin; Boldt, Vivien; Steininger, Anne; Port, Matthias; Ebert, Grit; Ullmann, Reinhard

2017-01-06

The analysis of DNA copy number variants (CNV) has increasing impact in the field of genetic diagnostics and research. However, the interpretation of CNV data derived from high resolution array CGH or NGS platforms is complicated by the considerable variability of the human genome. Therefore, tools for multidimensional data analysis and comparison of patient cohorts are needed to assist in the discrimination of clinically relevant CNVs from others. We developed GenomeCAT, a standalone Java application for the analysis and integrative visualization of CNVs. GenomeCAT is composed of three modules dedicated to the inspection of single cases, comparative analysis of multidimensional data and group comparisons aiming at the identification of recurrent aberrations in patients sharing the same phenotype, respectively. Its flexible import options ease the comparative analysis of own results derived from microarray or NGS platforms with data from literature or public depositories. Multidimensional data obtained from different experiment types can be merged into a common data matrix to enable common visualization and analysis. All results are stored in the integrated MySQL database, but can also be exported as tab delimited files for further statistical calculations in external programs. GenomeCAT offers a broad spectrum of visualization and analysis tools that assist in the evaluation of CNVs in the context of other experiment data and annotations. The use of GenomeCAT does not require any specialized computer skills. The various R packages implemented for data analysis are fully integrated into GenomeCATs graphical user interface and the installation process is supported by a wizard. The flexibility in terms of data import and export in combination with the ability to create a common data matrix makes the program also well suited as an interface between genomic data from heterogeneous sources and external software tools. Due to the modular architecture the functionality of GenomeCAT can be easily extended by further R packages or customized plug-ins to meet future requirements.

SparkSeq: fast, scalable and cloud-ready tool for the interactive genomic data analysis with nucleotide precision.

PubMed

Wiewiórka, Marek S; Messina, Antonio; Pacholewska, Alicja; Maffioletti, Sergio; Gawrysiak, Piotr; Okoniewski, Michał J

2014-09-15

Many time-consuming analyses of next -: generation sequencing data can be addressed with modern cloud computing. The Apache Hadoop-based solutions have become popular in genomics BECAUSE OF: their scalability in a cloud infrastructure. So far, most of these tools have been used for batch data processing rather than interactive data querying. The SparkSeq software has been created to take advantage of a new MapReduce framework, Apache Spark, for next-generation sequencing data. SparkSeq is a general-purpose, flexible and easily extendable library for genomic cloud computing. It can be used to build genomic analysis pipelines in Scala and run them in an interactive way. SparkSeq opens up the possibility of customized ad hoc secondary analyses and iterative machine learning algorithms. This article demonstrates its scalability and overall fast performance by running the analyses of sequencing datasets. Tests of SparkSeq also prove that the use of cache and HDFS block size can be tuned for the optimal performance on multiple worker nodes. Available under open source Apache 2.0 license: https://bitbucket.org/mwiewiorka/sparkseq/. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Individualised training to address variability of radiologists' performance

NASA Astrophysics Data System (ADS)

Sun, Shanghua; Taylor, Paul; Wilkinson, Louise; Khoo, Lisanne

2008-03-01

Computer-based tools are increasingly used for training and the continuing professional development of radiologists. We propose an adaptive training system to support individualised learning in mammography, based on a set of real cases, which are annotated with educational content by experienced breast radiologists. The system has knowledge of the strengths and weakness of each radiologist's performance: each radiologist is assessed to compute a profile showing how they perform on different sets of cases, classified by type of abnormality, breast density, and perceptual difficulty. We also assess variability in cognitive aspects of image perception, classifying errors made by radiologists as errors of search, recognition or decision. This is a novel element in our approach. The profile is used to select cases to present to the radiologist. The intelligent and flexible presentation of these cases distinguishes our system from existing training tools. The training cases are organised and indexed by an ontology we have developed for breast radiologist training, which is consistent with the radiologists' profile. Hence, the training system is able to select appropriate cases to compose an individualised training path, addressing the variability of the radiologists' performance. A substantial part of the system, the ontology has been evaluated on a large number of cases, and the training system is under implementation for further evaluation.

Teaching and learning the Hodgkin-Huxley model based on software developed in NEURON's programming language hoc.

PubMed

Hernández, Oscar E; Zurek, Eduardo E

2013-05-15

We present a software tool called SENB, which allows the geometric and biophysical neuronal properties in a simple computational model of a Hodgkin-Huxley (HH) axon to be changed. The aim of this work is to develop a didactic and easy-to-use computational tool in the NEURON simulation environment, which allows graphical visualization of both the passive and active conduction parameters and the geometric characteristics of a cylindrical axon with HH properties. The SENB software offers several advantages for teaching and learning electrophysiology. First, SENB offers ease and flexibility in determining the number of stimuli. Second, SENB allows immediate and simultaneous visualization, in the same window and time frame, of the evolution of the electrophysiological variables. Third, SENB calculates parameters such as time and space constants, stimuli frequency, cellular area and volume, sodium and potassium equilibrium potentials, and propagation velocity of the action potentials. Furthermore, it allows the user to see all this information immediately in the main window. Finally, with just one click SENB can save an image of the main window as evidence. The SENB software is didactic and versatile, and can be used to improve and facilitate the teaching and learning of the underlying mechanisms in the electrical activity of an axon using the biophysical properties of the squid giant axon.

Robust path planning for flexible needle insertion using Markov decision processes.

PubMed

Tan, Xiaoyu; Yu, Pengqian; Lim, Kah-Bin; Chui, Chee-Kong

2018-05-11

Flexible needle has the potential to accurately navigate to a treatment region in the least invasive manner. We propose a new planning method using Markov decision processes (MDPs) for flexible needle navigation that can perform robust path planning and steering under the circumstance of complex tissue-needle interactions. This method enhances the robustness of flexible needle steering from three different perspectives. First, the method considers the problem caused by soft tissue deformation. The method then resolves the common needle penetration failure caused by patterns of targets, while the last solution addresses the uncertainty issues in flexible needle motion due to complex and unpredictable tissue-needle interaction. Computer simulation and phantom experimental results show that the proposed method can perform robust planning and generate a secure control policy for flexible needle steering. Compared with a traditional method using MDPs, the proposed method achieves higher accuracy and probability of success in avoiding obstacles under complicated and uncertain tissue-needle interactions. Future work will involve experiment with biological tissue in vivo. The proposed robust path planning method can securely steer flexible needle within soft phantom tissues and achieve high adaptability in computer simulation.

Transformational electronics: a powerful way to revolutionize our information world

NASA Astrophysics Data System (ADS)

Rojas, Jhonathan P.; Torres Sevilla, Galo A.; Ghoneim, Mohamed T.; Hussain, Aftab M.; Ahmed, Sally M.; Nassar, Joanna M.; Bahabry, Rabab R.; Nour, Maha; Kutbee, Arwa T.; Byas, Ernesto; Al-Saif, Bidoor; Alamri, Amal M.; Hussain, Muhammad M.

2014-06-01

With the emergence of cloud computation, we are facing the rising waves of big data. It is our time to leverage such opportunity by increasing data usage both by man and machine. We need ultra-mobile computation with high data processing speed, ultra-large memory, energy efficiency and multi-functionality. Additionally, we have to deploy energy-efficient multi-functional 3D ICs for robust cyber-physical system establishment. To achieve such lofty goals we have to mimic human brain, which is inarguably the world's most powerful and energy efficient computer. Brain's cortex has folded architecture to increase surface area in an ultra-compact space to contain its neuron and synapses. Therefore, it is imperative to overcome two integration challenges: (i) finding out a low-cost 3D IC fabrication process and (ii) foldable substrates creation with ultra-large-scale-integration of high performance energy efficient electronics. Hence, we show a low-cost generic batch process based on trench-protect-peel-recycle to fabricate rigid and flexible 3D ICs as well as high performance flexible electronics. As of today we have made every single component to make a fully flexible computer including non-planar state-of-the-art FinFETs. Additionally we have demonstrated various solid-state memory, movable MEMS devices, energy harvesting and storage components. To show the versatility of our process, we have extended our process towards other inorganic semiconductor substrates such as silicon germanium and III-V materials. Finally, we report first ever fully flexible programmable silicon based microprocessor towards foldable brain computation and wirelessly programmable stretchable and flexible thermal patch for pain management for smart bionics.

Single-Point Mutation with a Rotamer Library Toolkit: Toward Protein Engineering.

PubMed

Pottel, Joshua; Moitessier, Nicolas

2015-12-28

Protein engineers have long been hard at work to harness biocatalysts as a natural source of regio-, stereo-, and chemoselectivity in order to carry out chemistry (reactions and/or substrates) not previously achieved with these enzymes. The extreme labor demands and exponential number of mutation combinations have induced computational advances in this domain. The first step in our virtual approach is to predict the correct conformations upon mutation of residues (i.e., rebuilding side chains). For this purpose, we opted for a combination of molecular mechanics and statistical data. In this work, we have developed automated computational tools to extract protein structural information and created conformational libraries for each amino acid dependent on a variable number of parameters (e.g., resolution, flexibility, secondary structure). We have also developed the necessary tool to apply the mutation and optimize the conformation accordingly. For side-chain conformation prediction, we obtained overall average root-mean-square deviations (RMSDs) of 0.91 and 1.01 Å for the 18 flexible natural amino acids within two distinct sets of over 3000 and 1500 side-chain residues, respectively. The commonly used dihedral angle differences were also evaluated and performed worse than the state of the art. These two metrics are also compared. Furthermore, we generated a family-specific library for kinases that produced an average 2% lower RMSD upon side-chain reconstruction and a residue-specific library that yielded a 17% improvement. Ultimately, since our protein engineering outlook involves using our docking software, Fitted/Impacts, we applied our mutation protocol to a benchmarked data set for self- and cross-docking. Our side-chain reconstruction does not hinder our docking software, demonstrating differences in pose prediction accuracy of approximately 2% (RMSD cutoff metric) for a set of over 200 protein/ligand structures. Similarly, when docking to a set of over 100 kinases, side-chain reconstruction (using both general and biased conformation libraries) had minimal detriment to the docking accuracy.

Designing a Hydro-Economic Collaborative Computer Decision Support System: Approaches, Best Practices, Lessons Learned, and Future Trends

NASA Astrophysics Data System (ADS)

Rosenberg, D. E.

2008-12-01

Designing and implementing a hydro-economic computer model to support or facilitate collaborative decision making among multiple stakeholders or users can be challenging and daunting. Collaborative modeling is distinguished and more difficult than non-collaborative efforts because of a large number of users with different backgrounds, disagreement or conflict among stakeholders regarding problem definitions, modeling roles, and analysis methods, plus evolving ideas of model scope and scale and needs for information and analysis as stakeholders interact, use the model, and learn about the underlying water system. This presentation reviews the lifecycle for collaborative model making and identifies some key design decisions that stakeholders and model developers must make to develop robust and trusted, verifiable and transparent, integrated and flexible, and ultimately useful models. It advances some best practices to implement and program these decisions. Among these best practices are 1) modular development of data- aware input, storage, manipulation, results recording and presentation components plus ways to couple and link to other models and tools, 2) explicitly structure both input data and the meta data that describes data sources, who acquired it, gaps, and modifications or translations made to put the data in a form usable by the model, 3) provide in-line documentation on model inputs, assumptions, calculations, and results plus ways for stakeholders to document their own model use and share results with others, and 4) flexibly program with graphical object-oriented properties and elements that allow users or the model maintainers to easily see and modify the spatial, temporal, or analysis scope as the collaborative process moves forward. We draw on examples of these best practices from the existing literature, the author's prior work, and some new applications just underway. The presentation concludes by identifying some future directions for collaborative modeling including geo-spatial display and analysis, real-time operations, and internet-based tools plus the design and programming needed to implement these capabilities.

A web-based system for neural network based classification in temporomandibular joint osteoarthritis.

PubMed

de Dumast, Priscille; Mirabel, Clément; Cevidanes, Lucia; Ruellas, Antonio; Yatabe, Marilia; Ioshida, Marcos; Ribera, Nina Tubau; Michoud, Loic; Gomes, Liliane; Huang, Chao; Zhu, Hongtu; Muniz, Luciana; Shoukri, Brandon; Paniagua, Beatriz; Styner, Martin; Pieper, Steve; Budin, Francois; Vimort, Jean-Baptiste; Pascal, Laura; Prieto, Juan Carlos

2018-07-01

The purpose of this study is to describe the methodological innovations of a web-based system for storage, integration and computation of biomedical data, using a training imaging dataset to remotely compute a deep neural network classifier of temporomandibular joint osteoarthritis (TMJOA). This study imaging dataset consisted of three-dimensional (3D) surface meshes of mandibular condyles constructed from cone beam computed tomography (CBCT) scans. The training dataset consisted of 259 condyles, 105 from control subjects and 154 from patients with diagnosis of TMJ OA. For the image analysis classification, 34 right and left condyles from 17 patients (39.9 ± 11.7 years), who experienced signs and symptoms of the disease for less than 5 years, were included as the testing dataset. For the integrative statistical model of clinical, biological and imaging markers, the sample consisted of the same 17 test OA subjects and 17 age and sex matched control subjects (39.4 ± 15.4 years), who did not show any sign or symptom of OA. For these 34 subjects, a standardized clinical questionnaire, blood and saliva samples were also collected. The technological methodologies in this study include a deep neural network classifier of 3D condylar morphology (ShapeVariationAnalyzer, SVA), and a flexible web-based system for data storage, computation and integration (DSCI) of high dimensional imaging, clinical, and biological data. The DSCI system trained and tested the neural network, indicating 5 stages of structural degenerative changes in condylar morphology in the TMJ with 91% close agreement between the clinician consensus and the SVA classifier. The DSCI remotely ran with a novel application of a statistical analysis, the Multivariate Functional Shape Data Analysis, that computed high dimensional correlations between shape 3D coordinates, clinical pain levels and levels of biological markers, and then graphically displayed the computation results. The findings of this study demonstrate a comprehensive phenotypic characterization of TMJ health and disease at clinical, imaging and biological levels, using novel flexible and versatile open-source tools for a web-based system that provides advanced shape statistical analysis and a neural network based classification of temporomandibular joint osteoarthritis. Published by Elsevier Ltd.

Reactive transport modeling in the subsurface environment with OGS-IPhreeqc

NASA Astrophysics Data System (ADS)

He, Wenkui; Beyer, Christof; Fleckenstein, Jan; Jang, Eunseon; Kalbacher, Thomas; Naumov, Dimitri; Shao, Haibing; Wang, Wenqing; Kolditz, Olaf

2015-04-01

Worldwide, sustainable water resource management becomes an increasingly challenging task due to the growth of population and extensive applications of fertilizer in agriculture. Moreover, climate change causes further stresses to both water quantity and quality. Reactive transport modeling in the coupled soil-aquifer system is a viable approach to assess the impacts of different land use and groundwater exploitation scenarios on the water resources. However, the application of this approach is usually limited in spatial scale and to simplified geochemical systems due to the huge computational expense involved. Such computational expense is not only caused by solving the high non-linearity of the initial boundary value problems of water flow in the unsaturated zone numerically with rather fine spatial and temporal discretization for the correct mass balance and numerical stability, but also by the intensive computational task of quantifying geochemical reactions. In the present study, a flexible and efficient tool for large scale reactive transport modeling in variably saturated porous media and its applications are presented. The open source scientific software OpenGeoSys (OGS) is coupled with the IPhreeqc module of the geochemical solver PHREEQC. The new coupling approach makes full use of advantages from both codes: OGS provides a flexible choice of different numerical approaches for simulation of water flow in the vadose zone such as the pressure-based or mixed forms of Richards equation; whereas the IPhreeqc module leads to a simplification of data storage and its communication with OGS, which greatly facilitates the coupling and code updating. Moreover, a parallelization scheme with MPI (Message Passing Interface) is applied, in which the computational task of water flow and mass transport is partitioned through domain decomposition, whereas the efficient parallelization of geochemical reactions is achieved by smart allocation of computational workload over multiple compute nodes. The plausibility of the new coupling is verified by several benchmark tests. In addition, the efficiency of the new coupling approach is demonstrated by its application in a large scale scenario, in which the environmental fate of pesticides in a complex soil-aquifer system is studied.

Reactive transport modeling in variably saturated porous media with OGS-IPhreeqc

NASA Astrophysics Data System (ADS)

He, W.; Beyer, C.; Fleckenstein, J. H.; Jang, E.; Kalbacher, T.; Shao, H.; Wang, W.; Kolditz, O.

2014-12-01

Worldwide, sustainable water resource management becomes an increasingly challenging task due to the growth of population and extensive applications of fertilizer in agriculture. Moreover, climate change causes further stresses to both water quantity and quality. Reactive transport modeling in the coupled soil-aquifer system is a viable approach to assess the impacts of different land use and groundwater exploitation scenarios on the water resources. However, the application of this approach is usually limited in spatial scale and to simplified geochemical systems due to the huge computational expense involved. Such computational expense is not only caused by solving the high non-linearity of the initial boundary value problems of water flow in the unsaturated zone numerically with rather fine spatial and temporal discretization for the correct mass balance and numerical stability, but also by the intensive computational task of quantifying geochemical reactions. In the present study, a flexible and efficient tool for large scale reactive transport modeling in variably saturated porous media and its applications are presented. The open source scientific software OpenGeoSys (OGS) is coupled with the IPhreeqc module of the geochemical solver PHREEQC. The new coupling approach makes full use of advantages from both codes: OGS provides a flexible choice of different numerical approaches for simulation of water flow in the vadose zone such as the pressure-based or mixed forms of Richards equation; whereas the IPhreeqc module leads to a simplification of data storage and its communication with OGS, which greatly facilitates the coupling and code updating. Moreover, a parallelization scheme with MPI (Message Passing Interface) is applied, in which the computational task of water flow and mass transport is partitioned through domain decomposition, whereas the efficient parallelization of geochemical reactions is achieved by smart allocation of computational workload over multiple compute nodes. The plausibility of the new coupling is verified by several benchmark tests. In addition, the efficiency of the new coupling approach is demonstrated by its application in a large scale scenario, in which the environmental fate of pesticides in a complex soil-aquifer system is studied.

Scalable Node Monitoring

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

Drotar, Alexander P.; Quinn, Erin E.; Sutherland, Landon D.

2012-07-30

Project description is: (1) Build a high performance computer; and (2) Create a tool to monitor node applications in Component Based Tool Framework (CBTF) using code from Lightweight Data Metric Service (LDMS). The importance of this project is that: (1) there is a need a scalable, parallel tool to monitor nodes on clusters; and (2) New LDMS plugins need to be able to be easily added to tool. CBTF stands for Component Based Tool Framework. It's scalable and adjusts to different topologies automatically. It uses MRNet (Multicast/Reduction Network) mechanism for information transport. CBTF is flexible and general enough to bemore » used for any tool that needs to do a task on many nodes. Its components are reusable and 'EASILY' added to a new tool. There are three levels of CBTF: (1) frontend node - interacts with users; (2) filter nodes - filters or concatenates information from backend nodes; and (3) backend nodes - where the actual work of the tool is done. LDMS stands for lightweight data metric servies. It's a tool used for monitoring nodes. Ltool is the name of the tool we derived from LDMS. It's dynamically linked and includes the following components: Vmstat, Meminfo, Procinterrupts and more. It works by: Ltool command is run on the frontend node; Ltool collects information from the backend nodes; backend nodes send information to the filter nodes; and filter nodes concatenate information and send to a database on the front end node. Ltool is a useful tool when it comes to monitoring nodes on a cluster because the overhead involved with running the tool is not particularly high and it will automatically scale to any size cluster.« less

Stability and control of flexible satellites. II - Control

NASA Technical Reports Server (NTRS)

Huang, T. C.; Das, A.

1980-01-01

It is demonstrated that by monitoring the deformations of the flexible elements of a satellite, the effectiveness of the satellite control system can be increased considerably. A simple model of a flexible satellite was analyzed in the first part of this work. The same model is used here for digital computer simulations.

Aircraft Survivability. Susceptibility Reduction. Fall 2010

DTIC Science & Technology

2010-01-01

limits flexibility when issues are encountered during development. Once a program enters Engineering, Manufacturing, and Development (EMD), the...using a flexible , efficient computational environment based on a credible set of components. Unfortunately, current survivability codes contain many...approach limits flexibility when issues are encountered during development. Once a program enters Engineering Manufacturing and Development (EMD), the

Modelling of structural flexiblity in multibody railroad vehicle systems

NASA Astrophysics Data System (ADS)

Escalona, José L.; Sugiyama, Hiroyuki; Shabana, Ahmed A.

2013-07-01

This paper presents a review of recent research investigations on the computer modelling of flexible bodies in railroad vehicle systems. The paper will also discuss the influence of the structural flexibility of various components, including the wheelset, the truck frames, tracks, pantograph/catenary systems, and car bodies, on the dynamics of railroad vehicles. While several formulations and computer techniques for modelling structural flexibility are discussed in this paper, a special attention is paid to the floating frame of reference formulation which is widely used and leads to reduced-order finite-element models for flexible bodies by employing component modes synthesis techniques. Other formulations and numerical methods such as semi-analytical approaches, absolute nodal coordinate formulation, finite-segment method, boundary elements method, and discrete elements method are also discussed. This investigation is motivated by the fact that the structural flexibility can have a significant effect on the overall dynamics of railroad vehicles, ride comfort, vibration suppression and noise level reduction, lateral stability, track response to vehicle forces, stress analysis, wheel-rail contact forces, wear and crashworthiness.

Neural networks as a control methodology

NASA Technical Reports Server (NTRS)

Mccullough, Claire L.

1990-01-01

While conventional computers must be programmed in a logical fashion by a person who thoroughly understands the task to be performed, the motivation behind neural networks is to develop machines which can train themselves to perform tasks, using available information about desired system behavior and learning from experience. There are three goals of this fellowship program: (1) to evaluate various neural net methods and generate computer software to implement those deemed most promising on a personal computer equipped with Matlab; (2) to evaluate methods currently in the professional literature for system control using neural nets to choose those most applicable to control of flexible structures; and (3) to apply the control strategies chosen in (2) to a computer simulation of a test article, the Control Structures Interaction Suitcase Demonstrator, which is a portable system consisting of a small flexible beam driven by a torque motor and mounted on springs tuned to the first flexible mode of the beam. Results of each are discussed.

Highly Efficient Computation of the Basal kon using Direct Simulation of Protein-Protein Association with Flexible Molecular Models.

PubMed

Saglam, Ali S; Chong, Lillian T

2016-01-14

An essential baseline for determining the extent to which electrostatic interactions enhance the kinetics of protein-protein association is the "basal" kon, which is the rate constant for association in the absence of electrostatic interactions. However, since such association events are beyond the milliseconds time scale, it has not been practical to compute the basal kon by directly simulating the association with flexible models. Here, we computed the basal kon for barnase and barstar, two of the most rapidly associating proteins, using highly efficient, flexible molecular simulations. These simulations involved (a) pseudoatomic protein models that reproduce the molecular shapes, electrostatic, and diffusion properties of all-atom models, and (b) application of the weighted ensemble path sampling strategy, which enhanced the efficiency of generating association events by >130-fold. We also examined the extent to which the computed basal kon is affected by inclusion of intermolecular hydrodynamic interactions in the simulations.

Flexible Launch Vehicle Stability Analysis Using Steady and Unsteady Computational Fluid Dynamics

NASA Technical Reports Server (NTRS)

Bartels, Robert E.

2012-01-01

Launch vehicles frequently experience a reduced stability margin through the transonic Mach number range. This reduced stability margin can be caused by the aerodynamic undamping one of the lower-frequency flexible or rigid body modes. Analysis of the behavior of a flexible vehicle is routinely performed with quasi-steady aerodynamic line loads derived from steady rigid aerodynamics. However, a quasi-steady aeroelastic stability analysis can be unconservative at the critical Mach numbers, where experiment or unsteady computational aeroelastic analysis show a reduced or even negative aerodynamic damping.Amethod of enhancing the quasi-steady aeroelastic stability analysis of a launch vehicle with unsteady aerodynamics is developed that uses unsteady computational fluid dynamics to compute the response of selected lower-frequency modes. The response is contained in a time history of the vehicle line loads. A proper orthogonal decomposition of the unsteady aerodynamic line-load response is used to reduce the scale of data volume and system identification is used to derive the aerodynamic stiffness, damping, and mass matrices. The results are compared with the damping and frequency computed from unsteady computational aeroelasticity and from a quasi-steady analysis. The results show that incorporating unsteady aerodynamics in this way brings the enhanced quasi-steady aeroelastic stability analysis into close agreement with the unsteady computational aeroelastic results.

Flexible services for the support of research.

PubMed

Turilli, Matteo; Wallom, David; Williams, Chris; Gough, Steve; Curran, Neal; Tarrant, Richard; Bretherton, Dan; Powell, Andy; Johnson, Matt; Harmer, Terry; Wright, Peter; Gordon, John

2013-01-28

Cloud computing has been increasingly adopted by users and providers to promote a flexible, scalable and tailored access to computing resources. Nonetheless, the consolidation of this paradigm has uncovered some of its limitations. Initially devised by corporations with direct control over large amounts of computational resources, cloud computing is now being endorsed by organizations with limited resources or with a more articulated, less direct control over these resources. The challenge for these organizations is to leverage the benefits of cloud computing while dealing with limited and often widely distributed computing resources. This study focuses on the adoption of cloud computing by higher education institutions and addresses two main issues: flexible and on-demand access to a large amount of storage resources, and scalability across a heterogeneous set of cloud infrastructures. The proposed solutions leverage a federated approach to cloud resources in which users access multiple and largely independent cloud infrastructures through a highly customizable broker layer. This approach allows for a uniform authentication and authorization infrastructure, a fine-grained policy specification and the aggregation of accounting and monitoring. Within a loosely coupled federation of cloud infrastructures, users can access vast amount of data without copying them across cloud infrastructures and can scale their resource provisions when the local cloud resources become insufficient.

Computation of Reacting Flows in Combustion Processes

NASA Technical Reports Server (NTRS)

Keith, Theo G., Jr.; Chen, Kuo-Huey

1997-01-01

The main objective of this research was to develop an efficient three-dimensional computer code for chemically reacting flows. The main computer code developed is ALLSPD-3D. The ALLSPD-3D computer program is developed for the calculation of three-dimensional, chemically reacting flows with sprays. The ALL-SPD code employs a coupled, strongly implicit solution procedure for turbulent spray combustion flows. A stochastic droplet model and an efficient method for treatment of the spray source terms in the gas-phase equations are used to calculate the evaporating liquid sprays. The chemistry treatment in the code is general enough that an arbitrary number of reaction and species can be defined by the users. Also, it is written in generalized curvilinear coordinates with both multi-block and flexible internal blockage capabilities to handle complex geometries. In addition, for general industrial combustion applications, the code provides both dilution and transpiration cooling capabilities. The ALLSPD algorithm, which employs the preconditioning and eigenvalue rescaling techniques, is capable of providing efficient solution for flows with a wide range of Mach numbers. Although written for three-dimensional flows in general, the code can be used for two-dimensional and axisymmetric flow computations as well. The code is written in such a way that it can be run in various computer platforms (supercomputers, workstations and parallel processors) and the GUI (Graphical User Interface) should provide a user-friendly tool in setting up and running the code.

SMOKE TOOL FOR MODELS-3 VERSION 4.1 STRUCTURE AND OPERATION DOCUMENTATION

EPA Science Inventory

The SMOKE Tool is a part of the Models-3 system, a flexible software system designed to simplify the development and use of air quality models and other environmental decision support tools. The SMOKE Tool is an input processor for SMOKE, (Sparse Matrix Operator Kernel Emissio...

MCAT to XCAT: The Evolution of 4-D Computerized Phantoms for Imaging Research: Computer models that take account of body movements promise to provide evaluation and improvement of medical imaging devices and technology.

PubMed

Paul Segars, W; Tsui, Benjamin M W

2009-12-01

Recent work in the development of computerized phantoms has focused on the creation of ideal "hybrid" models that seek to combine the realism of a patient-based voxelized phantom with the flexibility of a mathematical or stylized phantom. We have been leading the development of such computerized phantoms for use in medical imaging research. This paper will summarize our developments dating from the original four-dimensional (4-D) Mathematical Cardiac-Torso (MCAT) phantom, a stylized model based on geometric primitives, to the current 4-D extended Cardiac-Torso (XCAT) and Mouse Whole-Body (MOBY) phantoms, hybrid models of the human and laboratory mouse based on state-of-the-art computer graphics techniques. This paper illustrates the evolution of computerized phantoms toward more accurate models of anatomy and physiology. This evolution was catalyzed through the introduction of nonuniform rational b-spline (NURBS) and subdivision (SD) surfaces, tools widely used in computer graphics, as modeling primitives to define a more ideal hybrid phantom. With NURBS and SD surfaces as a basis, we progressed from a simple geometrically based model of the male torso (MCAT) containing only a handful of structures to detailed, whole-body models of the male and female (XCAT) anatomies (at different ages from newborn to adult), each containing more than 9000 structures. The techniques we applied for modeling the human body were similarly used in the creation of the 4-D MOBY phantom, a whole-body model for the mouse designed for small animal imaging research. From our work, we have found the NURBS and SD surface modeling techniques to be an efficient and flexible way to describe the anatomy and physiology for realistic phantoms. Based on imaging data, the surfaces can accurately model the complex organs and structures in the body, providing a level of realism comparable to that of a voxelized phantom. In addition, they are very flexible. Like stylized models, they can easily be manipulated to model anatomical variations and patient motion. With the vast improvement in realism, the phantoms developed in our lab can be combined with accurate models of the imaging process (SPECT, PET, CT, magnetic resonance imaging, and ultrasound) to generate simulated imaging data close to that from actual human or animal subjects. As such, they can provide vital tools to generate predictive imaging data from many different subjects under various scanning parameters from which to quantitatively evaluate and improve imaging devices and techniques. From the MCAT to XCAT, we will demonstrate how NURBS and SD surface modeling have resulted in a major evolutionary advance in the development of computerized phantoms for imaging research.

Effect of multiple forming tools on geometrical and mechanical properties in incremental sheet forming

NASA Astrophysics Data System (ADS)

Wernicke, S.; Dang, T.; Gies, S.; Tekkaya, A. E.

2018-05-01

The tendency to a higher variety of products requires economical manufacturing processes suitable for the production of prototypes and small batches. In the case of complex hollow-shaped parts, single point incremental forming (SPIF) represents a highly flexible process. The flexibility of this process comes along with a very long process time. To decrease the process time, a new incremental forming approach with multiple forming tools is investigated. The influence of two incremental forming tools on the resulting mechanical and geometrical component properties compared to SPIF is presented. Sheets made of EN AW-1050A were formed to frustums of a pyramid using different tool-path strategies. Furthermore, several variations of the tool-path strategy are analyzed. A time saving between 40% and 60% was observed depending on the tool-path and the radii of the forming tools while the mechanical properties remained unchanged. This knowledge can increase the cost efficiency of incremental forming processes.

Evidence of common and separate eye and hand accumulators underlying flexible eye-hand coordination

PubMed Central

Jana, Sumitash; Gopal, Atul

2016-01-01

Eye and hand movements are initiated by anatomically separate regions in the brain, and yet these movements can be flexibly coupled and decoupled, depending on the need. The computational architecture that enables this flexible coupling of independent effectors is not understood. Here, we studied the computational architecture that enables flexible eye-hand coordination using a drift diffusion framework, which predicts that the variability of the reaction time (RT) distribution scales with its mean. We show that a common stochastic accumulator to threshold, followed by a noisy effector-dependent delay, explains eye-hand RT distributions and their correlation in a visual search task that required decision-making, while an interactive eye and hand accumulator model did not. In contrast, in an eye-hand dual task, an interactive model better predicted the observed correlations and RT distributions than a common accumulator model. Notably, these two models could only be distinguished on the basis of the variability and not the means of the predicted RT distributions. Additionally, signatures of separate initiation signals were also observed in a small fraction of trials in the visual search task, implying that these distinct computational architectures were not a manifestation of the task design per se. Taken together, our results suggest two unique computational architectures for eye-hand coordination, with task context biasing the brain toward instantiating one of the two architectures. NEW & NOTEWORTHY Previous studies on eye-hand coordination have considered mainly the means of eye and hand reaction time (RT) distributions. Here, we leverage the approximately linear relationship between the mean and standard deviation of RT distributions, as predicted by the drift-diffusion model, to propose the existence of two distinct computational architectures underlying coordinated eye-hand movements. These architectures, for the first time, provide a computational basis for the flexible coupling between eye and hand movements. PMID:27784809

OpenMI: the essential concepts and their implications for legacy software

NASA Astrophysics Data System (ADS)

Gregersen, J. B.; Gijsbers, P. J. A.; Westen, S. J. P.; Blind, M.

2005-08-01

Information & Communication Technology (ICT) tools such as computational models are very helpful in designing river basin management plans (rbmp-s). However, in the scientific world there is consensus that a single integrated modelling system to support e.g. the implementation of the Water Framework Directive cannot be developed and that integrated systems need to be very much tailored to the local situation. As a consequence there is an urgent need to increase the flexibility of modelling systems, such that dedicated model systems can be developed from available building blocks. The HarmonIT project aims at precisely that. Its objective is to develop and implement a standard interface for modelling components and other relevant tools: The Open Modelling Interface (OpenMI) standard. The OpenMI standard has been completed and documented. It relies entirely on the "pull" principle, where data are pulled by one model from the previous model in the chain. This paper gives an overview of the OpenMI standard, explains the foremost concepts and the rational behind it.

Technical integration of hippocampus, Basal Ganglia and physical models for spatial navigation.

PubMed

Fox, Charles; Humphries, Mark; Mitchinson, Ben; Kiss, Tamas; Somogyvari, Zoltan; Prescott, Tony

2009-01-01

Computational neuroscience is increasingly moving beyond modeling individual neurons or neural systems to consider the integration of multiple models, often constructed by different research groups. We report on our preliminary technical integration of recent hippocampal formation, basal ganglia and physical environment models, together with visualisation tools, as a case study in the use of Python across the modelling tool-chain. We do not present new modeling results here. The architecture incorporates leaky-integrator and rate-coded neurons, a 3D environment with collision detection and tactile sensors, 3D graphics and 2D plots. We found Python to be a flexible platform, offering a significant reduction in development time, without a corresponding significant increase in execution time. We illustrate this by implementing a part of the model in various alternative languages and coding styles, and comparing their execution times. For very large-scale system integration, communication with other languages and parallel execution may be required, which we demonstrate using the BRAHMS framework's Python bindings.

Parametric Dependencies in Aero-Elastic, Articulated, Flapping Flight

NASA Astrophysics Data System (ADS)

Willis, D. J.; Persson, P.; Peraire, J.; Breuer, K. S.

2006-11-01

Aero-elastic coupling and wing articulation both play a vital role in the generation of lift and propulsion in birds, bats and fish. We present results from a computational study that employs several tools of varying fidelity to explore the role of flexible structures on the performance and efficiency of bird and bat flight mechanics. The tools (both 2-D and 3-D) include a Wake only ``Betz'' analysis following the work of Hall, Pigott and Hall (J. Aircaft, 1998), a potential flow model coupled to a free-vortex wake (Willis, Peraire & White, AIAA 2005-0854), and lastly, a discontinuous Galerkin solver (Persson & Peraire, AIAA 2006-0113) for the full Navier-Stokes equations. Structural models include springs, beams and membranes to represent compliant biological structures. The results demonstrate the changes in efficiency that can be achieved by different parametric variations in the flight behavior, including the effects of increasing kinematic degrees of freedom (e.g. articulated wings) and the effect of compliance in wing and skeletal structures.

Platform-independent software for medical image processing on the Internet

NASA Astrophysics Data System (ADS)

Mancuso, Michael E.; Pathak, Sayan D.; Kim, Yongmin

1997-05-01

We have developed a software tool for image processing over the Internet. The tool is a general purpose, easy to use, flexible, platform independent image processing software package with functions most commonly used in medical image processing.It provides for processing of medical images located wither remotely on the Internet or locally. The software was written in Java - the new programming language developed by Sun Microsystems. It was compiled and tested using Microsoft's Visual Java 1.0 and Microsoft's Just in Time Compiler 1.00.6211. The software is simple and easy to use. In order to use the tool, the user needs to download the software from our site before he/she runs it using any Java interpreter, such as those supplied by Sun, Symantec, Borland or Microsoft. Future versions of the operating systems supplied by Sun, Microsoft, Apple, IBM, and others will include Java interpreters. The software is then able to access and process any image on the iNternet or on the local computer. Using a 512 X 512 X 8-bit image, a 3 X 3 convolution took 0.88 seconds on an Intel Pentium Pro PC running at 200 MHz with 64 Mbytes of memory. A window/level operation took 0.38 seconds while a 3 X 3 median filter took 0.71 seconds. These performance numbers demonstrate the feasibility of using this software interactively on desktop computes. Our software tool supports various image processing techniques commonly used in medical image processing and can run without the need of any specialized hardware. It can become an easily accessible resource over the Internet to promote the learning and of understanding image processing algorithms. Also, it could facilitate sharing of medical image databases and collaboration amongst researchers and clinicians, regardless of location.

Development of an Adaptable Display and Diagnostic System for the Evaluation of Tropical Cyclone Forecasts

NASA Astrophysics Data System (ADS)

Kucera, P. A.; Burek, T.; Halley-Gotway, J.

2015-12-01

NCAR's Joint Numerical Testbed Program (JNTP) focuses on the evaluation of experimental forecasts of tropical cyclones (TCs) with the goal of developing new research tools and diagnostic evaluation methods that can be transitioned to operations. Recent activities include the development of new TC forecast verification methods and the development of an adaptable TC display and diagnostic system. The next generation display and diagnostic system is being developed to support evaluation needs of the U.S. National Hurricane Center (NHC) and broader TC research community. The new hurricane display and diagnostic capabilities allow forecasters and research scientists to more deeply examine the performance of operational and experimental models. The system is built upon modern and flexible technology that includes OpenLayers Mapping tools that are platform independent. The forecast track and intensity along with associated observed track information are stored in an efficient MySQL database. The system provides easy-to-use interactive display system, and provides diagnostic tools to examine forecast track stratified by intensity. Consensus forecasts can be computed and displayed interactively. The system is designed to display information for both real-time and for historical TC cyclones. The display configurations are easily adaptable to meet the needs of the end-user preferences. Ongoing enhancements include improving capabilities for stratification and evaluation of historical best tracks, development and implementation of additional methods to stratify and compute consensus hurricane track and intensity forecasts, and improved graphical display tools. The display is also being enhanced to incorporate gridded forecast, satellite, and sea surface temperature fields. The presentation will provide an overview of the display and diagnostic system development and demonstration of the current capabilities.

medplot: a web application for dynamic summary and analysis of longitudinal medical data based on R.

PubMed

Ahlin, Črt; Stupica, Daša; Strle, Franc; Lusa, Lara

2015-01-01

In biomedical studies the patients are often evaluated numerous times and a large number of variables are recorded at each time-point. Data entry and manipulation of longitudinal data can be performed using spreadsheet programs, which usually include some data plotting and analysis capabilities and are straightforward to use, but are not designed for the analyses of complex longitudinal data. Specialized statistical software offers more flexibility and capabilities, but first time users with biomedical background often find its use difficult. We developed medplot, an interactive web application that simplifies the exploration and analysis of longitudinal data. The application can be used to summarize, visualize and analyze data by researchers that are not familiar with statistical programs and whose knowledge of statistics is limited. The summary tools produce publication-ready tables and graphs. The analysis tools include features that are seldom available in spreadsheet software, such as correction for multiple testing, repeated measurement analyses and flexible non-linear modeling of the association of the numerical variables with the outcome. medplot is freely available and open source, it has an intuitive graphical user interface (GUI), it is accessible via the Internet and can be used within a web browser, without the need for installing and maintaining programs locally on the user's computer. This paper describes the application and gives detailed examples describing how to use the application on real data from a clinical study including patients with early Lyme borreliosis.

R-SWAT-FME user's guide

USGS Publications Warehouse

Wu, Yiping; Liu, Shu-Guang

2012-01-01

R program language-Soil and Water Assessment Tool-Flexible Modeling Environment (R-SWAT-FME) (Wu and Liu, 2012) is a comprehensive modeling framework that adopts an R package, Flexible Modeling Environment (FME) (Soetaert and Petzoldt, 2010), for the Soil and Water Assessment Tool (SWAT) model (Arnold and others, 1998; Neitsch and others, 2005). This framework provides the functionalities of parameter identifiability, model calibration, and sensitivity and uncertainty analysis with instant visualization. This user's guide shows how to apply this framework for a customized SWAT project.

Controlling flexible robot arms using a high speed dynamics process

NASA Technical Reports Server (NTRS)

Jain, Abhinandan (Inventor); Rodriguez, Guillermo (Inventor)

1992-01-01

Described here is a robot controller for a flexible manipulator arm having plural bodies connected at respective movable hinges, and flexible in plural deformation modes. It is operated by computing articulated body qualities for each of the bodies from the respective modal spatial influence vectors, obtaining specified body forces for each of the bodies, and computing modal deformation accelerations of the nodes and hinge accelerations of the hinges from the specified body forces, from the articulated body quantities and from the modal spatial influence vectors. In one embodiment of the invention, the controller further operates by comparing the accelerations thus computed to desired manipulator motion to determine a motion discrepancy, and correcting the specified body forces so as to reduce the motion discrepancy. The manipulator bodies and hinges are characterized by respective vectors of deformation and hinge configuration variables. Computing modal deformation accelerations and hinge accelerations is carried out for each of the bodies, beginning with the outermost body by computing a residual body force from a residual body force of a previous body, computing a resultant hinge acceleration from the body force, and then, for each one of the bodies beginning with the innermost body, computing a modal body acceleration from a modal body acceleration of a previous body, computing a modal deformation acceleration and hinge acceleration from the resulting hinge acceleration and from the modal body acceleration.

Reciprocal inhibition of inhibition: A circuit motif for flexible categorization in stimulus selection

PubMed Central

Knudsen, Eric I.

2011-01-01

As a precursor to the selection of a stimulus for gaze and attention, a midbrain network categorizes stimuli into “strongest” and “others.” The categorization tracks flexibly, in real-time, the absolute strength of the strongest stimulus. In this study, we take a first principles approach to computations that are essential for such categorization. We demonstrate that classical feedforward lateral inhibition cannot produce flexible categorization. However, circuits in which the strength of lateral inhibition varies with the relative strength of competing stimuli categorize successfully. One particular implementation - reciprocal inhibition of feedforward lateral inhibition – is structurally the simplest, and it outperforms others in flexibly categorizing rapidly and reliably. Strong predictions of this anatomically supported circuit model are validated by neural responses measured in the owl midbrain. The results demonstrate the extraordinary power of a remarkably simple, neurally grounded circuit motif in producing flexible categorization, a computation fundamental to attention, perception, and decision-making. PMID:22243757

Ensemble-based evaluation for protein structure models.

PubMed

Jamroz, Michal; Kolinski, Andrzej; Kihara, Daisuke

2016-06-15

Comparing protein tertiary structures is a fundamental procedure in structural biology and protein bioinformatics. Structure comparison is important particularly for evaluating computational protein structure models. Most of the model structure evaluation methods perform rigid body superimposition of a structure model to its crystal structure and measure the difference of the corresponding residue or atom positions between them. However, these methods neglect intrinsic flexibility of proteins by treating the native structure as a rigid molecule. Because different parts of proteins have different levels of flexibility, for example, exposed loop regions are usually more flexible than the core region of a protein structure, disagreement of a model to the native needs to be evaluated differently depending on the flexibility of residues in a protein. We propose a score named FlexScore for comparing protein structures that consider flexibility of each residue in the native state of proteins. Flexibility information may be extracted from experiments such as NMR or molecular dynamics simulation. FlexScore considers an ensemble of conformations of a protein described as a multivariate Gaussian distribution of atomic displacements and compares a query computational model with the ensemble. We compare FlexScore with other commonly used structure similarity scores over various examples. FlexScore agrees with experts' intuitive assessment of computational models and provides information of practical usefulness of models. https://bitbucket.org/mjamroz/flexscore dkihara@purdue.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Ensemble-based evaluation for protein structure models

PubMed Central

Jamroz, Michal; Kolinski, Andrzej; Kihara, Daisuke

2016-01-01

Motivation: Comparing protein tertiary structures is a fundamental procedure in structural biology and protein bioinformatics. Structure comparison is important particularly for evaluating computational protein structure models. Most of the model structure evaluation methods perform rigid body superimposition of a structure model to its crystal structure and measure the difference of the corresponding residue or atom positions between them. However, these methods neglect intrinsic flexibility of proteins by treating the native structure as a rigid molecule. Because different parts of proteins have different levels of flexibility, for example, exposed loop regions are usually more flexible than the core region of a protein structure, disagreement of a model to the native needs to be evaluated differently depending on the flexibility of residues in a protein. Results: We propose a score named FlexScore for comparing protein structures that consider flexibility of each residue in the native state of proteins. Flexibility information may be extracted from experiments such as NMR or molecular dynamics simulation. FlexScore considers an ensemble of conformations of a protein described as a multivariate Gaussian distribution of atomic displacements and compares a query computational model with the ensemble. We compare FlexScore with other commonly used structure similarity scores over various examples. FlexScore agrees with experts’ intuitive assessment of computational models and provides information of practical usefulness of models. Availability and implementation: https://bitbucket.org/mjamroz/flexscore Contact: dkihara@purdue.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307633

AIRNOISE: A Tool for Preliminary Noise-Abatement Terminal Approach Route Design

NASA Technical Reports Server (NTRS)

Li, Jinhua; Sridhar, Banavar; Xue, Min; Ng, Hok

2016-01-01

Noise from aircraft in the airport vicinity is one of the leading aviation-induced environmental issues. The FAA developed the Integrated Noise Model (INM) and its replacement Aviation Environmental Design Tool (AEDT) software to assess noise impact resulting from all aviation activities. However, a software tool is needed that is simple to use for terminal route modification, quick and reasonably accurate for preliminary noise impact evaluation and flexible to be used for iterative design of optimal noise-abatement terminal routes. In this paper, we extend our previous work on developing a noise-abatement terminal approach route design tool, named AIRNOISE, to satisfy this criterion. First, software efficiency has been significantly increased by over tenfold using the C programming language instead of MATLAB. Moreover, a state-of-the-art high performance GPU-accelerated computing module is implemented that was tested to be hundreds time faster than the C implementation. Secondly, a Graphical User Interface (GUI) was developed allowing users to import current terminal approach routes and modify the routes interactively to design new terminal approach routes. The corresponding noise impacts are then calculated and displayed in the GUI in seconds. Finally, AIRNOISE was applied to Baltimore-Washington International Airport terminal approach route to demonstrate its usage.

PNF and Other Flexibility Techniques.

ERIC Educational Resources Information Center

Cornelius, William L.

Effective flexibility procedures are one of the essential tools by which excellence can be attained. Although stretching exercises provide obvious benefits, negative outcomes can result unless effective stretching procedures are incoroporated. Characteristics of effective stretching include warmup before stretching, stretch before and after…

ReactPRED: a tool to predict and analyze biochemical reactions.

PubMed

Sivakumar, Tadi Venkata; Giri, Varun; Park, Jin Hwan; Kim, Tae Yong; Bhaduri, Anirban

2016-11-15

Biochemical pathways engineering is often used to synthesize or degrade target chemicals. In silico screening of the biochemical transformation space allows predicting feasible reactions, constituting these pathways. Current enabling tools are customized to predict reactions based on pre-defined biochemical transformations or reaction rule sets. Reaction rule sets are usually curated manually and tailored to specific applications. They are not exhaustive. In addition, current systems are incapable of regulating and refining data with an aim to tune specificity and sensitivity. A robust and flexible tool that allows automated reaction rule set creation along with regulated pathway prediction and analyses is a need. ReactPRED aims to address the same. ReactPRED is an open source flexible and customizable tool enabling users to predict biochemical reactions and pathways. The tool allows automated reaction rule creation from a user defined reaction set. Additionally, reaction rule degree and rule tolerance features allow refinement of predicted data. It is available as a flexible graphical user interface and a console application. ReactPRED is available at: https://sourceforge.net/projects/reactpred/ CONTACT: anirban.b@samsung.com or ty76.kim@samsung.comSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Sense-making for intelligence analysis on social media data

NASA Astrophysics Data System (ADS)

Pritzkau, Albert

2016-05-01

Social networks, in particular online social networks as a subset, enable the analysis of social relationships which are represented by interaction, collaboration, or other sorts of influence between people. Any set of people and their internal social relationships can be modelled as a general social graph. These relationships are formed by exchanging emails, making phone calls, or carrying out a range of other activities that build up the network. This paper presents an overview of current approaches to utilizing social media as a ubiquitous sensor network in the context of national and global security. Exploitation of social media is usually an interdisciplinary endeavour, in which the relevant technologies and methods are identified and linked in order ultimately demonstrate selected applications. Effective and efficient intelligence is usually accomplished in a combined human and computer effort. Indeed, the intelligence process heavily depends on combining a human's flexibility, creativity, and cognitive ability with the bandwidth and processing power of today's computers. To improve the usability and accuracy of the intelligence analysis we will have to rely on data-processing tools at the level of natural language. Especially the collection and transformation of unstructured data into actionable, structured data requires scalable computational algorithms ranging from Artificial Intelligence, via Machine Learning, to Natural Language Processing (NLP). To support intelligence analysis on social media data, social media analytics is concerned with developing and evaluating computational tools and frameworks to collect, monitor, analyze, summarize, and visualize social media data. Analytics methods are employed to extract of significant patterns that might not be obvious. As a result, different data representations rendering distinct aspects of content and interactions serve as a means to adapt the focus of the intelligence analysis to specific information requests.

BASINS Climate Assessment Tool Tutorials

EPA Pesticide Factsheets

The BASINS Climate Assessment Tool (CAT) provides a flexible set of capabilities for exploring the potential effects of climate change on streamflow and water quality using different watershed models in BASINS.

RABIX: AN OPEN-SOURCE WORKFLOW EXECUTOR SUPPORTING RECOMPUTABILITY AND INTEROPERABILITY OF WORKFLOW DESCRIPTIONS

PubMed Central

Ivkovic, Sinisa; Simonovic, Janko; Tijanic, Nebojsa; Davis-Dusenbery, Brandi; Kural, Deniz

2016-01-01

As biomedical data has become increasingly easy to generate in large quantities, the methods used to analyze it have proliferated rapidly. Reproducible and reusable methods are required to learn from large volumes of data reliably. To address this issue, numerous groups have developed workflow specifications or execution engines, which provide a framework with which to perform a sequence of analyses. One such specification is the Common Workflow Language, an emerging standard which provides a robust and flexible framework for describing data analysis tools and workflows. In addition, reproducibility can be furthered by executors or workflow engines which interpret the specification and enable additional features, such as error logging, file organization, optimizations1 to computation and job scheduling, and allow for easy computing on large volumes of data. To this end, we have developed the Rabix Executor a , an open-source workflow engine for the purposes of improving reproducibility through reusability and interoperability of workflow descriptions. PMID:27896971

RABIX: AN OPEN-SOURCE WORKFLOW EXECUTOR SUPPORTING RECOMPUTABILITY AND INTEROPERABILITY OF WORKFLOW DESCRIPTIONS.

PubMed

Kaushik, Gaurav; Ivkovic, Sinisa; Simonovic, Janko; Tijanic, Nebojsa; Davis-Dusenbery, Brandi; Kural, Deniz

2017-01-01

As biomedical data has become increasingly easy to generate in large quantities, the methods used to analyze it have proliferated rapidly. Reproducible and reusable methods are required to learn from large volumes of data reliably. To address this issue, numerous groups have developed workflow specifications or execution engines, which provide a framework with which to perform a sequence of analyses. One such specification is the Common Workflow Language, an emerging standard which provides a robust and flexible framework for describing data analysis tools and workflows. In addition, reproducibility can be furthered by executors or workflow engines which interpret the specification and enable additional features, such as error logging, file organization, optim1izations to computation and job scheduling, and allow for easy computing on large volumes of data. To this end, we have developed the Rabix Executor, an open-source workflow engine for the purposes of improving reproducibility through reusability and interoperability of workflow descriptions.

Clinician accessible tools for GUI computational models of transcranial electrical stimulation: BONSAI and SPHERES.

PubMed

Truong, Dennis Q; Hüber, Mathias; Xie, Xihe; Datta, Abhishek; Rahman, Asif; Parra, Lucas C; Dmochowski, Jacek P; Bikson, Marom

2014-01-01

Computational models of brain current flow during transcranial electrical stimulation (tES), including transcranial direct current stimulation (tDCS) and transcranial alternating current stimulation (tACS), are increasingly used to understand and optimize clinical trials. We propose that broad dissemination requires a simple graphical user interface (GUI) software that allows users to explore and design montages in real-time, based on their own clinical/experimental experience and objectives. We introduce two complimentary open-source platforms for this purpose: BONSAI and SPHERES. BONSAI is a web (cloud) based application (available at neuralengr.com/bonsai) that can be accessed through any flash-supported browser interface. SPHERES (available at neuralengr.com/spheres) is a stand-alone GUI application that allow consideration of arbitrary montages on a concentric sphere model by leveraging an analytical solution. These open-source tES modeling platforms are designed go be upgraded and enhanced. Trade-offs between open-access approaches that balance ease of access, speed, and flexibility are discussed. Copyright © 2014 Elsevier Inc. All rights reserved.

Enabling smart personalized healthcare: a hybrid mobile-cloud approach for ECG telemonitoring.

PubMed

Wang, Xiaoliang; Gui, Qiong; Liu, Bingwei; Jin, Zhanpeng; Chen, Yu

2014-05-01

The severe challenges of the skyrocketing healthcare expenditure and the fast aging population highlight the needs for innovative solutions supporting more accurate, affordable, flexible, and personalized medical diagnosis and treatment. Recent advances of mobile technologies have made mobile devices a promising tool to manage patients' own health status through services like telemedicine. However, the inherent limitations of mobile devices make them less effective in computation- or data-intensive tasks such as medical monitoring. In this study, we propose a new hybrid mobile-cloud computational solution to enable more effective personalized medical monitoring. To demonstrate the efficacy and efficiency of the proposed approach, we present a case study of mobile-cloud based electrocardiograph monitoring and analysis and develop a mobile-cloud prototype. The experimental results show that the proposed approach can significantly enhance the conventional mobile-based medical monitoring in terms of diagnostic accuracy, execution efficiency, and energy efficiency, and holds the potential in addressing future large-scale data analysis in personalized healthcare.

Using virtual machine monitors to overcome the challenges of monitoring and managing virtualized cloud infrastructures

NASA Astrophysics Data System (ADS)

Bamiah, Mervat Adib; Brohi, Sarfraz Nawaz; Chuprat, Suriayati

2012-01-01

Virtualization is one of the hottest research topics nowadays. Several academic researchers and developers from IT industry are designing approaches for solving security and manageability issues of Virtual Machines (VMs) residing on virtualized cloud infrastructures. Moving the application from a physical to a virtual platform increases the efficiency, flexibility and reduces management cost as well as effort. Cloud computing is adopting the paradigm of virtualization, using this technique, memory, CPU and computational power is provided to clients' VMs by utilizing the underlying physical hardware. Beside these advantages there are few challenges faced by adopting virtualization such as management of VMs and network traffic, unexpected additional cost and resource allocation. Virtual Machine Monitor (VMM) or hypervisor is the tool used by cloud providers to manage the VMs on cloud. There are several heterogeneous hypervisors provided by various vendors that include VMware, Hyper-V, Xen and Kernel Virtual Machine (KVM). Considering the challenge of VM management, this paper describes several techniques to monitor and manage virtualized cloud infrastructures.

Computer-aided design of biological circuits using TinkerCell.

PubMed

Chandran, Deepak; Bergmann, Frank T; Sauro, Herbert M

2010-01-01

Synthetic biology is an engineering discipline that builds on modeling practices from systems biology and wet-lab techniques from genetic engineering. As synthetic biology advances, efficient procedures will be developed that will allow a synthetic biologist to design, analyze, and build biological networks. In this idealized pipeline, computer-aided design (CAD) is a necessary component. The role of a CAD application would be to allow efficient transition from a general design to a final product. TinkerCell is a design tool for serving this purpose in synthetic biology. In TinkerCell, users build biological networks using biological parts and modules. The network can be analyzed using one of several functions provided by TinkerCell or custom programs from third-party sources. Since best practices for modeling and constructing synthetic biology networks have not yet been established, TinkerCell is designed as a flexible and extensible application that can adjust itself to changes in the field. © 2010 Landes Bioscience