Modular design of synthetic gene circuits with biological parts and pools.

PubMed

Marchisio, Mario Andrea

2015-01-01

Synthetic gene circuits can be designed in an electronic fashion by displaying their basic components-Standard Biological Parts and Pools of molecules-on the computer screen and connecting them with hypothetical wires. This procedure, achieved by our add-on for the software ProMoT, was successfully applied to bacterial circuits. Recently, we have extended this design-methodology to eukaryotic cells. Here, highly complex components such as promoters and Pools of mRNA contain hundreds of species and reactions whose calculation demands a rule-based modeling approach. We showed how to build such complex modules via the joint employment of the software BioNetGen (rule-based modeling) and ProMoT (modularization). In this chapter, we illustrate how to utilize our computational tool for synthetic biology with the in silico implementation of a simple eukaryotic gene circuit that performs the logic AND operation.

Modernized build and test infrastructure for control software at ESO: highly flexible building, testing, and automatic quality practices for telescope control software

NASA Astrophysics Data System (ADS)

Pellegrin, F.; Jeram, B.; Haucke, J.; Feyrin, S.

2016-07-01

The paper describes the introduction of a new automatized build and test infrastructure, based on the open-source software Jenkins1, into the ESO Very Large Telescope control software to replace the preexisting in-house solution. A brief introduction to software quality practices is given, a description of the previous solution, the limitations of it and new upcoming requirements. Modifications required to adapt the new system are described, how these were implemented to current software and the results obtained. An overview on how the new system may be used in future projects is also presented.

Virtual building environments (VBE) - Applying information modeling to buildings

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

Bazjanac, Vladimir

2004-06-21

A Virtual Building Environment (VBE) is a ''place'' where building industry project staffs can get help in creating Building Information Models (BIM) and in the use of virtual buildings. It consists of a group of industry software that is operated by industry experts who are also experts in the use of that software. The purpose of a VBE is to facilitate expert use of appropriate software applications in conjunction with each other to efficiently support multidisciplinary work. This paper defines BIM and virtual buildings, and describes VBE objectives, set-up and characteristics of operation. It informs about the VBE Initiative andmore » the benefits from a couple of early VBE projects.« less

Programming Makes Software; Support Makes Users

NASA Astrophysics Data System (ADS)

Batcheller, A. L.

2010-12-01

Skilled software engineers may build fantastic software for climate modeling, yet fail to achieve their project’s objectives. Software support and related activities are just as critical as writing software. This study followed three different software projects in the climate sciences, using interviews, observation, and document analysis to examine the value added by support work. Supporting the project and interacting with users was a key task for software developers, who often spent 50% of their time on it. Such support work most often involved replying to questions on an email list, but also included talking to users on teleconference calls and in person. Software support increased adoption by building the software’s reputation and showing individuals how the software can meet their needs. In the process of providing support, developers often learned new of requirements as users reported features they desire and bugs they found. As software matures and gains widespread use, support work often increases. In fact, such increases can be one signal that the software has achieved broad acceptance. Maturing projects also find demand for instructional classes, online tutorials and detailed examples of how to use the software. The importance of support highlights the fact that building software systems involves both social and technical aspects. Yes, we need to build the software, but we also need to “build” the users and practices that can take advantage of it.

ATLAS software configuration and build tool optimisation

NASA Astrophysics Data System (ADS)

Rybkin, Grigory; Atlas Collaboration

2014-06-01

ATLAS software code base is over 6 million lines organised in about 2000 packages. It makes use of some 100 external software packages, is developed by more than 400 developers and used by more than 2500 physicists from over 200 universities and laboratories in 6 continents. To meet the challenge of configuration and building of this software, the Configuration Management Tool (CMT) is used. CMT expects each package to describe its build targets, build and environment setup parameters, dependencies on other packages in a text file called requirements, and each project (group of packages) to describe its policies and dependencies on other projects in a text project file. Based on the effective set of configuration parameters read from the requirements files of dependent packages and project files, CMT commands build the packages, generate the environment for their use, or query the packages. The main focus was on build time performance that was optimised within several approaches: reduction of the number of reads of requirements files that are now read once per package by a CMT build command that generates cached requirements files for subsequent CMT build commands; introduction of more fine-grained build parallelism at package task level, i.e., dependent applications and libraries are compiled in parallel; code optimisation of CMT commands used for build; introduction of package level build parallelism, i. e., parallelise the build of independent packages. By default, CMT launches NUMBER-OF-PROCESSORS build commands in parallel. The other focus was on CMT commands optimisation in general that made them approximately 2 times faster. CMT can generate a cached requirements file for the environment setup command, which is especially useful for deployment on distributed file systems like AFS or CERN VMFS. The use of parallelism, caching and code optimisation significantly-by several times-reduced software build time, environment setup time, increased the efficiency of multi-core computing resources utilisation, and considerably improved software developer and user experience.

Software packager user's guide

NASA Technical Reports Server (NTRS)

Callahan, John R.

1995-01-01

Software integration is a growing area of concern for many programmers and software managers because the need to build new programs quickly from existing components is greater than ever. This includes building versions of software products for multiple hardware platforms and operating systems, building programs from components written in different languages, and building systems from components that must execute on different machines in a distributed network. The goal of software integration is to make building new programs from existing components more seamless -- programmers should pay minimal attention to the underlying configuration issues involved. Libraries of reusable components and classes are important tools but only partial solutions to software development problems. Even though software components may have compatible interfaces, there may be other reasons, such as differences between execution environments, why they cannot be integrated. Often, components must be adapted or reimplemented to fit into another application because of implementation differences -- they are implemented in different programming languages, dependent on different operating system resources, or must execute on different physical machines. The software packager is a tool that allows programmers to deal with interfaces between software components and ignore complex integration details. The packager takes modular descriptions of the structure of a software system written in the package specification language and produces an integration program in the form of a makefile. If complex integration tools are needed to integrate a set of components, such as remote procedure call stubs, their use is implied by the packager automatically and stub generation tools are invoked in the corresponding makefile. The programmer deals only with the components themselves and not the details of how to build the system on any given platform.

Analysis of Software Development Methodologies to Build Safety Software Applications for the SATEX-II: A Mexican Experimental Satellite

NASA Astrophysics Data System (ADS)

Aguilar Cisneros, Jorge; Vargas Martinez, Hector; Pedroza Melendez, Alejandro; Alonso Arevalo, Miguel

2013-09-01

Mexico is a country where the experience to build software for satellite applications is beginning. This is a delicate situation because in the near future we will need to develop software for the SATEX-II (Mexican Experimental Satellite). SATEX- II is a SOMECyTA's project (the Mexican Society of Aerospace Science and Technology). We have experienced applying software development methodologies, like TSP (Team Software Process) and SCRUM in other areas. Then, we analyzed these methodologies and we concluded: these can be applied to develop software for the SATEX-II, also, we supported these methodologies with SSP-05-0 Standard in particular with ESA PSS-05-11. Our analysis was focusing on main characteristics of each methodology and how these methodologies could be used with the ESA PSS 05-0 Standards. Our outcomes, in general, may be used by teams who need to build small satellites, but, in particular, these are going to be used when we will build the on board software applications for the SATEX-II.

Automatic Nanodesign Using Evolutionary Techniques

NASA Technical Reports Server (NTRS)

Globus, Al; Saini, Subhash (Technical Monitor)

1998-01-01

Many problems associated with the development of nanotechnology require custom designed molecules. We use genetic graph software, a new development, to automatically evolve molecules of interest when only the requirements are known. Genetic graph software designs molecules, and potentially nanoelectronic circuits, given a fitness function that determines which of two molecules is better. A set of molecules, the first generation, is generated at random then tested with the fitness function, Subsequent generations are created by randomly choosing two parent molecules with a bias towards high scoring molecules, tearing each molecules in two at random, and mating parts from the mother and father to create two children. This procedure is repeated until a satisfactory molecule is found. An atom pair similarity test is currently used as the fitness function to evolve molecules similar to existing pharmaceuticals.

Browndye: A software package for Brownian dynamics

NASA Astrophysics Data System (ADS)

Huber, Gary A.; McCammon, J. Andrew

2010-11-01

A new software package, Browndye, is presented for simulating the diffusional encounter of two large biological molecules. It can be used to estimate second-order rate constants and encounter probabilities, and to explore reaction trajectories. Browndye builds upon previous knowledge and algorithms from software packages such as UHBD, SDA, and Macrodox, while implementing algorithms that scale to larger systems. Program summaryProgram title: Browndye Catalogue identifier: AEGT_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGT_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: MIT license, included in distribution No. of lines in distributed program, including test data, etc.: 143 618 No. of bytes in distributed program, including test data, etc.: 1 067 861 Distribution format: tar.gz Programming language: C++, OCaml ( http://caml.inria.fr/) Computer: PC, Workstation, Cluster Operating system: Linux Has the code been vectorised or parallelized?: Yes. Runs on multiple processors with shared memory using pthreads RAM: Depends linearly on size of physical system Classification: 3 External routines: uses the output of APBS [1] ( http://www.poissonboltzmann.org/apbs/) as input. APBS must be obtained and installed separately. Expat 2.0.1, CLAPACK, ocaml-expat, Mersenne Twister. These are included in the Browndye distribution. Nature of problem: Exploration and determination of rate constants of bimolecular interactions involving large biological molecules. Solution method: Brownian dynamics with electrostatic, excluded volume, van der Waals, and desolvation forces. Running time: Depends linearly on size of physical system and quadratically on precision of results. The included example executes in a few minutes.

ETICS: the international software engineering service for the grid

NASA Astrophysics Data System (ADS)

Meglio, A. D.; Bégin, M.-E.; Couvares, P.; Ronchieri, E.; Takacs, E.

2008-07-01

The ETICS system is a distributed software configuration, build and test system designed to fulfil the needs of improving the quality, reliability and interoperability of distributed software in general and grid software in particular. The ETICS project is a consortium of five partners (CERN, INFN, Engineering Ingegneria Informatica, 4D Soft and the University of Wisconsin-Madison). The ETICS service consists of a build and test job execution system based on the Metronome software and an integrated set of web services and software engineering tools to design, maintain and control build and test scenarios. The ETICS system allows taking into account complex dependencies among applications and middleware components and provides a rich environment to perform static and dynamic analysis of the software and execute deployment, system and interoperability tests. This paper gives an overview of the system architecture and functionality set and then describes how the EC-funded EGEE, DILIGENT and OMII-Europe projects are using the software engineering services to build, validate and distribute their software. Finally a number of significant use and test cases will be described to show how ETICS can be used in particular to perform interoperability tests of grid middleware using the grid itself.

Tutorial for the structure elucidation of small molecules by means of the LSD software.

PubMed

Nuzillard, Jean-Marc; Plainchont, Bertrand

2018-06-01

Automatic structure elucidation of small molecules by means of the "logic for structure elucidation" (LSD) software is introduced in the context of the automatic exploitation of chemical shift correlation data and with minimal input from chemical shift values. The first step in solving a structural problem by means of LSD is the extraction of pertinent data from the 1D and 2D spectra. This operation requires the labeling of the resonances and of their correlations; its reliability highly depends on the quality of the spectra. The combination of COSY, HSQC, and HMBC spectra results in proximity relationships between nonhydrogen atoms that are associated in order to build the possible solutions of a problem. A simple molecule, camphor, serves as an example for the writing of an LSD input file and to show how solution structures are obtained. An input file for LSD must contain a nonambiguous description of each atom, or atom status, which includes the chemical element symbol, the hybridization state, the number of bound hydrogen atoms and the formal electric charge. In case of atom status ambiguity, the pyLSD program performs clarification by systematically generating the status of the atoms. PyLSD also proposes the use of the nmrshiftdb algorithm in order to rank the solutions of a problem according to the quality of the fit between the experimental carbon-13 chemical shifts, and the ones predicted from the proposed structures. To conclude, some hints toward future uses and developments of computer-assisted structure elucidation by LSD are proposed. Copyright © 2017 John Wiley & Sons, Ltd.

Automatic Molecular Design using Evolutionary Techniques

NASA Technical Reports Server (NTRS)

Globus, Al; Lawton, John; Wipke, Todd; Saini, Subhash (Technical Monitor)

1998-01-01

Molecular nanotechnology is the precise, three-dimensional control of materials and devices at the atomic scale. An important part of nanotechnology is the design of molecules for specific purposes. This paper describes early results using genetic software techniques to automatically design molecules under the control of a fitness function. The fitness function must be capable of determining which of two arbitrary molecules is better for a specific task. The software begins by generating a population of random molecules. The population is then evolved towards greater fitness by randomly combining parts of the better individuals to create new molecules. These new molecules then replace some of the worst molecules in the population. The unique aspect of our approach is that we apply genetic crossover to molecules represented by graphs, i.e., sets of atoms and the bonds that connect them. We present evidence suggesting that crossover alone, operating on graphs, can evolve any possible molecule given an appropriate fitness function and a population containing both rings and chains. Prior work evolved strings or trees that were subsequently processed to generate molecular graphs. In principle, genetic graph software should be able to evolve other graph representable systems such as circuits, transportation networks, metabolic pathways, computer networks, etc.

Development of Automated Procedures to Generate Reference Building Models for ASHRAE Standard 90.1 and India’s Building Energy Code and Implementation in OpenStudio

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

Parker, Andrew; Haves, Philip; Jegi, Subhash

This paper describes a software system for automatically generating a reference (baseline) building energy model from the proposed (as-designed) building energy model. This system is built using the OpenStudio Software Development Kit (SDK) and is designed to operate on building energy models in the OpenStudio file format.

Detailed analysis of complex single molecule FRET data with the software MASH

NASA Astrophysics Data System (ADS)

Hadzic, Mélodie C. A. S.; Kowerko, Danny; Börner, Richard; Zelger-Paulus, Susann; Sigel, Roland K. O.

2016-04-01

The processing and analysis of surface-immobilized single molecule FRET (Förster resonance energy transfer) data follows systematic steps (e.g. single molecule localization, clearance of different sources of noise, selection of the conformational and kinetic model, etc.) that require a solid knowledge in optics, photophysics, signal processing and statistics. The present proceeding aims at standardizing and facilitating procedures for single molecule detection by guiding the reader through an optimization protocol for a particular experimental data set. Relevant features were determined from single molecule movies (SMM) imaging Cy3- and Cy5-labeled Sc.ai5γ group II intron molecules synthetically recreated, to test the performances of four different detection algorithms. Up to 120 different parameterizations per method were routinely evaluated to finally establish an optimum detection procedure. The present protocol is adaptable to any movie displaying surface-immobilized molecules, and can be easily reproduced with our home-written software MASH (multifunctional analysis software for heterogeneous data) and script routines (both available in the download section of www.chem.uzh.ch/rna).

Integrating and Managing Bim in GIS, Software Review

NASA Astrophysics Data System (ADS)

El Meouche, R.; Rezoug, M.; Hijazi, I.

2013-08-01

Since the advent of Computer-Aided Design (CAD) and Geographical Information System (GIS) tools, project participants have been increasingly leveraging these tools throughout the different phases of a civil infrastructure project. In recent years the number of GIS software that provides tools to enable the integration of Building information in geo context has risen sharply. More and more GIS software are added tools for this purposes and other software projects are regularly extending these tools. However, each software has its different strength and weakness and its purpose of use. This paper provides a thorough review to investigate the software capabilities and clarify its purpose. For this study, Autodesk Revit 2012 i.e. BIM editor software was used to create BIMs. In the first step, three building models were created, the resulted models were converted to BIM format and then the software was used to integrate it. For the evaluation of the software, general characteristics was studied such as the user interface, what formats are supported (import/export), and the way building information are imported.

Transportable Payload Operations Control Center reusable software: Building blocks for quality ground data systems

NASA Technical Reports Server (NTRS)

Mahmot, Ron; Koslosky, John T.; Beach, Edward; Schwarz, Barbara

1994-01-01

The Mission Operations Division (MOD) at Goddard Space Flight Center builds Mission Operations Centers which are used by Flight Operations Teams to monitor and control satellites. Reducing system life cycle costs through software reuse has always been a priority of the MOD. The MOD's Transportable Payload Operations Control Center development team established an extensive library of 14 subsystems with over 100,000 delivered source instructions of reusable, generic software components. Nine TPOCC-based control centers to date support 11 satellites and achieved an average software reuse level of more than 75 percent. This paper shares experiences of how the TPOCC building blocks were developed and how building block developer's, mission development teams, and users are all part of the process.

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

McCann, Billy W.; Silva, Nuwan De; Windus, Theresa L.

Computer-aided molecular design and high-throughput screening of viable host architectures can significantly reduce the efforts in the design of novel ligands for efficient extraction of rare earth elements. This paper presents a computational approach to the deliberate design of bis-phosphine oxide host architectures that are structurally organized for complexation of trivalent lanthanides. Molecule building software, HostDesigner, was interfaced with molecular mechanics software, PCModel, providing a tool for generating and screening millions of potential R 2(O)P-link-P(O)R 2 ligand geometries. The molecular mechanics ranking of ligand structures is consistent with both the solution-phase free energies of complexation obtained with density functional theorymore » and the performance of known bis-phosphine oxide extractants. For the case where link is -CH 2-, evaluation of the ligand geometry provides the first characterization of a steric origin for the ‘anomalous aryl strengthening’ effect. The design approach has identified a number of novel bis-phosphine oxide ligands that are better organized for lanthanide complexation than previously studied examples.« less

A Team Building Model for Software Engineering Courses Term Projects

ERIC Educational Resources Information Center

Sahin, Yasar Guneri

2011-01-01

This paper proposes a new model for team building, which enables teachers to build coherent teams rapidly and fairly for the term projects of software engineering courses. Moreover, the model can also be used to build teams for any type of project, if the team member candidates are students, or if they are inexperienced on a certain subject. The…

Toward Generalization of Iterative Small Molecule Synthesis

PubMed Central

Lehmann, Jonathan W.; Blair, Daniel J.; Burke, Martin D.

2018-01-01

Small molecules have extensive untapped potential to benefit society, but access to this potential is too often restricted by limitations inherent to the customized approach currently used to synthesize this class of chemical matter. In contrast, the “building block approach”, i.e., generalized iterative assembly of interchangeable parts, has now proven to be a highly efficient and flexible way to construct things ranging all the way from skyscrapers to macromolecules to artificial intelligence algorithms. The structural redundancy found in many small molecules suggests that they possess a similar capacity for generalized building block-based construction. It is also encouraging that many customized iterative synthesis methods have been developed that improve access to specific classes of small molecules. There has also been substantial recent progress toward the iterative assembly of many different types of small molecules, including complex natural products, pharmaceuticals, biological probes, and materials, using common building blocks and coupling chemistry. Collectively, these advances suggest that a generalized building block approach for small molecule synthesis may be within reach. PMID:29696152

Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments

PubMed Central

Patmanidis, Ilias

2018-01-01

In bionanotechnology, the field of creating functional materials consisting of bio-inspired molecules, the function and shape of a nanostructure only appear through the assembly of many small molecules together. The large number of building blocks required to define a nanostructure combined with the many degrees of freedom in packing small molecules has long precluded molecular simulations, but recent advances in computational hardware as well as software have made classical simulations available to this strongly expanding field. Here, we review the state of the art in simulations of self-assembling bio-inspired supramolecular systems. We will first discuss progress in force fields, simulation protocols and enhanced sampling techniques using recent examples. Secondly, we will focus on efforts to enable the comparison of experimentally accessible observables and computational results. Experimental quantities that can be measured by microscopy, spectroscopy and scattering can be linked to simulation output either directly or indirectly, via quantum mechanical or semi-empirical techniques. Overall, we aim to provide an overview of the various computational approaches to understand not only the molecular architecture of nanostructures, but also the mechanism of their formation. PMID:29688238

A theoretical-electron-density databank using a model of real and virtual spherical atoms.

PubMed

Nassour, Ayoub; Domagala, Slawomir; Guillot, Benoit; Leduc, Theo; Lecomte, Claude; Jelsch, Christian

2017-08-01

A database describing the electron density of common chemical groups using combinations of real and virtual spherical atoms is proposed, as an alternative to the multipolar atom modelling of the molecular charge density. Theoretical structure factors were computed from periodic density functional theory calculations on 38 crystal structures of small molecules and the charge density was subsequently refined using a density model based on real spherical atoms and additional dummy charges on the covalent bonds and on electron lone-pair sites. The electron-density parameters of real and dummy atoms present in a similar chemical environment were averaged on all the molecules studied to build a database of transferable spherical atoms. Compared with the now-popular databases of transferable multipolar parameters, the spherical charge modelling needs fewer parameters to describe the molecular electron density and can be more easily incorporated in molecular modelling software for the computation of electrostatic properties. The construction method of the database is described. In order to analyse to what extent this modelling method can be used to derive meaningful molecular properties, it has been applied to the urea molecule and to biotin/streptavidin, a protein/ligand complex.

An Ontology for Software Engineering Education

ERIC Educational Resources Information Center

Ling, Thong Chee; Jusoh, Yusmadi Yah; Adbullah, Rusli; Alwi, Nor Hayati

2013-01-01

Software agents communicate using ontology. It is important to build an ontology for specific domain such as Software Engineering Education. Building an ontology from scratch is not only hard, but also incur much time and cost. This study aims to propose an ontology through adaptation of the existing ontology which is originally built based on a…

Dave Roberts | NREL

Science.gov Websites

Engineer in Colorado. He has expertise in building science, building energy simulation, and software simulation and software development projects, and served as product manager for the REM/Rate(tm) home energy

HashDist: Reproducible, Relocatable, Customizable, Cross-Platform Software Stacks for Open Hydrological Science

NASA Astrophysics Data System (ADS)

Ahmadia, A. J.; Kees, C. E.

2014-12-01

Developing scientific software is a continuous balance between not reinventing the wheel and getting fragile codes to interoperate with one another. Binary software distributions such as Anaconda provide a robust starting point for many scientific software packages, but this solution alone is insufficient for many scientific software developers. HashDist provides a critical component of the development workflow, enabling highly customizable, source-driven, and reproducible builds for scientific software stacks, available from both the IPython Notebook and the command line. To address these issues, the Coastal and Hydraulics Laboratory at the US Army Engineer Research and Development Center has funded the development of HashDist in collaboration with Simula Research Laboratories and the University of Texas at Austin. HashDist is motivated by a functional approach to package build management, and features intelligent caching of sources and builds, parametrized build specifications, and the ability to interoperate with system compilers and packages. HashDist enables the easy specification of "software stacks", which allow both the novice user to install a default environment and the advanced user to configure every aspect of their build in a modular fashion. As an advanced feature, HashDist builds can be made relocatable, allowing the easy redistribution of binaries on all three major operating systems as well as cloud, and supercomputing platforms. As a final benefit, all HashDist builds are reproducible, with a build hash specifying exactly how each component of the software stack was installed. This talk discusses the role of HashDist in the hydrological sciences, including its use by the Coastal and Hydraulics Laboratory in the development and deployment of the Proteus Toolkit as well as the Rapid Operational Access and Maneuver Support project. We demonstrate HashDist in action, and show how it can effectively support development, deployment, teaching, and reproducibility for scientists working in the hydrological sciences. The HashDist documentation is available from: http://hashdist.readthedocs.org/en/latest/ HashDist is currently hosted at: https://github.com/hashdist/hashdist

Using open source computational tools for predicting human metabolic stability and additional absorption, distribution, metabolism, excretion, and toxicity properties.

PubMed

Gupta, Rishi R; Gifford, Eric M; Liston, Ted; Waller, Chris L; Hohman, Moses; Bunin, Barry A; Ekins, Sean

2010-11-01

Ligand-based computational models could be more readily shared between researchers and organizations if they were generated with open source molecular descriptors [e.g., chemistry development kit (CDK)] and modeling algorithms, because this would negate the requirement for proprietary commercial software. We initially evaluated open source descriptors and model building algorithms using a training set of approximately 50,000 molecules and a test set of approximately 25,000 molecules with human liver microsomal metabolic stability data. A C5.0 decision tree model demonstrated that CDK descriptors together with a set of Smiles Arbitrary Target Specification (SMARTS) keys had good statistics [κ = 0.43, sensitivity = 0.57, specificity = 0.91, and positive predicted value (PPV) = 0.64], equivalent to those of models built with commercial Molecular Operating Environment 2D (MOE2D) and the same set of SMARTS keys (κ = 0.43, sensitivity = 0.58, specificity = 0.91, and PPV = 0.63). Extending the dataset to ∼193,000 molecules and generating a continuous model using Cubist with a combination of CDK and SMARTS keys or MOE2D and SMARTS keys confirmed this observation. When the continuous predictions and actual values were binned to get a categorical score we observed a similar κ statistic (0.42). The same combination of descriptor set and modeling method was applied to passive permeability and P-glycoprotein efflux data with similar model testing statistics. In summary, open source tools demonstrated predictive results comparable to those of commercial software with attendant cost savings. We discuss the advantages and disadvantages of open source descriptors and the opportunity for their use as a tool for organizations to share data precompetitively, avoiding repetition and assisting drug discovery.

Software Build and Delivery Systems

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

Robey, Robert W.

2016-07-10

This presentation deals with the hierarchy of software build and delivery systems. One of the goals is to maximize the success rate of new users and developers when first trying your software. First impressions are important. Early successes are important. This also reduces critical documentation costs. This is a presentation focused on computer science and goes into detail about code documentation.

IMS - MS Data Extractor

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

2015-10-20

An automated drift time extraction and computed associated collision cross section software tool for small molecule analysis with ion mobility spectrometry-mass spectrometry (IMS-MS). The software automatically extracts drift times and computes associated collision cross sections for small molecules analyzed using ion mobility spectrometry-mass spectrometry (IMS-MS) based on a target list of expected ions provided by the user.

Re-Writing the Construction History of Boughton House (northamptonshire, Uk) with the Help of DOCU-TOOLS®

NASA Astrophysics Data System (ADS)

Schuster, J. C.

2017-08-01

The tablet-based software docu-tools digitize the documentation of buildings, simplifies construction and facility management and the data analysis in building and construction-history research. As a plan-based software, `pins' can be set to record data (images, audio, text etc.), each data point containing a time and date stamp. Once a pin is set and information recorded, it can never be deleted from the system, creating clear contentious-free documentation. Reports to any/all data recorded can immediately be generated through various templates in order to share, document, analyze and archive the information gathered. The software both digitizes building condition assessment, as well as simplifies the fully documented management and solving of problems and monitoring of a building. Used both in the construction industry and for documenting and analyzing historic buildings, docu-tools is a versatile and flexible tool that has become integral to my work as a building historian working on the conservation and curating of the historic built environment in Europe. I used the software at Boughton House, Northamptonshire, UK, during a one-year research project into the construction history of the building. The details of how docu-tools was used during this project will be discussed in this paper.

Reconfigurable Software for Mission Operations

NASA Technical Reports Server (NTRS)

Trimble, Jay

2014-01-01

We developed software that provides flexibility to mission organizations through modularity and composability. Modularity enables removal and addition of functionality through the installation of plug-ins. Composability enables users to assemble software from pre-built reusable objects, thus reducing or eliminating the walls associated with traditional application architectures and enabling unique combinations of functionality. We have used composable objects to reduce display build time, create workflows, and build scenarios to test concepts for lunar roving operations. The software is open source, and may be downloaded from https:github.comnasamct.

Software Solution Builds Project Consensus.

ERIC Educational Resources Information Center

Graue, David

2003-01-01

Describes the use of Autodesk Revit, a computer software system for design and documentation of buildings, in the planning of the University Center of Chicago, a large residence hall involving the cooperation of DePaul University, Columbia College, and Roosevelt University. (EV)

LCG/AA build infrastructure

NASA Astrophysics Data System (ADS)

Hodgkins, Alex Liam; Diez, Victor; Hegner, Benedikt

2012-12-01

The Software Process & Infrastructure (SPI) project provides a build infrastructure for regular integration testing and release of the LCG Applications Area software stack. In the past, regular builds have been provided using a system which has been constantly growing to include more features like server-client communication, long-term build history and a summary web interface using present-day web technologies. However, the ad-hoc style of software development resulted in a setup that is hard to monitor, inflexible and difficult to expand. The new version of the infrastructure is based on the Django Python framework, which allows for a structured and modular design, facilitating later additions. Transparency in the workflows and ease of monitoring has been one of the priorities in the design. Formerly missing functionality like on-demand builds or release triggering will support the transition to a more agile development process.

Early experiences building a software quality prediction model

NASA Technical Reports Server (NTRS)

Agresti, W. W.; Evanco, W. M.; Smith, M. C.

1990-01-01

Early experiences building a software quality prediction model are discussed. The overall research objective is to establish a capability to project a software system's quality from an analysis of its design. The technical approach is to build multivariate models for estimating reliability and maintainability. Data from 21 Ada subsystems were analyzed to test hypotheses about various design structures leading to failure-prone or unmaintainable systems. Current design variables highlight the interconnectivity and visibility of compilation units. Other model variables provide for the effects of reusability and software changes. Reported results are preliminary because additional project data is being obtained and new hypotheses are being developed and tested. Current multivariate regression models are encouraging, explaining 60 to 80 percent of the variation in error density of the subsystems.

LHCb Build and Deployment Infrastructure for run 2

NASA Astrophysics Data System (ADS)

Clemencic, M.; Couturier, B.

2015-12-01

After the successful run 1 of the LHC, the LHCb Core software team has taken advantage of the long shutdown to consolidate and improve its build and deployment infrastructure. Several of the related projects have already been presented like the build system using Jenkins, as well as the LHCb Performance and Regression testing infrastructure. Some components are completely new, like the Software Configuration Database (using the Graph DB Neo4j), or the new packaging installation using RPM packages. Furthermore all those parts are integrated to allow easier and quicker releases of the LHCb Software stack, therefore reducing the risk of operational errors. Integration and Regression tests are also now easier to implement, allowing to improve further the software checks.

A Study of the Use of Ontologies for Building Computer-Aided Control Engineering Self-Learning Educational Software

ERIC Educational Resources Information Center

García, Isaías; Benavides, Carmen; Alaiz, Héctor; Alonso, Angel

2013-01-01

This paper describes research on the use of knowledge models (ontologies) for building computer-aided educational software in the field of control engineering. Ontologies are able to represent in the computer a very rich conceptual model of a given domain. This model can be used later for a number of purposes in different software applications. In…

Quantitative evaluation of software packages for single-molecule localization microscopy.

PubMed

Sage, Daniel; Kirshner, Hagai; Pengo, Thomas; Stuurman, Nico; Min, Junhong; Manley, Suliana; Unser, Michael

2015-08-01

The quality of super-resolution images obtained by single-molecule localization microscopy (SMLM) depends largely on the software used to detect and accurately localize point sources. In this work, we focus on the computational aspects of super-resolution microscopy and present a comprehensive evaluation of localization software packages. Our philosophy is to evaluate each package as a whole, thus maintaining the integrity of the software. We prepared synthetic data that represent three-dimensional structures modeled after biological components, taking excitation parameters, noise sources, point-spread functions and pixelation into account. We then asked developers to run their software on our data; most responded favorably, allowing us to present a broad picture of the methods available. We evaluated their results using quantitative and user-interpretable criteria: detection rate, accuracy, quality of image reconstruction, resolution, software usability and computational resources. These metrics reflect the various tradeoffs of SMLM software packages and help users to choose the software that fits their needs.

Feasibility of Close-Range Photogrammetric Models for Geographic Information System

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

Zhou, Luke; /Rice U.

2011-06-22

The objective of this project was to determine the feasibility of using close-range architectural photogrammetry as an alternative three dimensional modeling technique in order to place the digital models in a geographic information system (GIS) at SLAC. With the available equipment and Australis photogrammetry software, the creation of full and accurate models of an example building, Building 281 on SLAC campus, was attempted. After conducting several equipment tests to determine the precision achievable, a complete photogrammetric survey was attempted. The dimensions of the resulting models were then compared against the true dimensions of the building. A complete building model wasmore » not evidenced to be obtainable using the current equipment and software. This failure was likely attributable to the limits of the software rather than the precision of the physical equipment. However, partial models of the building were shown to be accurate and determined to still be usable in a GIS. With further development of the photogrammetric software and survey procedure, the desired generation of a complete three dimensional model is likely still feasible.« less

Building Energy Simulation Test for Existing Homes (BESTEST-EX) (Presentation)

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

Judkoff, R.; Neymark, J.; Polly, B.

2011-12-01

This presentation discusses the goals of NREL Analysis Accuracy R&D; BESTEST-EX goals; what BESTEST-EX is; how it works; 'Building Physics' cases; 'Building Physics' reference results; 'utility bill calibration' cases; limitations and potential future work. Goals of NREL Analysis Accuracy R&D are: (1) Provide industry with the tools and technical information needed to improve the accuracy and consistency of analysis methods; (2) Reduce the risks associated with purchasing, financing, and selling energy efficiency upgrades; and (3) Enhance software and input collection methods considering impacts on accuracy, cost, and time of energy assessments. BESTEST-EX Goals are: (1) Test software predictions of retrofitmore » energy savings in existing homes; (2) Ensure building physics calculations and utility bill calibration procedures perform up to a minimum standard; and (3) Quantify impact of uncertainties in input audit data and occupant behavior. BESTEST-EX is a repeatable procedure that tests how well audit software predictions compare to the current state of the art in building energy simulation. There is no direct truth standard. However, reference software have been subjected to validation testing, including comparisons with empirical data.« less

LIMAO: Cross-platform software for simulating laser-induced alignment and orientation dynamics of linear-, symmetric- and asymmetric tops

NASA Astrophysics Data System (ADS)

Szidarovszky, Tamás; Jono, Maho; Yamanouchi, Kaoru

2018-07-01

A user-friendly and cross-platform software called Laser-Induced Molecular Alignment and Orientation simulator (LIMAO) has been developed. The program can be used to simulate within the rigid rotor approximation the rotational dynamics of gas phase molecules induced by linearly polarized intense laser fields at a given temperature. The software is implemented in the Java and Mathematica programming languages. The primary aim of LIMAO is to aid experimental scientists in predicting and analyzing experimental data representing laser-induced spatial alignment and orientation of molecules.

Spatial modeling of cell signaling networks.

PubMed

Cowan, Ann E; Moraru, Ion I; Schaff, James C; Slepchenko, Boris M; Loew, Leslie M

2012-01-01

The shape of a cell, the sizes of subcellular compartments, and the spatial distribution of molecules within the cytoplasm can all control how molecules interact to produce a cellular behavior. This chapter describes how these spatial features can be included in mechanistic mathematical models of cell signaling. The Virtual Cell computational modeling and simulation software is used to illustrate the considerations required to build a spatial model. An explanation of how to appropriately choose between physical formulations that implicitly or explicitly account for cell geometry and between deterministic versus stochastic formulations for molecular dynamics is provided, along with a discussion of their respective strengths and weaknesses. As a first step toward constructing a spatial model, the geometry needs to be specified and associated with the molecules, reactions, and membrane flux processes of the network. Initial conditions, diffusion coefficients, velocities, and boundary conditions complete the specifications required to define the mathematics of the model. The numerical methods used to solve reaction-diffusion problems both deterministically and stochastically are then described and some guidance is provided in how to set up and run simulations. A study of cAMP signaling in neurons ends the chapter, providing an example of the insights that can be gained in interpreting experimental results through the application of spatial modeling. Copyright © 2012 Elsevier Inc. All rights reserved.

How Nasa's Independent Verification and Validation (IVandV) Program Builds Reliability into a Space Mission Software System (SMSS)

NASA Technical Reports Server (NTRS)

Fisher, Marcus S.; Northey, Jeffrey; Stanton, William

2014-01-01

The purpose of this presentation is to outline how the NASA Independent Verification and Validation (IVV) Program helps to build reliability into the Space Mission Software Systems (SMSSs) that its customers develop.

Computer-Aided Molecular Design of Bis-phosphine Oxide Lanthanide Extractants

DOE PAGES

McCann, Billy W.; Silva, Nuwan De; Windus, Theresa L.; ...

2016-02-17

Computer-aided molecular design and high-throughput screening of viable host architectures can significantly reduce the efforts in the design of novel ligands for efficient extraction of rare earth elements. This paper presents a computational approach to the deliberate design of bis-phosphine oxide host architectures that are structurally organized for complexation of trivalent lanthanides. Molecule building software, HostDesigner, was interfaced with molecular mechanics software, PCModel, providing a tool for generating and screening millions of potential R 2(O)P-link-P(O)R 2 ligand geometries. The molecular mechanics ranking of ligand structures is consistent with both the solution-phase free energies of complexation obtained with density functional theorymore » and the performance of known bis-phosphine oxide extractants. For the case where link is -CH 2-, evaluation of the ligand geometry provides the first characterization of a steric origin for the ‘anomalous aryl strengthening’ effect. The design approach has identified a number of novel bis-phosphine oxide ligands that are better organized for lanthanide complexation than previously studied examples.« less

[Extraction of buildings three-dimensional information from high-resolution satellite imagery based on Barista software].

PubMed

Zhang, Pei-feng; Hu, Yuan-man; He, Hong-shi

2010-05-01

The demand for accurate and up-to-date spatial information of urban buildings is becoming more and more important for urban planning, environmental protection, and other vocations. Today's commercial high-resolution satellite imagery offers the potential to extract the three-dimensional information of urban buildings. This paper extracted the three-dimensional information of urban buildings from QuickBird imagery, and validated the precision of the extraction based on Barista software. It was shown that the extraction of three-dimensional information of the buildings from high-resolution satellite imagery based on Barista software had the advantages of low professional level demand, powerful universality, simple operation, and high precision. One pixel level of point positioning and height determination accuracy could be achieved if the digital elevation model (DEM) and sensor orientation model had higher precision and the off-Nadir View Angle was relatively perfect.

BIM cost analysis of transport infrastructure projects

NASA Astrophysics Data System (ADS)

Volkov, Andrey; Chelyshkov, Pavel; Grossman, Y.; Khromenkova, A.

2017-10-01

The article describes the method of analysis of the energy costs of transport infrastructure objects using BIM software. The paper consideres several options of orientation of a building using SketchUp and IES VE software programs. These options allow to choose the best direction of the building facades. Particular attention is given to a distribution of a temperature field in a cross-section of the wall according to the calculation made in the ELCUT software. The issues related to calculation of solar radiation penetration into a building and selection of translucent structures are considered in the paper. The article presents data on building codes relating to the transport sector, on the basis of which the calculations were made. The author emphasizes that BIM-programs should be implemented and used in order to optimize a thermal behavior of a building and increase its energy efficiency using climatic data.

[Dynamic changes of urban architecture landscape based on Barista: a case study in Tiexi District of Shenyang City].

PubMed

Zhang, Pei-feng; Hu, Yuan-man; He, Hong-shi; Xiong, Zai-ping; Liu, Miao

2010-12-01

In this paper, three-dimensional building information was extracted from high resolution satellite image based on Barista software. Combined with ArcGIS software, the dynamic changes of the building landscape in Tiexi District of Shenyang City during urban renewal process were analyzed from the conversion contribution rate, building density, average building height, and built-up area rate. It was found that during this urban renewal process, four dominant landscape types (vacant lot, residential building, industrial building, and road) were the main parts of the landscape changes. The areas of vacant lot, residential building, commercial building, and road increased, while that of industrial building decreased. The building density decreased, while the average building height increased. There was an obvious regional variation in building landscape. The building density in industrial district was higher than that in residential district, while the average building height was in adverse. The further from the city center, the lower the building density and building average height.

From Bridges and Rockets, Lessons for Software Systems

NASA Technical Reports Server (NTRS)

Holloway, C. Michael

2004-01-01

Although differences exist between building software systems and building physical structures such as bridges and rockets, enough similarities exist that software engineers can learn lessons from failures in traditional engineering disciplines. This paper draws lessons from two well-known failures the collapse of the Tacoma Narrows Bridge in 1940 and the destruction of the space shuttle Challenger in 1986 and applies these lessons to software system development. The following specific applications are made: (1) the verification and validation of a software system should not be based on a single method, or a single style of methods; (2) the tendency to embrace the latest fad should be overcome; and (3) the introduction of software control into safety-critical systems should be done cautiously.

Direct NOE simulation from long MD trajectories.

PubMed

Chalmers, G; Glushka, J N; Foley, B L; Woods, R J; Prestegard, J H

2016-04-01

A software package, MD2NOE, is presented which calculates Nuclear Overhauser Effect (NOE) build-up curves directly from molecular dynamics (MD) trajectories. It differs from traditional approaches in that it calculates correlation functions directly from the trajectory instead of extracting inverse sixth power distance terms as an intermediate step in calculating NOEs. This is particularly important for molecules that sample conformational states on a timescale similar to molecular reorientation. The package is tested on sucrose and results are shown to differ in small but significant ways from those calculated using an inverse sixth power assumption. Results are also compared to experiment and found to be in reasonable agreement despite an expected underestimation of water viscosity by the water model selected. Copyright © 2016 Elsevier Inc. All rights reserved.

Building Energy Management Open Source Software

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

Rahman, Saifur

Funded by the U.S. Department of Energy in November 2013, a Building Energy Management Open Source Software (BEMOSS) platform was engineered to improve sensing and control of equipment in small- and medium-sized commercial buildings. According to the Energy Information Administration (EIA), small- (5,000 square feet or smaller) and medium-sized (between 5,001 to 50,000 square feet) commercial buildings constitute about 95% of all commercial buildings in the U.S. These buildings typically do not have Building Automation Systems (BAS) to monitor and control building operation. While commercial BAS solutions exist, including those from Siemens, Honeywell, Johnsons Controls and many more, they aremore » not cost effective in the context of small- and medium-sized commercial buildings, and typically work with specific controller products from the same company. BEMOSS targets small and medium-sized commercial buildings to address this gap.« less

Software Management for the NOνAExperiment

NASA Astrophysics Data System (ADS)

Davies, G. S.; Davies, J. P.; C Group; Rebel, B.; Sachdev, K.; Zirnstein, J.

2015-12-01

The NOvAsoftware (NOνASoft) is written in C++, and built on the Fermilab Computing Division's art framework that uses ROOT analysis software. NOνASoftmakes use of more than 50 external software packages, is developed by more than 50 developers and is used by more than 100 physicists from over 30 universities and laboratories in 3 continents. The software builds are handled by Fermilab's custom version of Software Release Tools (SRT), a UNIX based software management system for large, collaborative projects that is used by several experiments at Fermilab. The system provides software version control with SVN configured in a client-server mode and is based on the code originally developed by the BaBar collaboration. In this paper, we present efforts towards distributing the NOvA software via the CernVM File System distributed file system. We will also describe our recent work to use a CMake build system and Jenkins, the open source continuous integration system, for NOνASoft.

Improving the Accuracy of Software-Based Energy Analysis for Residential Buildings (Presentation)

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

Polly, B.

2011-09-01

This presentation describes the basic components of software-based energy analysis for residential buildings, explores the concepts of 'error' and 'accuracy' when analysis predictions are compared to measured data, and explains how NREL is working to continuously improve the accuracy of energy analysis methods.

Building the Scientific Modeling Assistant: An interactive environment for specialized software design

NASA Technical Reports Server (NTRS)

Keller, Richard M.

1991-01-01

The construction of scientific software models is an integral part of doing science, both within NASA and within the scientific community at large. Typically, model-building is a time-intensive and painstaking process, involving the design of very large, complex computer programs. Despite the considerable expenditure of resources involved, completed scientific models cannot easily be distributed and shared with the larger scientific community due to the low-level, idiosyncratic nature of the implemented code. To address this problem, we have initiated a research project aimed at constructing a software tool called the Scientific Modeling Assistant. This tool provides automated assistance to the scientist in developing, using, and sharing software models. We describe the Scientific Modeling Assistant, and also touch on some human-machine interaction issues relevant to building a successful tool of this type.

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

Chen, Yixing; Zhang, Jianshun; Pelken, Michael

Executive Summary The objective of this study was to develop a “Virtual Design Studio (VDS)”: a software platform for integrated, coordinated and optimized design of green building systems with low energy consumption, high indoor environmental quality (IEQ), and high level of sustainability. This VDS is intended to assist collaborating architects, engineers and project management team members throughout from the early phases to the detailed building design stages. It can be used to plan design tasks and workflow, and evaluate the potential impacts of various green building strategies on the building performance by using the state of the art simulation toolsmore » as well as industrial/professional standards and guidelines for green building system design. Engaged in the development of VDS was a multi-disciplinary research team that included architects, engineers, and software developers. Based on the review and analysis of how existing professional practices in building systems design operate, particularly those used in the U.S., Germany and UK, a generic process for performance-based building design, construction and operation was proposed. It distinguishes the whole process into five distinct stages: Assess, Define, Design, Apply, and Monitoring (ADDAM). The current VDS is focused on the first three stages. The VDS considers building design as a multi-dimensional process, involving multiple design teams, design factors, and design stages. The intersection among these three dimensions defines a specific design task in terms of “who”, “what” and “when”. It also considers building design as a multi-objective process that aims to enhance the five aspects of performance for green building systems: site sustainability, materials and resource efficiency, water utilization efficiency, energy efficiency and impacts to the atmospheric environment, and IEQ. The current VDS development has been limited to energy efficiency and IEQ performance, with particular focus on evaluating thermal performance, air quality and lighting environmental quality because of their strong interaction with the energy performance of buildings. The VDS software framework contains four major functions: 1) Design coordination: It enables users to define tasks using the Input-Process-Output flow approach, which specifies the anticipated activities (i.e., the process), required input and output information, and anticipated interactions with other tasks. It also allows task scheduling to define the work flow, and sharing of the design data and information via the internet. 2) Modeling and simulation: It enables users to perform building simulations to predict the energy consumption and IEQ conditions at any of the design stages by using EnergyPlus and a combined heat, air, moisture and pollutant simulation (CHAMPS) model. A method for co-simulation was developed to allow the use of both models at the same time step for the combined energy and indoor air quality analysis. 3) Results visualization: It enables users to display a 3-D geometric design of the building by reading BIM (building information model) file generated by design software such as SketchUp, and the predicted results of heat, air, moisture, pollutant and light distributions in the building. 4) Performance evaluation: It enables the users to compare the performance of a proposed building design against a reference building that is defined for the same type of buildings under the same climate condition, and predicts the percent of improvements over the minimum requirements specified in ASHRAE Standard 55-2010, 62.1-2010 and 90.1-2010. An approach was developed to estimate the potential impact of a design factor on the whole building performance, and hence can assist the user to identify areas that have most pay back for investment. The VDS software was developed by using C++ with the conventional Model, View and Control (MVC) software architecture. The software has been verified by using a simple 3-zone case building. The application of the VDS concepts and framework for building design and performance analysis has been illustrated by using a medium-sized, five story office building that received LEED Platinum Certification from USGBC.« less

Project based, Collaborative, Algorithmic Robotics for High School Students: Programming Self Driving Race Cars at MIT

DTIC Science & Technology

2017-02-19

software systems: the students design and build robotics software towards real-world applications, without being distracted by hardware issues; (ii) it...high school students require the students to focus on building and integrating the hardware that make up the robot, at the expense of designing and...robotics programs focus on the mechanics; as a result, they do not have room for students to design and implement relatively complex software systems, as

NASA's Core Trajectory Sub-System Project: Using JBoss Enterprise Middleware for Building Software Systems Used to Support Spacecraft Trajectory Operations

NASA Technical Reports Server (NTRS)

Stensrud, Kjell C.; Hamm, Dustin

2007-01-01

NASA's Johnson Space Center (JSC) / Flight Design and Dynamics Division (DM) has prototyped the use of Open Source middleware technology for building its next generation spacecraft mission support system. This is part of a larger initiative to use open standards and open source software as building blocks for future mission and safety critical systems. JSC is hoping to leverage standardized enterprise architectures, such as Java EE, so that its internal software development efforts can be focused on the core aspects of their problem domain. This presentation will outline the design and implementation of the Trajectory system and the lessons learned during the exercise.

CrossTalk: The Journal of Defense Software Engineering. Volume 23, Number 4, July/August 2010

DTIC Science & Technology

2010-08-01

Anita Carleton, Del Kellogg, and Jeff Schwalb Building Critical Systems as a Cyborg As outrageous as it may seem, adapting cybernetics to defense...software is a real possibility in building complex software systems. Ball discusses the history of cybernetics, what a “ cyborg ” really is, and how...What Is a Cyborg ? We want both kinds of the behavior that I’ve talked about, with predictable systems that follow established rules and proce- dures

Development of a web-based tool for automated processing and cataloging of a unique combinatorial drug screen.

PubMed

Dalecki, Alex G; Wolschendorf, Frank

2016-07-01

Facing totally resistant bacteria, traditional drug discovery efforts have proven to be of limited use in replenishing our depleted arsenal of therapeutic antibiotics. Recently, the natural anti-bacterial properties of metal ions in synergy with metal-coordinating ligands have shown potential for generating new molecule candidates with potential therapeutic downstream applications. We recently developed a novel combinatorial screening approach to identify compounds with copper-dependent anti-bacterial properties. Through a parallel screening technique, the assay distinguishes between copper-dependent and independent activities against Mycobacterium tuberculosis with hits being defined as compounds with copper-dependent activities. These activities must then be linked to a compound master list to process and analyze the data and to identify the hit molecules, a labor intensive and mistake-prone analysis. Here, we describe a software program built to automate this analysis in order to streamline our workflow significantly. We conducted a small, 1440 compound screen against M. tuberculosis and used it as an example framework to build and optimize the software. Though specifically adapted to our own needs, it can be readily expanded for any small- to medium-throughput screening effort, parallel or conventional. Further, by virtue of the underlying Linux server, it can be easily adapted for chemoinformatic analysis of screens through packages such as OpenBabel. Overall, this setup represents an easy-to-use solution for streamlining processing and analysis of biological screening data, as well as offering a scaffold for ready functionality expansion. Copyright © 2016 Elsevier B.V. All rights reserved.

Sensor Suitcase Tablet Software

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

The Retrocommissioning Sensor Suitcase is targeted for use in small commercial buildings of less than 50,000 square feet of floor space that regularly receive basic services such as maintenance and repair, but don't have in-house energy management staff or buildings experts. The Suitcase is designed to be easy-to-use by building maintenance staff, or other professionals such as telecom and alarm technicians. The software in the hand-held is designed to guide the staff to input the building and system information, deploy the sensors in proper location, configure the sensor hardware, and start the data collection.

Software augmented buildings: Exploiting existing infrastructure to improve energy efficiency and comfort in commercial buildings

NASA Astrophysics Data System (ADS)

Balaji, Bharathan

Commercial buildings consume 19% of energy in the US as of 2010, and traditionally, their energy use has been optimized through improved equipment efficiency and retrofits. Beyond improved hardware and infrastructure, there exists a tremendous potential in reducing energy use through better monitoring and operation. We present several applications that we developed and deployed to support our thesis that building energy use can be reduced through sensing, monitoring and optimization software that modulates use of building subsystems including HVAC. We focus on HVAC systems as these constitute 48-55% of building energy use. Specifically, in case of sensing, we describe an energy apportionment system that enables us to estimate real-time zonal HVAC power consumption by analyzing existing sensor information. With this energy breakdown, we can measure effectiveness of optimization solutions and identify inefficiencies. Central to energy efficiency improvement is determination of human occupancy in buildings. But this information is often unavailable or expensive to obtain using wide scale sensor deployment. We present our system that infers room level occupancy inexpensively by leveraging existing WiFi infrastructure. Occupancy information can be used not only to directly control HVAC but also to infer state of the building for predictive control. Building energy use is strongly influenced by human behaviors, and timely feedback mechanisms can encourage energy saving behavior. Occupants interact with HVAC using thermostats which has shown to be inadequate for thermal comfort. Building managers are responsible for incorporating energy efficiency measures, but our interviews reveal that they struggle to maintain efficiency due to lack of analytical tools and contextual information. We present our software services that provide energy feedback to occupants and building managers, improves comfort with personalized control and identifies energy wasting faults. For wide scale deployment of such energy saving software, they need to be portable across multiple buildings. However, buildings consist of heterogeneous equipment and use inconsistent naming schema, and developers need extensive domain knowledge to map sensor information to a standard format. To enable portability, we present an active learning algorithm that automates mapping building sensor metadata to a standard naming schema.

Validation and extraction of molecular-geometry information from small-molecule databases.

PubMed

Long, Fei; Nicholls, Robert A; Emsley, Paul; Graǽulis, Saulius; Merkys, Andrius; Vaitkus, Antanas; Murshudov, Garib N

2017-02-01

A freely available small-molecule structure database, the Crystallography Open Database (COD), is used for the extraction of molecular-geometry information on small-molecule compounds. The results are used for the generation of new ligand descriptions, which are subsequently used by macromolecular model-building and structure-refinement software. To increase the reliability of the derived data, and therefore the new ligand descriptions, the entries from this database were subjected to very strict validation. The selection criteria made sure that the crystal structures used to derive atom types, bond and angle classes are of sufficiently high quality. Any suspicious entries at a crystal or molecular level were removed from further consideration. The selection criteria included (i) the resolution of the data used for refinement (entries solved at 0.84 Å resolution or higher) and (ii) the structure-solution method (structures must be from a single-crystal experiment and all atoms of generated molecules must have full occupancies), as well as basic sanity checks such as (iii) consistency between the valences and the number of connections between atoms, (iv) acceptable bond-length deviations from the expected values and (v) detection of atomic collisions. The derived atom types and bond classes were then validated using high-order moment-based statistical techniques. The results of the statistical analyses were fed back to fine-tune the atom typing. The developed procedure was repeated four times, resulting in fine-grained atom typing, bond and angle classes. The procedure will be repeated in the future as and when new entries are deposited in the COD. The whole procedure can also be applied to any source of small-molecule structures, including the Cambridge Structural Database and the ZINC database.

A method for the complete analysis of NORM building materials by γ-ray spectrometry using HPGe detectors.

PubMed

Quintana, B; Pedrosa, M C; Vázquez-Canelas, L; Santamaría, R; Sanjuán, M A; Puertas, F

2018-04-01

A methodology including software tools for analysing NORM building materials and residues by low-level gamma-ray spectrometry has been developed. It comprises deconvolution of gamma-ray spectra using the software GALEA with focus on the natural radionuclides and Monte Carlo simulations for efficiency and true coincidence summing corrections. The methodology has been tested on a range of building materials and validated against reference materials. Copyright © 2017 Elsevier Ltd. All rights reserved.

A Scalable Software Architecture Booting and Configuring Nodes in the Whitney Commodity Computing Testbed

NASA Technical Reports Server (NTRS)

Fineberg, Samuel A.; Kutler, Paul (Technical Monitor)

1997-01-01

The Whitney project is integrating commodity off-the-shelf PC hardware and software technology to build a parallel supercomputer with hundreds to thousands of nodes. To build such a system, one must have a scalable software model, and the installation and maintenance of the system software must be completely automated. We describe the design of an architecture for booting, installing, and configuring nodes in such a system with particular consideration given to scalability and ease of maintenance. This system has been implemented on a 40-node prototype of Whitney and is to be used on the 500 processor Whitney system to be built in 1998.

Hunter Syndrome

MedlinePlus

... enough of the enzyme to break down certain complex molecules, the molecules build up in harmful amounts. ... chromosome, an enzyme that's needed to break down complex sugar molecules is missing or malfunctioning. Without this ...

Synthesis of most polyene natural product motifs using just twelve building blocks and one coupling reaction

PubMed Central

Woerly, Eric M.; Roy, Jahnabi; Burke, Martin D.

2014-01-01

The inherent modularity of polypeptides, oligonucleotides, and oligosaccharides has been harnessed to achieve generalized building block-based synthesis platforms. Importantly, like these other targets, most small molecule natural products are biosynthesized via iterative coupling of bifunctional building blocks. This suggests that many small molecules also possess inherent modularity commensurate with systematic building block-based construction. Supporting this hypothesis, here we report that the polyene motifs found in >75% of all known polyene natural products can be synthesized using just 12 building blocks and one coupling reaction. Using the same general retrosynthetic algorithm and reaction conditions, this platform enabled the synthesis of a wide range of polyene frameworks covering all of this natural product chemical space, and first total syntheses of the polyene natural products asnipyrone B, physarigin A, and neurosporaxanthin β-D-glucopyranoside. Collectively, these results suggest the potential for a more generalized approach for making small molecules in the laboratory. PMID:24848233

A Lossless Network for Data Acquisition

NASA Astrophysics Data System (ADS)

Jereczek, Grzegorz; Lehmann Miotto, Giovanna; Malone, David; Walukiewicz, Miroslaw

2017-06-01

The bursty many-to-one communication pattern, typical for data acquisition systems, is particularly demanding for commodity TCP/IP and Ethernet technologies. We expand the study of lossless switching in software running on commercial off-the-shelf servers, using the ATLAS experiment as a case study. In this paper, we extend the popular software switch, Open vSwitch, with a dedicated, throughput-oriented buffering mechanism for data acquisition. We compare the performance under heavy congestion on typical Ethernet switches to a commodity server acting as a switch. Our results indicate that software switches with large buffers perform significantly better. Next, we evaluate the scalability of the system when building a larger topology of interconnected software switches, exploiting the integration with software-defined networking technologies. We build an IP-only leaf-spine network consisting of eight software switches running on distinct physical servers as a demonstrator.

NREL Improves Building Energy Simulation Programs Through Diagnostic Testing (Fact Sheet)

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

Not Available

2012-01-01

This technical highlight describes NREL research to develop Building Energy Simulation Test for Existing Homes (BESTEST-EX) to increase the quality and accuracy of energy analysis tools for the building retrofit market. Researchers at the National Renewable Energy Laboratory (NREL) have developed a new test procedure to increase the quality and accuracy of energy analysis tools for the building retrofit market. The Building Energy Simulation Test for Existing Homes (BESTEST-EX) is a test procedure that enables software developers to evaluate the performance of their audit tools in modeling energy use and savings in existing homes when utility bills are available formore » model calibration. Similar to NREL's previous energy analysis tests, such as HERS BESTEST and other BESTEST suites included in ANSI/ASHRAE Standard 140, BESTEST-EX compares software simulation findings to reference results generated with state-of-the-art simulation tools such as EnergyPlus, SUNREL, and DOE-2.1E. The BESTEST-EX methodology: (1) Tests software predictions of retrofit energy savings in existing homes; (2) Ensures building physics calculations and utility bill calibration procedures perform to a minimum standard; and (3) Quantifies impacts of uncertainties in input audit data and occupant behavior. BESTEST-EX includes building physics and utility bill calibration test cases. The diagram illustrates the utility bill calibration test cases. Participants are given input ranges and synthetic utility bills. Software tools use the utility bills to calibrate key model inputs and predict energy savings for the retrofit cases. Participant energy savings predictions using calibrated models are compared to NREL predictions using state-of-the-art building energy simulation programs.« less

A New Three-Dimensional Educational Model Kit for Building DNA and RNA Molecules: Development and Evaluation

ERIC Educational Resources Information Center

Beltramini, Leila Maria; Araujo, Ana Paula Ulian; de Oliveira, Tales Henrique Goncalves; dos Santos Abel, Luciano Douglas; da Silva, Aparecido Rodrigues; dos Santos, Neusa Fernandes

2006-01-01

International specialized literature focused on research in biology education is sadly scarce, especially regarding biochemical and molecular aspects. In this light, researchers from this Centre for Structural Molecular Biotechnology developed and evaluated a three-dimensional educational model named "Building Life Molecules DNA and RNA." The…

Student Computer Attitudes, Experience and Perceptions about the Use of Two Software Applications in Building Engineering

ERIC Educational Resources Information Center

Chiner, Esther; Garcia-Vera, Victoria E.

2017-01-01

The purpose of this study was to examine students' computer attitudes and experience, as well as students' perceptions about the use of two specific software applications (Google Drive Spreadsheets and Arquimedes) in the Building Engineering context. The relationships among these variables were also examined. Ninety-two students took part in this…

JavaGenes Molecular Evolution

NASA Technical Reports Server (NTRS)

Lohn, Jason; Smith, David; Frank, Jeremy; Globus, Al; Crawford, James

2007-01-01

JavaGenes is a general-purpose, evolutionary software system written in Java. It implements several versions of a genetic algorithm, simulated annealing, stochastic hill climbing, and other search techniques. This software has been used to evolve molecules, atomic force field parameters, digital circuits, Earth Observing Satellite schedules, and antennas. This version differs from version 0.7.28 in that it includes the molecule evolution code and other improvements. Except for the antenna code, JaveGenes is available for NASA Open Source distribution.

PUS Services Software Building Block Automatic Generation for Space Missions

NASA Astrophysics Data System (ADS)

Candia, S.; Sgaramella, F.; Mele, G.

2008-08-01

The Packet Utilization Standard (PUS) has been specified by the European Committee for Space Standardization (ECSS) and issued as ECSS-E-70-41A to define the application-level interface between Ground Segments and Space Segments. The ECSS-E- 70-41A complements the ECSS-E-50 and the Consultative Committee for Space Data Systems (CCSDS) recommendations for packet telemetry and telecommand. The ECSS-E-70-41A characterizes the identified PUS Services from a functional point of view and the ECSS-E-70-31 standard specifies the rules for their mission-specific tailoring. The current on-board software design for a space mission implies the production of several PUS terminals, each providing a specific tailoring of the PUS services. The associated on-board software building blocks are developed independently, leading to very different design choices and implementations even when the mission tailoring requires very similar services (from the Ground operative perspective). In this scenario, the automatic production of the PUS services building blocks for a mission would be a way to optimize the overall mission economy and improve the robusteness and reliability of the on-board software and of the Ground-Space interactions. This paper presents the Space Software Italia (SSI) activities for the development of an integrated environment to support: the PUS services tailoring activity for a specific mission. the mission-specific PUS services configuration. the generation the UML model of the software building block implementing the mission-specific PUS services and the related source code, support documentation (software requirements, software architecture, test plans/procedures, operational manuals), and the TM/TC database. The paper deals with: (a) the project objectives, (b) the tailoring, configuration, and generation process, (c) the description of the environments supporting the process phases, (d) the characterization of the meta-model used for the generation, (e) the characterization of the reference avionics architecture and of the reference on- board software high-level architecture.

UML as a cell and biochemistry modeling language.

PubMed

Webb, Ken; White, Tony

2005-06-01

The systems biology community is building increasingly complex models and simulations of cells and other biological entities, and are beginning to look at alternatives to traditional representations such as those provided by ordinary differential equations (ODE). The lessons learned over the years by the software development community in designing and building increasingly complex telecommunication and other commercial real-time reactive systems, can be advantageously applied to the problems of modeling in the biology domain. Making use of the object-oriented (OO) paradigm, the unified modeling language (UML) and Real-Time Object-Oriented Modeling (ROOM) visual formalisms, and the Rational Rose RealTime (RRT) visual modeling tool, we describe a multi-step process we have used to construct top-down models of cells and cell aggregates. The simple example model described in this paper includes membranes with lipid bilayers, multiple compartments including a variable number of mitochondria, substrate molecules, enzymes with reaction rules, and metabolic pathways. We demonstrate the relevance of abstraction, reuse, objects, classes, component and inheritance hierarchies, multiplicity, visual modeling, and other current software development best practices. We show how it is possible to start with a direct diagrammatic representation of a biological structure such as a cell, using terminology familiar to biologists, and by following a process of gradually adding more and more detail, arrive at a system with structure and behavior of arbitrary complexity that can run and be observed on a computer. We discuss our CellAK (Cell Assembly Kit) approach in terms of features found in SBML, CellML, E-CELL, Gepasi, Jarnac, StochSim, Virtual Cell, and membrane computing systems.

Synthesis of most polyene natural product motifs using just 12 building blocks and one coupling reaction.

PubMed

Woerly, Eric M; Roy, Jahnabi; Burke, Martin D

2014-06-01

The inherent modularity of polypeptides, oligonucleotides and oligosaccharides has been harnessed to achieve generalized synthesis platforms. Importantly, like these other targets, most small-molecule natural products are biosynthesized via iterative coupling of bifunctional building blocks. This suggests that many small molecules also possess inherent modularity commensurate with systematic building block-based construction. Supporting this hypothesis, here we report that the polyene motifs found in >75% of all known polyene natural products can be synthesized using just 12 building blocks and one coupling reaction. Using the same general retrosynthetic algorithm and reaction conditions, this platform enabled both the synthesis of a wide range of polyene frameworks that covered all of this natural-product chemical space and the first total syntheses of the polyene natural products asnipyrone B, physarigin A and neurosporaxanthin b-D-glucopyranoside. Collectively, these results suggest the potential for a more generalized approach to making small molecules in the laboratory.

Synthesis of most polyene natural product motifs using just 12 building blocks and one coupling reaction

NASA Astrophysics Data System (ADS)

Woerly, Eric M.; Roy, Jahnabi; Burke, Martin D.

2014-06-01

The inherent modularity of polypeptides, oligonucleotides and oligosaccharides has been harnessed to achieve generalized synthesis platforms. Importantly, like these other targets, most small-molecule natural products are biosynthesized via iterative coupling of bifunctional building blocks. This suggests that many small molecules also possess inherent modularity commensurate with systematic building block-based construction. Supporting this hypothesis, here we report that the polyene motifs found in >75% of all known polyene natural products can be synthesized using just 12 building blocks and one coupling reaction. Using the same general retrosynthetic algorithm and reaction conditions, this platform enabled both the synthesis of a wide range of polyene frameworks that covered all of this natural-product chemical space and the first total syntheses of the polyene natural products asnipyrone B, physarigin A and neurosporaxanthin β-D-glucopyranoside. Collectively, these results suggest the potential for a more generalized approach to making small molecules in the laboratory.

Aro: a machine learning approach to identifying single molecules and estimating classification error in fluorescence microscopy images.

PubMed

Wu, Allison Chia-Yi; Rifkin, Scott A

2015-03-27

Recent techniques for tagging and visualizing single molecules in fixed or living organisms and cell lines have been revolutionizing our understanding of the spatial and temporal dynamics of fundamental biological processes. However, fluorescence microscopy images are often noisy, and it can be difficult to distinguish a fluorescently labeled single molecule from background speckle. We present a computational pipeline to distinguish the true signal of fluorescently labeled molecules from background fluorescence and noise. We test our technique using the challenging case of wide-field, epifluorescence microscope image stacks from single molecule fluorescence in situ experiments on nematode embryos where there can be substantial out-of-focus light and structured noise. The software recognizes and classifies individual mRNA spots by measuring several features of local intensity maxima and classifying them with a supervised random forest classifier. A key innovation of this software is that, by estimating the probability that each local maximum is a true spot in a statistically principled way, it makes it possible to estimate the error introduced by image classification. This can be used to assess the quality of the data and to estimate a confidence interval for the molecule count estimate, all of which are important for quantitative interpretations of the results of single-molecule experiments. The software classifies spots in these images well, with >95% AUROC on realistic artificial data and outperforms other commonly used techniques on challenging real data. Its interval estimates provide a unique measure of the quality of an image and confidence in the classification.

Real-time single-molecule imaging of quantum interference.

PubMed

Juffmann, Thomas; Milic, Adriana; Müllneritsch, Michael; Asenbaum, Peter; Tsukernik, Alexander; Tüxen, Jens; Mayor, Marcel; Cheshnovsky, Ori; Arndt, Markus

2012-03-25

The observation of interference patterns in double-slit experiments with massive particles is generally regarded as the ultimate demonstration of the quantum nature of these objects. Such matter-wave interference has been observed for electrons, neutrons, atoms and molecules and, in contrast to classical physics, quantum interference can be observed when single particles arrive at the detector one by one. The build-up of such patterns in experiments with electrons has been described as the "most beautiful experiment in physics". Here, we show how a combination of nanofabrication and nano-imaging allows us to record the full two-dimensional build-up of quantum interference patterns in real time for phthalocyanine molecules and for derivatives of phthalocyanine molecules, which have masses of 514 AMU and 1,298 AMU respectively. A laser-controlled micro-evaporation source was used to produce a beam of molecules with the required intensity and coherence, and the gratings were machined in 10-nm-thick silicon nitride membranes to reduce the effect of van der Waals forces. Wide-field fluorescence microscopy detected the position of each molecule with an accuracy of 10 nm and revealed the build-up of a deterministic ensemble interference pattern from single molecules that arrived stochastically at the detector. In addition to providing this particularly clear demonstration of wave-particle duality, our approach could also be used to study larger molecules and explore the boundary between quantum and classical physics.

Real-time single-molecule imaging of quantum interference

NASA Astrophysics Data System (ADS)

Juffmann, Thomas; Milic, Adriana; Müllneritsch, Michael; Asenbaum, Peter; Tsukernik, Alexander; Tüxen, Jens; Mayor, Marcel; Cheshnovsky, Ori; Arndt, Markus

2012-05-01

The observation of interference patterns in double-slit experiments with massive particles is generally regarded as the ultimate demonstration of the quantum nature of these objects. Such matter-wave interference has been observed for electrons, neutrons, atoms and molecules and, in contrast to classical physics, quantum interference can be observed when single particles arrive at the detector one by one. The build-up of such patterns in experiments with electrons has been described as the ``most beautiful experiment in physics''. Here, we show how a combination of nanofabrication and nano-imaging allows us to record the full two-dimensional build-up of quantum interference patterns in real time for phthalocyanine molecules and for derivatives of phthalocyanine molecules, which have masses of 514 AMU and 1,298 AMU respectively. A laser-controlled micro-evaporation source was used to produce a beam of molecules with the required intensity and coherence, and the gratings were machined in 10-nm-thick silicon nitride membranes to reduce the effect of van der Waals forces. Wide-field fluorescence microscopy detected the position of each molecule with an accuracy of 10 nm and revealed the build-up of a deterministic ensemble interference pattern from single molecules that arrived stochastically at the detector. In addition to providing this particularly clear demonstration of wave-particle duality, our approach could also be used to study larger molecules and explore the boundary between quantum and classical physics.

Analysis of sulfates on low molecular weight heparin using mass spectrometry: structural characterization of enoxaparin.

PubMed

Gupta, Rohitesh; Ponnusamy, Moorthy P

2018-05-31

Structural characterization of low molecular weight heparin (LMWH) is critical to meet biosimilarity standards. In this context, the review focuses on structural analysis of labile sulfates attached to the side-groups of LMWH using mass spectrometry. A comprehensive review of this topic will help readers to identify key strategies for tackling the problem related to sulfate loss. At the same time, various mass spectrometry techniques are presented to facilitate compositional analysis of LMWH, mainly enoxaparin. Areas covered: This review summarizes findings on mass spectrometry application for LMWH, including modulation of sulfates, using enzymology and sample preparation approaches. Furthermore, popular open-source software packages for automated spectral data interpretation are also discussed. Successful use of LC/MS can decipher structural composition for LMWH and help evaluate their sameness or biosimilarity with the innovator molecule. Overall, the literature has been searched using PubMed by typing various search queries such as 'enoxaparin', 'mass spectrometry', 'low molecular weight heparin', 'structural characterization', etc. Expert commentary: This section highlights clinically relevant areas that need improvement to achieve satisfactory commercialization of LMWHs. It also primarily emphasizes the advancements in instrumentation related to mass spectrometry, and discusses building automated software for data interpretation and analysis.

DrugECs: An Ensemble System with Feature Subspaces for Accurate Drug-Target Interaction Prediction

PubMed Central

Jiang, Jinjian; Wang, Nian; Zhang, Jun

2017-01-01

Background Drug-target interaction is key in drug discovery, especially in the design of new lead compound. However, the work to find a new lead compound for a specific target is complicated and hard, and it always leads to many mistakes. Therefore computational techniques are commonly adopted in drug design, which can save time and costs to a significant extent. Results To address the issue, a new prediction system is proposed in this work to identify drug-target interaction. First, drug-target pairs are encoded with a fragment technique and the software “PaDEL-Descriptor.” The fragment technique is for encoding target proteins, which divides each protein sequence into several fragments in order and encodes each fragment with several physiochemical properties of amino acids. The software “PaDEL-Descriptor” creates encoding vectors for drug molecules. Second, the dataset of drug-target pairs is resampled and several overlapped subsets are obtained, which are then input into kNN (k-Nearest Neighbor) classifier to build an ensemble system. Conclusion Experimental results on the drug-target dataset showed that our method performs better and runs faster than the state-of-the-art predictors. PMID:28744468

A LEGO Mindstorms Brewster angle microscope

NASA Astrophysics Data System (ADS)

Fernsler, Jonathan; Nguyen, Vincent; Wallum, Alison; Benz, Nicholas; Hamlin, Matthew; Pilgram, Jessica; Vanderpoel, Hunter; Lau, Ryan

2017-09-01

A Brewster Angle Microscope (BAM) built from a LEGO Mindstorms kit, additional LEGO bricks, and several standard optics components, is described. The BAM was built as part of an undergraduate senior project and was designed, calibrated, and used to image phospholipid, cholesterol, soap, and oil films on the surface of water. A BAM uses p-polarized laser light reflected off a surface at the Brewster angle, which ideally yields zero reflectivity. When a film of different refractive index is added to the surface a small amount of light is reflected, which can be imaged in a microscope camera. Films of only one molecule (approximately 1 nm) thick, a monolayer, can be observed easily in the BAM. The BAM was used in a junior-level Physical Chemistry class to observe phase transitions of a monolayer and the collapse of a monolayer deposited on the water surface in a Langmuir trough. Using a photometric calculation, students observed a change in thickness of a monolayer during a phase transition of 7 Å, which was accurate to within 1 Å of the value determined by more advanced methods. As supplementary material, we provide a detailed manual on how to build the BAM, software to control the BAM and camera, and image processing software.

Software Tools for Development on the Peregrine System | High-Performance

Science.gov Websites

Computing | NREL Software Tools for Development on the Peregrine System Software Tools for and manage software at the source code level. Cross-Platform Make and SCons The "Cross-Platform Make" (CMake) package is from Kitware, and SCons is a modern software build tool based on Python

A molecular fragment cheminformatics roadmap for mesoscopic simulation.

PubMed

Truszkowski, Andreas; Daniel, Mirco; Kuhn, Hubert; Neumann, Stefan; Steinbeck, Christoph; Zielesny, Achim; Epple, Matthias

2014-12-01

Mesoscopic simulation studies the structure, dynamics and properties of large molecular ensembles with millions of atoms: Its basic interacting units (beads) are no longer the nuclei and electrons of quantum chemical ab-initio calculations or the atom types of molecular mechanics but molecular fragments, molecules or even larger molecular entities. For its simulation setup and output a mesoscopic simulation kernel software uses abstract matrix (array) representations for bead topology and connectivity. Therefore a pure kernel-based mesoscopic simulation task is a tedious, time-consuming and error-prone venture that limits its practical use and application. A consequent cheminformatics approach tackles these problems and provides solutions for a considerably enhanced accessibility. This study aims at outlining a complete cheminformatics roadmap that frames a mesoscopic Molecular Fragment Dynamics (MFD) simulation kernel to allow its efficient use and practical application. The molecular fragment cheminformatics roadmap consists of four consecutive building blocks: An adequate fragment structure representation (1), defined operations on these fragment structures (2), the description of compartments with defined compositions and structural alignments (3), and the graphical setup and analysis of a whole simulation box (4). The basis of the cheminformatics approach (i.e. building block 1) is a SMILES-like line notation (denoted f SMILES) with connected molecular fragments to represent a molecular structure. The f SMILES notation and the following concepts and methods for building blocks 2-4 are outlined with examples and practical usage scenarios. It is shown that the requirements of the roadmap may be partly covered by already existing open-source cheminformatics software. Mesoscopic simulation techniques like MFD may be considerably alleviated and broadened for practical use with a consequent cheminformatics layer that successfully tackles its setup subtleties and conceptual usage hurdles. Molecular Fragment Cheminformatics may be regarded as a crucial accelerator to propagate MFD and similar mesoscopic simulation techniques in the molecular sciences. Graphical abstractA molecular fragment cheminformatics roadmap for mesoscopic simulation.

Averting Denver Airports on a Chip

NASA Technical Reports Server (NTRS)

Sullivan, Kevin J.

1995-01-01

As a result of recent advances in software engineering capabilities, we are now in a more stable environment. De-facto hardware and software standards are emerging. Work on software architecture and design patterns signals a consensus on the importance of early system-level design decisions, and agreements on the uses of certain paradigmatic software structures. We now routinely build systems that would have been risky or infeasible a few years ago. Unfortunately, technological developments threaten to destabilize software design again. Systems designed around novel computing and peripheral devices will spark ambitious new projects that will stress current software design and engineering capabilities. Micro-electro-mechanical systems (MEMS) and related technologies provide the physical basis for new systems with the potential to produce this kind of destabilizing effect. One important response to anticipated software engineering and design difficulties is carefully directed engineering-scientific research. Two specific problems meriting substantial research attention are: A lack of sufficient means to build software systems by generating, extending, specializing, and integrating large-scale reusable components; and a lack of adequate computational and analytic tools to extend and aid engineers in maintaining intellectual control over complex software designs.

Economic and Environmental Assessment of a 1 MW Grid Connected Rooftop Solar PV System for Energy Efficient Building in Bangladesh

NASA Astrophysics Data System (ADS)

Chakraborty, Sanjib; Hosain, Rubayet; Rahman, Toufiqur; Rabbi, Ahmead Fazle

This paper evaluates the potentiality of a 1 MW grid connected rooftop solar PV system for an Energy Efficient Building in Bangladesh, which was estimated by utilizing NASA SSE solar radiation data, PVsyst simulation software and RETScreen simulation software. Economic and environmental viability for a ten-storied building with roof area of 6,500 m2 in the Capital City of Bangladesh, Dhaka was assessed by using the RETScreen simulation software. The yearly electricity production of the proposed system was 1,581 MWh estimated by PVsyst where the technical prospective of gird-connected solar PV in Bangladesh was calculated as about 50,174 MW. The economic assessments were determined the simple payback in such a way that the generated electricity first fulfills the demand of the building, and then the rest of the energy is supplied to the grid. The result indicates that the roof top solar PV system for an Energy efficient building in Dhaka city has a favorable condition for development both in economic and environmental point of view.

Enhancing reproducibility in scientific computing: Metrics and registry for Singularity containers.

PubMed

Sochat, Vanessa V; Prybol, Cameron J; Kurtzer, Gregory M

2017-01-01

Here we present Singularity Hub, a framework to build and deploy Singularity containers for mobility of compute, and the singularity-python software with novel metrics for assessing reproducibility of such containers. Singularity containers make it possible for scientists and developers to package reproducible software, and Singularity Hub adds automation to this workflow by building, capturing metadata for, visualizing, and serving containers programmatically. Our novel metrics, based on custom filters of content hashes of container contents, allow for comparison of an entire container, including operating system, custom software, and metadata. First we will review Singularity Hub's primary use cases and how the infrastructure has been designed to support modern, common workflows. Next, we conduct three analyses to demonstrate build consistency, reproducibility metric and performance and interpretability, and potential for discovery. This is the first effort to demonstrate a rigorous assessment of measurable similarity between containers and operating systems. We provide these capabilities within Singularity Hub, as well as the source software singularity-python that provides the underlying functionality. Singularity Hub is available at https://singularity-hub.org, and we are excited to provide it as an openly available platform for building, and deploying scientific containers.

Enhancing reproducibility in scientific computing: Metrics and registry for Singularity containers

PubMed Central

Prybol, Cameron J.; Kurtzer, Gregory M.

2017-01-01

Here we present Singularity Hub, a framework to build and deploy Singularity containers for mobility of compute, and the singularity-python software with novel metrics for assessing reproducibility of such containers. Singularity containers make it possible for scientists and developers to package reproducible software, and Singularity Hub adds automation to this workflow by building, capturing metadata for, visualizing, and serving containers programmatically. Our novel metrics, based on custom filters of content hashes of container contents, allow for comparison of an entire container, including operating system, custom software, and metadata. First we will review Singularity Hub’s primary use cases and how the infrastructure has been designed to support modern, common workflows. Next, we conduct three analyses to demonstrate build consistency, reproducibility metric and performance and interpretability, and potential for discovery. This is the first effort to demonstrate a rigorous assessment of measurable similarity between containers and operating systems. We provide these capabilities within Singularity Hub, as well as the source software singularity-python that provides the underlying functionality. Singularity Hub is available at https://singularity-hub.org, and we are excited to provide it as an openly available platform for building, and deploying scientific containers. PMID:29186161

78 FR 31916 - Increasing Market and Planning Efficiency Through Improved Software; Supplemental Agenda Notice

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-28

... Market and Planning Efficiency Through Improved Software; Supplemental Agenda Notice Take notice that... for increasing real-time and day-ahead market efficiency through improved software. A detailed agenda..., the software industry, government, research centers and academia and is intended to build on the...

Test-driven programming

NASA Astrophysics Data System (ADS)

Georgiev, Bozhidar; Georgieva, Adriana

2013-12-01

In this paper, are presented some possibilities concerning the implementation of a test-driven development as a programming method. Here is offered a different point of view for creation of advanced programming techniques (build tests before programming source with all necessary software tools and modules respectively). Therefore, this nontraditional approach for easier programmer's work through building tests at first is preferable way of software development. This approach allows comparatively simple programming (applied with different object-oriented programming languages as for example JAVA, XML, PYTHON etc.). It is predictable way to develop software tools and to provide help about creating better software that is also easier to maintain. Test-driven programming is able to replace more complicated casual paradigms, used by many programmers.

Third-Party Software's Trust Quagmire.

PubMed

Voas, J; Hurlburt, G

2015-12-01

Current software development has trended toward the idea of integrating independent software sub-functions to create more complete software systems. Software sub-functions are often not homegrown - instead they are developed by unknown 3 rd party organizations and reside in software marketplaces owned or controlled by others. Such software sub-functions carry plausible concern in terms of quality, origins, functionality, security, interoperability, to name a few. This article surveys key technical difficulties in confidently building systems from acquired software sub-functions by calling out the principle software supply chain actors.

Fluxonium-Based Artificial Molecule with a Tunable Magnetic Moment

NASA Astrophysics Data System (ADS)

Kou, A.; Smith, W. C.; Vool, U.; Brierley, R. T.; Meier, H.; Frunzio, L.; Girvin, S. M.; Glazman, L. I.; Devoret, M. H.

2017-07-01

Engineered quantum systems allow us to observe phenomena that are not easily accessible naturally. The LEGO®-like nature of superconducting circuits makes them particularly suited for building and coupling artificial atoms. Here, we introduce an artificial molecule, composed of two strongly coupled fluxonium atoms, which possesses a tunable magnetic moment. Using an applied external flux, one can tune the molecule between two regimes: one in which the ground-excited state manifold has a magnetic dipole moment and one in which the ground-excited state manifold has only a magnetic quadrupole moment. By varying the applied external flux, we find the coherence of the molecule to be limited by local flux noise. The ability to engineer and control artificial molecules paves the way for building more complex circuits for quantum simulation and protected qubits.

Direct-coupled microcomputer-based building emulator for building energy management and control systems

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

Lam, H.N.

1999-07-01

In this paper, the development and implementation of a direct-coupled building emulator for a building energy management and control system (EMCS) is presented. The building emulator consists of a microcomputer and a computer model of an air-conditioning system implemented in a modular dynamic simulation software package for direct-coupling to an EMCS, without using analog-to-digital and digital-to-analog converters. The building emulator can be used to simulate in real time the behavior of the air-conditioning system under a given operating environment and subject to a given usage pattern. Software modules for data communication, graphical display, dynamic data exchange, and synchronization of simulationmore » outputs with real time have been developed to achieve direct digital data transfer between the building emulator and a commercial EMCS. Based on the tests conducted, the validity of the building emulator has been established and the proportional-plus-integral control function of the EMCS assessed.« less

Working Notes from the 1992 AAAI Workshop on Automating Software Design. Theme: Domain Specific Software Design

NASA Technical Reports Server (NTRS)

Keller, Richard M. (Editor); Barstow, David; Lowry, Michael R.; Tong, Christopher H.

1992-01-01

The goal of this workshop is to identify different architectural approaches to building domain-specific software design systems and to explore issues unique to domain-specific (vs. general-purpose) software design. Some general issues that cut across the particular software design domain include: (1) knowledge representation, acquisition, and maintenance; (2) specialized software design techniques; and (3) user interaction and user interface.

RNA and RNP as Building Blocks for Nanotechnology and Synthetic Biology.

PubMed

Ohno, Hirohisa; Saito, Hirohide

2016-01-01

Recent technologies that aimed to elucidate cellular function have revealed essential roles for RNA molecules in living systems. Our knowledge concerning functional and structural information of naturally occurring RNA and RNA-protein (RNP) complexes is increasing rapidly. RNA and RNP interaction motifs are structural units that function as building blocks to constitute variety of complex structures. RNA-central synthetic biology and nanotechnology are constructive approaches that employ the accumulated information and build synthetic RNA (RNP)-based circuits and nanostructures. Here, we describe how to design and construct synthetic RNA (RNP)-based devices and structures at the nanometer-scale for biological and future therapeutic applications. RNA/RNP nanostructures can also be utilized as the molecular scaffold to control the localization or interactions of target molecule(s). Moreover, RNA motifs recognized by RNA-binding proteins can be applied to make protein-responsive translational "switches" that can turn gene expression "on" or "off" depending on the intracellular environment. This "synthetic RNA and RNP world" will expand tools for nanotechnology and synthetic biology. In addition, these reconstructive approaches would lead to a greater understanding of building principle in naturally occurring RNA/RNP molecules and systems. Copyright © 2016 Elsevier Inc. All rights reserved.

User systems guidelines for software projects

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

Abrahamson, L.

1986-04-01

This manual presents guidelines for software standards which were developed so that software project-development teams and management involved in approving the software could have a generalized view of all phases in the software production procedure and the steps involved in completing each phase. Guidelines are presented for six phases of software development: project definition, building a user interface, designing software, writing code, testing code, and preparing software documentation. The discussions for each phase include examples illustrating the recommended guidelines. 45 refs. (DWL)

Building Diagnostic Market Deployment - Final Report

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

Katipamula, S.; Gayeski, N.

2012-04-30

Operational faults are pervasive across the commercial buildings sector, wasting energy and increasing energy costs by up to about 30% (Mills 2009, Liu et al. 2003, Claridge et al. 2000, Katipamula and Brambley 2008, and Brambley and Katipamula 2009). Automated fault detection and diagnostic (AFDD) tools provide capabilities essential for detecting and correcting these problems and eliminating the associated energy waste and costs. The U.S. Department of Energy's (DOE) Building Technology Program (BTP) has previously invested in developing and testing of such diagnostic tools for whole-building (and major system) energy use, air handlers, chillers, cooling towers, chilled-water distribution systems, andmore » boilers. These diagnostic processes can be used to make the commercial buildings more energy efficient. The work described in this report was done as part of a Cooperative Research and Development Agreement (CRADA) between the U.S. Department of Energy's Pacific Northwest National Laboratory (PNNL) and KGS Building LLC (KGS). PNNL and KGS both believe that the widespread adoption of AFDD tools will result in significant reduction to energy and peak energy consumption. The report provides an introduction and summary of the various tasks performed under the CRADA. The CRADA project had three major focus areas: (1) Technical Assistance for Whole Building Energy Diagnostician (WBE) Commercialization, (2) Market Transfer of the Outdoor Air/Economizer Diagnostician (OAE), and (3) Development and Deployment of Automated Diagnostics to Improve Large Commercial Building Operations. PNNL has previously developed two diagnostic tools: (1) whole building energy (WBE) diagnostician and (2) outdoor air/economizer (OAE) diagnostician. WBE diagnostician is currently licensed non-exclusively to one company. As part of this CRADA, PNNL developed implementation documentation and provided technical support to KGS to implement the tool into their software suite, Clockworks. PNNL also provided validation data sets and the WBE software tool to validate the KGS implementation. OAE diagnostician automatically detects and diagnoses problems with outdoor air ventilation and economizer operation for air handling units (AHUs) in commercial buildings using data available from building automation systems (BASs). As part of this CRADA, PNNL developed implementation documentation and provided technical support to KGS to implement the tool into their software suite. PNNL also provided validation data sets and the OAE software tool to validate the KGS implementation. Finally, as part of this CRADA project, PNNL developed new processes to automate parts of the re-tuning process and transfer those process to KGS for integration into their software product. The transfer of DOE-funded technologies will transform the commercial buildings sector by making buildings more energy efficient and also reducing the carbon footprint from the buildings. As part of the CRADA with PNNL, KGS implemented the whole building energy diagnostician, a portion of outdoor air economizer diagnostician and a number of measures that automate the identification of re-tuning measures.« less

SYVA: A program to analyze symmetry of molecules based on vector algebra

NASA Astrophysics Data System (ADS)

Gyevi-Nagy, László; Tasi, Gyula

2017-06-01

Symmetry is a useful concept in physics and chemistry. It can be used to find out some simple properties of a molecule or simplify complex calculations. In this paper a simple vector algebraic method is described to determine all symmetry elements of an arbitrary molecule. To carry out the symmetry analysis, a program has been written, which is also capable of generating the framework group of the molecule, revealing the symmetry properties of normal modes of vibration and symmetrizing the structure. To demonstrate the capabilities of the program, it is compared to other common widely used stand-alone symmetry analyzer (SYMMOL, Symmetrizer) and molecular modeling (NWChem, ORCA, MRCC) software. SYVA can generate input files for molecular modeling programs, e.g. Gaussian, using precisely symmetrized molecular structures. Possible applications are also demonstrated by integrating SYVA with the GAMESS and MRCC software.

Building the Core Architecture of a Multiagent System Product Line: With an example from a future NASA Mission

NASA Technical Reports Server (NTRS)

Pena, Joaquin; Hinchey, Michael G.; Ruiz-Cortes, Antonio

2006-01-01

The field of Software Product Lines (SPL) emphasizes building a core architecture for a family of software products from which concrete products can be derived rapidly. This helps to reduce time-to-market, costs, etc., and can result in improved software quality and safety. Current AOSE methodologies are concerned with developing a single Multiagent System. We propose an initial approach to developing the core architecture of a Multiagent Systems Product Line (MAS-PL), exemplifying our approach with reference to a concept NASA mission based on multiagent technology.

Teaching Model Building to High School Students: Theory and Reality.

ERIC Educational Resources Information Center

Roberts, Nancy; Barclay, Tim

1988-01-01

Builds on a National Science Foundation (NSF) microcomputer based laboratory project to introduce system dynamics into the precollege setting. Focuses on providing students with powerful and investigatory theory building tools. Discusses developed hardware, software, and curriculum materials used to introduce model building and simulations into…

Luigi Gentile Polese | NREL

Science.gov Websites

software development of next-generation whole-building energy modeling, analysis, and simulation tools technical positions in networking protocol specifications, call control software, and requirements

Home | BEopt

Science.gov Websites

BEopt - Building Energy Optimization BEopt NREL - National Renewable Energy Laboratory Primary Energy Optimization) software provides capabilities to evaluate residential building designs and identify sequential search optimization technique used by BEopt: Finds minimum-cost building designs at different

RETScreen Plus Software Tutorial

NASA Technical Reports Server (NTRS)

Ganoe, Rene D.; Stackhouse, Paul W., Jr.; DeYoung, Russell J.

2014-01-01

Greater emphasis is being placed on reducing both the carbon footprint and energy cost of buildings. A building's energy usage depends upon many factors one of the most important is the local weather and climate conditions to which it's electrical, heating and air conditioning systems must respond. Incorporating renewable energy systems, including solar systems, to supplement energy supplies and increase energy efficiency is important to saving costs and reducing emissions. Also retrofitting technologies to buildings requires knowledge of building performance in its current state, potential future climate state, projection of potential savings with capital investment, and then monitoring the performance once the improvements are made. RETScreen Plus is a performance analysis software module that supplies the needed functions of monitoring current building performance, targeting projected energy efficiency improvements and verifying improvements once completed. This tutorial defines the functions of RETScreen Plus as well as outlines the general procedure for monitoring and reporting building energy performance.

Measurements of the LHCb software stack on the ARM architecture

NASA Astrophysics Data System (ADS)

Vijay Kartik, S.; Couturier, Ben; Clemencic, Marco; Neufeld, Niko

2014-06-01

The ARM architecture is a power-efficient design that is used in most processors in mobile devices all around the world today since they provide reasonable compute performance per watt. The current LHCb software stack is designed (and thus expected) to build and run on machines with the x86/x86_64 architecture. This paper outlines the process of measuring the performance of the LHCb software stack on the ARM architecture - specifically, the ARMv7 architecture on Cortex-A9 processors from NVIDIA and on full-fledged ARM servers with chipsets from Calxeda - and makes comparisons with the performance on x86_64 architectures on the Intel Xeon L5520/X5650 and AMD Opteron 6272. The paper emphasises the aspects of performance per core with respect to the power drawn by the compute nodes for the given performance - this ensures a fair real-world comparison with much more 'powerful' Intel/AMD processors. The comparisons of these real workloads in the context of LHCb are also complemented with the standard synthetic benchmarks HEPSPEC and Coremark. The pitfalls and solutions for the non-trivial task of porting the source code to build for the ARMv7 instruction set are presented. The specific changes in the build process needed for ARM-specific portions of the software stack are described, to serve as pointers for further attempts taken up by other groups in this direction. Cases where architecture-specific tweaks at the assembler lever (both in ROOT and the LHCb software stack) were needed for a successful compile are detailed - these cases are good indicators of where/how the software stack as well as the build system can be made more portable and multi-arch friendly. The experience gained from the tasks described in this paper are intended to i) assist in making an informed choice about ARM-based server solutions as a feasible low-power alternative to the current compute nodes, and ii) revisit the software design and build system for portability and generic improvements.

Selecting Really Excellent Software for Young Adults.

ERIC Educational Resources Information Center

Polly, Jean Armour

1985-01-01

This article discusses criteria of a good computer software package to aid the public librarian in the building, weeding, and maintenance of a software collection for young adults. Highlights include manuals or documentation; bells, whistles, and color; and the true test of time. (EJS)

Advances in the treatment of explicit water molecules in docking and binding free energy calculations.

PubMed

Hu, Xiao; Maffucci, Irene; Contini, Alessandro

2018-05-13

The inclusion of direct effects mediated by water during the ligand-receptor recognition is a hot-topic of modern computational chemistry applied to drug discovery and development. Docking or virtual screening with explicit hydration is still debatable, despite the successful cases that have been presented in the last years. Indeed, how to select the water molecules that will be included in the docking process or how the included waters should be treated remain open questions. In this review, we will discuss some of the most recent methods that can be used in computational drug discovery and drug development when the effect of a single water, or of a small network of interacting waters, needs to be explicitly considered. Here, we analyse software to aid the selection, or to predict the position, of water molecules that are going to be explicitly considered in later docking studies. We also present software and protocols able to efficiently treat flexible water molecules during docking, including examples of applications. Finally, we discuss methods based on molecular dynamics simulations that can be used to integrate docking studies or to reliably and efficiently compute binding energies of ligands in presence of interfacial or bridging water molecules. Software applications aiding the design of new drugs that exploit water molecules, either as displaceable residues or as bridges to the receptor, are constantly being developed. Although further validation is needed, workflows that explicitly consider water will probably become a standard for computational drug discovery soon. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

SRA Real Math Building Blocks PreK. What Works Clearinghouse Intervention Report

ERIC Educational Resources Information Center

What Works Clearinghouse, 2007

2007-01-01

"SRA Real Math Building Blocks PreK" (also referred to as "Building Blocks for Math") is a supplemental mathematics curriculum designed to develop preschool children's early mathematical knowledge through various individual and small- and large-group activities. It uses "Building Blocks for Math PreK" software,…

Top Value Added Chemicals from Biomass - Volume I, Results of Screening for Potential Candidates from Sugars and Synthesis Gas

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

None

2004-08-01

This report identifies twelve building block chemicals that can be produced from sugars via biological or chemical conversions. The twelve building blocks can be subsequently converted to a number of high-value bio-based chemicals or materials. Building block chemicals, as considered for this analysis, are molecules with multiple functional groups that possess the potential to be transformed into new families of useful molecules. The twelve sugar-based building blocks are 1,4-diacids (succinic, fumaric and malic), 2,5-furan dicarboxylic acid, 3-hydroxy propionic acid, aspartic acid, glucaric acid, glutamic acid, itaconic acid, levulinic acid, 3-hydroxybutyrolactone, glycerol, sorbitol, and xylitol/arabinitol.

Top Value Added Chemicals from Biomass: Volume I -- Results of Screening for Potential Candidates from Sugars and Synthesis Gas

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

Werpy, T.; Petersen, G.

2004-08-01

This report identifies twelve building block chemicals that can be produced from sugars via biological or chemical conversions. The twelve building blocks can be subsequently converted to a number of high-value bio-based chemicals or materials. Building block chemicals, as considered for this analysis, are molecules with multiple functional groups that possess the potential to be transformed into new families of useful molecules. The twelve sugar-based building blocks are 1,4-diacids (succinic, fumaric and malic), 2,5-furan dicarboxylic acid, 3-hydroxy propionic acid, aspartic acid, glucaric acid, glutamic acid, itaconic acid, levulinic acid, 3-hydroxybutyrolactone, glycerol, sorbitol, and xylitol/arabinitol.

Ontology for Life-Cycle Modeling of Electrical Distribution Systems: Model View Definition

DTIC Science & Technology

2013-06-01

building information models ( BIM ) at the coordinated design stage of building construction. 1.3 Approach To...standard for exchanging Building Information Modeling ( BIM ) data, which defines hundreds of classes for common use in software, currently supported by...specifications, Construction Operations Building in- formation exchange (COBie), Building Information Modeling ( BIM ) 16. SECURITY CLASSIFICATION OF:

Rapid Deployment of Optimal Control for Building HVAC Systems Using Innovative Software Tools and a Hybrid Heuristic/Model Based Control Approach

DTIC Science & Technology

2017-03-21

for public release; distribution is unlimited 13. SUPPLEMENTARY NOTES None 14. ABSTRACT ESTCP project EW-201409 aimed at demonstrating the benefits ...of innovative software technology for building HV AC systems. These benefits included reduced system energy use and cost as wetl as improved...Control Approach March 2017 This document has been cleared for public release; Distribution Statement A

Defense Facility Condition: Revised Guidance Needed to Improve Oversight of Assessments and Ratings

DTIC Science & Technology

2016-06-01

are to implement the standardized process in part by assessing the condition of buildings, pavement , and rail using the same set of software tools...facility to current standards; costs for labor, equipment, materials, and currency exchange rates overseas; costs for project planning and design ...example, the services are to assess the condition of buildings, pavement , and rail using Sustainment Management System software tools developed by the

Teaching and Assessment of Mathematical Principles for Software Correctness Using a Reasoning Concept Inventory

ERIC Educational Resources Information Center

Drachova-Strang, Svetlana V.

2013-01-01

As computing becomes ubiquitous, software correctness has a fundamental role in ensuring the safety and security of the systems we build. To design and develop software correctly according to their formal contracts, CS students, the future software practitioners, need to learn a critical set of skills that are necessary and sufficient for…

Automatic Generation of Just-in-Time Online Assessments from Software Design Models

ERIC Educational Resources Information Center

Zualkernan, Imran A.; El-Naaj, Salim Abou; Papadopoulos, Maria; Al-Amoudi, Budoor K.; Matthews, Charles E.

2009-01-01

Computer software is pervasive in today's society. The rate at which new versions of computer software products are released is phenomenal when compared to the release rate of new products in traditional industries such as aircraft building. This rapid rate of change can partially explain why most certifications in the software industry are…

Accuracy Assessment of a Complex Building 3d Model Reconstructed from Images Acquired with a Low-Cost Uas

NASA Astrophysics Data System (ADS)

Oniga, E.; Chirilă, C.; Stătescu, F.

2017-02-01

Nowadays, Unmanned Aerial Systems (UASs) are a wide used technique for acquisition in order to create buildings 3D models, providing the acquisition of a high number of images at very high resolution or video sequences, in a very short time. Since low-cost UASs are preferred, the accuracy of a building 3D model created using this platforms must be evaluated. To achieve results, the dean's office building from the Faculty of "Hydrotechnical Engineering, Geodesy and Environmental Engineering" of Iasi, Romania, has been chosen, which is a complex shape building with the roof formed of two hyperbolic paraboloids. Seven points were placed on the ground around the building, three of them being used as GCPs, while the remaining four as Check points (CPs) for accuracy assessment. Additionally, the coordinates of 10 natural CPs representing the building characteristic points were measured with a Leica TCR 405 total station. The building 3D model was created as a point cloud which was automatically generated based on digital images acquired with the low-cost UASs, using the image matching algorithm and different software like 3DF Zephyr, Visual SfM, PhotoModeler Scanner and Drone2Map for ArcGIS. Except for the PhotoModeler Scanner software, the interior and exterior orientation parameters were determined simultaneously by solving a self-calibrating bundle adjustment. Based on the UAS point clouds, automatically generated by using the above mentioned software and GNSS data respectively, the parameters of the east side hyperbolic paraboloid were calculated using the least squares method and a statistical blunder detection. Then, in order to assess the accuracy of the building 3D model, several comparisons were made for the facades and the roof with reference data, considered with minimum errors: TLS mesh for the facades and GNSS mesh for the roof. Finally, the front facade of the building was created in 3D based on its characteristic points using the PhotoModeler Scanner software, resulting a CAD (Computer Aided Design) model. The results showed the high potential of using low-cost UASs for building 3D model creation and if the building 3D model is created based on its characteristic points the accuracy is significantly improved.

An Overview of Biological Macromolecule Crystallization

PubMed Central

Krauss, Irene Russo; Merlino, Antonello; Vergara, Alessandro; Sica, Filomena

2013-01-01

The elucidation of the three dimensional structure of biological macromolecules has provided an important contribution to our current understanding of many basic mechanisms involved in life processes. This enormous impact largely results from the ability of X-ray crystallography to provide accurate structural details at atomic resolution that are a prerequisite for a deeper insight on the way in which bio-macromolecules interact with each other to build up supramolecular nano-machines capable of performing specialized biological functions. With the advent of high-energy synchrotron sources and the development of sophisticated software to solve X-ray and neutron crystal structures of large molecules, the crystallization step has become even more the bottleneck of a successful structure determination. This review introduces the general aspects of protein crystallization, summarizes conventional and innovative crystallization methods and focuses on the new strategies utilized to improve the success rate of experiments and increase crystal diffraction quality. PMID:23727935

Software For Genetic Algorithms

NASA Technical Reports Server (NTRS)

Wang, Lui; Bayer, Steve E.

1992-01-01

SPLICER computer program is genetic-algorithm software tool used to solve search and optimization problems. Provides underlying framework and structure for building genetic-algorithm application program. Written in Think C.

Automatic building information model query generation

DOE PAGES

Jiang, Yufei; Yu, Nan; Ming, Jiang; ...

2015-12-01

Energy efficient building design and construction calls for extensive collaboration between different subfields of the Architecture, Engineering and Construction (AEC) community. Performing building design and construction engineering raises challenges on data integration and software interoperability. Using Building Information Modeling (BIM) data hub to host and integrate building models is a promising solution to address those challenges, which can ease building design information management. However, the partial model query mechanism of current BIM data hub collaboration model has several limitations, which prevents designers and engineers to take advantage of BIM. To address this problem, we propose a general and effective approachmore » to generate query code based on a Model View Definition (MVD). This approach is demonstrated through a software prototype called QueryGenerator. In conclusion, by demonstrating a case study using multi-zone air flow analysis, we show how our approach and tool can help domain experts to use BIM to drive building design with less labour and lower overhead cost.« less

Automatic building information model query generation

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

Jiang, Yufei; Yu, Nan; Ming, Jiang

Energy efficient building design and construction calls for extensive collaboration between different subfields of the Architecture, Engineering and Construction (AEC) community. Performing building design and construction engineering raises challenges on data integration and software interoperability. Using Building Information Modeling (BIM) data hub to host and integrate building models is a promising solution to address those challenges, which can ease building design information management. However, the partial model query mechanism of current BIM data hub collaboration model has several limitations, which prevents designers and engineers to take advantage of BIM. To address this problem, we propose a general and effective approachmore » to generate query code based on a Model View Definition (MVD). This approach is demonstrated through a software prototype called QueryGenerator. In conclusion, by demonstrating a case study using multi-zone air flow analysis, we show how our approach and tool can help domain experts to use BIM to drive building design with less labour and lower overhead cost.« less

Evan Weaver | NREL

Science.gov Websites

Evan Weaver Photo of Evan Weaver Evan Weaver Researcher III-Software Engineering Evan.Weaver , he works as a software engineer developing whole-building energy modeling tools. Prior to joining NREL, he worked in the biomedical industry as a software engineer, specializing in graphical user

S-Cube: Enabling the Next Generation of Software Services

NASA Astrophysics Data System (ADS)

Metzger, Andreas; Pohl, Klaus

The Service Oriented Architecture (SOA) paradigm is increasingly adopted by industry for building distributed software systems. However, when designing, developing and operating innovative software services and servicebased systems, several challenges exist. Those challenges include how to manage the complexity of those systems, how to establish, monitor and enforce Quality of Service (QoS) and Service Level Agreements (SLAs), as well as how to build those systems such that they can proactively adapt to dynamically changing requirements and context conditions. Developing foundational solutions for those challenges requires joint efforts of different research communities such as Business Process Management, Grid Computing, Service Oriented Computing and Software Engineering. This paper provides an overview of S-Cube, the European Network of Excellence on Software Services and Systems. S-Cube brings together researchers from leading research institutions across Europe, who join their competences to develop foundations, theories as well as methods and tools for future service-based systems.

Descriptions of Free and Freeware Software in the Mathematics Teaching

NASA Astrophysics Data System (ADS)

Antunes de Macedo, Josue; Neves de Almeida, Samara; Voelzke, Marcos Rincon

2016-05-01

This paper presents the analysis and the cataloging of free and freeware mathematical software available on the internet, a brief explanation of them, and types of licenses for use in teaching and learning. The methodology is based on the qualitative research. Among the different types of software found, it stands out in algebra, the Winmat, that works with linear algebra, matrices and linear systems. In geometry, the GeoGebra, which can be used in the study of functions, plan and spatial geometry, algebra and calculus. For graphing, can quote the Graph and Graphequation. With Graphmatica software, it is possible to build various graphs of mathematical equations on the same screen, representing cartesian equations, inequalities, parametric among other functions. The Winplot allows the user to build graphics in two and three dimensions functions and mathematical equations. Thus, this work aims to present the teachers some free math software able to be used in the classroom.

Requirements Engineering in Building Climate Science Software

NASA Astrophysics Data System (ADS)

Batcheller, Archer L.

Software has an important role in supporting scientific work. This dissertation studies teams that build scientific software, focusing on the way that they determine what the software should do. These requirements engineering processes are investigated through three case studies of climate science software projects. The Earth System Modeling Framework assists modeling applications, the Earth System Grid distributes data via a web portal, and the NCAR (National Center for Atmospheric Research) Command Language is used to convert, analyze and visualize data. Document analysis, observation, and interviews were used to investigate the requirements-related work. The first research question is about how and why stakeholders engage in a project, and what they do for the project. Two key findings arise. First, user counts are a vital measure of project success, which makes adoption important and makes counting tricky and political. Second, despite the importance of quantities of users, a few particular "power users" develop a relationship with the software developers and play a special role in providing feedback to the software team and integrating the system into user practice. The second research question focuses on how project objectives are articulated and how they are put into practice. The team seeks to both build a software system according to product requirements but also to conduct their work according to process requirements such as user support. Support provides essential communication between users and developers that assists with refining and identifying requirements for the software. It also helps users to learn and apply the software to their real needs. User support is a vital activity for scientific software teams aspiring to create infrastructure. The third research question is about how change in scientific practice and knowledge leads to changes in the software, and vice versa. The "thickness" of a layer of software infrastructure impacts whether the software team or users have control and responsibility for making changes in response to new scientific ideas. Thick infrastructure provides more functionality for users, but gives them less control of it. The stability of infrastructure trades off against the responsiveness that the infrastructure can have to user needs.

From synthesis to function via iterative assembly of N-methyliminodiacetic acid boronate building blocks.

PubMed

Li, Junqi; Grillo, Anthony S; Burke, Martin D

2015-08-18

The study and optimization of small molecule function is often impeded by the time-intensive and specialist-dependent process that is typically used to make such compounds. In contrast, general and automated platforms have been developed for making peptides, oligonucleotides, and increasingly oligosaccharides, where synthesis is simplified to iterative applications of the same reactions. Inspired by the way natural products are biosynthesized via the iterative assembly of a defined set of building blocks, we developed a platform for small molecule synthesis involving the iterative coupling of haloboronic acids protected as the corresponding N-methyliminodiacetic acid (MIDA) boronates. Here we summarize our efforts thus far to develop this platform into a generalized and automated approach for small molecule synthesis. We and others have employed this approach to access many polyene-based compounds, including the polyene motifs found in >75% of all polyene natural products. This platform further allowed us to derivatize amphotericin B, the powerful and resistance-evasive but also highly toxic last line of defense in treating systemic fungal infections, and thereby understand its mechanism of action. This synthesis-enabled mechanistic understanding has led us to develop less toxic derivatives currently under evaluation as improved antifungal agents. To access more Csp(3)-containing small molecules, we gained a stereocontrolled entry into chiral, non-racemic α-boryl aldehydes through the discovery of a chiral derivative of MIDA. These α-boryl aldehydes are versatile intermediates for the synthesis of many Csp(3) boronate building blocks that are otherwise difficult to access. In addition, we demonstrated the utility of these types of building blocks in accessing pharmaceutically relevant targets via an iterative Csp(3) cross-coupling cycle. We have further expanded the scope of the platform to include stereochemically complex macrocyclic and polycyclic molecules using a linear-to-cyclized strategy, in which Csp(3) boronate building blocks are iteratively assembled into linear precursors that are then cyclized into the cyclic frameworks found in many natural products and natural product-like structures. Enabled by the serendipitous discovery of a catch-and-release protocol for generally purifying MIDA boronate intermediates, the platform has been automated. The synthesis of 14 distinct classes of small molecules, including pharmaceuticals, materials components, and polycyclic natural products, has been achieved using this new synthesis machine. It is anticipated that the scope of small molecules accessible by this platform will continue to expand via further developments in building block synthesis, Csp(3) cross-coupling methodologies, and cyclization strategies. Achieving these goals will enable the more generalized synthesis of small molecules and thereby help shift the rate-limiting step in small molecule science from synthesis to function.

Sivasathya Pradha Balamurugan | NREL

Science.gov Websites

Researcher II-Software Engineering SivasathyaPradha.Balamurugan@nrel.gov | 303-275-3883 Sivasathya joined NREL in 2017. Her research is focused on developing and supporting software for energy management in buildings. Her background is in software development, applied cryptography, and hardware. Education M.S

Proposal for constructing an advanced software tool for planetary atmospheric modeling

NASA Technical Reports Server (NTRS)

Keller, Richard M.; Sims, Michael H.; Podolak, Esther; Mckay, Christopher P.; Thompson, David E.

1990-01-01

Scientific model building can be a time intensive and painstaking process, often involving the development of large and complex computer programs. Despite the effort involved, scientific models cannot easily be distributed and shared with other scientists. In general, implemented scientific models are complex, idiosyncratic, and difficult for anyone but the original scientist/programmer to understand. We believe that advanced software techniques can facilitate both the model building and model sharing process. We propose to construct a scientific modeling software tool that serves as an aid to the scientist in developing and using models. The proposed tool will include an interactive intelligent graphical interface and a high level, domain specific, modeling language. As a testbed for this research, we propose development of a software prototype in the domain of planetary atmospheric modeling.

Development and Analysis of a Bi-Directional Tidal Turbine

DTIC Science & Technology

2012-03-01

commercial CFD software ANSYS CFX was utilized to build a turbine map. The basic turbine map was developed for a 25 blade bi-axial turbine under...directional turbine created for this purpose. In the present study, the commercial CFD software ANSYS CFX was utilized to build a turbine map. The...sheath C. PROBLEM SPECIFICATIONS AND BOUNDARY CONDITIONS The simulation definition was created using ANSYS CFX -Pre. The best measurements to determine

Ben Polly | NREL

Science.gov Websites

joined NREL in 2009. He specializes in the development, validation, and application of energy analysis approaches for individual buildings and collections of buildings. He has developed and applied software (e.g., building energy storage). In addition to his work at NREL, Ben serves on the Building

Advanced information processing system: Local system services

NASA Technical Reports Server (NTRS)

Burkhardt, Laura; Alger, Linda; Whittredge, Roy; Stasiowski, Peter

1989-01-01

The Advanced Information Processing System (AIPS) is a multi-computer architecture composed of hardware and software building blocks that can be configured to meet a broad range of application requirements. The hardware building blocks are fault-tolerant, general-purpose computers, fault-and damage-tolerant networks (both computer and input/output), and interfaces between the networks and the computers. The software building blocks are the major software functions: local system services, input/output, system services, inter-computer system services, and the system manager. The foundation of the local system services is an operating system with the functions required for a traditional real-time multi-tasking computer, such as task scheduling, inter-task communication, memory management, interrupt handling, and time maintenance. Resting on this foundation are the redundancy management functions necessary in a redundant computer and the status reporting functions required for an operator interface. The functional requirements, functional design and detailed specifications for all the local system services are documented.

Toward a Progress Indicator for Machine Learning Model Building and Data Mining Algorithm Execution: A Position Paper.

PubMed

Luo, Gang

2017-12-01

For user-friendliness, many software systems offer progress indicators for long-duration tasks. A typical progress indicator continuously estimates the remaining task execution time as well as the portion of the task that has been finished. Building a machine learning model often takes a long time, but no existing machine learning software supplies a non-trivial progress indicator. Similarly, running a data mining algorithm often takes a long time, but no existing data mining software provides a nontrivial progress indicator. In this article, we consider the problem of offering progress indicators for machine learning model building and data mining algorithm execution. We discuss the goals and challenges intrinsic to this problem. Then we describe an initial framework for implementing such progress indicators and two advanced, potential uses of them, with the goal of inspiring future research on this topic.

Toward a Progress Indicator for Machine Learning Model Building and Data Mining Algorithm Execution: A Position Paper

PubMed Central

Luo, Gang

2017-01-01

For user-friendliness, many software systems offer progress indicators for long-duration tasks. A typical progress indicator continuously estimates the remaining task execution time as well as the portion of the task that has been finished. Building a machine learning model often takes a long time, but no existing machine learning software supplies a non-trivial progress indicator. Similarly, running a data mining algorithm often takes a long time, but no existing data mining software provides a nontrivial progress indicator. In this article, we consider the problem of offering progress indicators for machine learning model building and data mining algorithm execution. We discuss the goals and challenges intrinsic to this problem. Then we describe an initial framework for implementing such progress indicators and two advanced, potential uses of them, with the goal of inspiring future research on this topic. PMID:29177022

Eric Bonnema | NREL

Science.gov Websites

contributes to the research efforts for commercial buildings. This effort is dedicated to studying the , commercial sector whole-building energy simulation, scientific computing, and software configuration and

A SOFTWARE TOOL TO COMPARE MEASURED AND SIMULATED BUILDING ENERGY PERFORMANCE DATA

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

Maile, Tobias; Bazjanac, Vladimir; O'Donnell, James

2011-11-01

Building energy performance is often inadequate when compared to design goals. To link design goals to actual operation one can compare measured with simulated energy performance data. Our previously developed comparison approach is the Energy Performance Comparison Methodology (EPCM), which enables the identification of performance problems based on a comparison of measured and simulated performance data. In context of this method, we developed a software tool that provides graphing and data processing capabilities of the two performance data sets. The software tool called SEE IT (Stanford Energy Efficiency Information Tool) eliminates the need for manual generation of data plots andmore » data reformatting. SEE IT makes the generation of time series, scatter and carpet plots independent of the source of data (measured or simulated) and provides a valuable tool for comparing measurements with simulation results. SEE IT also allows assigning data points on a predefined building object hierarchy and supports different versions of simulated performance data. This paper briefly introduces the EPCM, describes the SEE IT tool and illustrates its use in the context of a building case study.« less

Top Value Added Chemicals From Biomass: I. Results of Screening for Potential Candidates from Sugars and Synthesis Gas

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

Werpy, Todd A.; Holladay, John E.; White, James F.

2004-11-01

This report identifies twelve building block chemicals that can be produced from sugars via biological or chemical conversions. The twelve building blocks can be subsequently converted to a number of high-value bio-based chemicals or materials. Building block chemicals, as considered for this analysis, are molecules with multiple functional groups that possess the potential to be transformed into new families of useful molecules. The twelve sugar-based building blocks are 1,4-diacids (succinic, fumaric and malic), 2,5-furan dicarboxylic acid, 3-hydroxy propionic acid, aspartic acid, glucaric acid, glutamic acid, itaconic acid, levulinic acid, 3-hydroxybutyrolactone, glycerol, sorbitol, and xylitol/arabinitol. In addition to building blocks, themore » report outlines the central technical barriers that are preventing the widespread use of biomass for products and chemicals.« less

Computational Design of Metal Ion Sequestering Agents

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

Hay, Benjamin P.; Rapko, Brian M.

Organic ligands that exhibit a high degree of metal ion recognition are essential precursors for developing separation processes and sensors for metal ions. Since the beginning of the nuclear era, much research has focused on discovering ligands that target specific radionuclides. Members of the Group 1A and 2A cations (e.g., Cs, Sr, Ra) and the f-block metals (actinides and lanthanides) are of primary concern to DOE. Although there has been some success in identifying ligand architectures that exhibit a degree of metal ion recognition, the ability to control binding affinity and selectivity remains a significant challenge. The traditional approach formore » discovering such ligands has involved lengthy programs of organic synthesis and testing that, in the absence of reliable methods for screening compounds before synthesis, have resulted in much wasted research effort. This project seeks to enhance and strengthen the traditional approach through computer-aided design of new and improved host molecules. Accurate electronic structure calculations are coupled with experimental data to provide fundamental information about ligand structure and the nature of metal-donor group interactions (design criteria). This fundamental information then is used in a molecular mechanics model (MM) that helps us rapidly screen proposed ligand architectures and select the best members from a set of potential candidates. By using combinatorial methods, molecule building software has been developed that generates large numbers of candidate architectures for a given set of donor groups. The specific goals of this project are: • further understand the structural and energetic aspects of individual donor group- metal ion interactions and incorporate this information within the MM framework • further develop and evaluate approaches for correlating ligand structure with reactivity toward metal ions, in other words, screening capability • use molecule structure building software to generate large numbers of candidate ligand architectures for given sets of donor groups • screen candidates and identify ligand architectures that will exhibit enhanced metal ion recognition. These new capabilities are being applied to ligand systems identified under other DOEsponsored projects where studies have suggested that modifying existing architectures will lead to dramatic enhancements in metal ion binding affinity and selectivity. With this in mind, we are collaborating with Professors R. T. Paine (University of New Mexico), K. N. Raymond (University of California, Berkeley), and J. E. Hutchison (University of Oregon), and Dr. B. A. Moyer (Oak Ridge National Laboratory) to obtain experimental validation of the predicted new ligand structures. Successful completion of this study will yield molecular-level insight into the role that ligand architecture plays in controlling metal ion complexation and will provide a computational approach to ligand design.« less

Synthesis of many different types of organic small molecules using one automated process.

PubMed

Li, Junqi; Ballmer, Steven G; Gillis, Eric P; Fujii, Seiko; Schmidt, Michael J; Palazzolo, Andrea M E; Lehmann, Jonathan W; Morehouse, Greg F; Burke, Martin D

2015-03-13

Small-molecule synthesis usually relies on procedures that are highly customized for each target. A broadly applicable automated process could greatly increase the accessibility of this class of compounds to enable investigations of their practical potential. Here we report the synthesis of 14 distinct classes of small molecules using the same fully automated process. This was achieved by strategically expanding the scope of a building block-based synthesis platform to include even C(sp3)-rich polycyclic natural product frameworks and discovering a catch-and-release chromatographic purification protocol applicable to all of the corresponding intermediates. With thousands of compatible building blocks already commercially available, many small molecules are now accessible with this platform. More broadly, these findings illuminate an actionable roadmap to a more general and automated approach for small-molecule synthesis. Copyright © 2015, American Association for the Advancement of Science.

Magnetically-refreshable receptor platform structures for reusable nano-biosensor chips

NASA Astrophysics Data System (ADS)

Yoo, Haneul; Lee, Dong Jun; Cho, Dong-guk; Park, Juhun; Nam, Ki Wan; Tak Cho, Young; Park, Jae Yeol; Chen, Xing; Hong, Seunghun

2016-01-01

We developed a magnetically-refreshable receptor platform structure which can be integrated with quite versatile nano-biosensor structures to build reusable nano-biosensor chips. This structure allows one to easily remove used receptor molecules from a biosensor surface and reuse the biosensor for repeated sensing operations. Using this structure, we demonstrated reusable immunofluorescence biosensors. Significantly, since our method allows one to place receptor molecules very close to a nano-biosensor surface, it can be utilized to build reusable carbon nanotube transistor-based biosensors which require receptor molecules within a Debye length from the sensor surface. Furthermore, we also show that a single sensor chip can be utilized to detect two different target molecules simply by replacing receptor molecules using our method. Since this method does not rely on any chemical reaction to refresh sensor chips, it can be utilized for versatile biosensor structures and virtually-general receptor molecular species.

Computers and Young Children. Storyboard Software: Flannel Boards in the Computer Age.

ERIC Educational Resources Information Center

Shade, Daniel D.

1995-01-01

Describes storyboard software as computer programs with which children can build a story using visuals. Notes the importance of such programs from preliterate or nonreading children. Describes a new storyboard program, "Wiggins in Storyland," and its features. Lists recommended storyboard software programs, with publishers and compatible…

Modeling and MBL: Software Tools for Science.

ERIC Educational Resources Information Center

Tinker, Robert F.

Recent technological advances and new software packages put unprecedented power for experimenting and theory-building in the hands of students at all levels. Microcomputer-based laboratory (MBL) and model-solving tools illustrate the educational potential of the technology. These tools include modeling software and three MBL packages (which are…

Methods and Software for Building Bibliographic Data Bases.

ERIC Educational Resources Information Center

Daehn, Ralph M.

1985-01-01

This in-depth look at database management systems (DBMS) for microcomputers covers data entry, information retrieval, security, DBMS software and design, and downloading of literature search results. The advantages of in-house systems versus online search vendors are discussed, and specifications of three software packages and 14 sources are…

Moving Secure Software Assurance into Higher Education: A Roadmap for Change

DTIC Science & Technology

2011-06-02

Summarized: The Issue: 6/2/20118 Software defects are currently a fact of life Software defects are avenues of security vulnerabilities that cyber ... criminals , terrorists, or hostile nations can exploit. We (THE ENTIRE INDUSTY) need to change the way we build systems Decrease the number of defects

Building Software Development Capacity to Advance the State of Educational Technology

ERIC Educational Resources Information Center

Luterbach, Kenneth J.

2013-01-01

Educational technologists may advance the state of the field by increasing capacity to develop software tools and instructional applications. Presently, few academic programs in educational technology require even a single computer programming course. Further, the educational technologists who develop software generally work independently or in…

Eric Wilson | NREL

Science.gov Websites

, developing an analysis framework and data visualization for national residential building stock models, and include developing multifamily modeling capabilities for the BEopt building energy optimization software

Hardware and software improvements to a low-cost horizontal parallax holographic video monitor.

PubMed

Henrie, Andrew; Codling, Jesse R; Gneiting, Scott; Christensen, Justin B; Awerkamp, Parker; Burdette, Mark J; Smalley, Daniel E

2018-01-01

Displays capable of true holographic video have been prohibitively expensive and difficult to build. With this paper, we present a suite of modularized hardware components and software tools needed to build a HoloMonitor with basic "hacker-space" equipment, highlighting improvements that have enabled the total materials cost to fall to $820, well below that of other holographic displays. It is our hope that the current level of simplicity, development, design flexibility, and documentation will enable the lay engineer, programmer, and scientist to relatively easily replicate, modify, and build upon our designs, bringing true holographic video to the masses.

Using ChEMBL web services for building applications and data processing workflows relevant to drug discovery.

PubMed

Nowotka, Michał M; Gaulton, Anna; Mendez, David; Bento, A Patricia; Hersey, Anne; Leach, Andrew

2017-08-01

ChEMBL is a manually curated database of bioactivity data on small drug-like molecules, used by drug discovery scientists. Among many access methods, a REST API provides programmatic access, allowing the remote retrieval of ChEMBL data and its integration into other applications. This approach allows scientists to move from a world where they go to the ChEMBL web site to search for relevant data, to one where ChEMBL data can be simply integrated into their everyday tools and work environment. Areas covered: This review highlights some of the audiences who may benefit from using the ChEMBL API, and the goals they can address, through the description of several use cases. The examples cover a team communication tool (Slack), a data analytics platform (KNIME), batch job management software (Luigi) and Rich Internet Applications. Expert opinion: The advent of web technologies, cloud computing and micro services oriented architectures have made REST APIs an essential ingredient of modern software development models. The widespread availability of tools consuming RESTful resources have made them useful for many groups of users. The ChEMBL API is a valuable resource of drug discovery bioactivity data for professional chemists, chemistry students, data scientists, scientific and web developers.

MassCascade: Visual Programming for LC-MS Data Processing in Metabolomics.

PubMed

Beisken, Stephan; Earll, Mark; Portwood, David; Seymour, Mark; Steinbeck, Christoph

2014-04-01

Liquid chromatography coupled to mass spectrometry (LC-MS) is commonly applied to investigate the small molecule complement of organisms. Several software tools are typically joined in custom pipelines to semi-automatically process and analyse the resulting data. General workflow environments like the Konstanz Information Miner (KNIME) offer the potential of an all-in-one solution to process LC-MS data by allowing easy integration of different tools and scripts. We describe MassCascade and its workflow plug-in for processing LC-MS data. The Java library integrates frequently used algorithms in a modular fashion, thus enabling it to serve as back-end for graphical front-ends. The functions available in MassCascade have been encapsulated in a plug-in for the workflow environment KNIME, allowing combined use with e.g. statistical workflow nodes from other providers and making the tool intuitive to use without knowledge of programming. The design of the software guarantees a high level of modularity where processing functions can be quickly replaced or concatenated. MassCascade is an open-source library for LC-MS data processing in metabolomics. It embraces the concept of visual programming through its KNIME plug-in, simplifying the process of building complex workflows. The library was validated using open data.

Ry Horsey | NREL

Science.gov Websites

Ry Horsey Photo of Henry Horsey Ry Horsey Software Developer - Commercial Buildings Energy Modeling the field of commercial building energy modeling. He is particularly interested in the increasing tools to support large-scale commercial building energy modeling. This work has led to contributions to

Software-engineering challenges of building and deploying reusable problem solvers.

PubMed

O'Connor, Martin J; Nyulas, Csongor; Tu, Samson; Buckeridge, David L; Okhmatovskaia, Anna; Musen, Mark A

2009-11-01

Problem solving methods (PSMs) are software components that represent and encode reusable algorithms. They can be combined with representations of domain knowledge to produce intelligent application systems. A goal of research on PSMs is to provide principled methods and tools for composing and reusing algorithms in knowledge-based systems. The ultimate objective is to produce libraries of methods that can be easily adapted for use in these systems. Despite the intuitive appeal of PSMs as conceptual building blocks, in practice, these goals are largely unmet. There are no widely available tools for building applications using PSMs and no public libraries of PSMs available for reuse. This paper analyzes some of the reasons for the lack of widespread adoptions of PSM techniques and illustrate our analysis by describing our experiences developing a complex, high-throughput software system based on PSM principles. We conclude that many fundamental principles in PSM research are useful for building knowledge-based systems. In particular, the task-method decomposition process, which provides a means for structuring knowledge-based tasks, is a powerful abstraction for building systems of analytic methods. However, despite the power of PSMs in the conceptual modeling of knowledge-based systems, software engineering challenges have been seriously underestimated. The complexity of integrating control knowledge modeled by developers using PSMs with the domain knowledge that they model using ontologies creates a barrier to widespread use of PSM-based systems. Nevertheless, the surge of recent interest in ontologies has led to the production of comprehensive domain ontologies and of robust ontology-authoring tools. These developments present new opportunities to leverage the PSM approach.

GABBs: Cyberinfrastructure for Self-Service Geospatial Data Exploration, Computation, and Sharing

NASA Astrophysics Data System (ADS)

Song, C. X.; Zhao, L.; Biehl, L. L.; Merwade, V.; Villoria, N.

2016-12-01

Geospatial data are present everywhere today with the proliferation of location-aware computing devices. This is especially true in the scientific community where large amounts of data are driving research and education activities in many domains. Collaboration over geospatial data, for example, in modeling, data analysis and visualization, must still overcome the barriers of specialized software and expertise among other challenges. In addressing these needs, the Geospatial data Analysis Building Blocks (GABBs) project aims at building geospatial modeling, data analysis and visualization capabilities in an open source web platform, HUBzero. Funded by NSF's Data Infrastructure Building Blocks initiative, GABBs is creating a geospatial data architecture that integrates spatial data management, mapping and visualization, and interfaces in the HUBzero platform for scientific collaborations. The geo-rendering enabled Rappture toolkit, a generic Python mapping library, geospatial data exploration and publication tools, and an integrated online geospatial data management solution are among the software building blocks from the project. The GABBS software will be available through Amazon's AWS Marketplace VM images and open source. Hosting services are also available to the user community. The outcome of the project will enable researchers and educators to self-manage their scientific data, rapidly create GIS-enable tools, share geospatial data and tools on the web, and build dynamic workflows connecting data and tools, all without requiring significant software development skills, GIS expertise or IT administrative privileges. This presentation will describe the GABBs architecture, toolkits and libraries, and showcase the scientific use cases that utilize GABBs capabilities, as well as the challenges and solutions for GABBs to interoperate with other cyberinfrastructure platforms.

Software-engineering challenges of building and deploying reusable problem solvers

PubMed Central

O’CONNOR, MARTIN J.; NYULAS, CSONGOR; TU, SAMSON; BUCKERIDGE, DAVID L.; OKHMATOVSKAIA, ANNA; MUSEN, MARK A.

2012-01-01

Problem solving methods (PSMs) are software components that represent and encode reusable algorithms. They can be combined with representations of domain knowledge to produce intelligent application systems. A goal of research on PSMs is to provide principled methods and tools for composing and reusing algorithms in knowledge-based systems. The ultimate objective is to produce libraries of methods that can be easily adapted for use in these systems. Despite the intuitive appeal of PSMs as conceptual building blocks, in practice, these goals are largely unmet. There are no widely available tools for building applications using PSMs and no public libraries of PSMs available for reuse. This paper analyzes some of the reasons for the lack of widespread adoptions of PSM techniques and illustrate our analysis by describing our experiences developing a complex, high-throughput software system based on PSM principles. We conclude that many fundamental principles in PSM research are useful for building knowledge-based systems. In particular, the task–method decomposition process, which provides a means for structuring knowledge-based tasks, is a powerful abstraction for building systems of analytic methods. However, despite the power of PSMs in the conceptual modeling of knowledge-based systems, software engineering challenges have been seriously underestimated. The complexity of integrating control knowledge modeled by developers using PSMs with the domain knowledge that they model using ontologies creates a barrier to widespread use of PSM-based systems. Nevertheless, the surge of recent interest in ontologies has led to the production of comprehensive domain ontologies and of robust ontology-authoring tools. These developments present new opportunities to leverage the PSM approach. PMID:23565031

Molecular building blocks and their architecture in biologically/environmentally compatible soft matter chemical machinery.

PubMed

Toyota, Taro; Banno, Taisuke; Nitta, Sachiko; Takinoue, Masahiro; Nomoto, Tomonori; Natsume, Yuno; Matsumura, Shuichi; Fujinami, Masanori

2014-01-01

This review briefly summarizes recent developments in the construction of biologically/environmentally compatible chemical machinery composed of soft matter. Since environmental and living systems are open systems, chemical machinery must continuously fulfill its functions not only through the influx and generation of molecules but also via the degradation and dissipation of molecules. If the degradation or dissipation of soft matter molecular building blocks and biomaterial molecules/polymers can be achieved, soft matter particles composed of them can be used to realize chemical machinery such as selfpropelled droplets, drug delivery carriers, tissue regeneration scaffolds, protocell models, cell-/tissuemarkers, and molecular computing systems.

Matriarch: A Python Library for Materials Architecture.

PubMed

Giesa, Tristan; Jagadeesan, Ravi; Spivak, David I; Buehler, Markus J

2015-10-12

Biological materials, such as proteins, often have a hierarchical structure ranging from basic building blocks at the nanoscale (e.g., amino acids) to assembled structures at the macroscale (e.g., fibers). Current software for materials engineering allows the user to specify polypeptide chains and simple secondary structures prior to molecular dynamics simulation, but is not flexible in terms of the geometric arrangement of unequilibrated structures. Given some knowledge of a larger-scale structure, instructing the software to create it can be very difficult and time-intensive. To this end, the present paper reports a mathematical language, using category theory, to describe the architecture of a material, i.e., its set of building blocks and instructions for combining them. While this framework applies to any hierarchical material, here we concentrate on proteins. We implement this mathematical language as an open-source Python library called Matriarch. It is a domain-specific language that gives the user the ability to create almost arbitrary structures with arbitrary amino acid sequences and, from them, generate Protein Data Bank (PDB) files. In this way, Matriarch is more powerful than commercial software now available. Matriarch can be used in tandem with molecular dynamics simulations and helps engineers design and modify biologically inspired materials based on their desired functionality. As a case study, we use our software to alter both building blocks and building instructions for tropocollagen, and determine their effect on its structure and mechanical properties.

Property Graph vs RDF Triple Store: A Comparison on Glycan Substructure Search

PubMed Central

Alocci, Davide; Mariethoz, Julien; Horlacher, Oliver; Bolleman, Jerven T.; Campbell, Matthew P.; Lisacek, Frederique

2015-01-01

Resource description framework (RDF) and Property Graph databases are emerging technologies that are used for storing graph-structured data. We compare these technologies through a molecular biology use case: glycan substructure search. Glycans are branched tree-like molecules composed of building blocks linked together by chemical bonds. The molecular structure of a glycan can be encoded into a direct acyclic graph where each node represents a building block and each edge serves as a chemical linkage between two building blocks. In this context, Graph databases are possible software solutions for storing glycan structures and Graph query languages, such as SPARQL and Cypher, can be used to perform a substructure search. Glycan substructure searching is an important feature for querying structure and experimental glycan databases and retrieving biologically meaningful data. This applies for example to identifying a region of the glycan recognised by a glycan binding protein (GBP). In this study, 19,404 glycan structures were selected from GlycomeDB (www.glycome-db.org) and modelled for being stored into a RDF triple store and a Property Graph. We then performed two different sets of searches and compared the query response times and the results from both technologies to assess performance and accuracy. The two implementations produced the same results, but interestingly we noted a difference in the query response times. Qualitative measures such as portability were also used to define further criteria for choosing the technology adapted to solving glycan substructure search and other comparable issues. PMID:26656740

Gate-to-gate Life-Cycle Inventory of Hardboard Production in North America

Treesearch

Richard Bergman

2014-01-01

Whole-building life-cycle assessments (LCAs) populated by life-cycle inventory (LCI) data are incorporated into environmental footprint software tools for establishing green building certification by building professionals and code. However, LCI data on some wood building products are still needed to help fill gaps in the data and thus provide a more complete picture...

The US Army Corps of Engineers Roadmap for Life-Cycle Building Information Modeling (BIM)

DTIC Science & Technology

2012-11-01

Building Information Modeling ( BIM ) En gi ne er R es ea rc h an...Abstract Building Information Modeling ( BIM ) technology has rapidly gained ac- ceptance throughout the planning, architecture, engineering...the Industry Foundation Class (IFC) definitions to create vendor-neutral data exchanges for use in BIM software tools. Building Information Modeling

Validation of Tendril TrueHome Using Software-to-Software Comparison

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

Maguire, Jeffrey B; Horowitz, Scott G; Moore, Nathan

This study performed comparative evaluation of EnergyPlus version 8.6 and Tendril TrueHome, two physics-based home energy simulation models, to identify differences in energy consumption predictions between the two programs and resolve discrepancies between them. EnergyPlus is considered a benchmark, best-in-class software tool for building energy simulation. This exercise sought to improve both software tools through additional evaluation/scrutiny.

Toward Reusable Graphics Components in Ada

DTIC Science & Technology

1993-03-01

Then alternatives for obtaining well- engineered reusable software components were examined. Finally, the alternatives were analyzed, and the most...reusable software components. Chapter 4 describes detailed design and implementation strategies in building a well- engineered reusable set of components in...study. 2.2 The Object-Oriented Paradigm 2.2.1 The Need for Object-Oriented Techniques. Among software engineers the software crisis is a well known

PD5: a general purpose library for primer design software.

PubMed

Riley, Michael C; Aubrey, Wayne; Young, Michael; Clare, Amanda

2013-01-01

Complex PCR applications for large genome-scale projects require fast, reliable and often highly sophisticated primer design software applications. Presently, such applications use pipelining methods to utilise many third party applications and this involves file parsing, interfacing and data conversion, which is slow and prone to error. A fully integrated suite of software tools for primer design would considerably improve the development time, the processing speed, and the reliability of bespoke primer design software applications. The PD5 software library is an open-source collection of classes and utilities, providing a complete collection of software building blocks for primer design and analysis. It is written in object-oriented C(++) with an emphasis on classes suitable for efficient and rapid development of bespoke primer design programs. The modular design of the software library simplifies the development of specific applications and also integration with existing third party software where necessary. We demonstrate several applications created using this software library that have already proved to be effective, but we view the project as a dynamic environment for building primer design software and it is open for future development by the bioinformatics community. Therefore, the PD5 software library is published under the terms of the GNU General Public License, which guarantee access to source-code and allow redistribution and modification. The PD5 software library is downloadable from Google Code and the accompanying Wiki includes instructions and examples: http://code.google.com/p/primer-design.

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

Foucar, James G.; Salinger, Andrew G.; Deakin, Michael

CIME is the software infrastructure for configuring, building, running, and testing an Earth system model. It can be developed and tested as stand-alone software, but its main role is to be integrating into the CESM and ACME Earth system models.

Software Reviews.

ERIC Educational Resources Information Center

Miller, Anne, Ed.; Radziemski, Cathy, Ed.

1988-01-01

Three pieces of computer software are described and reviewed: HyperCard, to build and use varied applications; Iggy's Gnees, for problem solving with shapes in grades kindergarten-two; and Algebra Shop, for practicing skills and problem solving. (MNS)

Key ingredients needed when building large data processing systems for scientists

NASA Technical Reports Server (NTRS)

Miller, K. C.

2002-01-01

Why is building a large science software system so painful? Weren't teams of software engineers supposed to make life easier for scientists? Does it sometimes feel as if it would be easier to write the million lines of code in Fortran 77 yourself? The cause of this dissatisfaction is that many of the needs of the science customer remain hidden in discussions with software engineers until after a system has already been built. In fact, many of the hidden needs of the science customer conflict with stated needs and are therefore very difficult to meet unless they are addressed from the outset in a system's architectural requirements. What's missing is the consideration of a small set of key software properties in initial agreements about the requirements, the design and the cost of the system.

A Roadmap to Continuous Integration for ATLAS Software Development

NASA Astrophysics Data System (ADS)

Elmsheuser, J.; Krasznahorkay, A.; Obreshkov, E.; Undrus, A.; ATLAS Collaboration

2017-10-01

The ATLAS software infrastructure facilitates efforts of more than 1000 developers working on the code base of 2200 packages with 4 million lines of C++ and 1.4 million lines of python code. The ATLAS offline code management system is the powerful, flexible framework for processing new package versions requests, probing code changes in the Nightly Build System, migration to new platforms and compilers, deployment of production releases for worldwide access and supporting physicists with tools and interfaces for efficient software use. It maintains multi-stream, parallel development environment with about 70 multi-platform branches of nightly releases and provides vast opportunities for testing new packages, for verifying patches to existing software and for migrating to new platforms and compilers. The system evolution is currently aimed on the adoption of modern continuous integration (CI) practices focused on building nightly releases early and often, with rigorous unit and integration testing. This paper describes the CI incorporation program for the ATLAS software infrastructure. It brings modern open source tools such as Jenkins and GitLab into the ATLAS Nightly System, rationalizes hardware resource allocation and administrative operations, provides improved feedback and means to fix broken builds promptly for developers. Once adopted, ATLAS CI practices will improve and accelerate innovation cycles and result in increased confidence in new software deployments. The paper reports the status of Jenkins integration with the ATLAS Nightly System as well as short and long term plans for the incorporation of CI practices.

Software is a Product...Not

DTIC Science & Technology

1992-09-01

understand the process if we consider software as a service , not a prod- uct. Let me expand on this statement. I do not believe we must do any of the... software -building activities differently. Instead, from the perspective of schedul- ing, budgeting, and delivering software , we should use the service ...While we’re not perfect, we do a fairly its upgrades. The pricing scheme be- good job of managing hardware engi- Software as a service . What is a

Home | Simulation Research

Science.gov Websites

Group specializes in the research, development and deployment of software that support the design and controls design, the Spawn of EnergyPlus next-generation simulation engine, for building and control energy systems tools for OpenBuildingControl to support control design, deployment and verification of building

Inorganic-Organic Molecules and Solids with Nanometer-Sized Pores

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

Maverick, Andrew W

2011-12-17

We are constructing porous inorganic-organic hybrid molecules and solids, many of which contain coordinatively unsaturated metal centers. In this work, we use multifunctional ²-diketone ligands as building blocks to prepare extended-solid and molecular porous materials that are capable of reacting with a variety of guest molecules.

Building Your Own Web Course: The Case for Off-the-Shelf Component Software.

ERIC Educational Resources Information Center

Kaplan, Howard

1998-01-01

Compares the features, advantages, and disadvantages of two major software options available for designing web courses: (1) component, off-the shelf software that allows for creation of audio slide lectures, course materials, discussion forums, animations, synchronous chat groups, quiz creators, and electronic mail, and (2) integrated packages…

Methodology to Assess No Touch Audit Software Using Simulated Building Utility Data

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

Cheung, Howard; Braun, James E.; Langner, M. Rois

This report describes a methodology developed for assessing the performance of no touch building audit tools and presents results for an available tool. Building audits are conducted in many commercial buildings to reduce building energy costs and improve building operation. Because the audits typically require significant input obtained by building engineers, they are usually only affordable for larger commercial building owners. In an effort to help small building and business owners gain the benefits of an audit at a lower cost, no touch building audit tools have been developed to remotely analyze a building's energy consumption.

PNNL’s Building Operations Control Center

ScienceCinema

Belew, Shan

2018-01-16

PNNL's Building Operations Control Center (BOCC) video provides an overview of the center, its capabilities, and its objectives. The BOCC was relocated to PNNL's new 3820 Systems Engineering Building in 2015. Although a key focus of the BOCC is on monitoring and improving the operations of PNNL buildings, the center's state-of-the-art computational, software and visualization resources also have provided a platform for PNNL buildings-related research projects.

SCIL Executive Summaries.

ERIC Educational Resources Information Center

Samuels, Alan R.; And Others

1987-01-01

These five papers by speakers at the Small Computers in Libraries 1987 conference include: "Acquiring and Using Shareware in Building Small Scale Automated Information systems" (Samuels); "A Software Lending Collection" (Talab); "Providing Subject Access to Microcomputer Software" (Mitchell); "Interfacing Vendor…

Ingredients for Life Artist Concept

NASA Image and Video Library

2005-07-27

This artist conception symbolically represents complex organic molecules, known as polycyclic aromatic hydrocarbons, seen in the early universe. These large molecules, comprised of carbon and hydrogen, are considered among the building blocks of life.

Mapping Ad Hoc Communications Network of a Large Number Fixed-Wing UAV Swarm

DTIC Science & Technology

2017-03-01

partitioned sub-swarms. The work covered in this thesis is to build a model of the NPS swarm’s communication network in ns-3 simulation software and use...partitioned sub- swarms. The work covered in this thesis is to build a model of the NPS swarm’s communication network in ns-3 simulation software and...NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA THESIS MAPPING AD HOC COMMUNICATIONS NETWORK OF A LARGE NUMBER FIXED-WING UAV SWARM by Alexis

Scaling Retro-Commissioning to Small Commercial Buildings: A Turnkey Automated Hardware-Software Solution

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

Lin, Guanjing; Granderson, J.; Brambley, Michael R.

2015-07-01

In the United States, small commercial buildings represent 51% of total floor space of all commercial buildings and consume nearly 3 quadrillion Btu (3.2 quintillion joule) of site energy annually, presenting an enormous opportunity for energy savings. Retro-commissioning (RCx), the process through which professional energy service providers identify and correct operational problems, has proven to be a cost-effective means to achieve median energy savings of 16%. However, retro-commissioning is not typically conducted at scale throughout the commercial stock. Very few small commercial buildings are retro-commissioned because utility expenses are relatively modest, margins are tighter, and capital for improvements is limited.more » In addition, small buildings do not have in-house staff with the expertise to identify improvement opportunities. In response, a turnkey hardware-software solution was developed to enable cost-effective, monitoring-based RCx of small commercial buildings. This highly tailored solution enables non-commissioning providers to identify energy and comfort problems, as well as associated cost impacts and remedies. It also facilitates scale by offering energy service providers the means to streamline their existing processes and reduce costs by more than half. The turnkey RCx sensor suitcase consists of two primary components: a suitcase of sensors for short-term building data collection that guides users through the process of deploying and retrieving their data and a software application that automates analysis of sensor data, identifies problems and generates recommendations. This paper presents the design and testing of prototype models, including descriptions of the hardware design, analysis algorithms, performance testing, and plans for dissemination.« less

Reuse Metrics for Object Oriented Software

NASA Technical Reports Server (NTRS)

Bieman, James M.

1998-01-01

One way to increase the quality of software products and the productivity of software development is to reuse existing software components when building new software systems. In order to monitor improvements in reuse, the level of reuse must be measured. In this NASA supported project we (1) derived a suite of metrics which quantify reuse attributes for object oriented, object based, and procedural software, (2) designed prototype tools to take these measurements in Ada, C++, Java, and C software, (3) evaluated the reuse in available software, (4) analyzed the relationship between coupling, cohesion, inheritance, and reuse, (5) collected object oriented software systems for our empirical analyses, and (6) developed quantitative criteria and methods for restructuring software to improve reusability.

Development of Efficient Authoring Software for e-Learning Contents

NASA Astrophysics Data System (ADS)

Kozono, Kazutake; Teramoto, Akemi; Akiyama, Hidenori

The contents creation in e-Learning system becomes an important problem. The contents of e-Learning should include figure and voice media for a high-level educational effect. However, the use of figure and voice complicates the operation of authoring software considerably. A new authoring software, which can build e-Learning contents efficiently, has been developed to solve this problem. This paper reports development results of the authoring software.

Safe Software for Space Applications: Building on the DO-178 Experience

NASA Astrophysics Data System (ADS)

Dorsey, Cheryl A.; Dorsey, Timothy A.

2013-09-01

DO-178, Software Considerations in Airborne Systems and Equipment Certification, is the well-known international standard dealing with the assurance of software used in airborne systems [1,2]. Insights into the DO-178 experiences, strengths and weaknesses can benefit the international space community. As DO-178 is an excellent standard for safe software development when used appropriately, this paper provides lessons learned and suggestions for using it effectively.

Rapid Building Assessment Project

DTIC Science & Technology

2014-05-01

ongoing management of commercial energy efficiency. No other company offers all of these proven services on a seamless, integrated Software -as-a- Service ...FirstFuel has added a suite of additional Software -as-a- Service analytics capabilities to support the entire energy efficiency lifecycle, including...the client side. In this document, we refer to the service side software as “BUILDER” and the client software as “BuilderRED,” following the Army

Reliability Engineering for Service Oriented Architectures

DTIC Science & Technology

2013-02-01

Common Object Request Broker Architecture Ecosystem In software , an ecosystem is a set of applications and/or services that grad- ually build up over time...Enterprise Service Bus Foreign In an SOA context: Any SOA, service or software which the owners of the calling software do not have control of, either...SOA Service Oriented Architecture SRE Software Reliability Engineering System Mode Many systems exhibit different modes of operation. E.g. the cockpit

Investigation into the development of computer aided design software for space based sensors

NASA Technical Reports Server (NTRS)

Pender, C. W.; Clark, W. L.

1987-01-01

The described effort is phase one of the development of a Computer Aided Design (CAD) software to be used to perform radiometric sensor design. The software package will be referred to as SCAD and is directed toward the preliminary phase of the design of space based sensor system. The approach being followed is to develop a modern, graphic intensive, user friendly software package using existing software as building blocks. The emphasis will be directed toward the development of a shell containing menus, smart defaults, and interfaces, which can accommodate a wide variety of existing application software packages. The shell will offer expected utilities such as graphics, tailored menus, and a variety of drivers for I/O devices. Following the development of the shell, the development of SCAD is planned as chiefly selection and integration of appropriate building blocks. The phase one development activities have included: the selection of hardware which will be used with SCAD; the determination of the scope of SCAD; the preliminary evaluation of a number of software packages for applicability to SCAD; determination of a method for achieving required capabilities where voids exist; and then establishing a strategy for binding the software modules into an easy to use tool kit.

WinHPC System Programming | High-Performance Computing | NREL

Science.gov Websites

Programming WinHPC System Programming Learn how to build and run an MPI (message passing interface (mpi.h) and library (msmpi.lib) are. To build from the command line, run... Start > Intel Software Development Tools > Intel C++ Compiler Professional... > C++ Build Environment for applications running

Advancing Knowledge-Building Discourse through Judgments of Promising Ideas

ERIC Educational Resources Information Center

Chen, Bodong; Scardamalia, Marlene; Bereiter, Carl

2015-01-01

Evaluating promisingness of ideas is an important but underdeveloped aspect of knowledge building. The goal of this research was to examine the extent to which Grade 3 students could make promisingness judgments to facilitate knowledge-building discourse. A Promising Ideas Tool was added to Knowledge Forum software to better support…

Hemojuvelin-hepcidin axis modeled and analyzed using Petri nets.

PubMed

Formanowicz, Dorota; Kozak, Adam; Głowacki, Tomasz; Radom, Marcin; Formanowicz, Piotr

2013-12-01

Systems biology approach to investigate biological phenomena seems to be very promising because it is capable to capture one of the fundamental properties of living organisms, i.e. their inherent complexity. It allows for analysis biological entities as complex systems of interacting objects. The first and necessary step of such an analysis is building a precise model of the studied biological system. This model is expressed in the language of some branch of mathematics, as for example, differential equations. During the last two decades the theory of Petri nets has appeared to be very well suited for building models of biological systems. The structure of these nets reflects the structure of interacting biological molecules and processes. Moreover, on one hand, Petri nets have intuitive graphical representation being very helpful in understanding the structure of the system and on the other hand, there is a lot of mathematical methods and software tools supporting an analysis of the properties of the nets. In this paper a Petri net based model of the hemojuvelin-hepcidin axis involved in the maintenance of the human body iron homeostasis is presented. The analysis based mainly on T-invariants of the model properties has been made and some biological conclusions have been drawn. Copyright © 2013 Elsevier Inc. All rights reserved.

Final Technical Report - Center for Technology for Advanced Scientific Component Software (TASCS)

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

Sussman, Alan

2014-10-21

This is a final technical report for the University of Maryland work in the SciDAC Center for Technology for Advanced Scientific Component Software (TASCS). The Maryland work focused on software tools for coupling parallel software components built using the Common Component Architecture (CCA) APIs. Those tools are based on the Maryland InterComm software framework that has been used in multiple computational science applications to build large-scale simulations of complex physical systems that employ multiple separately developed codes.

Building Successful GitHub Communities

NASA Astrophysics Data System (ADS)

Smith, A.

2014-12-01

Building successful online communities is hard, whether it's in open source software or web-based citizen science. In this presentation I'll share some lessons learned and outline some techniques employed by successful open source projects.

Simulation-based Testing of Control Software

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

Ozmen, Ozgur; Nutaro, James J.; Sanyal, Jibonananda

It is impossible to adequately test complex software by examining its operation in a physical prototype of the system monitored. Adequate test coverage can require millions of test cases, and the cost of equipment prototypes combined with the real-time constraints of testing with them makes it infeasible to sample more than a small number of these tests. Model based testing seeks to avoid this problem by allowing for large numbers of relatively inexpensive virtual prototypes that operate in simulation time at a speed limited only by the available computing resources. In this report, we describe how a computer system emulatormore » can be used as part of a model based testing environment; specifically, we show that a complete software stack including operating system and application software - can be deployed within a simulated environment, and that these simulations can proceed as fast as possible. To illustrate this approach to model based testing, we describe how it is being used to test several building control systems that act to coordinate air conditioning loads for the purpose of reducing peak demand. These tests involve the use of ADEVS (A Discrete Event System Simulator) and QEMU (Quick Emulator) to host the operational software within the simulation, and a building model developed with the MODELICA programming language using Buildings Library and packaged as an FMU (Functional Mock-up Unit) that serves as the virtual test environment.« less

An Approach for On-Board Software Building Blocks Cooperation and Interfaces Definition

NASA Astrophysics Data System (ADS)

Pascucci, Dario; Campolo, Giovanni; Candia, Sante; Lisio, Giovanni

2010-08-01

This paper provides an insight on the Avionic SW architecture developed by Thales Alenia Space Italy (TAS-I) to achieve structuring of the OBSW as a set of self-standing and re-usable building blocks. It is initially described the underlying framework for building blocks cooperation, which is based on ECSSE-70 packets forwarding (for services request to a building block) and standard parameters exchange for data communication. Subsequently it is discussed the high level of flexibility and scalability of the resulting architecture, reporting as example an implementation of the Failure Detection, Isolation and Recovery (FDIR) function which exploits the proposed architecture. The presented approach evolves from avionic SW architecture developed in the scope of the project PRIMA (Mult-Purpose Italian Re-configurable Platform) and has been adopted for the Sentinel-1 Avionic Software (ASW).

Sustaining Open Source Communities through Hackathons - An Example from the ASPECT Community

NASA Astrophysics Data System (ADS)

Heister, T.; Hwang, L.; Bangerth, W.; Kellogg, L. H.

2016-12-01

The ecosystem surrounding a successful scientific open source software package combines both social and technical aspects. Much thought has been given to the technology side of writing sustainable software for large infrastructure projects and software libraries, but less about building the human capacity to perpetuate scientific software used in computational modeling. One effective format for building capacity is regular multi-day hackathons. Scientific hackathons bring together a group of science domain users and scientific software contributors to make progress on a specific software package. Innovation comes through the chance to work with established and new collaborations. Especially in the domain sciences with small communities, hackathons give geographically distributed scientists an opportunity to connect face-to-face. They foster lively discussions amongst scientists with different expertise, promote new collaborations, and increase transparency in both the technical and scientific aspects of code development. ASPECT is an open source, parallel, extensible finite element code to simulate thermal convection, that began development in 2011 under the Computational Infrastructure for Geodynamics. ASPECT hackathons for the past 3 years have grown the number of authors to >50, training new code maintainers in the process. Hackathons begin with leaders establishing project-specific conventions for development, demonstrating the workflow for code contributions, and reviewing relevant technical skills. Each hackathon expands the developer community. Over 20 scientists add >6,000 lines of code during the >1 week event. Participants grow comfortable contributing to the repository and over half continue to contribute afterwards. A high return rate of participants ensures continuity and stability of the group as well as mentoring for novice members. We hope to build other software communities on this model, but anticipate each to bring their own unique challenges.

Geospatial-enabled Data Exploration and Computation through Data Infrastructure Building Blocks

NASA Astrophysics Data System (ADS)

Song, C. X.; Biehl, L. L.; Merwade, V.; Villoria, N.

2015-12-01

Geospatial data are present everywhere today with the proliferation of location-aware computing devices and sensors. This is especially true in the scientific community where large amounts of data are driving research and education activities in many domains. Collaboration over geospatial data, for example, in modeling, data analysis and visualization, must still overcome the barriers of specialized software and expertise among other challenges. The GABBs project aims at enabling broader access to geospatial data exploration and computation by developing spatial data infrastructure building blocks that leverage capabilities of end-to-end application service and virtualized computing framework in HUBzero. Funded by NSF Data Infrastructure Building Blocks (DIBBS) initiative, GABBs provides a geospatial data architecture that integrates spatial data management, mapping and visualization and will make it available as open source. The outcome of the project will enable users to rapidly create tools and share geospatial data and tools on the web for interactive exploration of data without requiring significant software development skills, GIS expertise or IT administrative privileges. This presentation will describe the development of geospatial data infrastructure building blocks and the scientific use cases that help drive the software development, as well as seek feedback from the user communities.

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

DOE PAGES

Brettin, Thomas; Davis, James J.; Disz, Terry; ...

2015-02-10

The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offersmore » a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.« less

Healthy Air: Signs of Potential Problems in the Workplace

MedlinePlus

... The U.S. Environmental Protection Agency has developed free software to help building professionals identify, solve and prevent ... Privacy Policy | Sitemap Our Family Of Sites nonprofit software Join the fight for healthy lungs and healthy ...

Building a Library Web Server on a Budget.

ERIC Educational Resources Information Center

Orr, Giles

1998-01-01

Presents a method for libraries with limited budgets to create reliable Web servers with existing hardware and free software available via the Internet. Discusses staff, hardware and software requirements, and security; outlines the assembly process. (PEN)

Complex Dipolar Matter

DTIC Science & Technology

2014-11-10

opportunities for advanced material development and quantum simulators. These molecules include (1) the already quantum degenerate bi- alkali singlet sigma...case potassium-rubidium (KRb) and related molecules; (2) opto-electrically trapped symmetric top molecules soon to reach quantum degeneracy and...rubidium; (C) a correction of phase diagrams for dipolar gases necessary to understand experimental measurements and build accurate quantum simulators

Object-oriented software design in semiautomatic building extraction

NASA Astrophysics Data System (ADS)

Guelch, Eberhard; Mueller, Hardo

1997-08-01

Developing a system for semiautomatic building acquisition is a complex process, that requires constant integration and updating of software modules and user interfaces. To facilitate these processes we apply an object-oriented design not only for the data but also for the software involved. We use the unified modeling language (UML) to describe the object-oriented modeling of the system in different levels of detail. We can distinguish between use cases from the users point of view, that represent a sequence of actions, yielding in an observable result and the use cases for the programmers, who can use the system as a class library to integrate the acquisition modules in their own software. The structure of the system is based on the model-view-controller (MVC) design pattern. An example from the integration of automated texture extraction for the visualization of results demonstrate the feasibility of this approach.

The Ettention software package.

PubMed

Dahmen, Tim; Marsalek, Lukas; Marniok, Nico; Turoňová, Beata; Bogachev, Sviatoslav; Trampert, Patrick; Nickels, Stefan; Slusallek, Philipp

2016-02-01

We present a novel software package for the problem "reconstruction from projections" in electron microscopy. The Ettention framework consists of a set of modular building-blocks for tomographic reconstruction algorithms. The well-known block iterative reconstruction method based on Kaczmarz algorithm is implemented using these building-blocks, including adaptations specific to electron tomography. Ettention simultaneously features (1) a modular, object-oriented software design, (2) optimized access to high-performance computing (HPC) platforms such as graphic processing units (GPU) or many-core architectures like Xeon Phi, and (3) accessibility to microscopy end-users via integration in the IMOD package and eTomo user interface. We also provide developers with a clean and well-structured application programming interface (API) that allows for extending the software easily and thus makes it an ideal platform for algorithmic research while hiding most of the technical details of high-performance computing. Copyright © 2015 Elsevier B.V. All rights reserved.

Empirical Evaluation of Hunk Metrics as Bug Predictors

NASA Astrophysics Data System (ADS)

Ferzund, Javed; Ahsan, Syed Nadeem; Wotawa, Franz

Reducing the number of bugs is a crucial issue during software development and maintenance. Software process and product metrics are good indicators of software complexity. These metrics have been used to build bug predictor models to help developers maintain the quality of software. In this paper we empirically evaluate the use of hunk metrics as predictor of bugs. We present a technique for bug prediction that works at smallest units of code change called hunks. We build bug prediction models using random forests, which is an efficient machine learning classifier. Hunk metrics are used to train the classifier and each hunk metric is evaluated for its bug prediction capabilities. Our classifier can classify individual hunks as buggy or bug-free with 86 % accuracy, 83 % buggy hunk precision and 77% buggy hunk recall. We find that history based and change level hunk metrics are better predictors of bugs than code level hunk metrics.

Student computer attitudes, experience and perceptions about the use of two software applications in Building Engineering

NASA Astrophysics Data System (ADS)

Chiner, Esther; Garcia-Vera, Victoria E.

2017-11-01

The purpose of this study was to examine students' computer attitudes and experience, as well as students' perceptions about the use of two specific software applications (Google Drive Spreadsheets and Arquimedes) in the Building Engineering context. The relationships among these variables were also examined. Ninety-two students took part in this study. Results suggest that students hold favourable computer attitudes. Moreover, it was found a significant positive relationship among students' attitudes and their computer experience. Findings also show that students find Arquimedes software more useful and with higher output quality than Google Drive Spreadsheets, while the latter is perceived to be easier to use. Regarding the relationship among students' attitudes towards the use of computers and their perceptions about the use of both software applications, only a significant positive relationship in the case of Arquimedes was found. Findings are discussed in terms of its implications for practice and further research.

SOA Governance: A Critical SOA Success Factor

DTIC Science & Technology

2010-04-01

Software Perspective Service Consumer Service Providers Interface Optimize tomorrow today. ® Building Blocks...of a SOA Service – Software implemented capability that is well-defined, self contained and does not depend on context or state of other services ... Service Consumer – Service , application or other software component that requires a specific service . – Located through registry – Initiates service

Genetics Home Reference: mitochondrial neurogastrointestinal encephalopathy disease

MedlinePlus

... modification) is used as a building block of DNA . Thymidine phosphorylase breaks down thymidine into smaller molecules, ... molecule is damaging to a particular kind of DNA known as mitochondrial DNA or mtDNA. Mitochondria are ...

Genetics Home Reference: glycine encephalopathy

MedlinePlus

... a molecule called glycine. This molecule is an amino acid , which is a building block of proteins. Glycine ... Additional Information & Resources MedlinePlus (3 links) Health Topic: Amino Acid Metabolism Disorders Health Topic: Genetic Brain Disorders Health ...

Software on the Peregrine System | High-Performance Computing | NREL

Science.gov Websites

. Development Tools View list of tools for build automation, version control, and high-level or specialized scripting. Toolchains Learn about the available toolchains to build applications from source code

Data and Tools | Integrated Energy Solutions | NREL

Science.gov Websites

for a research campus eQUEST. Detailed analysis of today's state-of-the-art building design source software tools to support whole building energy modeling and advanced daylight analysis BESTEST-EX

Single molecule magnets from magnetic building blocks

NASA Astrophysics Data System (ADS)

Kroener, W.; Paretzki, A.; Cervetti, C.; Hohloch, S.; Rauschenbach, S.; Kern, K.; Dressel, M.; Bogani, L.; M&üLler, P.

2013-03-01

We provide a basic set of magnetic building blocks that can be rationally assembled, similar to magnetic LEGO bricks, in order to create a huge variety of magnetic behavior. Using rare-earth centers and multipyridine ligands, fine-tuning of intra and intermolecular exchange interaction is demonstrated. We have investigated a series of molecules with monomeric, dimeric and trimeric lanthanide centers using SQUID susceptometry and Hall bar magnetometry. A home-made micro-Hall-probe magnetometer was used to measure magnetic hysteresis loops at mK temperatures and fields up to 17 T. All compounds show hysteresis below blocking temperatures of 3 to 4 K. The correlation of the assembly of the building blocks with the magnetic properties will be discussed.

Cradle-to-Gate Life-Cycle Inventory of Hardboard and Engineered Wood Siding and Trim Produced in North America

Treesearch

Richard D. Bergman

2015-01-01

Developing wood product LCI data helps construct product LCAs that are then incorporated into developing whole building LCAs in environmental footprint software such as the Athena Impact Estimator for Buildings (ASMI 2015). Conducting whole building LCAs provide for points that go toward green building certification in rating systems such as LEED v4, Green Globes, and...

Metabolon, Inc.

PubMed

Ryals, John; Lawton, Kay; Stevens, Daniel; Milburn, Michael

2007-07-01

Metabolon is an emerging technology company developing proprietary analytical methods and software for biomarker discovery using metabolomics. The company's aim is to measure all small molecules (<1500 Da) in a biological sample. These small-molecule compounds include biochemicals of cellular metabolism and xenobiotics from diet and environment. Our proprietary mLIMStrade mark system contains advanced metabolomic software and automated data-processing tools that use a variety of data-analysis and quality-control algorithms to convert raw mass-spectrometry data to identified, quantitated compounds. Metabolon's primary focus is a fee-for-service business that exploits this technology for pharmaceutical and biotechnology companies, with additional clients in the consumer goods, cosmetics and agricultural industries. Fee-for-service studies are often collaborations with groups that employ a variety of technologies for biomarker discovery. Metabolon's goal is to develop technology that will automatically analyze any sample for the small-molecule components present and become a standard technology for applications in health and related sciences.

Drawing the PDB: Protein-Ligand Complexes in Two Dimensions.

PubMed

Stierand, Katrin; Rarey, Matthias

2010-12-09

The two-dimensional representation of molecules is a popular communication medium in chemistry and the associated scientific fields. Computational methods for drawing small molecules with and without manual investigation are well-established and widely spread in terms of numerous software tools. Concerning the planar depiction of molecular complexes, there is considerably less choice. We developed the software PoseView, which automatically generates two-dimensional diagrams of macromolecular complexes, showing the ligand, the interactions, and the interacting residues. All depicted molecules are drawn on an atomic level as structure diagrams; thus, the output plots are clearly structured and easily readable for the scientist. We tested the performance of PoseView in a large-scale application on nearly all druglike complexes of the PDB (approximately 200000 complexes); for more than 92% of the complexes considered for drawing, a layout could be computed. In the following, we will present the results of this application study.

NREL Announces Third Round of Start-Ups to Participate in the Wells Fargo

Science.gov Websites

innovative commercial building technologies Photo of NREL researchers talking. George Lee and Steven Low that provide scalable solutions to reduce the energy impact of commercial buildings. Including Round 3 kit for commercial buildings. Referred to apply to program by University of Colorado Boulder Software

Efficient and Robust Optimization for Building Energy Simulation

PubMed Central

Pourarian, Shokouh; Kearsley, Anthony; Wen, Jin; Pertzborn, Amanda

2016-01-01

Efficiently, robustly and accurately solving large sets of structured, non-linear algebraic and differential equations is one of the most computationally expensive steps in the dynamic simulation of building energy systems. Here, the efficiency, robustness and accuracy of two commonly employed solution methods are compared. The comparison is conducted using the HVACSIM+ software package, a component based building system simulation tool. The HVACSIM+ software presently employs Powell’s Hybrid method to solve systems of nonlinear algebraic equations that model the dynamics of energy states and interactions within buildings. It is shown here that the Powell’s method does not always converge to a solution. Since a myriad of other numerical methods are available, the question arises as to which method is most appropriate for building energy simulation. This paper finds considerable computational benefits result from replacing the Powell’s Hybrid method solver in HVACSIM+ with a solver more appropriate for the challenges particular to numerical simulations of buildings. Evidence is provided that a variant of the Levenberg-Marquardt solver has superior accuracy and robustness compared to the Powell’s Hybrid method presently used in HVACSIM+. PMID:27325907

Efficient and Robust Optimization for Building Energy Simulation.

PubMed

Pourarian, Shokouh; Kearsley, Anthony; Wen, Jin; Pertzborn, Amanda

2016-06-15

Efficiently, robustly and accurately solving large sets of structured, non-linear algebraic and differential equations is one of the most computationally expensive steps in the dynamic simulation of building energy systems. Here, the efficiency, robustness and accuracy of two commonly employed solution methods are compared. The comparison is conducted using the HVACSIM+ software package, a component based building system simulation tool. The HVACSIM+ software presently employs Powell's Hybrid method to solve systems of nonlinear algebraic equations that model the dynamics of energy states and interactions within buildings. It is shown here that the Powell's method does not always converge to a solution. Since a myriad of other numerical methods are available, the question arises as to which method is most appropriate for building energy simulation. This paper finds considerable computational benefits result from replacing the Powell's Hybrid method solver in HVACSIM+ with a solver more appropriate for the challenges particular to numerical simulations of buildings. Evidence is provided that a variant of the Levenberg-Marquardt solver has superior accuracy and robustness compared to the Powell's Hybrid method presently used in HVACSIM+.

Lucid Provides Energy Reduction Software to DC Government

EPA Pesticide Factsheets

Earlier this year, Lucid, a 2014 U.S. EPA SBIR award recipient, announced that the D.C. government was using Lucid's BuildingOS® software in order to reach an an energy reduction target of 20 percent in 20 months

Evaluation of Software for Introducing Protein Structure: Visualization and Simulation

ERIC Educational Resources Information Center

White, Brian; Kahriman, Azmin; Luberice, Lois; Idleh, Farhia

2010-01-01

Communicating an understanding of the forces and factors that determine a protein's structure is an important goal of many biology and biochemistry courses at a variety of levels. Many educators use computer software that allows visualization of these complex molecules for this purpose. Although visualization is in wide use and has been associated…

Secure Video Surveillance System Acquisition Software

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

2009-12-04

The SVSS Acquisition Software collects and displays video images from two cameras through a VPN, and store the images onto a collection controller. The software is configured to allow a user to enter a time window to display up to 2 1/2, hours of video review. The software collects images from the cameras at a rate of 1 image per second and automatically deletes images older than 3 hours. The software code operates in a linux environment and can be run in a virtual machine on Windows XP. The Sandia software integrates the different COTS software together to build themore » video review system.« less

Energy performance evaluation of AAC

NASA Astrophysics Data System (ADS)

Aybek, Hulya

The U.S. building industry constitutes the largest consumer of energy (i.e., electricity, natural gas, petroleum) in the world. The building sector uses almost 41 percent of the primary energy and approximately 72 percent of the available electricity in the United States. As global energy-generating resources are being depleted at exponential rates, the amount of energy consumed and wasted cannot be ignored. Professionals concerned about the environment have placed a high priority on finding solutions that reduce energy consumption while maintaining occupant comfort. Sustainable design and the judicious combination of building materials comprise one solution to this problem. A future including sustainable energy may result from using energy simulation software to accurately estimate energy consumption and from applying building materials that achieve the potential results derived through simulation analysis. Energy-modeling tools assist professionals with making informed decisions about energy performance during the early planning phases of a design project, such as determining the most advantageous combination of building materials, choosing mechanical systems, and determining building orientation on the site. By implementing energy simulation software to estimate the effect of these factors on the energy consumption of a building, designers can make adjustments to their designs during the design phase when the effect on cost is minimal. The primary objective of this research consisted of identifying a method with which to properly select energy-efficient building materials and involved evaluating the potential of these materials to earn LEED credits when properly applied to a structure. In addition, this objective included establishing a framework that provides suggestions for improvements to currently available simulation software that enhance the viability of the estimates concerning energy efficiency and the achievements of LEED credits. The primary objective was accomplished by using conducting several simulation models to determine the relative energy efficiency of wood-framed, metal-framed, and Aerated Autoclaved Concrete (AAC) wall structures for both commercial and residential buildings.

The software architecture to control the Cherenkov Telescope Array

NASA Astrophysics Data System (ADS)

Oya, I.; Füßling, M.; Antonino, P. O.; Conforti, V.; Hagge, L.; Melkumyan, D.; Morgenstern, A.; Tosti, G.; Schwanke, U.; Schwarz, J.; Wegner, P.; Colomé, J.; Lyard, E.

2016-07-01

The Cherenkov Telescope Array (CTA) project is an initiative to build two large arrays of Cherenkov gamma- ray telescopes. CTA will be deployed as two installations, one in the northern and the other in the southern hemisphere, containing dozens of telescopes of different sizes. CTA is a big step forward in the field of ground- based gamma-ray astronomy, not only because of the expected scientific return, but also due to the order-of- magnitude larger scale of the instrument to be controlled. The performance requirements associated with such a large and distributed astronomical installation require a thoughtful analysis to determine the best software solutions. The array control and data acquisition (ACTL) work-package within the CTA initiative will deliver the software to control and acquire the data from the CTA instrumentation. In this contribution we present the current status of the formal ACTL system decomposition into software building blocks and the relationships among them. The system is modelled via the Systems Modelling Language (SysML) formalism. To cope with the complexity of the system, this architecture model is sub-divided into different perspectives. The relationships with the stakeholders and external systems are used to create the first perspective, the context of the ACTL software system. Use cases are employed to describe the interaction of those external elements with the ACTL system and are traced to a hierarchy of functionalities (abstract system functions) describing the internal structure of the ACTL system. These functions are then traced to fully specified logical elements (software components), the deployment of which as technical elements, is also described. This modelling approach allows us to decompose the ACTL software in elements to be created and the ow of information within the system, providing us with a clear way to identify sub-system interdependencies. This architectural approach allows us to build the ACTL system model and trace requirements to deliverables (source code, documentation, etc.), and permits the implementation of a flexible use-case driven software development approach thanks to the traceability from use cases to the logical software elements. The Alma Common Software (ACS) container/component framework, used for the control of the Atacama Large Millimeter/submillimeter Array (ALMA) is the basis for the ACTL software and as such it is considered as an integral part of the software architecture.

Effect of electric field on adsorption of formaldehyde by β-cellobiose in micro-scale

NASA Astrophysics Data System (ADS)

Xu, Bo; Chen, Zhenqian

2018-05-01

To provide a microcosmic theoretical support for the reduction of formaldehyde in building material by the effect of electric fields, the adsorption between formaldehyde molecule and β-cellobiose was studied by density function theory (DFT). Details of geometric structures, molecule bonds and adsorption energy were discussed respectively. The obtained results indicated the energy of formaldehyde molecule decreased while the energy of β-cellobiose increased with greater electric intensity. In addition, the adsorption energy between formaldehyde molecule and β-cellobiose was greatly influenced by external electric field. The adsorption energy reduced gradually with greater electric intensity, and the changing curve of adsorption energy could be fitted as an exponential function, verified by the experiment. The results of this study confirmed the external electric field would be a good strategy for decreasing formaldehyde within building materials in the microcosmic view.

A General Water Resources Regulation Software System in China

NASA Astrophysics Data System (ADS)

LEI, X.

2017-12-01

To avoid iterative development of core modules in water resource normal regulation and emergency regulation and improve the capability of maintenance and optimization upgrading of regulation models and business logics, a general water resources regulation software framework was developed based on the collection and analysis of common demands for water resources regulation and emergency management. It can provide a customizable, secondary developed and extensible software framework for the three-level platform "MWR-Basin-Province". Meanwhile, this general software system can realize business collaboration and information sharing of water resources regulation schemes among the three-level platforms, so as to improve the decision-making ability of national water resources regulation. There are four main modules involved in the general software system: 1) A complete set of general water resources regulation modules allows secondary developer to custom-develop water resources regulation decision-making systems; 2) A complete set of model base and model computing software released in the form of Cloud services; 3) A complete set of tools to build the concept map and model system of basin water resources regulation, as well as a model management system to calibrate and configure model parameters; 4) A database which satisfies business functions and functional requirements of general water resources regulation software can finally provide technical support for building basin or regional water resources regulation models.

A Buyer Behaviour Framework for the Development and Design of Software Agents in E-Commerce.

ERIC Educational Resources Information Center

Sproule, Susan; Archer, Norm

2000-01-01

Software agents are computer programs that run in the background and perform tasks autonomously as delegated by the user. This paper blends models from marketing research and findings from the field of decision support systems to build a framework for the design of software agents to support in e-commerce buying applications. (Contains 35…

Modular modeling system for building distributed hydrologic models with a user-friendly software package

NASA Astrophysics Data System (ADS)

Wi, S.; Ray, P. A.; Brown, C.

2015-12-01

A software package developed to facilitate building distributed hydrologic models in a modular modeling system is presented. The software package provides a user-friendly graphical user interface that eases its practical use in water resources-related research and practice. The modular modeling system organizes the options available to users when assembling models according to the stages of hydrological cycle, such as potential evapotranspiration, soil moisture accounting, and snow/glacier melting processes. The software is intended to be a comprehensive tool that simplifies the task of developing, calibrating, validating, and using hydrologic models through the inclusion of intelligent automation to minimize user effort, and reduce opportunities for error. Processes so far automated include the definition of system boundaries (i.e., watershed delineation), climate and geographical input generation, and parameter calibration. Built-in post-processing toolkits greatly improve the functionality of the software as a decision support tool for water resources system management and planning. Example post-processing toolkits enable streamflow simulation at ungauged sites with predefined model parameters, and perform climate change risk assessment by means of the decision scaling approach. The software is validated through application to watersheds representing a variety of hydrologic regimes.

Building Interactive Simulations in Web Pages without Programming.

PubMed

Mailen Kootsey, J; McAuley, Grant; Bernal, Julie

2005-01-01

A software system is described for building interactive simulations and other numerical calculations in Web pages. The system is based on a new Java-based software architecture named NumberLinX (NLX) that isolates each function required to build the simulation so that a library of reusable objects could be assembled. The NLX objects are integrated into a commercial Web design program for coding-free page construction. The model description is entered through a wizard-like utility program that also functions as a model editor. The complete system permits very rapid construction of interactive simulations without coding. A wide range of applications are possible with the system beyond interactive calculations, including remote data collection and processing and collaboration over a network.

Acceptance test procedure bldg. 271-U remote monitoring of project W-059 B-Plant canyon exhaust system

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

MCDANIEL, K.S.

1999-09-01

The test procedure provides for verifying indications and alarms The test procedure provides for verifying indications and alarms associated with the B Plant Canyon Ventilation System as they are being displayed on a remote monitoring workstation located in building 271-U. The system application software was installed by PLCS Plus under contract from B&W Hanford Company. The application software was installed on an existing operator workstation in building 271U which is owned and operated by Bechtel Hanford Inc.

Where to attach dye molecules to a protein: lessons from the computer program WHAT IF

NASA Astrophysics Data System (ADS)

Altenberg-Greulich, B.; Vriend, G.

2001-10-01

Genomic and proteomic projects are producing a flood of data that all require interpretation which often is best performed based on a three dimensional structure of the molecule(s) involved. These structures can be determined experimentally, or modelled by homology. Because of the complexity of the questions and the heterogeneity of the data, the software used for modelling proteins must become even more versatile. We describe several case studies in which the questions asked, the data, and the requirements on the software all are very different. It is shown how structural knowledge about a protein helps to determine the best place to bind a fluorescent dye. Such dyes are needed to determine protein-protein, protein-DNA interactions or intrinsic fluorescence microscopy. Further, using dyes you can trace molecules in the cell and thus get a handle on subcellular localisation. The first example (OCT-1) involves the search for free amino groups in a protein-DNA complex. The second example (BPTI) is a case, in which the amino acid distribution shows that amino groups are spread all over the structure, so that the natural structure has to be modified to get an answer. The third example (HFE) involves a model built by homology. In this case the amino group distribution can also be predicted. All these studies were performed using the WHAT IF software package. This package is available including source code, documentation, etc. See http://www.cmbi.kun.nl/whatif/

Investigating the Acquisition of Software Systems that Rely on Open Architecture and Open Source Software

DTIC Science & Technology

2010-03-01

associated with certain software systems [Breaux and Anton 2008]. With this basis to build on, it is now possible to analyze the alignment of...Kazman, R., (2003). Software Architecture in Practice, 2nd Edition, Addison-Wesley Pro- fessional, New York.. Breaux, T.D. and Anton , A.I. (2008... calculus for license rights and obligations in license and context models. Using them, we calculate rights and obligations for specific sys- tems, identify

Large-scale visualization projects for teaching software engineering.

PubMed

Müller, Christoph; Reina, Guido; Burch, Michael; Weiskopf, Daniel

2012-01-01

The University of Stuttgart's software engineering major complements the traditional computer science major with more practice-oriented education. Two-semester software projects in various application areas offered by the university's different computer science institutes are a successful building block in the curriculum. With this realistic, complex project setting, students experience the practice of software engineering, including software development processes, technologies, and soft skills. In particular, visualization-based projects are popular with students. Such projects offer them the opportunity to gain profound knowledge that would hardly be possible with only regular lectures and homework assignments.

Seismic vulnerability assessment to earthquake at urban scale: A case of Mostaganem city in Algeria

PubMed Central

Benanane, Abdelkader; Boutaraa, Zohra

2018-01-01

The focus of this study was the seismic vulnerability assessment of buildings constituting Mostaganem city in Algeria. Situated 320 km to the west of Algiers, Mostaganem city encompasses a valuable cultural and architectural built heritage. The city has suffered several moderate earthquakes in recent years; this has led to extensive structural damage to old structures, especially unreinforced historical buildings. This study was divided into two essential steps, the first step being to establish fragility curves based on a non-linear static pushover analysis for each typology and height of buildings. Twenty-seven pushover analyses were performed by means of SAP2000 software (three analyses for each type of building). The second step was to adopt the US HAZUS software and to modify it to suit the typical setting and parameters of the city of Mostaganem. A seismic vulnerability analysis of Mostaganem city was conducted using HAZUS software after inputting the new parameters of the fragility curves established within the first step. The results indicated that the number of poor-quality buildings expected to be totally destroyed under a 5.5 Mw earthquake scenario could reach more than 28 buildings. Three percent of unreinforced masonry (URM) buildings were completely damaged and 10% were extensively damaged. Of the concrete frame buildings, 6% were extensively damaged and 19% were moderately damaged. According to the built year, 6% of both concrete frame and URM buildings built before 1980 are estimated to be collapsing. Buildings constructed between 1980 and 1999 are more resistant; 8% of those structures were extensively damaged and 18% were moderately damaged. Only 10% of buildings constructed after 1999 were moderately damaged. The results also show that the main hospital of the city, built before 1960, will be extensively damaged during an earthquake of 5.5 Mw. The number of human casualties could reach several hundreds – 10.5% of residents of URM buildings are injured or dead. Compared with the URM buildings, concrete frame buildings have lower casualty rates of 1.5% and 0.5% for those built before and after 1980, respectively. It was concluded that Mostaganem city belongs to seismic vulnerable zones in Algeria; in this regard, an action plan is needed for the rehabilitation of old constructions. In addition, the effectiveness of establishing and introducing new and appropriate fragility curves was demonstrated.

Determining position inside building via laser rangefinder and handheld computer

DOEpatents

Ramsey, Jr James L. [Albuquerque, NM; Finley, Patrick [Albuquerque, NM; Melton, Brad [Albuquerque, NM

2010-01-12

An apparatus, computer software, and a method of determining position inside a building comprising selecting on a PDA at least two walls of a room in a digitized map of a building or a portion of a building, pointing and firing a laser rangefinder at corresponding physical walls, transmitting collected range information to the PDA, and computing on the PDA a position of the laser rangefinder within the room.

Autotune Calibrates Models to Building Use Data

ScienceCinema

None

2018-01-16

Models of existing buildings are currently unreliable unless calibrated manually by a skilled professional. Autotune, as the name implies, automates this process by calibrating the model of an existing building to measured data, and is now available as open source software. This enables private businesses to incorporate Autotune into their products so that their customers can more effectively estimate cost savings of reduced energy consumption measures in existing buildings.

Assigning Robust Default Values in Building Performance Simulation Software for Improved Decision-Making in the Initial Stages of Building Design.

PubMed

Hiyama, Kyosuke

2015-01-01

Applying data mining techniques on a database of BIM models could provide valuable insights in key design patterns implicitly present in these BIM models. The architectural designer would then be able to use previous data from existing building projects as default values in building performance simulation software for the early phases of building design. The author has proposed the method to minimize the magnitude of the variation in these default values in subsequent design stages. This approach maintains the accuracy of the simulation results in the initial stages of building design. In this study, a more convincing argument is presented to demonstrate the significance of the new method. The variation in the ideal default values for different building design conditions is assessed first. Next, the influence of each condition on these variations is investigated. The space depth is found to have a large impact on the ideal default value of the window to wall ratio. In addition, the presence or absence of lighting control and natural ventilation has a significant influence on the ideal default value. These effects can be used to identify the types of building conditions that should be considered to determine the ideal default values.

Assigning Robust Default Values in Building Performance Simulation Software for Improved Decision-Making in the Initial Stages of Building Design

PubMed Central

2015-01-01

Applying data mining techniques on a database of BIM models could provide valuable insights in key design patterns implicitly present in these BIM models. The architectural designer would then be able to use previous data from existing building projects as default values in building performance simulation software for the early phases of building design. The author has proposed the method to minimize the magnitude of the variation in these default values in subsequent design stages. This approach maintains the accuracy of the simulation results in the initial stages of building design. In this study, a more convincing argument is presented to demonstrate the significance of the new method. The variation in the ideal default values for different building design conditions is assessed first. Next, the influence of each condition on these variations is investigated. The space depth is found to have a large impact on the ideal default value of the window to wall ratio. In addition, the presence or absence of lighting control and natural ventilation has a significant influence on the ideal default value. These effects can be used to identify the types of building conditions that should be considered to determine the ideal default values. PMID:26090512

Advanced Software V&V for Civil Aviation and Autonomy

NASA Technical Reports Server (NTRS)

Brat, Guillaume P.

2017-01-01

With the advances in high-computing platform (e.g., advanced graphical processing units or multi-core processors), computationally-intensive software techniques such as the ones used in artificial intelligence or formal methods have provided us with an opportunity to further increase safety in the aviation industry. Some of these techniques have facilitated building safety at design time, like in aircraft engines or software verification and validation, and others can introduce safety benefits during operations as long as we adapt our processes. In this talk, I will present how NASA is taking advantage of these new software techniques to build in safety at design time through advanced software verification and validation, which can be applied earlier and earlier in the design life cycle and thus help also reduce the cost of aviation assurance. I will then show how run-time techniques (such as runtime assurance or data analytics) offer us a chance to catch even more complex problems, even in the face of changing and unpredictable environments. These new techniques will be extremely useful as our aviation systems become more complex and more autonomous.

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

Hart, William Eugene

These slides describe different strategies for installing Python software. Although I am a big fan of Python software development, robust strategies for software installation remains a challenge. This talk describes several different installation scenarios. The Good: the user has administrative privileges - Installing on Windows with an installer executable, Installing with Linux application utility, Installing a Python package from the PyPI repository, and Installing a Python package from source. The Bad: the user does not have administrative privileges - Using a virtual environment to isolate package installations, and Using an installer executable on Windows with a virtual environment. The Ugly:more » the user needs to install an extension package from source - Installing a Python extension package from source, and PyCoinInstall - Managing builds for Python extension packages. The last item referring to PyCoinInstall describes a utility being developed for the COIN-OR software, which is used within the operations research community. COIN-OR includes a variety of Python and C++ software packages, and this script uses a simple plug-in system to support the management of package builds and installation.« less

Lipidomics informatics for life-science.

PubMed

Schwudke, D; Shevchenko, A; Hoffmann, N; Ahrends, R

2017-11-10

Lipidomics encompasses analytical approaches that aim to identify and quantify the complete set of lipids, defined as lipidome in a given cell, tissue or organism as well as their interactions with other molecules. The majority of lipidomics workflows is based on mass spectrometry and has been proven as a powerful tool in system biology in concert with other Omics disciplines. Unfortunately, bioinformatics infrastructures for this relatively young discipline are limited only to some specialists. Search engines, quantification algorithms, visualization tools and databases developed by the 'Lipidomics Informatics for Life-Science' (LIFS) partners will be restructured and standardized to provide broad access to these specialized bioinformatics pipelines. There are many medical challenges related to lipid metabolic alterations that will be fostered by capacity building suggested by LIFS. LIFS as member of the 'German Network for Bioinformatics' (de.NBI) node for 'Bioinformatics for Proteomics' (BioInfra.Prot) and will provide access to the described software as well as to tutorials and consulting services via a unified web-portal. Copyright © 2017 Elsevier B.V. All rights reserved.

Chemical markup, XML and the World-Wide Web. 3. Toward a signed semantic chemical web of trust.

PubMed

Gkoutos, G V; Murray-Rust, P; Rzepa, H S; Wright, M

2001-01-01

We describe how a collection of documents expressed in XML-conforming languages such as CML and XHTML can be authenticated and validated against digital signatures which make use of established X.509 certificate technology. These can be associated either with specific nodes in the XML document or with the entire document. We illustrate this with two examples. An entire journal article expressed in XML has its individual components digitally signed by separate authors, and the collection is placed in an envelope and again signed. The second example involves using a software robot agent to acquire a collection of documents from a specified URL, to perform various operations and transformations on the content, including expressing molecules in CML, and to automatically sign the various components and deposit the result in a repository. We argue that these operations can used as components for building what we term an authenticated and semantic chemical web of trust.

FRETBursts: An Open Source Toolkit for Analysis of Freely-Diffusing Single-Molecule FRET

PubMed Central

Lerner, Eitan; Chung, SangYoon; Weiss, Shimon; Michalet, Xavier

2016-01-01

Single-molecule Förster Resonance Energy Transfer (smFRET) allows probing intermolecular interactions and conformational changes in biomacromolecules, and represents an invaluable tool for studying cellular processes at the molecular scale. smFRET experiments can detect the distance between two fluorescent labels (donor and acceptor) in the 3-10 nm range. In the commonly employed confocal geometry, molecules are free to diffuse in solution. When a molecule traverses the excitation volume, it emits a burst of photons, which can be detected by single-photon avalanche diode (SPAD) detectors. The intensities of donor and acceptor fluorescence can then be related to the distance between the two fluorophores. While recent years have seen a growing number of contributions proposing improvements or new techniques in smFRET data analysis, rarely have those publications been accompanied by software implementation. In particular, despite the widespread application of smFRET, no complete software package for smFRET burst analysis is freely available to date. In this paper, we introduce FRETBursts, an open source software for analysis of freely-diffusing smFRET data. FRETBursts allows executing all the fundamental steps of smFRET bursts analysis using state-of-the-art as well as novel techniques, while providing an open, robust and well-documented implementation. Therefore, FRETBursts represents an ideal platform for comparison and development of new methods in burst analysis. We employ modern software engineering principles in order to minimize bugs and facilitate long-term maintainability. Furthermore, we place a strong focus on reproducibility by relying on Jupyter notebooks for FRETBursts execution. Notebooks are executable documents capturing all the steps of the analysis (including data files, input parameters, and results) and can be easily shared to replicate complete smFRET analyzes. Notebooks allow beginners to execute complex workflows and advanced users to customize the analysis for their own needs. By bundling analysis description, code and results in a single document, FRETBursts allows to seamless share analysis workflows and results, encourages reproducibility and facilitates collaboration among researchers in the single-molecule community. PMID:27532626

User News. Volume 17, Number 1 -- Spring 1996

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

NONE

This is a newsletter for users of the DOE-2, PowerDOE, SPARK, and BLAST building energy simulation programs. The topics for the Spring 1996 issue include the SPARK simulation environment, DOE-2 validation, listing of free fenestration software from LBNL, Web sites for building energy efficiency, the heat balance method of calculating building heating and cooling loads.

LARGE BUILDING HVAC SIMULATION

EPA Science Inventory

The report discusses the monitoring and collection of data relating to indoor pressures and radon concentrations under several test conditions in a large school building in Bartow, Florida. The Florida Solar Energy Center (FSEC) used an integrated computational software, FSEC 3.0...

pyam: Python Implementation of YaM

NASA Technical Reports Server (NTRS)

Myint, Steven; Jain, Abhinandan

2012-01-01

pyam is a software development framework with tools for facilitating the rapid development of software in a concurrent software development environment. pyam provides solutions for development challenges associated with software reuse, managing multiple software configurations, developing software product lines, and multiple platform development and build management. pyam uses release-early, release-often development cycles to allow developers to integrate their changes incrementally into the system on a continual basis. It facilitates the creation and merging of branches to support the isolated development of immature software to avoid impacting the stability of the development effort. It uses modules and packages to organize and share software across multiple software products, and uses the concepts of link and work modules to reduce sandbox setup times even when the code-base is large. One sidebenefit is the enforcement of a strong module-level encapsulation of a module s functionality and interface. This increases design transparency, system stability, and software reuse. pyam is written in Python and is organized as a set of utilities on top of the open source SVN software version control package. All development software is organized into a collection of modules. pyam packages are defined as sub-collections of the available modules. Developers can set up private sandboxes for module/package development. All module/package development takes place on private SVN branches. High-level pyam commands support the setup, update, and release of modules and packages. Released and pre-built versions of modules are available to developers. Developers can tailor the source/link module mix for their sandboxes so that new sandboxes (even large ones) can be built up easily and quickly by pointing to pre-existing module releases. All inter-module interfaces are publicly exported via links. A minimal, but uniform, convention is used for building modules.

Assessment Environment for Complex Systems Software Guide

NASA Technical Reports Server (NTRS)

2013-01-01

This Software Guide (SG) describes the software developed to test the Assessment Environment for Complex Systems (AECS) by the West Virginia High Technology Consortium (WVHTC) Foundation's Mission Systems Group (MSG) for the National Aeronautics and Space Administration (NASA) Aeronautics Research Mission Directorate (ARMD). This software is referred to as the AECS Test Project throughout the remainder of this document. AECS provides a framework for developing, simulating, testing, and analyzing modern avionics systems within an Integrated Modular Avionics (IMA) architecture. The purpose of the AECS Test Project is twofold. First, it provides a means to test the AECS hardware and system developed by MSG. Second, it provides an example project upon which future AECS research may be based. This Software Guide fully describes building, installing, and executing the AECS Test Project as well as its architecture and design. The design of the AECS hardware is described in the AECS Hardware Guide. Instructions on how to configure, build and use the AECS are described in the User's Guide. Sample AECS software, developed by the WVHTC Foundation, is presented in the AECS Software Guide. The AECS Hardware Guide, AECS User's Guide, and AECS Software Guide are authored by MSG. The requirements set forth for AECS are presented in the Statement of Work for the Assessment Environment for Complex Systems authored by NASA Dryden Flight Research Center (DFRC). The intended audience for this document includes software engineers, hardware engineers, project managers, and quality assurance personnel from WVHTC Foundation (the suppliers of the software), NASA (the customer), and future researchers (users of the software). Readers are assumed to have general knowledge in the field of real-time, embedded computer software development.

Investigation of wind behaviour around high-rise buildings

NASA Astrophysics Data System (ADS)

Mat Isa, Norasikin; Fitriah Nasir, Nurul; Sadikin, Azmahani; Ariff Hairul Bahara, Jamil

2017-09-01

A study on the investigation of wind behaviour around the high-rise buildings is done through an experiment using a wind tunnel and computational fluid dynamics. High-rise buildings refer to buildings or structures that have more than 12 floors. Wind is invisible to the naked eye; thus, it is hard to see and analyse its flow around and over buildings without the use of proper methods, such as the use of wind tunnel and computational fluid dynamics software.The study was conducted on buildings located in Presint 4, Putrajaya, Malaysia which is the Ministry of Rural and Regional Development, Ministry of Information Communications and Culture, Ministry of Urban Wellbeing, Housing and Local Government and the Ministry of Women, Family, and Community by making scaled models of the buildings. The parameters in which this study is conducted on are, four different wind velocities used based on the seasonal monsoons, and wind direction. ANSYS Fluent workbench software is used to compute the simulations in order to achieve the objectives of this study. The data from the computational fluid dynamics are validated with the experiment done through the wind tunnel. From the results obtained through the use of the computation fluid dynamics, this study can identify the characteristics of wind around buildings, including boundary layer of the buildings, separation flow, wake region and etc. Then analyses is conducted on the occurance resulting from the wind that passes the buildings based on the velocity difference between before and after the wind passes the buildings.

TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD.

PubMed

Vermaas, Josh V; Hardy, David J; Stone, John E; Tajkhorshid, Emad; Kohlmeyer, Axel

2016-06-27

Molecular dynamics (MD) simulation engines use a variety of different approaches for modeling molecular systems with force fields that govern their dynamics and describe their topology. These different approaches introduce incompatibilities between engines, and previously published software bridges the gaps between many popular MD packages, such as between CHARMM and AMBER or GROMACS and LAMMPS. While there are many structure building tools available that generate topologies and structures in CHARMM format, only recently have mechanisms been developed to convert their results into GROMACS input. We present an approach to convert CHARMM-formatted topology and parameters into a format suitable for simulation with GROMACS by expanding the functionality of TopoTools, a plugin integrated within the widely used molecular visualization and analysis software VMD. The conversion process was diligently tested on a comprehensive set of biological molecules in vacuo. The resulting comparison between energy terms shows that the translation performed was lossless as the energies were unchanged for identical starting configurations. By applying the conversion process to conventional benchmark systems that mimic typical modestly sized MD systems, we explore the effect of the implementation choices made in CHARMM, NAMD, and GROMACS. The newly available automatic conversion capability breaks down barriers between simulation tools and user communities and allows users to easily compare simulation programs and leverage their unique features without the tedium of constructing a topology twice.

Systemic Vulnerabilities

DTIC Science & Technology

2014-10-01

CRm CAL FA~WR£S Q I • Software Engineering Institute I Ccamt>gw l\\~llon Lniwndty 34 Basic attack tree Destroy Building Generate Sufficient...by computer-security company marketing literature that touts 11hacker proof software,11 11triple-DES security,11 and the like. In truth, unbreakable

A review of building information modelling

NASA Astrophysics Data System (ADS)

Wang, Wen; Han, Rui

2018-05-01

Building Information Modelling (BIM) is widely seen as a catalyst for innovation and productivity. It is becoming standard for new construction and is the most significant technology changing how we design, build, use and manage the building. It is a dominant technological trend in the software industry and although the theoretical groundwork was laid in the previous century, it is a popular topic in academic research. BIM is discussed in this study, which results can provide better and more comprehensive choices for building owners, designers, and developers in future.

Addressing failures in exascale computing

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

Snir, Marc; Wisniewski, Robert W.; Abraham, Jacob A.

2014-05-01

We present here a report produced by a workshop on “Addressing Failures in Exascale Computing” held in Park City, Utah, August 4–11, 2012. The charter of this workshop was to establish a common taxonomy about resilience across all the levels in a computing system; discuss existing knowledge on resilience across the various hardware and software layers of an exascale system; and build on those results, examining potential solutions from both a hardware and software perspective and focusing on a combined approach. The workshop brought together participants with expertise in applications, system software, and hardware; they came from industry, government, andmore » academia; and their interests ranged from theory to implementation. The combination allowed broad and comprehensive discussions and led to this document, which summarizes and builds on those discussions.« less

Addressing Failures in Exascale Computing

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

Snir, Marc; Wisniewski, Robert; Abraham, Jacob

2014-01-01

We present here a report produced by a workshop on Addressing failures in exascale computing' held in Park City, Utah, 4-11 August 2012. The charter of this workshop was to establish a common taxonomy about resilience across all the levels in a computing system, discuss existing knowledge on resilience across the various hardware and software layers of an exascale system, and build on those results, examining potential solutions from both a hardware and software perspective and focusing on a combined approach. The workshop brought together participants with expertise in applications, system software, and hardware; they came from industry, government, andmore » academia, and their interests ranged from theory to implementation. The combination allowed broad and comprehensive discussions and led to this document, which summarizes and builds on those discussions.« less

Comparison of different approaches of modelling in a masonry building

NASA Astrophysics Data System (ADS)

Saba, M.; Meloni, D.

2017-12-01

The present work has the objective to model a simple masonry building, through two different modelling methods in order to assess their validity in terms of evaluation of static stresses. Have been chosen two of the most commercial software used to address this kind of problem, which are of S.T.A. Data S.r.l. and Sismicad12 of Concrete S.r.l. While the 3Muri software adopts the Frame by Macro Elements Method (FME), which should be more schematic and more efficient, Sismicad12 software uses the Finite Element Method (FEM), which guarantees accurate results, with greater computational burden. Remarkably differences of the static stresses, for such a simple structure between the two approaches have been found, and an interesting comparison and analysis of the reasons is proposed.

Introductory Molecular Orbital Theory: An Honors General Chemistry Computational Lab as Implemented Using Three-Dimensional Modeling Software

ERIC Educational Resources Information Center

Ruddick, Kristie R.; Parrill, Abby L.; Petersen, Richard L.

2012-01-01

In this study, a computational molecular orbital theory experiment was implemented in a first-semester honors general chemistry course. Students used the GAMESS (General Atomic and Molecular Electronic Structure System) quantum mechanical software (as implemented in ChemBio3D) to optimize the geometry for various small molecules. Extended Huckel…

Permuting input for more effective sampling of 3D conformer space

NASA Astrophysics Data System (ADS)

Carta, Giorgio; Onnis, Valeria; Knox, Andrew J. S.; Fayne, Darren; Lloyd, David G.

2006-03-01

SMILES strings and other classic 2D structural formats offer a convenient way to represent molecules as a simplistic connection table, with the inherent advantages of ease of handling and storage. In the context of virtual screening, chemical databases to be screened are often initially represented by canonicalised SMILES strings that can be filtered and pre-processed in a number of ways, resulting in molecules that occupy similar regions of chemical space to active compounds of a therapeutic target. A wide variety of software exists to convert molecules into SMILES format, namely, Mol2smi (Daylight Inc.), MOE (Chemical Computing Group) and Babel (Openeye Scientific Software). Depending on the algorithm employed, the atoms of a SMILES string defining a molecule can be ordered differently. Upon conversion to 3D coordinates they result in the production of ostensibly the same molecule. In this work we show how different permutations of a SMILES string can affect conformer generation, affecting reliability and repeatability of the results. Furthermore, we propose a novel procedure for the generation of conformers, taking advantage of the permutation of the input strings—both SMILES and other 2D formats, leading to more effective sampling of conformation space in output, and also implementing fingerprint and principal component analyses step to post process and visualise the results.

Modeling of diatomic molecule using the Morse potential and the Verlet algorithm

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

Fidiani, Elok

Performing molecular modeling usually uses special software for Molecular Dynamics (MD) such as: GROMACS, NAMD, JMOL etc. Molecular dynamics is a computational method to calculate the time dependent behavior of a molecular system. In this work, MATLAB was used as numerical method for a simple modeling of some diatomic molecules: HCl, H{sub 2} and O{sub 2}. MATLAB is a matrix based numerical software, in order to do numerical analysis, all the functions and equations describing properties of atoms and molecules must be developed manually in MATLAB. In this work, a Morse potential was generated to describe the bond interaction betweenmore » the two atoms. In order to analyze the simultaneous motion of molecules, the Verlet Algorithm derived from Newton’s Equations of Motion (classical mechanics) was operated. Both the Morse potential and the Verlet algorithm were integrated using MATLAB to derive physical properties and the trajectory of the molecules. The data computed by MATLAB is always in the form of a matrix. To visualize it, Visualized Molecular Dynamics (VMD) was performed. Such method is useful for development and testing some types of interaction on a molecular scale. Besides, this can be very helpful for describing some basic principles of molecular interaction for educational purposes.« less

3D modeling based on CityEngine

NASA Astrophysics Data System (ADS)

Jia, Guangyin; Liao, Kaiju

2017-03-01

Currently, there are many 3D modeling softwares, like 3DMAX, AUTOCAD, and more populous BIM softwares represented by REVIT. CityEngine modeling software introduced in this paper can fully utilize the existing GIS data and combine other built models to make 3D modeling on internal and external part of buildings in a rapid and batch manner, so as to improve the 3D modeling efficiency.

Logic Model Checking of Unintended Acceleration Claims in Toyota Vehicles

NASA Technical Reports Server (NTRS)

Gamble, Ed

2012-01-01

Part of the US Department of Transportation investigation of Toyota sudden unintended acceleration (SUA) involved analysis of the throttle control software, JPL Laboratory for Reliable Software applied several techniques including static analysis and logic model checking, to the software; A handful of logic models were build, Some weaknesses were identified; however, no cause for SUA was found; The full NASA report includes numerous other analyses

A graph-based approach to construct target-focused libraries for virtual screening.

PubMed

Naderi, Misagh; Alvin, Chris; Ding, Yun; Mukhopadhyay, Supratik; Brylinski, Michal

2016-01-01

Due to exorbitant costs of high-throughput screening, many drug discovery projects commonly employ inexpensive virtual screening to support experimental efforts. However, the vast majority of compounds in widely used screening libraries, such as the ZINC database, will have a very low probability to exhibit the desired bioactivity for a given protein. Although combinatorial chemistry methods can be used to augment existing compound libraries with novel drug-like compounds, the broad chemical space is often too large to be explored. Consequently, the trend in library design has shifted to produce screening collections specifically tailored to modulate the function of a particular target or a protein family. Assuming that organic compounds are composed of sets of rigid fragments connected by flexible linkers, a molecule can be decomposed into its building blocks tracking their atomic connectivity. On this account, we developed eSynth, an exhaustive graph-based search algorithm to computationally synthesize new compounds by reconnecting these building blocks following their connectivity patterns. We conducted a series of benchmarking calculations against the Directory of Useful Decoys, Enhanced database. First, in a self-benchmarking test, the correctness of the algorithm is validated with the objective to recover a molecule from its building blocks. Encouragingly, eSynth can efficiently rebuild more than 80 % of active molecules from their fragment components. Next, the capability to discover novel scaffolds is assessed in a cross-benchmarking test, where eSynth successfully reconstructed 40 % of the target molecules using fragments extracted from chemically distinct compounds. Despite an enormous chemical space to be explored, eSynth is computationally efficient; half of the molecules are rebuilt in less than a second, whereas 90 % take only about a minute to be generated. eSynth can successfully reconstruct chemically feasible molecules from molecular fragments. Furthermore, in a procedure mimicking the real application, where one expects to discover novel compounds based on a small set of already developed bioactives, eSynth is capable of generating diverse collections of molecules with the desired activity profiles. Thus, we are very optimistic that our effort will contribute to targeted drug discovery. eSynth is freely available to the academic community at www.brylinski.org/content/molecular-synthesis.Graphical abstractAssuming that organic compounds are composed of sets of rigid fragments connected by flexible linkers, a molecule can be decomposed into its building blocks tracking their atomic connectivity. Here, we developed eSynth, an automated method to synthesize new compounds by reconnecting these building blocks following the connectivity patterns via an exhaustive graph-based search algorithm. eSynth opens up a possibility to rapidly construct virtual screening libraries for targeted drug discovery.

ControlShell - A real-time software framework

NASA Technical Reports Server (NTRS)

Schneider, Stanley A.; Ullman, Marc A.; Chen, Vincent W.

1991-01-01

ControlShell is designed to enable modular design and impplementation of real-time software. It is an object-oriented tool-set for real-time software system programming. It provides a series of execution and data interchange mechansims that form a framework for building real-time applications. These mechanisms allow a component-based approach to real-time software generation and mangement. By defining a set of interface specifications for intermodule interaction, ControlShell provides a common platform that is the basis for real-time code development and exchange.

Software management tools: Lessons learned from use

NASA Technical Reports Server (NTRS)

Reifer, D. J.; Valett, J.; Knight, J.; Wenneson, G.

1985-01-01

Experience in inserting software project planning tools into more than 100 projects producing mission critical software are discussed. The problems the software project manager faces are listed along with methods and tools available to handle them. Experience is reported with the Project Manager's Workstation (PMW) and the SoftCost-R cost estimating package. Finally, the results of a survey, which looked at what could be done in the future to overcome the problems experienced and build a set of truly useful tools, are presented.

Tonal Interface to MacroMolecules (TIMMol): A Textual and Tonal Tool for Molecular Visualization

ERIC Educational Resources Information Center

Cordes, Timothy J.; Carlson, C. Britt; Forest, Katrina T.

2008-01-01

We developed the three-dimensional visualization software, Tonal Interface to MacroMolecules or TIMMol, for studying atomic coordinates of protein structures. Key features include audio tones indicating x, y, z location, identification of the cursor location in one-dimensional and three-dimensional space, textual output that can be easily linked…

Teaching Introductory Mineralogy With the GeoWall

NASA Astrophysics Data System (ADS)

Anderson, C. D.; Haymon, R. M.

2003-12-01

Mineralogy, like many topics in Earth Sciences, contains inherently three-dimensional topics that are difficult to teach. Concepts such as crystal symmetry and forms, Miller indices, the polymerization of silica tetrahedra and resulting structures of silicate mineral groups, and the interaction of light and minerals are particularly difficult. Two-dimensional diagrams are limited in their effectiveness, and physical models, while effective, are expensive and do not work as well in large class settings. The GeoWall system brings the effectiveness of physical models to the large classroom. In Fall 2003, we will integrate the GeoWall into our introductory mineralogy classes at UCSB using a combination of commercial software, atomic structure models available on the web, and custom content created in-house. The commercial software SHAPE (www.shapesoftware.com) allows users to build and display crystal shapes and their symmetry. Though not designed for the GeoWall, the software's stereopair display mode works perfectly on the system. Using the Chime web browser plug-in (www.mdl.com), computer models of silicate minerals available from the Virtual Museum of Minerals and Molecules (www.soils.umn.eduvirtual_museum) provide an interactive display of silicate mineral structure that illustrates the tetrahedral framework. Again, while not developed for the GeoWall, the Chime plug-in works seamlessly with the GeoWall hardware. 3-D GeoWall images that display light paths through minerals, and reveal relationships between crystal symmetry and optical indicatrix properties, have been developed in-house using a combination of SHAPE and 3D modeling software. The 3-D GeoWall images should convey in an instant these difficult concepts that students historically have struggled to visualize. Initial assessment of the GeoWall's effectiveness as a mineralogy teaching aid at UCSB in Fall 2003 will come from the instructor's impressions and by comparing test scores with classes from previous years.

Systems Engineering Building Advances Power Grid Research

ScienceCinema

Virden, Jud; Huang, Henry; Skare, Paul; Dagle, Jeff; Imhoff, Carl; Stoustrup, Jakob; Melton, Ron; Stiles, Dennis; Pratt, Rob

2018-01-16

Researchers and industry are now better equipped to tackle the nation’s most pressing energy challenges through PNNL’s new Systems Engineering Building – including challenges in grid modernization, buildings efficiency and renewable energy integration. This lab links real-time grid data, software platforms, specialized laboratories and advanced computing resources for the design and demonstration of new tools to modernize the grid and increase buildings energy efficiency.

Analysis of a school building damaged by the 2015 Ranau earthquake Malaysia

NASA Astrophysics Data System (ADS)

Takano, Shugo; Saito, Taiki

2017-10-01

On June 5th, 2015 a severe earthquake with a moment Magnitude of 6.0 occurred in Ranau, Malaysia. Depth of the epicenter is 10 km. Due to the earthquake, many facilities were damaged and 18 people were killed due to rockfalls [1]. Because the British Standard (BS) is adopted as a regulation for built buildings in Malaysia, the seismic force is not considered in the structural design. Therefore, the seismic resistance of Malaysian buildings is unclear. To secure the human life and building safety, it is important to grasp seismic resistance of the building. The objective of this study is to evaluate the seismic resistance of the existing buildings in Malaysia built by the British Standard. A school building that was damaged at the Ranau earthquake is selected as the target building. The building is a four story building and the ground floor is designed to be a parking space for the staff. The structural types are infill masonries where main frame is configured by reinforced concrete columns and beams and brick is installed inside the frame as walls. Analysis is performed using the STERA_3D software that is the software to analyze the seismic performance of buildings developed by one of the authors. Firstly, the natural period of the building is calculated and compared with the result of micro-tremor measurement. Secondly, the nonlinear push-over analysis was conducted to evaluate the horizontal load bearing capacity of the building. Thirdly, the earthquake response analysis was conducted using the time history acceleration data measured at the Ranau earthquake by the seismograph installed at Kota Kinabalu. By comparing the results of earthquake response analysis and the actual damage of the building, the reason that caused damage to the building is clarified.

Managing a Real-Time Embedded Linux Platform with Buildroot

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

Diamond, J.; Martin, K.

2015-01-01

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

RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules.

PubMed

Garcia-Martin, Juan Antonio; Dotu, Ivan; Clote, Peter

2015-07-01

Several algorithms for RNA inverse folding have been used to design synthetic riboswitches, ribozymes and thermoswitches, whose activity has been experimentally validated. The RNAiFold software is unique among approaches for inverse folding in that (exhaustive) constraint programming is used instead of heuristic methods. For that reason, RNAiFold can generate all sequences that fold into the target structure or determine that there is no solution. RNAiFold 2.0 is a complete overhaul of RNAiFold 1.0, rewritten from the now defunct COMET language to C++. The new code properly extends the capabilities of its predecessor by providing a user-friendly pipeline to design synthetic constructs having the functionality of given Rfam families. In addition, the new software supports amino acid constraints, even for proteins translated in different reading frames from overlapping coding sequences; moreover, structure compatibility/incompatibility constraints have been expanded. With these features, RNAiFold 2.0 allows the user to design single RNA molecules as well as hybridization complexes of two RNA molecules. the web server, source code and linux binaries are publicly accessible at http://bioinformatics.bc.edu/clotelab/RNAiFold2.0. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Role of step edges on the structure formation of α-6T on Ag(441)

NASA Astrophysics Data System (ADS)

Wagner, Thorsten; Fritz, Daniel Roman; Rudolfová, Zdena; Zeppenfeld, Peter

2018-01-01

Controlling the orientation of organic molecules on surfaces is important in order to tune the physical properties of the organic thin films and, thereby, increase the performance of organic thin film devices. Here, we present a scanning tunneling microscopy (STM) and photoelectron emission microscopy (PEEM) study of the deposition of the organic dye pigment α-sexithiophene (α-6T) on the vicinal Ag(441) surface. In the presence of the steps on the Ag(441) surface, the α-6T molecules exclusively align parallel to the step edges oriented along the [1 1 bar0]-direction of the substrate. The STM results further reveal that the adsorption of the α-6T molecules is accompanied by various restructuring of the substrate surface: Initially, the molecules prefer the Ag(551) building blocks of the Ag(441) surface. The Ag(551) termination of the terraces is then changed to a predominately Ag(331) one upon completion of the first α-6T monolayer. When closing the two layer thick wetting layer, the original ratio of Ag(331) and Ag(551) building blocks ( ≈ 1:1) is recovered, but a phase separation into microfacets, which are composed either of Ag(331) or of Ag(551) building blocks, is found.

An ontology for major histocompatibility restriction.

PubMed

Vita, Randi; Overton, James A; Seymour, Emily; Sidney, John; Kaufman, Jim; Tallmadge, Rebecca L; Ellis, Shirley; Hammond, John; Butcher, Geoff W; Sette, Alessandro; Peters, Bjoern

2016-01-01

MHC molecules are a highly diverse family of proteins that play a key role in cellular immune recognition. Over time, different techniques and terminologies have been developed to identify the specific type(s) of MHC molecule involved in a specific immune recognition context. No consistent nomenclature exists across different vertebrate species. To correctly represent MHC related data in The Immune Epitope Database (IEDB), we built upon a previously established MHC ontology and created an ontology to represent MHC molecules as they relate to immunological experiments. This ontology models MHC protein chains from 16 species, deals with different approaches used to identify MHC, such as direct sequencing verses serotyping, relates engineered MHC molecules to naturally occurring ones, connects genetic loci, alleles, protein chains and multi-chain proteins, and establishes evidence codes for MHC restriction. Where available, this work is based on existing ontologies from the OBO foundry. Overall, representing MHC molecules provides a challenging and practically important test case for ontology building, and could serve as an example of how to integrate other ontology building efforts into web resources.

Molecule kernels: a descriptor- and alignment-free quantitative structure-activity relationship approach.

PubMed

Mohr, Johannes A; Jain, Brijnesh J; Obermayer, Klaus

2008-09-01

Quantitative structure activity relationship (QSAR) analysis is traditionally based on extracting a set of molecular descriptors and using them to build a predictive model. In this work, we propose a QSAR approach based directly on the similarity between the 3D structures of a set of molecules measured by a so-called molecule kernel, which is independent of the spatial prealignment of the compounds. Predictors can be build using the molecule kernel in conjunction with the potential support vector machine (P-SVM), a recently proposed machine learning method for dyadic data. The resulting models make direct use of the structural similarities between the compounds in the test set and a subset of the training set and do not require an explicit descriptor construction. We evaluated the predictive performance of the proposed method on one classification and four regression QSAR datasets and compared its results to the results reported in the literature for several state-of-the-art descriptor-based and 3D QSAR approaches. In this comparison, the proposed molecule kernel method performed better than the other QSAR methods.

SNPversity: A web-based tool for visualizing diversity

USDA-ARS?s Scientific Manuscript database

Background: Many stand-alone desktop software suites exist to visualize single nucleotide polymorphisms (SNP) diversity, but web-based software that can be easily implemented and used for biological databases is absent. SNPversity was created to answer this need by building an open-source visualizat...

Teacher-Pedagogy Approach for Sustainable Proficiency

ERIC Educational Resources Information Center

Nath, Baiju K.; Balan, Meera

2010-01-01

Quality concerns of an institution shall be explained in terms of hardware and software. The hardware comprises of building and other infrastructural facilities and software involves teachers, students and administrative staff. Various agencies such as National Council for Educational Research & Training (NCERT), National Council for Teacher…

RESEARCH AND DESIGN ABOUT VERSATILE 3D-CAD ENGINE FOR CONSTRUCTION

NASA Astrophysics Data System (ADS)

Tanaka, Shigenori; Kubota, Satoshi; Kitagawa, Etsuji; Monobe, Kantaro; Nakamura, Kenji

In the construction field of Japan, it is an important subject to build the environment where 3D-CAD data is used for CALS/EC, information construction, and an improvement in productivity. However, in the construction field, 3D-CAD software does not exist under the present circumstances. Then, in order to support development of domestic 3D-CAD software, it is required to develop a 3D-CAD engine. In this research, in order to familiarize the 3D-CAD software at low cost and quickly and build the environment where the 3D-CAD software is utilizable, investigation for designing a 3D-CAD engine is proposed. The target for investigation are the use scene of 3D-CAD, the seeds which accompany 3D-CAD, a standardization trend, existing products, IT component engineering. Based on results of the investigation, the functional requirements for the 3D-CAD engine for the construction field were concluded.

Scalable geocomputation: evolving an environmental model building platform from single-core to supercomputers

NASA Astrophysics Data System (ADS)

Schmitz, Oliver; de Jong, Kor; Karssenberg, Derek

2017-04-01

There is an increasing demand to run environmental models on a big scale: simulations over large areas at high resolution. The heterogeneity of available computing hardware such as multi-core CPUs, GPUs or supercomputer potentially provides significant computing power to fulfil this demand. However, this requires detailed knowledge of the underlying hardware, parallel algorithm design and the implementation thereof in an efficient system programming language. Domain scientists such as hydrologists or ecologists often lack this specific software engineering knowledge, their emphasis is (and should be) on exploratory building and analysis of simulation models. As a result, models constructed by domain specialists mostly do not take full advantage of the available hardware. A promising solution is to separate the model building activity from software engineering by offering domain specialists a model building framework with pre-programmed building blocks that they combine to construct a model. The model building framework, consequently, needs to have built-in capabilities to make full usage of the available hardware. Developing such a framework providing understandable code for domain scientists and being runtime efficient at the same time poses several challenges on developers of such a framework. For example, optimisations can be performed on individual operations or the whole model, or tasks need to be generated for a well-balanced execution without explicitly knowing the complexity of the domain problem provided by the modeller. Ideally, a modelling framework supports the optimal use of available hardware whichsoever combination of model building blocks scientists use. We demonstrate our ongoing work on developing parallel algorithms for spatio-temporal modelling and demonstrate 1) PCRaster, an environmental software framework (http://www.pcraster.eu) providing spatio-temporal model building blocks and 2) parallelisation of about 50 of these building blocks using the new Fern library (https://github.com/geoneric/fern/), an independent generic raster processing library. Fern is a highly generic software library and its algorithms can be configured according to the configuration of a modelling framework. With manageable programming effort (e.g. matching data types between programming and domain language) we created a binding between Fern and PCRaster. The resulting PCRaster Python multicore module can be used to execute existing PCRaster models without having to make any changes to the model code. We show initial results on synthetic and geoscientific models indicating significant runtime improvements provided by parallel local and focal operations. We further outline challenges in improving remaining algorithms such as flow operations over digital elevation maps and further potential improvements like enhancing disk I/O.

ControlShell: A real-time software framework

NASA Technical Reports Server (NTRS)

Schneider, Stanley A.; Chen, Vincent W.; Pardo-Castellote, Gerardo

1994-01-01

The ControlShell system is a programming environment that enables the development and implementation of complex real-time software. It includes many building tools for complex systems, such as a graphical finite state machine (FSM) tool to provide strategic control. ControlShell has a component-based design, providing interface definitions and mechanisms for building real-time code modules along with providing basic data management. Some of the system-building tools incorporated in ControlShell are a graphical data flow editor, a component data requirement editor, and a state-machine editor. It also includes a distributed data flow package, an execution configuration manager, a matrix package, and an object database and dynamic binding facility. This paper presents an overview of ControlShell's architecture and examines the functions of several of its tools.

Streamlining the Design-to-Build Transition with Build-Optimization Software Tools.

PubMed

Oberortner, Ernst; Cheng, Jan-Fang; Hillson, Nathan J; Deutsch, Samuel

2017-03-17

Scaling-up capabilities for the design, build, and test of synthetic biology constructs holds great promise for the development of new applications in fuels, chemical production, or cellular-behavior engineering. Construct design is an essential component in this process; however, not every designed DNA sequence can be readily manufactured, even using state-of-the-art DNA synthesis methods. Current biological computer-aided design and manufacture tools (bioCAD/CAM) do not adequately consider the limitations of DNA synthesis technologies when generating their outputs. Designed sequences that violate DNA synthesis constraints may require substantial sequence redesign or lead to price-premiums and temporal delays, which adversely impact the efficiency of the DNA manufacturing process. We have developed a suite of build-optimization software tools (BOOST) to streamline the design-build transition in synthetic biology engineering workflows. BOOST incorporates knowledge of DNA synthesis success determinants into the design process to output ready-to-build sequences, preempting the need for sequence redesign. The BOOST web application is available at https://boost.jgi.doe.gov and its Application Program Interfaces (API) enable integration into automated, customized DNA design processes. The herein presented results highlight the effectiveness of BOOST in reducing DNA synthesis costs and timelines.

BIM and IoT: A Synopsis from GIS Perspective

NASA Astrophysics Data System (ADS)

Isikdag, U.

2015-10-01

Internet-of-Things (IoT) focuses on enabling communication between all devices, things that are existent in real life or that are virtual. Building Information Models (BIMs) and Building Information Modelling is a hype that has been the buzzword of the construction industry for last 15 years. BIMs emerged as a result of a push by the software companies, to tackle the problems of inefficient information exchange between different software and to enable true interoperability. In BIM approach most up-to-date an accurate models of a building are stored in shared central databases during the design and the construction of a project and at post-construction stages. GIS based city monitoring / city management applications require the fusion of information acquired from multiple resources, BIMs, City Models and Sensors. This paper focuses on providing a method for facilitating the GIS based fusion of information residing in digital building "Models" and information acquired from the city objects i.e. "Things". Once this information fusion is accomplished, many fields ranging from Emergency Response, Urban Surveillance, Urban Monitoring to Smart Buildings will have potential benefits.

Occupy Hard Drives: Making your work more valuable by giving it away

NASA Astrophysics Data System (ADS)

Weiner, Benjamin J.

2014-01-01

Astronomy is more than ever reliant on scientist-built software, but our systems of supporting research and giving credit for research work have failed to evolve with this reality. Both the perception of short term advantage, and an artificial distinction between "tools" and "science," lead to software and data remaining proprietary or unpublished. The lack of incentives to build and maintain software leads to both a decay of the software infrastructure, and a potential for growing class inequality, a pundit-technician divide. Top-down efforts to direct the field such as the recent US decadal survey have not adequately addressed this future. I argue that writing, freely releasing, and publishing your software is currently not adequately funded, rewarded, or credited, and that you should do it anyway. Writing your software as if you plan to release it is better for you and for the code. Releasing software can get credit from the rest of the community beyond your circle of collaborators or letter-writers, and it can benefit you and everyone else by making astronomy a better place to work. Building a culture of cooperation will be a more effective approach to reforming the system of credit than waiting for leadership from above or outside, but requires that each of us consciously encourage process, values, and behavior that support such a change.

76 FR 4864 - Submission for OMB Review; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-27

...: National Institute of Standards and Technology (NIST). Title: BEES (Building for Environmental and Economic.... Needs and Uses: Building for Environmental and Economic Sustainability (BEES) Please is a voluntary... may be evaluated scientifically using the BEES software. These data include product-specific materials...

Knowledge-intensive software design systems: Can too much knowledge be a burden?

NASA Technical Reports Server (NTRS)

Keller, Richard M.

1992-01-01

While acknowledging the considerable benefits of domain-specific, knowledge-intensive approaches to automated software engineering, it is prudent to carefully examine the costs of such approaches, as well. In adding domain knowledge to a system, a developer makes a commitment to understanding, representing, maintaining, and communicating that knowledge. This substantial overhead is not generally associated with domain-independent approaches. In this paper, I examine the downside of incorporating additional knowledge, and illustrate with examples based on our experience in building the SIGMA system. I also offer some guidelines for developers building domain-specific systems.

Knowledge-intensive software design systems: Can too much knowledge be a burden?

NASA Technical Reports Server (NTRS)

Keller, Richard M.

1992-01-01

While acknowledging the considerable benefits of domain-specific, knowledge-intensive approaches to automated software engineering, it is prudent to carefully examine the costs of such approaches, as well. In adding domain knowledge to a system, a developer makes a commitment to understanding, representing, maintaining, and communicating that knowledge. This substantial overhead is not generally associated with domain-independent approaches. In this paper, I examine the downside of incorporating additional knowledge, and illustrate with examples based on our experiences building the SIGMA system. I also offer some guidelines for developers building domain-specific systems.

Survivability as a Tool for Evaluating Open Source Software

DTIC Science & Technology

2015-06-01

the thesis limited the program development, so it is only able to process project issues (bugs or feature requests), which is an important metric for...Ideally, these insights may provide an analytic framework to generate guidance for decision makers that may support the inclusion of OSS to more...refine their efforts to build quality software and to strengthen their software development communities. 1.4 Research Questions This thesis addresses

Complex small-molecule architectures regulate phenotypic plasticity in a nematode.

PubMed

Bose, Neelanjan; Ogawa, Akira; von Reuss, Stephan H; Yim, Joshua J; Ragsdale, Erik J; Sommer, Ralf J; Schroeder, Frank C

2012-12-07

Chemistry the worm's way: The nematode Pristionchus pacificus constructs elaborate small molecules from modified building blocks of primary metabolism, including an unusual xylopyranose-based nucleoside (see scheme). These compounds act as signaling molecules to control adult phenotypic plasticity and dauer development and provide examples of modular generation of structural diversity in metazoans. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

User-Driven Quality Certification of Workplace Software, the UsersAward Experience

DTIC Science & Technology

2004-06-01

the set of criteria and the chosen level of approval was sufficiently balanced . Furthermore, the fact that both software providers experienced... Worklife - Building Social Capacity - European Approaches, Edition sigma Berlin. Lind, T. (2002). IT-kartan, användare och IT-system i svenskt

Communal Resources in Open Source Software Development

ERIC Educational Resources Information Center

Spaeth, Sebastian; Haefliger, Stefan; von Krogh, Georg; Renzl, Birgit

2008-01-01

Introduction: Virtual communities play an important role in innovation. The paper focuses on the particular form of collective action in virtual communities underlying as Open Source software development projects. Method: Building on resource mobilization theory and private-collective innovation, we propose a theory of collective action in…

DecoyFinder: an easy-to-use python GUI application for building target-specific decoy sets.

PubMed

Cereto-Massagué, Adrià; Guasch, Laura; Valls, Cristina; Mulero, Miquel; Pujadas, Gerard; Garcia-Vallvé, Santiago

2012-06-15

Decoys are molecules that are presumed to be inactive against a target (i.e. will not likely bind to the target) and are used to validate the performance of molecular docking or a virtual screening workflow. The Directory of Useful Decoys database (http://dud.docking.org/) provides a free directory of decoys for use in virtual screening, though it only contains a limited set of decoys for 40 targets.To overcome this limitation, we have developed an application called DecoyFinder that selects, for a given collection of active ligands of a target, a set of decoys from a database of compounds. Decoys are selected if they are similar to active ligands according to five physical descriptors (molecular weight, number of rotational bonds, total hydrogen bond donors, total hydrogen bond acceptors and the octanol-water partition coefficient) without being chemically similar to any of the active ligands used as an input (according to the Tanimoto coefficient between MACCS fingerprints). To the best of our knowledge, DecoyFinder is the first application designed to build target-specific decoy sets. A complete description of the software is included on the application home page. A validation of DecoyFinder on 10 DUD targets is provided as Supplementary Table S1. DecoyFinder is freely available at http://URVnutrigenomica-CTNS.github.com/DecoyFinder.

Machine learning research 1989-90

NASA Technical Reports Server (NTRS)

Porter, Bruce W.; Souther, Arthur

1990-01-01

Multifunctional knowledge bases offer a significant advance in artificial intelligence because they can support numerous expert tasks within a domain. As a result they amortize the costs of building a knowledge base over multiple expert systems and they reduce the brittleness of each system. Due to the inevitable size and complexity of multifunctional knowledge bases, their construction and maintenance require knowledge engineering and acquisition tools that can automatically identify interactions between new and existing knowledge. Furthermore, their use requires software for accessing those portions of the knowledge base that coherently answer questions. Considerable progress was made in developing software for building and accessing multifunctional knowledge bases. A language was developed for representing knowledge, along with software tools for editing and displaying knowledge, a machine learning program for integrating new information into existing knowledge, and a question answering system for accessing the knowledge base.

Unidata: 30 Years of FOSS for the Geosciences

NASA Astrophysics Data System (ADS)

Davis, E.; Ramamurthy, M. K.; Young, J. W.; Fisher, W. I.; Rew, R. K.

2015-12-01

Unidata's core mission is to serve academic research and education communities by facilitating access and use of real-time weather data. To this end, Unidata develops, distributes, and supports several Free and Open Source Software (FOSS) packages. These packages are largely focused on data management, access, analysis and visualization. This presentation will discuss the lessons Unidata has gathered over thirty years of FOSS development, support, and community building. These lessons include what it takes to be a successful FOSS organization, how to adapt to changing "best practices" and the emergence of new FOSS tools and services, and techniques for dealing with software end-of-life. We will also discuss our approach when supporting a varied user community spanning end users and software developers. Strong user support has been an important key to Unidata's successful community building.

ATLAS software stack on ARM64

NASA Astrophysics Data System (ADS)

Smith, Joshua Wyatt; Stewart, Graeme A.; Seuster, Rolf; Quadt, Arnulf; ATLAS Collaboration

2017-10-01

This paper reports on the port of the ATLAS software stack onto new prototype ARM64 servers. This included building the “external” packages that the ATLAS software relies on. Patches were needed to introduce this new architecture into the build as well as patches that correct for platform specific code that caused failures on non-x86 architectures. These patches were applied such that porting to further platforms will need no or only very little adjustments. A few additional modifications were needed to account for the different operating system, Ubuntu instead of Scientific Linux 6 / CentOS7. Selected results from the validation of the physics outputs on these ARM 64-bit servers will be shown. CPU, memory and IO intensive benchmarks using ATLAS specific environment and infrastructure have been performed, with a particular emphasis on the performance vs. energy consumption.

Agile Acceptance Test–Driven Development of Clinical Decision Support Advisories: Feasibility of Using Open Source Software

PubMed Central

Baldwin, Krystal L; Kannan, Vaishnavi; Flahaven, Emily L; Parks, Cassandra J; Ott, Jason M; Willett, Duwayne L

2018-01-01

Background Moving to electronic health records (EHRs) confers substantial benefits but risks unintended consequences. Modern EHRs consist of complex software code with extensive local configurability options, which can introduce defects. Defects in clinical decision support (CDS) tools are surprisingly common. Feasible approaches to prevent and detect defects in EHR configuration, including CDS tools, are needed. In complex software systems, use of test–driven development and automated regression testing promotes reliability. Test–driven development encourages modular, testable design and expanding regression test coverage. Automated regression test suites improve software quality, providing a “safety net” for future software modifications. Each automated acceptance test serves multiple purposes, as requirements (prior to build), acceptance testing (on completion of build), regression testing (once live), and “living” design documentation. Rapid-cycle development or “agile” methods are being successfully applied to CDS development. The agile practice of automated test–driven development is not widely adopted, perhaps because most EHR software code is vendor-developed. However, key CDS advisory configuration design decisions and rules stored in the EHR may prove amenable to automated testing as “executable requirements.” Objective We aimed to establish feasibility of acceptance test–driven development of clinical decision support advisories in a commonly used EHR, using an open source automated acceptance testing framework (FitNesse). Methods Acceptance tests were initially constructed as spreadsheet tables to facilitate clinical review. Each table specified one aspect of the CDS advisory’s expected behavior. Table contents were then imported into a test suite in FitNesse, which queried the EHR database to automate testing. Tests and corresponding CDS configuration were migrated together from the development environment to production, with tests becoming part of the production regression test suite. Results We used test–driven development to construct a new CDS tool advising Emergency Department nurses to perform a swallowing assessment prior to administering oral medication to a patient with suspected stroke. Test tables specified desired behavior for (1) applicable clinical settings, (2) triggering action, (3) rule logic, (4) user interface, and (5) system actions in response to user input. Automated test suite results for the “executable requirements” are shown prior to building the CDS alert, during build, and after successful build. Conclusions Automated acceptance test–driven development and continuous regression testing of CDS configuration in a commercial EHR proves feasible with open source software. Automated test–driven development offers one potential contribution to achieving high-reliability EHR configuration. Vetting acceptance tests with clinicians elicits their input on crucial configuration details early during initial CDS design and iteratively during rapid-cycle optimization. PMID:29653922

Agile Acceptance Test-Driven Development of Clinical Decision Support Advisories: Feasibility of Using Open Source Software.

PubMed

Basit, Mujeeb A; Baldwin, Krystal L; Kannan, Vaishnavi; Flahaven, Emily L; Parks, Cassandra J; Ott, Jason M; Willett, Duwayne L

2018-04-13

Moving to electronic health records (EHRs) confers substantial benefits but risks unintended consequences. Modern EHRs consist of complex software code with extensive local configurability options, which can introduce defects. Defects in clinical decision support (CDS) tools are surprisingly common. Feasible approaches to prevent and detect defects in EHR configuration, including CDS tools, are needed. In complex software systems, use of test-driven development and automated regression testing promotes reliability. Test-driven development encourages modular, testable design and expanding regression test coverage. Automated regression test suites improve software quality, providing a "safety net" for future software modifications. Each automated acceptance test serves multiple purposes, as requirements (prior to build), acceptance testing (on completion of build), regression testing (once live), and "living" design documentation. Rapid-cycle development or "agile" methods are being successfully applied to CDS development. The agile practice of automated test-driven development is not widely adopted, perhaps because most EHR software code is vendor-developed. However, key CDS advisory configuration design decisions and rules stored in the EHR may prove amenable to automated testing as "executable requirements." We aimed to establish feasibility of acceptance test-driven development of clinical decision support advisories in a commonly used EHR, using an open source automated acceptance testing framework (FitNesse). Acceptance tests were initially constructed as spreadsheet tables to facilitate clinical review. Each table specified one aspect of the CDS advisory's expected behavior. Table contents were then imported into a test suite in FitNesse, which queried the EHR database to automate testing. Tests and corresponding CDS configuration were migrated together from the development environment to production, with tests becoming part of the production regression test suite. We used test-driven development to construct a new CDS tool advising Emergency Department nurses to perform a swallowing assessment prior to administering oral medication to a patient with suspected stroke. Test tables specified desired behavior for (1) applicable clinical settings, (2) triggering action, (3) rule logic, (4) user interface, and (5) system actions in response to user input. Automated test suite results for the "executable requirements" are shown prior to building the CDS alert, during build, and after successful build. Automated acceptance test-driven development and continuous regression testing of CDS configuration in a commercial EHR proves feasible with open source software. Automated test-driven development offers one potential contribution to achieving high-reliability EHR configuration. Vetting acceptance tests with clinicians elicits their input on crucial configuration details early during initial CDS design and iteratively during rapid-cycle optimization. ©Mujeeb A Basit, Krystal L Baldwin, Vaishnavi Kannan, Emily L Flahaven, Cassandra J Parks, Jason M Ott, Duwayne L Willett. Originally published in JMIR Medical Informatics (http://medinform.jmir.org), 13.04.2018.

A Solution-Processable Molecule using Thieno[3,2-b]thiophene as Building Block for Efficient Organic Solar Cells.

PubMed

Wei, Huan; Chen, Weichao; Han, Liangliang; Wang, Ting; Bao, Xichang; Li, Xiaoyun; Liu, Jie; Zhou, Yuanhang; Yang, Renqiang

2015-08-01

A solution-processed acceptor-π-donor-π-acceptor (A-π-D-π-A) type small molecule, namely DCATT, has been designed and synthesized for the application as donor material in organic solar cells. The fused aromatic unit thieno[3,2-b]thiophene (TT) flanked with thiophene is applied as π bridge, while 4,8-bisthienyl substituted benzodithiophene (BDT) and 2-ethylhexyl cyanoacetate are chosen as the central building block and end group, respectively. Introduction of fused ring to the small molecule enhances the conjugation length of the main chain, and gives a strong tendency to form π-π stacking with a large overlapping area which favors to high charge carrier transport. Small-molecule organic solar cells based on blends of DCATT and fullerene acceptor exhibit power conversion efficiencies as high as 5.20 % under the illumination of AM 1.5G, 100 mW cm(-2) . © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chemistry Modeling for Aerothermodynamics and TPS

NASA Technical Reports Server (NTRS)

Wang, Dunyou; Stallcop, James R.; Dateo, Christopher e.; Schwenke, David W.; Halicioglu, Timur; Huo, winifred M.

2005-01-01

Recent advances in supercomputers and highly scalable quantum chemistry software render computational chemistry methods a viable means of providing chemistry data for aerothermal analysis at a specific level of confidence. Four examples of first principles quantum chemistry calculations will be presented. Study of the highly nonequilibrium rotational distribution of a nitrogen molecule from the exchange reaction N + N2 illustrates how chemical reactions can influence rotational distribution. The reaction C2H + H2 is one example of a radical reaction that occurs during hypersonic entry into an atmosphere containing methane. A study of the etching of a Si surface illustrates our approach to surface reactions. A recently developed web accessible database and software tool (DDD) that provides the radiation profile of diatomic molecules is also described.

Chemistry Modeling for Aerothermodynamics and TPS

NASA Technical Reports Server (NTRS)

Wang, Dun-You; Stallcop, James R.; Dateo, Christopher E.; Schwenke, David W.; Haliciogiu, Timur; Huo, Winifred

2004-01-01

Recent advances in supercomputers and highly scalable quantum chemistry software render computational chemistry methods a viable means of providing chemistry data for aerothermal analysis at a specific level of confidence. Four examples of first principles quantum chemistry calculations will be presented. The study of the highly nonequilibrium rotational distribution of nitrogen molecule from the exchange reaction N + N2 illustrates how chemical reactions can influence the rotational distribution. The reaction C2H + H2 is one example of a radical reaction that occurs during hypersonic entry into a methane containing atmosphere. A study of the etching of Si surface illustrates our approach to surface reactions. A recently developed web accessible database and software tool (DDD) that provides the radiation profile of diatomic molecules is also described.

SSMNG Software Service Manager: A Scalable Building Blocks Architecture for PUS Services & FDIR Management

NASA Astrophysics Data System (ADS)

Lisio, Giovanni; Candia, Sante; Campolo, Giovanni; Pascucci, Dario

2011-08-01

Thales Alenia Space Italy has carried out the definition of a configurable (on mission basis) PUS ECSS-E_70- 41A see [3] Centralised Services Layer, characterised by:- a mission-independent set of 'classes' implementing the services logic.- a mission-dependent set of configuration data and selection flags.The software components belonging to this layer implement the PUS standard services ECSS-E_70-41A and a set of mission-specific services. The design of this layer has been performed by separating the services mechanisms (mission-independent execution logic) from the services configuration information (mission-dependent data). Once instantiated for a specific mission, the PUS Centralised Services Layer offers a large set of capabilities available to the CSCI's Applications Layer. This paper describes the building blocks PUS architectural solution developed by Thales Alenia Space Italy, emphasizing the mechanisms which allow easy configuration of the Scalable PUS library to fulfill the requirements of different missions. This paper also focus the Thales Alenia Space solution to automatically generate the mission-specific "PUS Services" flight software based on mission specific requirements. Building the PUS services mechanisms, which are configurable on mission basis is part of the PRIMA (Multipurpose Spacecraft Bus ) 'missionisation' process improvement. PRIMA Platform Avionics Software (ASW) is continuously evolving to improve modularity and standardization of interfaces and of SW components (see references in [1]).

Minimizing pulling geometry errors in atomic force microscope single molecule force spectroscopy.

PubMed

Rivera, Monica; Lee, Whasil; Ke, Changhong; Marszalek, Piotr E; Cole, Daniel G; Clark, Robert L

2008-10-01

In atomic force microscopy-based single molecule force spectroscopy (AFM-SMFS), it is assumed that the pulling angle is negligible and that the force applied to the molecule is equivalent to the force measured by the instrument. Recent studies, however, have indicated that the pulling geometry errors can drastically alter the measured force-extension relationship of molecules. Here we describe a software-based alignment method that repositions the cantilever such that it is located directly above the molecule's substrate attachment site. By aligning the applied force with the measurement axis, the molecule is no longer undergoing combined loading, and the full force can be measured by the cantilever. Simulations and experimental results verify the ability of the alignment program to minimize pulling geometry errors in AFM-SMFS studies.

Investigating interoperability of the LSST data management software stack with Astropy

NASA Astrophysics Data System (ADS)

Jenness, Tim; Bosch, James; Owen, Russell; Parejko, John; Sick, Jonathan; Swinbank, John; de Val-Borro, Miguel; Dubois-Felsmann, Gregory; Lim, K.-T.; Lupton, Robert H.; Schellart, Pim; Krughoff, K. S.; Tollerud, Erik J.

2016-07-01

The Large Synoptic Survey Telescope (LSST) will be an 8.4m optical survey telescope sited in Chile and capable of imaging the entire sky twice a week. The data rate of approximately 15TB per night and the requirements to both issue alerts on transient sources within 60 seconds of observing and create annual data releases means that automated data management systems and data processing pipelines are a key deliverable of the LSST construction project. The LSST data management software has been in development since 2004 and is based on a C++ core with a Python control layer. The software consists of nearly a quarter of a million lines of code covering the system from fundamental WCS and table libraries to pipeline environments and distributed process execution. The Astropy project began in 2011 as an attempt to bring together disparate open source Python projects and build a core standard infrastructure that can be used and built upon by the astronomy community. This project has been phenomenally successful in the years since it has begun and has grown to be the de facto standard for Python software in astronomy. Astropy brings with it considerable expectations from the community on how astronomy Python software should be developed and it is clear that by the time LSST is fully operational in the 2020s many of the prospective users of the LSST software stack will expect it to be fully interoperable with Astropy. In this paper we describe the overlap between the LSST science pipeline software and Astropy software and investigate areas where the LSST software provides new functionality. We also discuss the possibilities of re-engineering the LSST science pipeline software to build upon Astropy, including the option of contributing affliated packages.

GERICOS: A Generic Framework for the Development of On-Board Software

NASA Astrophysics Data System (ADS)

Plasson, P.; Cuomo, C.; Gabriel, G.; Gauthier, N.; Gueguen, L.; Malac-Allain, L.

2016-08-01

This paper presents an overview of the GERICOS framework (GEneRIC Onboard Software), its architecture, its various layers and its future evolutions. The GERICOS framework, developed and qualified by LESIA, offers a set of generic, reusable and customizable software components for the rapid development of payload flight software. The GERICOS framework has a layered structure. The first layer (GERICOS::CORE) implements the concept of active objects and forms an abstraction layer over the top of real-time kernels. The second layer (GERICOS::BLOCKS) offers a set of reusable software components for building flight software based on generic solutions to recurrent functionalities. The third layer (GERICOS::DRIVERS) implements software drivers for several COTS IP cores of the LEON processor ecosystem.

Modular Software for Spacecraft Navigation Using the Global Positioning System (GPS)

NASA Technical Reports Server (NTRS)

Truong, S. H.; Hartman, K. R.; Weidow, D. A.; Berry, D. L.; Oza, D. H.; Long, A. C.; Joyce, E.; Steger, W. L.

1996-01-01

The Goddard Space Flight Center Flight Dynamics and Mission Operations Divisions have jointly investigated the feasibility of engineering modular Global Positioning SYSTEM (GPS) navigation software to support both real time flight and ground postprocessing configurations. The goals of this effort are to define standard GPS data interfaces and to engineer standard, reusable navigation software components that can be used to build a broad range of GPS navigation support applications. The paper discusses the GPS modular software (GMOD) system and operations concepts, major requirements, candidate software architecture, feasibility assessment and recommended software interface standards. In additon, ongoing efforts to broaden the scope of the initial study and to develop modular software to support autonomous navigation using GPS are addressed,

Validation of highly reliable, real-time knowledge-based systems

NASA Technical Reports Server (NTRS)

Johnson, Sally C.

1988-01-01

Knowledge-based systems have the potential to greatly increase the capabilities of future aircraft and spacecraft and to significantly reduce support manpower needed for the space station and other space missions. However, a credible validation methodology must be developed before knowledge-based systems can be used for life- or mission-critical applications. Experience with conventional software has shown that the use of good software engineering techniques and static analysis tools can greatly reduce the time needed for testing and simulation of a system. Since exhaustive testing is infeasible, reliability must be built into the software during the design and implementation phases. Unfortunately, many of the software engineering techniques and tools used for conventional software are of little use in the development of knowledge-based systems. Therefore, research at Langley is focused on developing a set of guidelines, methods, and prototype validation tools for building highly reliable, knowledge-based systems. The use of a comprehensive methodology for building highly reliable, knowledge-based systems should significantly decrease the time needed for testing and simulation. A proven record of delivering reliable systems at the beginning of the highly visible testing and simulation phases is crucial to the acceptance of knowledge-based systems in critical applications.

Independent verification and validation for Space Shuttle flight software

NASA Technical Reports Server (NTRS)

1992-01-01

The Committee for Review of Oversight Mechanisms for Space Shuttle Software was asked by the National Aeronautics and Space Administration's (NASA) Office of Space Flight to determine the need to continue independent verification and validation (IV&V) for Space Shuttle flight software. The Committee found that the current IV&V process is necessary to maintain NASA's stringent safety and quality requirements for man-rated vehicles. Therefore, the Committee does not support NASA's plan to eliminate funding for the IV&V effort in fiscal year 1993. The Committee believes that the Space Shuttle software development process is not adequate without IV&V and that elimination of IV&V as currently practiced will adversely affect the overall quality and safety of the software, both now and in the future. Furthermore, the Committee was told that no organization within NASA has the expertise or the manpower to replace the current IV&V function in a timely fashion, nor will building this expertise elsewhere necessarily reduce cost. Thus, the Committee does not recommend moving IV&V functions to other organizations within NASA unless the current IV&V is maintained for as long as it takes to build comparable expertise in the replacing organization.

BioSPICE: access to the most current computational tools for biologists.

PubMed

Garvey, Thomas D; Lincoln, Patrick; Pedersen, Charles John; Martin, David; Johnson, Mark

2003-01-01

The goal of the BioSPICE program is to create a framework that provides biologists access to the most current computational tools. At the program midpoint, the BioSPICE member community has produced a software system that comprises contributions from approximately 20 participating laboratories integrated under the BioSPICE Dashboard and a methodology for continued software integration. These contributed software modules are the BioSPICE Dashboard, a graphical environment that combines Open Agent Architecture and NetBeans software technologies in a coherent, biologist-friendly user interface. The current Dashboard permits data sources, models, simulation engines, and output displays provided by different investigators and running on different machines to work together across a distributed, heterogeneous network. Among several other features, the Dashboard enables users to create graphical workflows by configuring and connecting available BioSPICE components. Anticipated future enhancements to BioSPICE include a notebook capability that will permit researchers to browse and compile data to support model building, a biological model repository, and tools to support the development, control, and data reduction of wet-lab experiments. In addition to the BioSPICE software products, a project website supports information exchange and community building.

What Are HyperCard? (Part 2).

ERIC Educational Resources Information Center

Marcus, Stephen

1989-01-01

Presents the second article in a two-part series on HyperCard materials (computer software used to build structures that create patterns and connections) designed for English and language arts classes. Suggests assignments for use with early HyperCard software that can be adapted to a variety of nonverbal "stackware." (MM)

The Use of Geogebra Software as a Calculus Teaching and Learning Tool

ERIC Educational Resources Information Center

Nobre, Cristiane Neri; Meireles, Magali Rezende Gouvêa; Vieira, Niltom, Jr.; de Resende, Mônica Neli; da Costa, Lucivânia Ester; da Rocha, Rejane Corrêa

2016-01-01

Information and Communication Technologies (ICT) in education provide a new learning environment where the student builds his own knowledge, allowing his visualization and experimentation. This study evaluated the Geogebra software in the learning process of Calculus. It was observed that the proposed activities helped in the graphical…

Engaging New Software.

ERIC Educational Resources Information Center

Allen, Denise

1994-01-01

Reviews three educational computer software products: (1) a compact disc-read only memory (CD-ROM) bundle of five mathematics programs from the Apple Education Series; (2) "Sammy's Science House," with science activities for preschool through second grade (Edmark); and (3) "The Cat Came Back," an interactive CD-ROM game designed to build language…

Preventing Exploits Against Software of Uncertain Provenance (PEASOUP)

DTIC Science & Technology

2015-05-01

Together with Strata’s fine-grained confinement, they build up a robust sandbox environment for SOUP that can resist most kind of exploits...Guide to the World’s Most Popular Disassembler. 2008: No Starch Press. 60. Christey, S., 2011 CWE/SANS top 25 most dangerous software errors

Organization of functional interaction of corporate information systems

NASA Astrophysics Data System (ADS)

Safronov, V. V.; Barabanov, V. F.; Podvalniy, S. L.; Nuzhnyy, A. M.

2018-03-01

In this article the methods of specialized software systems integration are analyzed and the concept of seamless integration of production decisions is offered. In view of this concept developed structural and functional schemes of the specialized software are shown. The proposed schemes and models are improved for a machine-building enterprise.

Tips for Ensuring Successful Software Implementation

ERIC Educational Resources Information Center

Weathers, Robert

2013-01-01

Implementing an enterprise-level, mission-critical software system is an infrastructure project akin to other sizable projects, such as building a school. It's costly and complex, takes a year or more to complete, requires the collaboration of many different parties, involves uncertainties, results in a long-lived asset requiring ongoing…

Building Databases for Education. ERIC Digest.

ERIC Educational Resources Information Center

Klausmeier, Jane A.

This digest provides a brief explanation of what a database is; explains how a database can be used; identifies important factors that should be considered when choosing database management system software; and provides citations to sources for finding reviews and evaluations of database management software. The digest is concerned primarily with…

Locking Down the Software Development Environment

DTIC Science & Technology

2014-12-01

OpenSSL code [13]. The OpenSSL software is, as the name implies, open source, a result of many developers coding beginning in 1998 using the C...programming language to build crypto services. OpenSSL is used widely both on the Internet and in firmware [13], further delaying the ability of many

Constraint-Driven Software Design: An Escape from the Waterfall Model.

ERIC Educational Resources Information Center

de Hoog, Robert; And Others

1994-01-01

Presents the principles of a development methodology for software design based on a nonlinear, product-driven approach that integrates quality aspects. Two examples are given to show that the flexibility needed for building high quality systems leads to integrated development environments in which methodology, product, and tools are closely…

Institutional Logics, Indie Software Developers and Platform Governance

ERIC Educational Resources Information Center

Qiu, Yixin

2013-01-01

This two-essay dissertation aims to study institutional logics in the context of Apple's independent third-party software developers. In essay 1, I investigate the embedded agency aspect of the institutional logics theory. It builds on the premise that logics constrain preferences, interests and behaviors of individuals and organizations, thereby…

Improving Mathematics Learning of Kindergarten Students through Computer-Assisted Instruction

ERIC Educational Resources Information Center

Foster, Matthew E.; Anthony, Jason L.; Clements, Doug H.; Sarama, Julie; Williams, Jeffrey M.

2016-01-01

This study evaluated the effects of a mathematics software program, the Building Blocks software suite, on young children's mathematics performance. Participants included 247 Kindergartners from 37 classrooms in 9 schools located in low-income communities. Children within classrooms were randomly assigned to receive 21 weeks of computer-assisted…

Four Pillars for Improving the Quality of Safety-Critical Software-Reliant Systems

DTIC Science & Technology

2013-04-01

Studies of safety-critical software-reliant systems developed using the current practices of build-then-test show that requirements and architecture ... design defects make up approximately 70% of all defects, many system level related to operational quality attributes, and 80% of these defects are

Single Molecule Conductance of Oligothiophene Derivatives

NASA Astrophysics Data System (ADS)

Dell, Emma J.

This thesis studies the electronic properties of small organic molecules based on the thiophene motif. If we are to build next-generation devices, advanced materials must be designed which possess requisite electronic functionality. Molecules present attractive candidates for these ad- vanced materials since nanoscale devices are particularly sought after. However, selecting a molecule that is suited to a certain electronic function remains a challenge, and characterization of electronic behavior is therefore critical. Single molecule conductance measurements are a powerful tool to determine properties on the nanoscale and, as such, can be used to investigate novel building blocks that may fulfill the design requirements of next-generation devices. Combining these conductance results with strategic chemical synthesis allows for the development of new families of molecules that show attractive properties for future electronic devices. Since thiophene rings are the fruitflies of organic semiconductors on the bulk scale, they present an intriguing starting point for building functional materials on the nanoscale, and therefore form the structural basis of all molecules studied herein. First, the single-molecule conductance of a family of bithiophene derivatives was measured. A broad distribution in the single-molecule conductance of bithiophene was found compared with that of a biphenyl. This increased breadth in the conductance distribution was shown to be explained by the difference in 5-fold symmetry of thiophene rings as compared to the 6-fold symmetry of benzene rings. The reduced symmetry of thiophene rings results in a restriction on the torsion angle space available to these molecules when bound between two metal electrodes in a junction, causing each molecular junction to sample a different set of conformers in the conductance measurements. By contrast, the rotations of biphenyl are essentially unimpeded by junction binding, allowing each molecular junction to sample similar conformers. This work demonstrates that the conductance of bithiophene displays a strong dependence on the conformational fluctuations accessible within a given junction configuration, and that the symmetry of such small molecules can significantly influence their conductance behavior. Next, the single-molecule conductance of a family of oligothiophenes comprising one to six thiophene units was measured. An anomalous behavior was found: the peak of the conductance histogram distribution did not follow a clear exponential decay with increasing number of thiophene units in the chain. The electronic properties of the materials were characterized by optical spectroscopy and electrochemistry to gain an understanding of the factors affecting the conductance of these molecules. Different conformers in the junction were postulated to be a contributing factor to the anomalous trend in the observed conductance as a function of molecule length. Then, the electronic properties of the thiophene-1,1-dioxide unit were investigated. These motifs have become synthetically accessible in the last decade, due to Rozen's unprecedentedly potent oxidizing reagent - HOF˙CH 3CN - which has been shown to be powerful yet selective enough to oxidize thiophenes in various environments. The resulting thiophene-1,1-dioxides show great promise for electronic devices. The oxidation chemistry of thiophenes was expanded and tuning of the frontier energy levels was demonstrated through combining electron poor and electron rich units. Finally, charge carriers in single-molecule junctions were shown to be tunable within a family of molecules containing these thiophene-1,1-dioxide (TDO) building blocks. Oligomers of TDO were designed in order to increase electron affinity, maintain delocalized frontier orbitals, while significantly decreasing the transport gap. Through thermopower measurements, the dominant charge carriers were shown to change from holes to electrons as the number of TDO units was increased. This resulted in a unique system in which the charge carrier depends on backbone length, providing a new means to tune p- and n-type transport in organic materials. Taken together, the results presented in this thesis offer an insight into how molecular symme- try and the accessible conformers within a junction have important consequences on conductance behavior. Additionally, thiophene-1,1-dioxide is shown to be an exciting unit for single molecule devices, especially when combined with electron rich thiophene flanking groups. By demon- strating, for the first time, a change in conductance pathway with molecular length, this work provides a framework for using frontier orbital levels to strategically design electronic building blocks.

[Construction of educational software about personality disorders].

PubMed

Botti, Nadja Cristiane Lappann; Carneiro, Ana Luíza Marques; Almeida, Camila Souza; Pereira, Cíntia Braga Silva

2011-01-01

The study describes the experience of building educational software in the area of mental health. The software was developed to enable the nursing student identify personality disorders. In this process, we applied the pedagogical framework of Vygotsky and the theoretical framework of the diagnostic criteria defined by DSM-IV. From these references were identified personality disorders characters in stories and / or children's movies. The software development bank was built with multimedia graphics data, sound and explanatory. The software developed like educational game like questions with increasing levels of difficulty. The software was developed with Microsoft Office PowerPoint 2007. It is believed in the validity of this strategy for teaching-learning to the area of mental health nursing.

Thermal dynamic simulation of wall for building energy efficiency under varied climate environment

NASA Astrophysics Data System (ADS)

Wang, Xuejin; Zhang, Yujin; Hong, Jing

2017-08-01

Aiming at different kind of walls in five cities of different zoning for thermal design, using thermal instantaneous response factors method, the author develops software to calculation air conditioning cooling load temperature, thermal response factors, and periodic response factors. On the basis of the data, the author gives the net work analysis about the influence of dynamic thermal of wall on air-conditioning load and thermal environment in building of different zoning for thermal design regional, and put forward the strategy how to design thermal insulation and heat preservation wall base on dynamic thermal characteristic of wall under different zoning for thermal design regional. And then provide the theory basis and the technical references for the further study on the heat preservation with the insulation are in the service of energy saving wall design. All-year thermal dynamic load simulating and energy consumption analysis for new energy-saving building is very important in building environment. This software will provide the referable scientific foundation for all-year new thermal dynamic load simulation, energy consumption analysis, building environment systems control, carrying through farther research on thermal particularity and general particularity evaluation for new energy -saving walls building. Based on which, we will not only expediently design system of building energy, but also analyze building energy consumption and carry through scientific energy management. The study will provide the referable scientific foundation for carrying through farther research on thermal particularity and general particularity evaluation for new energy saving walls building.

Implementation of AN Unmanned Aerial Vehicle System for Large Scale Mapping

NASA Astrophysics Data System (ADS)

Mah, S. B.; Cryderman, C. S.

2015-08-01

Unmanned Aerial Vehicles (UAVs), digital cameras, powerful personal computers, and software have made it possible for geomatics professionals to capture aerial photographs and generate digital terrain models and orthophotographs without using full scale aircraft or hiring mapping professionals. This has been made possible by the availability of miniaturized computers and sensors, and software which has been driven, in part, by the demand for this technology in consumer items such as smartphones. The other force that is in play is the increasing number of Do-It-Yourself (DIY) people who are building UAVs as a hobby or for professional use. Building a UAV system for mapping is an alternative to purchasing a turnkey system. This paper describes factors to be considered when building a UAV mapping system, the choices made, and the test results of a project using this completed system.

Automating the design of scientific computing software

NASA Technical Reports Server (NTRS)

Kant, Elaine

1992-01-01

SINAPSE is a domain-specific software design system that generates code from specifications of equations and algorithm methods. This paper describes the system's design techniques (planning in a space of knowledge-based refinement and optimization rules), user interaction style (user has option to control decision making), and representation of knowledge (rules and objects). It also summarizes how the system knowledge has evolved over time and suggests some issues in building software design systems to facilitate reuse.

Compositional Specification of Software Architecture

NASA Technical Reports Server (NTRS)

Penix, John; Lau, Sonie (Technical Monitor)

1998-01-01

This paper describes our experience using parameterized algebraic specifications to model properties of software architectures. The goal is to model the decomposition of requirements independent of the style used to implement the architecture. We begin by providing an overview of the role of architecture specification in software development. We then describe how architecture specifications are build up from component and connector specifications and give an overview of insights gained from a case study used to validate the method.

Note: Tormenta: An open source Python-powered control software for camera based optical microscopy.

PubMed

Barabas, Federico M; Masullo, Luciano A; Stefani, Fernando D

2016-12-01

Until recently, PC control and synchronization of scientific instruments was only possible through closed-source expensive frameworks like National Instruments' LabVIEW. Nowadays, efficient cost-free alternatives are available in the context of a continuously growing community of open-source software developers. Here, we report on Tormenta, a modular open-source software for the control of camera-based optical microscopes. Tormenta is built on Python, works on multiple operating systems, and includes some key features for fluorescence nanoscopy based on single molecule localization.

Note: Tormenta: An open source Python-powered control software for camera based optical microscopy

NASA Astrophysics Data System (ADS)

Barabas, Federico M.; Masullo, Luciano A.; Stefani, Fernando D.

2016-12-01

Until recently, PC control and synchronization of scientific instruments was only possible through closed-source expensive frameworks like National Instruments' LabVIEW. Nowadays, efficient cost-free alternatives are available in the context of a continuously growing community of open-source software developers. Here, we report on Tormenta, a modular open-source software for the control of camera-based optical microscopes. Tormenta is built on Python, works on multiple operating systems, and includes some key features for fluorescence nanoscopy based on single molecule localization.

Application of the Software as a Service Model to the Control of Complex Building Systems

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

Stadler, Michael; Donadee, Jonathan; Marnay, Chris

2011-03-17

In an effort to create broad access to its optimization software, Lawrence Berkeley National Laboratory (LBNL), in collaboration with the University of California at Davis (UC Davis) and OSISoft, has recently developed a Software as a Service (SaaS) Model for reducing energy costs, cutting peak power demand, and reducing carbon emissions for multipurpose buildings. UC Davis currently collects and stores energy usage data from buildings on its campus. Researchers at LBNL sought to demonstrate that a SaaS application architecture could be built on top of this data system to optimize the scheduling of electricity and heat delivery in the building.more » The SaaS interface, known as WebOpt, consists of two major parts: a) the investment& planning and b) the operations module, which builds on the investment& planning module. The operational scheduling and load shifting optimization models within the operations module use data from load prediction and electrical grid emissions models to create an optimal operating schedule for the next week, reducing peak electricity consumption while maintaining quality of energy services. LBNL's application also provides facility managers with suggested energy infrastructure investments for achieving their energy cost and emission goals based on historical data collected with OSISoft's system. This paper describes these models as well as the SaaS architecture employed by LBNL researchers to provide asset scheduling services to UC Davis. The peak demand, emissions, and cost implications of the asset operation schedule and investments suggested by this optimization model are analysed.« less

Application of the Software as a Service Model to the Control of Complex Building Systems

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

Stadler, Michael; Donadee, Jon; Marnay, Chris

2011-03-18

In an effort to create broad access to its optimization software, Lawrence Berkeley National Laboratory (LBNL), in collaboration with the University of California at Davis (UC Davis) and OSISoft, has recently developed a Software as a Service (SaaS) Model for reducing energy costs, cutting peak power demand, and reducing carbon emissions for multipurpose buildings. UC Davis currently collects and stores energy usage data from buildings on its campus. Researchers at LBNL sought to demonstrate that a SaaS application architecture could be built on top of this data system to optimize the scheduling of electricity and heat delivery in the building.more » The SaaS interface, known as WebOpt, consists of two major parts: a) the investment& planning and b) the operations module, which builds on the investment& planning module. The operational scheduling and load shifting optimization models within the operations module use data from load prediction and electrical grid emissions models to create an optimal operating schedule for the next week, reducing peak electricity consumption while maintaining quality of energy services. LBNL's application also provides facility managers with suggested energy infrastructure investments for achieving their energy cost and emission goals based on historical data collected with OSISoft's system. This paper describes these models as well as the SaaS architecture employed by LBNL researchers to provide asset scheduling services to UC Davis. The peak demand, emissions, and cost implications of the asset operation schedule and investments suggested by this optimization model are analyzed.« less

The Web Resource Collaboration Center

ERIC Educational Resources Information Center

Dunlap, Joanna C.

2004-01-01

The Web Resource Collaboration Center (WRCC) is a web-based tool developed to help software engineers build their own web-based learning and performance support systems. Designed using various online communication and collaboration technologies, the WRCC enables people to: (1) build a learning and professional development resource that provides…

BESTEST-EX | Buildings | NREL

Science.gov Websites

method for testing home energy audit software and associated calibration methods. BESTEST-EX is one of Energy Analysis Model Calibration Methods. When completed, the ANSI/RESNET SMOT will specify test procedures for evaluating calibration methods used in conjunction with predicting building energy use and

Symbolic derivation of high-order Rayleigh-Schroedinger perturbation energies using computer algebra: Application to vibrational-rotational analysis of diatomic molecules

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

Herbert, John M.

1997-01-01

Rayleigh-Schroedinger perturbation theory is an effective and popular tool for describing low-lying vibrational and rotational states of molecules. This method, in conjunction with ab initio techniques for computation of electronic potential energy surfaces, can be used to calculate first-principles molecular vibrational-rotational energies to successive orders of approximation. Because of mathematical complexities, however, such perturbation calculations are rarely extended beyond the second order of approximation, although recent work by Herbert has provided a formula for the nth-order energy correction. This report extends that work and furnishes the remaining theoretical details (including a general formula for the Rayleigh-Schroedinger expansion coefficients) necessary formore » calculation of energy corrections to arbitrary order. The commercial computer algebra software Mathematica is employed to perform the prohibitively tedious symbolic manipulations necessary for derivation of generalized energy formulae in terms of universal constants, molecular constants, and quantum numbers. As a pedagogical example, a Hamiltonian operator tailored specifically to diatomic molecules is derived, and the perturbation formulae obtained from this Hamiltonian are evaluated for a number of such molecules. This work provides a foundation for future analyses of polyatomic molecules, since it demonstrates that arbitrary-order perturbation theory can successfully be applied with the aid of commercially available computer algebra software.« less

Experimental Raman and IR spectral and theoretical studies of vibrational spectrum and molecular structure of Pantothenic acid (vitamin B5)

NASA Astrophysics Data System (ADS)

Srivastava, Mayuri; Singh, N. P.; Yadav, R. A.

2014-08-01

Vibrational spectrum of Pantothenic acid has been investigated using experimental IR and Raman spectroscopies and density functional theory methods available with the Gaussian 09 software. Vibrational assignments of the observed IR and Raman bands have been proposed in light of the results obtained from computations. In order to assign the observed IR and Raman frequencies the potential energy distributions (PEDs) have also been computed using GAR2PED software. Optimized geometrical parameters suggest that the overall symmetry of the molecule is C1. The molecule is found to possess eight conformations. Conformational analysis was carried out to obtain the most stable configuration of the molecule. In the present paper the vibrational features of the lowest energy conformer C-I have been studied. The two methyl groups have slightly distorted symmetries from C3V. The acidic Osbnd H bond is found to be the smallest one. To investigate molecular stability and bond strength we have used natural bond orbital analysis (NBO). Charge transfer occurs in the molecule have been shown by the calculated highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) energies. The mapping of electron density iso-surface with electrostatic potential (ESP), has been carried out to get the information about the size, shape, charge density distribution and site of chemical reactivity of the molecule.

Single-Molecule Methods for Nucleotide Excision Repair: Building a System to Watch Repair in Real Time.

PubMed

Kong, Muwen; Beckwitt, Emily C; Springall, Luke; Kad, Neil M; Van Houten, Bennett

2017-01-01

Single-molecule approaches to solving biophysical problems are powerful tools that allow static and dynamic real-time observations of specific molecular interactions of interest in the absence of ensemble-averaging effects. Here, we provide detailed protocols for building an experimental system that employs atomic force microscopy and a single-molecule DNA tightrope assay based on oblique angle illumination fluorescence microscopy. Together with approaches for engineering site-specific lesions into DNA substrates, these complementary biophysical techniques are well suited for investigating protein-DNA interactions that involve target-specific DNA-binding proteins, such as those engaged in a variety of DNA repair pathways. In this chapter, we demonstrate the utility of the platform by applying these techniques in the studies of proteins participating in nucleotide excision repair. © 2017 Elsevier Inc. All rights reserved.

Kinetochores: if you build it, they will come.

PubMed

DeLuca, Jennifer G; Salmon, E D

2004-11-09

Successful mitosis depends critically on the segregation of chromosomes by kinetochore microtubules. A recent paper describes a conserved protein network from Caenorhabditis elegans that is composed of three classes of molecules, each of which contributes uniquely to the building of the kinetochore-microtubule attachment site.

WIRM: An Open Source Toolkit for Building Biomedical Web Applications

PubMed Central

Jakobovits, Rex M.; Rosse, Cornelius; Brinkley, James F.

2002-01-01

This article describes an innovative software toolkit that allows the creation of web applications that facilitate the acquisition, integration, and dissemination of multimedia biomedical data over the web, thereby reducing the cost of knowledge sharing. There is a lack of high-level web application development tools suitable for use by researchers, clinicians, and educators who are not skilled programmers. Our Web Interfacing Repository Manager (WIRM) is a software toolkit that reduces the complexity of building custom biomedical web applications. WIRM’s visual modeling tools enable domain experts to describe the structure of their knowledge, from which WIRM automatically generates full-featured, customizable content management systems. PMID:12386108

Design Automation in Synthetic Biology.

PubMed

Appleton, Evan; Madsen, Curtis; Roehner, Nicholas; Densmore, Douglas

2017-04-03

Design automation refers to a category of software tools for designing systems that work together in a workflow for designing, building, testing, and analyzing systems with a target behavior. In synthetic biology, these tools are called bio-design automation (BDA) tools. In this review, we discuss the BDA tools areas-specify, design, build, test, and learn-and introduce the existing software tools designed to solve problems in these areas. We then detail the functionality of some of these tools and show how they can be used together to create the desired behavior of two types of modern synthetic genetic regulatory networks. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

Ontology for Life-Cycle Modeling of Water Distribution Systems: Model View Definition

DTIC Science & Technology

2013-06-01

Research and Development Center, Construction Engineering Research Laboratory (ERDC-CERL) to develop a life-cycle building model have resulted in the...Laboratory (ERDC-CERL) to develop a life-cycle building model have resulted in the definition of a “core” building information model that contains...developed experimental BIM models us- ing commercial off-the-shelf (COTS) software. Those models represent three types of typical low-rise Army

Commercial Building Energy Saver, API

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

Hong, Tianzhen; Piette, Mary; Lee, Sang Hoon

2015-08-27

The CBES API provides Application Programming Interface to a suite of functions to improve energy efficiency of buildings, including building energy benchmarking, preliminary retrofit analysis using a pre-simulation database DEEP, and detailed retrofit analysis using energy modeling with the EnergyPlus simulation engine. The CBES API is used to power the LBNL CBES Web App. It can be adopted by third party developers and vendors into their software tools and platforms.

CosmoQuest Transient Tracker: Opensource Photometry & Astrometry software

NASA Astrophysics Data System (ADS)

Myers, Joseph L.; Lehan, Cory; Gay, Pamela; Richardson, Matthew; CosmoQuest Team

2018-01-01

CosmoQuest is moving from online citizen science, to observational astronomy with the creation of Transient Trackers. This open source software is designed to identify asteroids and other transient/variable objects in image sets. Transient Tracker’s features in final form will include: astrometric and photometric solutions, identification of moving/transient objects, identification of variable objects, and lightcurve analysis. In this poster we present our initial, v0.1 release and seek community input.This software builds on the existing NIH funded ImageJ libraries. Creation of this suite of opensource image manipulation routines is lead by Wayne Rasband and is released primarily under the MIT license. In this release, we are building on these libraries to add source identification for point / point-like sources, and to do astrometry. Our materials released under the Apache 2.0 license on github (http://github.com/CosmoQuestTeam) and documentation can be found at http://cosmoquest.org/TransientTracker.

The Computational Infrastructure for Geodynamics as a Community of Practice

NASA Astrophysics Data System (ADS)

Hwang, L.; Kellogg, L. H.

2016-12-01

Computational Infrastructure for Geodynamics (CIG), geodynamics.org, originated in 2005 out of community recognition that the efforts of individual or small groups of researchers to develop scientifically-sound software is impossible to sustain, duplicates effort, and makes it difficult for scientists to adopt state-of-the art computational methods that promote new discovery. As a community of practice, participants in CIG share an interest in computational modeling in geodynamics and work together on open source software to build the capacity to support complex, extensible, scalable, interoperable, reliable, and reusable software in an effort to increase the return on investment in scientific software development and increase the quality of the resulting software. The group interacts regularly to learn from each other and better their practices formally through webinar series, workshops, and tutorials and informally through listservs and hackathons. Over the past decade, we have learned that successful scientific software development requires at a minimum: collaboration between domain-expert researchers, software developers and computational scientists; clearly identified and committed lead developer(s); well-defined scientific and computational goals that are regularly evaluated and updated; well-defined benchmarks and testing throughout development; attention throughout development to usability and extensibility; understanding and evaluation of the complexity of dependent libraries; and managed user expectations through education, training, and support. CIG's code donation standards provide the basis for recently formalized best practices in software development (geodynamics.org/cig/dev/best-practices/). Best practices include use of version control; widely used, open source software libraries; extensive test suites; portable configuration and build systems; extensive documentation internal and external to the code; and structured, human readable input formats.

3-D Object Recognition from Point Cloud Data

NASA Astrophysics Data System (ADS)

Smith, W.; Walker, A. S.; Zhang, B.

2011-09-01

The market for real-time 3-D mapping includes not only traditional geospatial applications but also navigation of unmanned autonomous vehicles (UAVs). Massively parallel processes such as graphics processing unit (GPU) computing make real-time 3-D object recognition and mapping achievable. Geospatial technologies such as digital photogrammetry and GIS offer advanced capabilities to produce 2-D and 3-D static maps using UAV data. The goal is to develop real-time UAV navigation through increased automation. It is challenging for a computer to identify a 3-D object such as a car, a tree or a house, yet automatic 3-D object recognition is essential to increasing the productivity of geospatial data such as 3-D city site models. In the past three decades, researchers have used radiometric properties to identify objects in digital imagery with limited success, because these properties vary considerably from image to image. Consequently, our team has developed software that recognizes certain types of 3-D objects within 3-D point clouds. Although our software is developed for modeling, simulation and visualization, it has the potential to be valuable in robotics and UAV applications. The locations and shapes of 3-D objects such as buildings and trees are easily recognizable by a human from a brief glance at a representation of a point cloud such as terrain-shaded relief. The algorithms to extract these objects have been developed and require only the point cloud and minimal human inputs such as a set of limits on building size and a request to turn on a squaring option. The algorithms use both digital surface model (DSM) and digital elevation model (DEM), so software has also been developed to derive the latter from the former. The process continues through the following steps: identify and group 3-D object points into regions; separate buildings and houses from trees; trace region boundaries; regularize and simplify boundary polygons; construct complex roofs. Several case studies have been conducted using a variety of point densities, terrain types and building densities. The results have been encouraging. More work is required for better processing of, for example, forested areas, buildings with sides that are not at right angles or are not straight, and single trees that impinge on buildings. Further work may also be required to ensure that the buildings extracted are of fully cartographic quality. A first version will be included in production software later in 2011. In addition to the standard geospatial applications and the UAV navigation, the results have a further advantage: since LiDAR data tends to be accurately georeferenced, the building models extracted can be used to refine image metadata whenever the same buildings appear in imagery for which the GPS/IMU values are poorer than those for the LiDAR.

Introduction to Financial Projection Models. Business Management Instructional Software.

ERIC Educational Resources Information Center

Pomeroy, Robert W., III

This guidebook and teacher's guide accompany a personal computer software program and introduce the key elements of financial projection modeling to project the financial statements of an industrial enterprise. The student will then build a model on an electronic spreadsheet. The guidebook teaches the purpose of a financial model and the steps…

The MDE Diploma: First International Postgraduate Specialization in Model-Driven Engineering

ERIC Educational Resources Information Center

Cabot, Jordi; Tisi, Massimo

2011-01-01

Model-Driven Engineering (MDE) is changing the way we build, operate, and maintain our software-intensive systems. Several projects using MDE practices are reporting significant improvements in quality and performance but, to be able to handle these projects, software engineers need a set of technical and interpersonal skills that are currently…

A UNIMARC Bibliographic Format Database for ABCD

ERIC Educational Resources Information Center

Megnigbeto, Eustache

2012-01-01

Purpose: ABCD is a web-based open and free software suite for library management derived from the UNESCO CDS/ISIS software technology. The first version was launched officially in December 2009 with a MARC 21 bibliographic format database. This paper aims to detail the building of the UNIMARC bibliographic format database for ABCD.…

Default Parallels Plesk Panel Page

Science.gov Websites

services that small businesses want and need. Our software includes key building blocks of cloud service virtualized servers Service Provider Products Parallels® Automation Hosting, SaaS, and cloud computing , the leading hosting automation software. You see this page because there is no Web site at this

Generic Software Architecture for Launchers

NASA Astrophysics Data System (ADS)

Carre, Emilien; Gast, Philippe; Hiron, Emmanuel; Leblanc, Alain; Lesens, David; Mescam, Emmanuelle; Moro, Pierre

2015-09-01

The definition and reuse of generic software architecture for launchers is not so usual for several reasons: the number of European launcher families is very small (Ariane 5 and Vega for these last decades); the real time constraints (reactivity and determinism needs) are very hard; low levels of versatility are required (implying often an ad hoc development of the launcher mission). In comparison, satellites are often built on a generic platform made up of reusable hardware building blocks (processors, star-trackers, gyroscopes, etc.) and reusable software building blocks (middleware, TM/TC, On Board Control Procedure, etc.). If some of these reasons are still valid (e.g. the limited number of development), the increase of the available CPU power makes today an approach based on a generic time triggered middleware (ensuring the full determinism of the system) and a centralised mission and vehicle management (offering more flexibility in the design and facilitating the long term maintenance) achievable. This paper presents an example of generic software architecture which could be envisaged for future launchers, based on the previously described principles and supported by model driven engineering and automatic code generation.

Genoviz Software Development Kit: Java tool kit for building genomics visualization applications.

PubMed

Helt, Gregg A; Nicol, John W; Erwin, Ed; Blossom, Eric; Blanchard, Steven G; Chervitz, Stephen A; Harmon, Cyrus; Loraine, Ann E

2009-08-25

Visualization software can expose previously undiscovered patterns in genomic data and advance biological science. The Genoviz Software Development Kit (SDK) is an open source, Java-based framework designed for rapid assembly of visualization software applications for genomics. The Genoviz SDK framework provides a mechanism for incorporating adaptive, dynamic zooming into applications, a desirable feature of genome viewers. Visualization capabilities of the Genoviz SDK include automated layout of features along genetic or genomic axes; support for user interactions with graphical elements (Glyphs) in a map; a variety of Glyph sub-classes that promote experimentation with new ways of representing data in graphical formats; and support for adaptive, semantic zooming, whereby objects change their appearance depending on zoom level and zooming rate adapts to the current scale. Freely available demonstration and production quality applications, including the Integrated Genome Browser, illustrate Genoviz SDK capabilities. Separation between graphics components and genomic data models makes it easy for developers to add visualization capability to pre-existing applications or build new applications using third-party data models. Source code, documentation, sample applications, and tutorials are available at http://genoviz.sourceforge.net/.

A Study of the Use of Ontologies for Building Computer-Aided Control Engineering Self-Learning Educational Software

NASA Astrophysics Data System (ADS)

García, Isaías; Benavides, Carmen; Alaiz, Héctor; Alonso, Angel

2013-08-01

This paper describes research on the use of knowledge models (ontologies) for building computer-aided educational software in the field of control engineering. Ontologies are able to represent in the computer a very rich conceptual model of a given domain. This model can be used later for a number of purposes in different software applications. In this study, domain ontology about the field of lead-lag compensator design has been built and used for automatic exercise generation, graphical user interface population and interaction with the user at any level of detail, including explanations about why things occur. An application called Onto-CELE (ontology-based control engineering learning environment) uses the ontology for implementing a learning environment that can be used for self and lifelong learning purposes. The experience has shown that the use of knowledge models as the basis for educational software applications is capable of showing students the whole complexity of the analysis and design processes at any level of detail. A practical experience with postgraduate students has shown the mentioned benefits and possibilities of the approach.

Applying object-oriented software engineering at the BaBar collaboration

NASA Astrophysics Data System (ADS)

Jacobsen, Bob; BaBar Collaboration Reconstruction Software Group

1997-02-01

The BaBar experiment at SLAC will start taking data in 1999. We are attempting to build its reconstruction software using good software engineering practices, including the use of object-oriented technology. We summarize our experience to date with analysis and design activities, training, CASE and documentation tools, C++ programming practice and similar topics. The emphasis is on the practical issues of simultaneously introducing new techniques to a large collaboration while under a deadline for system delivery.

Building Energy Monitoring and Analysis

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

Hong, Tianzhen; Feng, Wei; Lu, Alison

This project aimed to develop a standard methodology for building energy data definition, collection, presentation, and analysis; apply the developed methods to a standardized energy monitoring platform, including hardware and software, to collect and analyze building energy use data; and compile offline statistical data and online real-time data in both countries for fully understanding the current status of building energy use. This helps decode the driving forces behind the discrepancy of building energy use between the two countries; identify gaps and deficiencies of current building energy monitoring, data collection, and analysis; and create knowledge and tools to collect and analyzemore » good building energy data to provide valuable and actionable information for key stakeholders.« less

Crawling The Web for Libre: Selecting, Integrating, Extending and Releasing Open Source Software

NASA Astrophysics Data System (ADS)

Truslove, I.; Duerr, R. E.; Wilcox, H.; Savoie, M.; Lopez, L.; Brandt, M.

2012-12-01

Libre is a project developed by the National Snow and Ice Data Center (NSIDC). Libre is devoted to liberating science data from its traditional constraints of publication, location, and findability. Libre embraces and builds on the notion of making knowledge freely available, and both Creative Commons licensed content and Open Source Software are crucial building blocks for, as well as required deliverable outcomes of the project. One important aspect of the Libre project is to discover cryospheric data published on the internet without prior knowledge of the location or even existence of that data. Inspired by well-known search engines and their underlying web crawling technologies, Libre has explored tools and technologies required to build a search engine tailored to allow users to easily discover geospatial data related to the polar regions. After careful consideration, the Libre team decided to base its web crawling work on the Apache Nutch project (http://nutch.apache.org). Nutch is "an open source web-search software project" written in Java, with good documentation, a significant user base, and an active development community. Nutch was installed and configured to search for the types of data of interest, and the team created plugins to customize the default Nutch behavior to better find and categorize these data feeds. This presentation recounts the Libre team's experiences selecting, using, and extending Nutch, and working with the Nutch user and developer community. We will outline the technical and organizational challenges faced in order to release the project's software as Open Source, and detail the steps actually taken. We distill these experiences into a set of heuristics and recommendations for using, contributing to, and releasing Open Source Software.

Towards Archetypes-Based Software Development

NASA Astrophysics Data System (ADS)

Piho, Gunnar; Roost, Mart; Perkins, David; Tepandi, Jaak

We present a framework for the archetypes based engineering of domains, requirements and software (Archetypes-Based Software Development, ABD). An archetype is defined as a primordial object that occurs consistently and universally in business domains and in business software systems. An archetype pattern is a collaboration of archetypes. Archetypes and archetype patterns are used to capture conceptual information into domain specific models that are utilized by ABD. The focus of ABD is on software factories - family-based development artefacts (domain specific languages, patterns, frameworks, tools, micro processes, and others) that can be used to build the family members. We demonstrate the usage of ABD for developing laboratory information management system (LIMS) software for the Clinical and Biomedical Proteomics Group, at the Leeds Institute of Molecular Medicine, University of Leeds.

Identification of vibrational signatures from short chains of interlinked molecule-nanoparticle junctions obtained by inelastic electron tunnelling spectroscopy

NASA Astrophysics Data System (ADS)

Jafri, S. H. M.; Löfås, H.; Fransson, J.; Blom, T.; Grigoriev, A.; Wallner, A.; Ahuja, R.; Ottosson, H.; Leifer, K.

2013-05-01

Short chains containing a series of metal-molecule-nanoparticle nanojunctions are a nano-material system with the potential to give electrical signatures close to those from single molecule experiments while enabling us to build portable devices on a chip. Inelastic electron tunnelling spectroscopy (IETS) measurements provide one of the most characteristic electrical signals of single and few molecules. In interlinked molecule-nanoparticle (NP) chains containing typically 5-7 molecules in a chain, the spectrum is expected to be a superposition of the vibrational signatures of individual molecules. We have established a stable and reproducible molecule-AuNP multi-junction by placing a few 1,8-octanedithiol (ODT) molecules onto a versatile and portable nanoparticle-nanoelectrode platform and measured for the first time vibrational molecular signatures at complex and coupled few-molecule-NP junctions. From quantum transport calculations, we model the IETS spectra and identify vibrational modes as well as the number of molecules contributing to the electron transport in the measured spectra.Short chains containing a series of metal-molecule-nanoparticle nanojunctions are a nano-material system with the potential to give electrical signatures close to those from single molecule experiments while enabling us to build portable devices on a chip. Inelastic electron tunnelling spectroscopy (IETS) measurements provide one of the most characteristic electrical signals of single and few molecules. In interlinked molecule-nanoparticle (NP) chains containing typically 5-7 molecules in a chain, the spectrum is expected to be a superposition of the vibrational signatures of individual molecules. We have established a stable and reproducible molecule-AuNP multi-junction by placing a few 1,8-octanedithiol (ODT) molecules onto a versatile and portable nanoparticle-nanoelectrode platform and measured for the first time vibrational molecular signatures at complex and coupled few-molecule-NP junctions. From quantum transport calculations, we model the IETS spectra and identify vibrational modes as well as the number of molecules contributing to the electron transport in the measured spectra. Electronic supplementary information (ESI) available: Methods and materials. Details of the ab initio calculation of molecular vibrations and inelastic spectra of ODT between two Au electrodes. A model of carrier transport through the molecular junctions. See DOI: 10.1039/c3nr00505d

Leveraging OpenStudio's Application Programming Interfaces: Preprint

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

Long, N.; Ball, B.; Goldwasser, D.

2013-11-01

OpenStudio development efforts have been focused on providing Application Programming Interfaces (APIs) where users are able to extend OpenStudio without the need to compile the open source libraries. This paper will discuss the basic purposes and functionalities of the core libraries that have been wrapped with APIs including the Building Model, Results Processing, Advanced Analysis, UncertaintyQuantification, and Data Interoperability through Translators. Several building energy modeling applications have been produced using OpenStudio's API and Software Development Kits (SDK) including the United States Department of Energy's Asset ScoreCalculator, a mobile-based audit tool, an energy design assistance reporting protocol, and a portfolio scalemore » incentive optimization analysismethodology. Each of these software applications will be discussed briefly and will describe how the APIs were leveraged for various uses including high-level modeling, data transformations from detailed building audits, error checking/quality assurance of models, and use of high-performance computing for mass simulations.« less

The relationships between software publications and software systems

NASA Astrophysics Data System (ADS)

Hogg, David W.

2017-01-01

When we build software systems or software tools for astronomy, we sometimes do and sometimes don't also write and publish standard scientific papers about those software systems. I will discuss the pros and cons of writing such publications. There are impacts of writing such papers immediately (they can affect the design and structure of the software project itself), in the short term (they can promote adoption and legitimize the software), in the medium term (they can provide a platform for all the literature's mechanisms for citation, criticism, and reuse), and in the long term (they can preserve ideas that are embodied in the software, possibly on timescales much longer than the lifetime of any software context). I will argue that as important as pure software contributions are to astronomy—and I am both a preacher and a practitioner—software contributions are even more valuable when they are associated with traditional scientific publications. There are exceptions and complexities of course, which I will discuss.

Building quality into medical product software design.

PubMed

Mallory, S R

1993-01-01

The software engineering and quality assurance disciplines are a requisite to the design of safe and effective software-based medical devices. It is in the areas of software methodology and process that the most beneficial application of these disciplines to software development can be made. Software is a product of complex operations and methodologies and is not amenable to the traditional electromechanical quality assurance processes. Software quality must be built in by the developers, with the software verification and validation engineers acting as the independent instruments for ensuring compliance with performance objectives and with development and maintenance standards. The implementation of a software quality assurance program is a complex process involving management support, organizational changes, and new skill sets, but the benefits are profound. Its rewards provide safe, reliable, cost-effective, maintainable, and manageable software, which may significantly speed the regulatory review process and therefore potentially shorten the overall time to market. The use of a trial project can greatly facilitate the learning process associated with the first-time application of a software quality assurance program.

Bim and Gis: when Parametric Modeling Meets Geospatial Data

NASA Astrophysics Data System (ADS)

Barazzetti, L.; Banfi, F.

2017-12-01

Geospatial data have a crucial role in several projects related to infrastructures and land management. GIS software are able to perform advanced geospatial analyses, but they lack several instruments and tools for parametric modelling typically available in BIM. At the same time, BIM software designed for buildings have limited tools to handle geospatial data. As things stand at the moment, BIM and GIS could appear as complementary solutions, notwithstanding research work is currently under development to ensure a better level of interoperability, especially at the scale of the building. On the other hand, the transition from the local (building) scale to the infrastructure (where geospatial data cannot be neglected) has already demonstrated that parametric modelling integrated with geoinformation is a powerful tool to simplify and speed up some phases of the design workflow. This paper reviews such mixed approaches with both simulated and real examples, demonstrating that integration is already a reality at specific scales, which are not dominated by "pure" GIS or BIM. The paper will also demonstrate that some traditional operations carried out with GIS software are also available in parametric modelling software for BIM, such as transformation between reference systems, DEM generation, feature extraction, and geospatial queries. A real case study is illustrated and discussed to show the advantage of a combined use of both technologies. BIM and GIS integration can generate greater usage of geospatial data in the AECOO (Architecture, Engineering, Construction, Owner and Operator) industry, as well as new solutions for parametric modelling with additional geoinformation.

Vibrational Spectral Studies of Gemfibrozil

NASA Astrophysics Data System (ADS)

Benitta, T. Asenath; Balendiran, G. K.; James, C.

2008-11-01

The Fourier Transform Raman and infrared spectra of the crystallized drug molecule 5-(2,5-Dimethylphenoxy)-2,2-dimethylpentanoic acid (Gemfibrozil) have been recorded and analyzed. Quantum chemical computational methods have been employed using Gaussian 03 software package based on Hartree Fock method for theoretically modeling the grown molecule. The optimized geometry and vibrational frequencies have been predicted. Observed vibrational modes have been assigned with the aid of normal coordinate analysis.

Building on prior knowledge without building it in.

PubMed

Hansen, Steven S; Lampinen, Andrew K; Suri, Gaurav; McClelland, James L

2017-01-01

Lake et al. propose that people rely on "start-up software," "causal models," and "intuitive theories" built using compositional representations to learn new tasks more efficiently than some deep neural network models. We highlight the many drawbacks of a commitment to compositional representations and describe our continuing effort to explore how the ability to build on prior knowledge and to learn new tasks efficiently could arise through learning in deep neural networks.

Study on Earthquake Emergency Evacuation Drill Trainer Development

NASA Astrophysics Data System (ADS)

ChangJiang, L.

2016-12-01

With the improvement of China's urbanization, to ensure people survive the earthquake needs scientific routine emergency evacuation drills. Drawing on cellular automaton, shortest path algorithm and collision avoidance, we designed a model of earthquake emergency evacuation drill for school scenes. Based on this model, we made simulation software for earthquake emergency evacuation drill. The software is able to perform the simulation of earthquake emergency evacuation drill by building spatial structural model and selecting the information of people's location grounds on actual conditions of constructions. Based on the data of simulation, we can operate drilling in the same building. RFID technology could be used here for drill data collection which read personal information and send it to the evacuation simulation software via WIFI. Then the simulation software would contrast simulative data with the information of actual evacuation process, such as evacuation time, evacuation path, congestion nodes and so on. In the end, it would provide a contrastive analysis report to report assessment result and optimum proposal. We hope the earthquake emergency evacuation drill software and trainer can provide overall process disposal concept for earthquake emergency evacuation drill in assembly occupancies. The trainer can make the earthquake emergency evacuation more orderly, efficient, reasonable and scientific to fulfill the increase in coping capacity of urban hazard.

A Theoretical and Experimental Study of DNA Self-assembly

NASA Astrophysics Data System (ADS)

Chandran, Harish

The control of matter and phenomena at the nanoscale is fast becoming one of the most important challenges of the 21st century with wide-ranging applications from energy and health care to computing and material science. Conventional top-down approaches to nanotechnology, having served us well for long, are reaching their inherent limitations. Meanwhile, bottom-up methods such as self-assembly are emerging as viable alternatives for nanoscale fabrication and manipulation. A particularly successful bottom up technique is DNA self-assembly where a set of carefully designed DNA strands form a nanoscale object as a consequence of specific, local interactions among the different components, without external direction. The final product of the self-assembly process might be a static nanostructure or a dynamic nanodevice that performs a specific function. Over the past two decades, DNA self-assembly has produced stunning nanoscale objects such as 2D and 3D lattices, polyhedra and addressable arbitrary shaped substrates, and a myriad of nanoscale devices such as molecular tweezers, computational circuits, biosensors and molecular assembly lines. In this dissertation we study multiple problems in the theory, simulations and experiments of DNA self-assembly. We extend the Turing-universal mathematical framework of self-assembly known as the Tile Assembly Model by incorporating randomization during the assembly process. This allows us to reduce the tile complexity of linear assemblies. We develop multiple techniques to build linear assemblies of expected length N using far fewer tile types than previously possible. We abstract the fundamental properties of DNA and develop a biochemical system, which we call meta-DNA, based entirely on strands of DNA as the only component molecule. We further develop various enzyme-free protocols to manipulate meta-DNA systems and provide strand level details along with abstract notations for these mechanisms. We simulate DNA circuits by providing detailed designs for local molecular computations that involve spatially contiguous molecules arranged on addressable substrates via enzyme-free DNA hybridization reaction cascades. We use the Visual DSD simulation software in conjunction with localized reaction rates obtained from biophysical modeling to create chemical reaction networks of localized hybridization circuits that are then model checked using the PRISM model checking software. We develop a DNA detection system employing the triggered self-assembly of a novel DNA dendritic nanostructure. Detection begins when a specific, single-stranded target DNA strand triggers a hybridization chain reaction between two distinct DNA hairpins. Each hairpin opens and hybridizes up to two copies of the other, and hence each layer of the growing dendritic nanostructure can in principle accommodate an exponentially increasing number of cognate molecules, generating a nanostructure with high molecular weight. We build linear activatable assemblies employing a novel protection/deprotection strategy to strictly enforce the direction of tiling assembly growth to ensure the robustness of the assembly process. Our system consists of two tiles that can form a linear co-polymer. These tiles, which are initially protected such that they do not react with each other, can be activated to form linear co-polymers via the use of a strand displacing enzyme.

Development and Demonstration of a Method to Evaluate Bio-Sampling Strategies Using Building Simulation and Sample Planning Software

PubMed Central

Dols, W. Stuart; Persily, Andrew K.; Morrow, Jayne B.; Matzke, Brett D.; Sego, Landon H.; Nuffer, Lisa L.; Pulsipher, Brent A.

2010-01-01

In an effort to validate and demonstrate response and recovery sampling approaches and technologies, the U.S. Department of Homeland Security (DHS), along with several other agencies, have simulated a biothreat agent release within a facility at Idaho National Laboratory (INL) on two separate occasions in the fall of 2007 and the fall of 2008. Because these events constitute only two realizations of many possible scenarios, increased understanding of sampling strategies can be obtained by virtually examining a wide variety of release and dispersion scenarios using computer simulations. This research effort demonstrates the use of two software tools, CONTAM, developed by the National Institute of Standards and Technology (NIST), and Visual Sample Plan (VSP), developed by Pacific Northwest National Laboratory (PNNL). The CONTAM modeling software was used to virtually contaminate a model of the INL test building under various release and dissemination scenarios as well as a range of building design and operation parameters. The results of these CONTAM simulations were then used to investigate the relevance and performance of various sampling strategies using VSP. One of the fundamental outcomes of this project was the demonstration of how CONTAM and VSP can be used together to effectively develop sampling plans to support the various stages of response to an airborne chemical, biological, radiological, or nuclear event. Following such an event (or prior to an event), incident details and the conceptual site model could be used to create an ensemble of CONTAM simulations which model contaminant dispersion within a building. These predictions could then be used to identify priority area zones within the building and then sampling designs and strategies could be developed based on those zones. PMID:27134782

Development and Demonstration of a Method to Evaluate Bio-Sampling Strategies Using Building Simulation and Sample Planning Software.

PubMed

Dols, W Stuart; Persily, Andrew K; Morrow, Jayne B; Matzke, Brett D; Sego, Landon H; Nuffer, Lisa L; Pulsipher, Brent A

2010-01-01

In an effort to validate and demonstrate response and recovery sampling approaches and technologies, the U.S. Department of Homeland Security (DHS), along with several other agencies, have simulated a biothreat agent release within a facility at Idaho National Laboratory (INL) on two separate occasions in the fall of 2007 and the fall of 2008. Because these events constitute only two realizations of many possible scenarios, increased understanding of sampling strategies can be obtained by virtually examining a wide variety of release and dispersion scenarios using computer simulations. This research effort demonstrates the use of two software tools, CONTAM, developed by the National Institute of Standards and Technology (NIST), and Visual Sample Plan (VSP), developed by Pacific Northwest National Laboratory (PNNL). The CONTAM modeling software was used to virtually contaminate a model of the INL test building under various release and dissemination scenarios as well as a range of building design and operation parameters. The results of these CONTAM simulations were then used to investigate the relevance and performance of various sampling strategies using VSP. One of the fundamental outcomes of this project was the demonstration of how CONTAM and VSP can be used together to effectively develop sampling plans to support the various stages of response to an airborne chemical, biological, radiological, or nuclear event. Following such an event (or prior to an event), incident details and the conceptual site model could be used to create an ensemble of CONTAM simulations which model contaminant dispersion within a building. These predictions could then be used to identify priority area zones within the building and then sampling designs and strategies could be developed based on those zones.

Rapid Risk Evaluation (ER2) Using MS Excel Spreadsheet: a Case Study of Fredericton (new Brunswick, Canada)

NASA Astrophysics Data System (ADS)

McGrath, H.; Stefanakis, E.; Nastev, M.

2016-06-01

Conventional knowledge of the flood hazard alone (extent and frequency) is not sufficient for informed decision-making. The public safety community needs tools and guidance to adequately undertake flood hazard risk assessment in order to estimate respective damages and social and economic losses. While many complex computer models have been developed for flood risk assessment, they require highly trained personnel to prepare the necessary input (hazard, inventory of the built environment, and vulnerabilities) and analyze model outputs. As such, tools which utilize open-source software or are built within popular desktop software programs are appealing alternatives. The recently developed Rapid Risk Evaluation (ER2) application runs scenario based loss assessment analyses in a Microsoft Excel spreadsheet. User input is limited to a handful of intuitive drop-down menus utilized to describe the building type, age, occupancy and the expected water level. In anticipation of local depth damage curves and other needed vulnerability parameters, those from the U.S. FEMA's Hazus-Flood software have been imported and temporarily accessed in conjunction with user input to display exposure and estimated economic losses related to the structure and the content of the building. Building types and occupancies representative of those most exposed to flooding in Fredericton (New Brunswick) were introduced and test flood scenarios were run. The algorithm was successfully validated against results from the Hazus-Flood model for the same building types and flood depths.

Swarming Robot Design, Construction and Software Implementation

NASA Technical Reports Server (NTRS)

Stolleis, Karl A.

2014-01-01

In this paper is presented an overview of the hardware design, construction overview, software design and software implementation for a small, low-cost robot to be used for swarming robot development. In addition to the work done on the robot, a full simulation of the robotic system was developed using Robot Operating System (ROS) and its associated simulation. The eventual use of the robots will be exploration of evolving behaviors via genetic algorithms and builds on the work done at the University of New Mexico Biological Computation Lab.

Achieving design reuse: a case study

NASA Astrophysics Data System (ADS)

Young, Peter J.; Nielsen, Jon J.; Roberts, William H.; Wilson, Greg M.

2008-08-01

The RSAA CICADA data acquisition and control software package uses an object-oriented approach to model astronomical instrumentation and a layered architecture for implementation. Emphasis has been placed on building reusable C++ class libraries and on the use of attribute/value tables for dynamic configuration. This paper details how the approach has been successfully used in the construction of the instrument control software for the Gemini NIFS and GSAOI instruments. The software is again being used for the new RSAA SkyMapper and WiFeS instruments.

Porting the Starlink Software Collection to GNU Autotools

NASA Astrophysics Data System (ADS)

Gray, N.; Jenness, T.; Allan, A.; Berry, D. S.; Currie, M. J.; Draper, P. W.; Taylor, M. B.; Cavanagh, B.

2005-12-01

The Starlink software collection currently runs on three different Unix platforms and contains around 100 separate software items, totaling 2.5 million lines of code, in a mixture of languages. We have changed the build system from a hand-maintained collection of makefiles with hard-wired OS variants to a scheme involving feature-discovery via GNU Autoconf. As a result of this work, we have already ported the collection to Mac OS X and Cygwin. This had some unexpected benefits and costs, and valuable lessons.

A Decision Support System for Planning, Control and Auditing of DoD Software Cost Estimation.

DTIC Science & Technology

1986-03-01

is frequently used in U. S. Air Force software cost estimates. Barry Boehm’s Constructive Cost Estimation Model (COCOMO) was recently selected for use...are considered basic to the proper development of software. Pressman , [Ref. 11], addresses these basic elements in a manner which attempts to integrate...H., Jr., and Carlson, Eric D., Building E fective Decision SUDDOrt Systems, Prentice-Hal, EnglewoodNJ, 1982 11. Pressman , Roger S., o A Practioner’s A

Static and Dynamic Analysis in Design of Exoskeleton Structure

NASA Astrophysics Data System (ADS)

Ivánkova, Ol'ga; Méri, Dávid; Vojteková, Eva

2017-10-01

This paper introduces a numerical experiment of creating the load bearing system of a high rise building. When designing the high-rise building, it is always an important task to find the right proportion between the height of the building and its perceptive width from the various angles of street view. Investigated high rise building in this article was designed according to these criteria. The load bearing structure of the analysed object consists of a reinforced core, plates and steel tubes of an exoskeleton. Eight models of the building were created using the spatial variant of FEM in Scia Engineer Software. Individual models varied in number and dimensions of diagrids in the exoskeleton. In the models, loadings due to the own weight, weight of external glass cladding, and due to the wind according to the Standard, have been considered. The building was loaded by wind load from all four main directions with respect to its shape. Wind load was calculated using the 3D wind generator, which is a part of the Scia Engineer Software. For each model the static analysis was performed. Its most important criterion was the maximum or minimum horizontal displacement (rotation) of the highest point of the building. This displacement was compared with the limit values of the displacement of the analysed high-rise building. By step-by-step adding diagrids and optimizing their dimensions the building model was obtained that complied with the criteria of the Limit Serviceability State. The last model building was assessed also for the Ultimate Limit State. This model was loaded also by seismic loads for comparison with the load due to the wind.

Fault Tree Analysis Application for Safety and Reliability

NASA Technical Reports Server (NTRS)

Wallace, Dolores R.

2003-01-01

Many commercial software tools exist for fault tree analysis (FTA), an accepted method for mitigating risk in systems. The method embedded in the tools identifies a root as use in system components, but when software is identified as a root cause, it does not build trees into the software component. No commercial software tools have been built specifically for development and analysis of software fault trees. Research indicates that the methods of FTA could be applied to software, but the method is not practical without automated tool support. With appropriate automated tool support, software fault tree analysis (SFTA) may be a practical technique for identifying the underlying cause of software faults that may lead to critical system failures. We strive to demonstrate that existing commercial tools for FTA can be adapted for use with SFTA, and that applied to a safety-critical system, SFTA can be used to identify serious potential problems long before integrator and system testing.

Building Real World Domain-Specific Social Network Websites as a Capstone Project

ERIC Educational Resources Information Center

Yue, Kwok-Bun; De Silva, Dilhar; Kim, Dan; Aktepe, Mirac; Nagle, Stewart; Boerger, Chris; Jain, Anubha; Verma, Sunny

2009-01-01

This paper describes our experience of using Content Management Software (CMS), specifically Joomla, to build a real world domain-specific social network site (SNS) as a capstone project for graduate information systems and computer science students. As Web 2.0 technologies become increasingly important in driving business application development,…

ecoSmart landscapes: a versatile SaaS platform for green infrastructure applications in urban environments

Treesearch

Greg McPherson; Qingfu Xiao; Joe Purohit; Mark Dietenberger; Charles (C.R.) Boardman; Jim Simpson; Paula Peper

2014-01-01

The urban environment offers significant opportunities to improve sustainability and optimize water resources. Historically, research and software applications have been focused on the built environment (buildings). Cost-effective, practical tools that can assess the impact of different landscape configurations and their interactions with buildings have not been widely...

Building Phylogenetic Trees from DNA Sequence Data: Investigating Polar Bear and Giant Panda Ancestry.

ERIC Educational Resources Information Center

Maier, Caroline Alexandra

2001-01-01

Presents an activity in which students seek answers to questions about evolutionary relationships by using genetic databases and bioinformatics software. Students build genetic distance matrices and phylogenetic trees based on molecular sequence data using web-based resources. Provides a flowchart of steps involved in accessing, retrieving, and…

A high-resolution radiation hybrid map of the bovine genome

USDA-ARS?s Scientific Manuscript database

We are building high-resolution radiation hybrid maps of all 29 bovine autosomes and chromosome X, using a 58,000-marker genotyping assay, and a 12,000-rad whole-genome radiation hybrid (RH) panel. To accommodate the large number of markers, and to automate the map building procedure, a software pip...

Techniques and Tools for Trustworthy Composition of Pre-Designed Embedded Software Components

DTIC Science & Technology

2012-07-01

following option choices. 1. A plain vanilla pi-trie algorithm set to build the entire pi-trie. 2. A pi-trie algorithm filtered for positive prime...implicates only. 3. A plain vanilla pi-trie algorithm to build the entire pi-trie, but recognize variable-disjoint subformulas. 4. A pi-trie

USING THE ECLPSS SOFTWARE ENVIRONMENT TO BUILD A SPATIALLY EXPLICIT COMPONENT-BASED MODEL OF OZONE EFFECTS ON FOREST ECOSYSTEMS. (R827958)

EPA Science Inventory

We have developed a modeling framework to support grid-based simulation of ecosystems at multiple spatial scales, the Ecological Component Library for Parallel Spatial Simulation (ECLPSS). ECLPSS helps ecologists to build robust spatially explicit simulations of ...

Effects of a Preschool Mathematics Curriculum: Summative Research on the "Building Blocks" Project

ERIC Educational Resources Information Center

Clements, Douglas H.; Sarama, Julie

2007-01-01

This study evaluated the efficacy of a preschool mathematics program based on a comprehensive model of developing research-based software and print curricula. Building Blocks, funded by the National Science Foundation, is a curriculum development project focused on creating research-based, technology-enhanced mathematics materials for pre-K…

A support architecture for reliable distributed computing systems

NASA Technical Reports Server (NTRS)

Dasgupta, Partha; Leblanc, Richard J., Jr.

1988-01-01

The Clouds project is well underway to its goal of building a unified distributed operating system supporting the object model. The operating system design uses the object concept of structuring software at all levels of the system. The basic operating system was developed and work is under progress to build a usable system.

Structural and vibrational study of a neurotransmitter molecule: Dopamine [4-(2-aminoethyl) benzene-1,2-diol

NASA Astrophysics Data System (ADS)

Jha, Omkant; Yadav, T. K.; Yadav, R. A.

2018-01-01

Structural and vibrational studies for the most stable conformer of dopamine {4-(2-Aminoethyl) benzene-1, 2-diol} have been carried out at the DFT/B3LYP/6-311 ++G** level using the Gaussian 09 software. The IR and Raman spectra have been recorded and analyzed in light of the computed vibrational parameters using the DFT and the PEDs computed with the help of the GAR2PED software. Some of the fundamentals have considerably changed frequencies in going from benzene to dopamine. Except the rocking and wagging modes of the NH2 group the other four modes are pure group modes. The rocking and wagging modes of the NH2 group show mixing with the other modes. The two Osbnd H stretching vibrations are highly localized modes. The Kekule phenyl ring stretching mode is found to remain almost unchanged. The HOMO-LUMO study suggests the existence of charge transfer within the molecule and the energy gap supports the pharmacological active property of the dopamine molecule. The NBO analysis has been carried out to understand the proper and improper hydrogen bonding.

Software Piracy among Technology Education Students: Investigating Property Rights in a Culture of Innovation

ERIC Educational Resources Information Center

Teston, George

2008-01-01

When asked about individual perceptions of "technology," 68% of Americans primarily equate the term to the computer. Although this perception under represents the true breadth of the field, the statistic does speak to the ubiquitous role the computer plays across many technology disciplines. Software has become the building block of all major…

A Comparison of the Effects of Lego TC Logo and Problem Solving Software on Elementary Students' Problem Solving Skills.

ERIC Educational Resources Information Center

Palumbo, Debra L; Palumbo, David B.

1993-01-01

Computer-based problem-solving software exposure was compared to Lego TC LOGO instruction. Thirty fifth graders received either Lego LOGO instruction, which couples Lego building block activities with LOGO computer programming, or instruction with various problem-solving computer programs. Although both groups showed significant progress, the Lego…

Beyond terrestrial biology: charting the chemical universe of α-amino acid structures.

PubMed

Meringer, Markus; Cleaves, H James; Freeland, Stephen J

2013-11-25

α-Amino acids are fundamental to biochemistry as the monomeric building blocks with which cells construct proteins according to genetic instructions. However, the 20 amino acids of the standard genetic code represent a tiny fraction of the number of α-amino acid chemical structures that could plausibly play such a role, both from the perspective of natural processes by which life emerged and evolved, and from the perspective of human-engineered genetically coded proteins. Until now, efforts to describe the structures comprising this broader set, or even estimate their number, have been hampered by the complex combinatorial properties of organic molecules. Here, we use computer software based on graph theory and constructive combinatorics in order to conduct an efficient and exhaustive search of the chemical structures implied by two careful and precise definitions of the α-amino acids relevant to coded biological proteins. Our results include two virtual libraries of α-amino acid structures corresponding to these different approaches, comprising 121 044 and 3 846 structures, respectively, and suggest a simple approach to exploring much larger, as yet uncomputed, libraries of interest.

Effector-Triggered Self-Replication in Coupled Subsystems.

PubMed

Komáromy, Dávid; Tezcan, Meniz; Schaeffer, Gaël; Marić, Ivana; Otto, Sijbren

2017-11-13

In living systems processes like genome duplication and cell division are carefully synchronized through subsystem coupling. If we are to create life de novo, similar control over essential processes such as self-replication need to be developed. Here we report that coupling two dynamic combinatorial subsystems, featuring two separate building blocks, enables effector-mediated control over self-replication. The subsystem based on the first building block shows only self-replication, whereas that based on the second one is solely responsive toward a specific external effector molecule. Mixing the subsystems arrests replication until the effector molecule is added, resulting in the formation of a host-effector complex and the liberation of the building block that subsequently engages in self-replication. The onset, rate and extent of self-replication is controlled by the amount of effector present. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Analysis of Decomposition for Structure I Methane Hydrate by Molecular Dynamics Simulation

NASA Astrophysics Data System (ADS)

Wei, Na; Sun, Wan-Tong; Meng, Ying-Feng; Liu, An-Qi; Zhou, Shou-Wei; Guo, Ping; Fu, Qiang; Lv, Xin

2018-05-01

Under multi-nodes of temperatures and pressures, microscopic decomposition mechanisms of structure I methane hydrate in contact with bulk water molecules have been studied through LAMMPS software by molecular dynamics simulation. Simulation system consists of 482 methane molecules in hydrate and 3027 randomly distributed bulk water molecules. Through analyses of simulation results, decomposition number of hydrate cages, density of methane molecules, radial distribution function for oxygen atoms, mean square displacement and coefficient of diffusion of methane molecules have been studied. A significant result shows that structure I methane hydrate decomposes from hydrate-bulk water interface to hydrate interior. As temperature rises and pressure drops, the stabilization of hydrate will weaken, decomposition extent will go deep, and mean square displacement and coefficient of diffusion of methane molecules will increase. The studies can provide important meanings for the microscopic decomposition mechanisms analyses of methane hydrate.

Design of magnetic system to produce intense beam of polarized molecules of H2 and D2

NASA Astrophysics Data System (ADS)

Yurchenko, A. V.; Nikolenko, D. M.; Rachek, I. A.; Shestakov, Yu V.; Toporkov, D. K.; Zorin, A. V.

2017-12-01

A magnetic-separating system is designed to produce polarized molecular high-density beams of H2/D2. The distribution of the magnetic field inside the aperture of the multipole magnet was calculated using the Mermaid software package. The calculation showed that the characteristic value of the magnetic field is 40 kGs, the field gradient is about 60 kGs/cm. A numerical calculation of the trajectories of the motion of molecules with different spin projections in this magnetic system is performed. The article discusses the possibility of using the magnetic system designed for the creation of a high-intensity source of polarized molecules. The expected intensity of this source is calculated. The expected flux of molecules focused in the receiver tube is 3.5·1016 mol/s for the hydrogen molecule and 2.0·1015 mol/s for the deuterium molecule.

Nanogap structures for molecular nanoelectronics.

PubMed

Motto, Paolo; Dimonte, Alice; Rattalino, Ismael; Demarchi, Danilo; Piccinini, Gianluca; Civera, Pierluigi

2012-02-09

This study is focused on the realization of nanodevices for nano and molecular electronics, based on molecular interactions in a metal-molecule-metal (M-M-M) structure. In an M-M-M system, the electronic function is a property of the structure and can be characterized through I/V measurements. The contact between the metals and the molecule was obtained by gold nanogaps (with a dimension of less than 10 nm), produced with the electromigration technique. The nanogap fabrication was controlled by a custom hardware and the related software system. The studies were carried out through experiments and simulations of organic molecules, in particular oligothiophenes.

Installing a Local Copy of the Reactome Web Site and Knowledgebase

PubMed Central

McKay, Sheldon J; Weiser, Joel

2015-01-01

The Reactome project builds, maintains, and publishes a knowledgebase of biological pathways. The information in the knowledgebase is gathered from the experts in the field, peer reviewed, and edited by Reactome editorial staff and then published to the Reactome Web site, http://www.reactome.org (see UNIT 8.7; Croft et al., 2013). The Reactome software is open source and builds on top of other open-source or freely available software. Reactome data and code can be freely downloaded in its entirety and the Web site installed locally. This allows for more flexible interrogation of the data and also makes it possible to add one’s own information to the knowledgebase. PMID:26087747

Photogrammetric 3d Building Reconstruction from Thermal Images

NASA Astrophysics Data System (ADS)

Maset, E.; Fusiello, A.; Crosilla, F.; Toldo, R.; Zorzetto, D.

2017-08-01

This paper addresses the problem of 3D building reconstruction from thermal infrared (TIR) images. We show that a commercial Computer Vision software can be used to automatically orient sequences of TIR images taken from an Unmanned Aerial Vehicle (UAV) and to generate 3D point clouds, without requiring any GNSS/INS data about position and attitude of the images nor camera calibration parameters. Moreover, we propose a procedure based on Iterative Closest Point (ICP) algorithm to create a model that combines high resolution and geometric accuracy of RGB images with the thermal information deriving from TIR images. The process can be carried out entirely by the aforesaid software in a simple and efficient way.

Property Specification Patterns for intelligence building software

NASA Astrophysics Data System (ADS)

Chun, Seungsu

2018-03-01

In this paper, through the property specification pattern research for Modal MU(μ) logical aspects present a single framework based on the pattern of intelligence building software. In this study, broken down by state property specification pattern classification of Dwyer (S) and action (A) and was subdivided into it again strong (A) and weaknesses (E). Through these means based on a hierarchical pattern classification of the property specification pattern analysis of logical aspects Mu(μ) was applied to the pattern classification of the examples used in the actual model checker. As a result, not only can a more accurate classification than the existing classification systems were easy to create and understand the attributes specified.

Building Energy Management Open Source Software

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

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

Urban Earthquake Shaking and Loss Assessment

NASA Astrophysics Data System (ADS)

Hancilar, U.; Tuzun, C.; Yenidogan, C.; Zulfikar, C.; Durukal, E.; Erdik, M.

2009-04-01

This study, conducted under the JRA-3 component of the EU NERIES Project, develops a methodology and software (ELER) for the rapid estimation of earthquake shaking and losses the Euro-Mediterranean region. This multi-level methodology developed together with researchers from Imperial College, NORSAR and ETH-Zurich is capable of incorporating regional variability and sources of uncertainty stemming from ground motion predictions, fault finiteness, site modifications, inventory of physical and social elements subjected to earthquake hazard and the associated vulnerability relationships. GRM Risk Management, Inc. of Istanbul serves as sub-contractor tor the coding of the ELER software. The methodology encompasses the following general steps: 1. Finding of the most likely location of the source of the earthquake using regional seismotectonic data base and basic source parameters, and if and when possible, by the estimation of fault rupture parameters from rapid inversion of data from on-line stations. 2. Estimation of the spatial distribution of selected ground motion parameters through region specific ground motion attenuation relationships and using shear wave velocity distributions.(Shake Mapping) 4. Incorporation of strong ground motion and other empirical macroseismic data for the improvement of Shake Map 5. Estimation of the losses (damage, casualty and economic) at different levels of sophistication (0, 1 and 2) that commensurate with the availability of inventory of human built environment (Loss Mapping) Level 2 analysis of the ELER Software (similar to HAZUS and SELENA) is essentially intended for earthquake risk assessment (building damage, consequential human casualties and macro economic loss quantifiers) in urban areas. The basic Shake Mapping is similar to the Level 0 and Level 1 analysis however, options are available for more sophisticated treatment of site response through externally entered data and improvement of the shake map through incorporation of accelerometric and other macroseismic data (similar to the USGS ShakeMap System). The building inventory data for the Level 2 analysis will consist of grid (geo-cell) based urban building and demographic inventories. For building grouping the European building typology developed within the EU-FP5 RISK-EU project is used. The building vulnerability/fragility relationships to be used can be user selected from a list of applicable relationships developed on the basis of a comprehensive study, Both empirical and analytical relationships (based on the Coefficient Method, Equivalent Linearization Method and the Reduction Factor Method of analysis) can be employed. Casualties in Level 2 analysis are estimated based on the number of buildings in different damaged states and the casualty rates for each building type and damage level. Modifications to the casualty rates can be used if necessary. ELER Level 2 analysis will include calculation of direct monetary losses as a result building damage that will allow for repair-cost estimations and specific investigations associated with earthquake insurance applications (PML and AAL estimations). ELER Level 2 analysis loss results obtained for Istanbul for a scenario earthquake using different techniques will be presented with comparisons using different earthquake damage assessment software. The urban earthquake shaking and loss information is intented for dissemination in a timely manner to related agencies for the planning and coordination of the post-earthquake emergency response. However the same software can also be used for scenario earthquake loss estimation, related Monte-Carlo type simulations and eathquake insurance applications.

Building a Snow Data Management System using Open Source Software (and IDL)

NASA Astrophysics Data System (ADS)

Goodale, C. E.; Mattmann, C. A.; Ramirez, P.; Hart, A. F.; Painter, T.; Zimdars, P. A.; Bryant, A.; Brodzik, M.; Skiles, M.; Seidel, F. C.; Rittger, K. E.

2012-12-01

At NASA's Jet Propulsion Laboratory free and open source software is used everyday to support a wide range of projects, from planetary to climate to research and development. In this abstract I will discuss the key role that open source software has played in building a robust science data processing pipeline for snow hydrology research, and how the system is also able to leverage programs written in IDL, making JPL's Snow Data System a hybrid of open source and proprietary software. Main Points: - The Design of the Snow Data System (illustrate how the collection of sub-systems are combined to create a complete data processing pipeline) - Discuss the Challenges of moving from a single algorithm on a laptop, to running 100's of parallel algorithms on a cluster of servers (lesson's learned) - Code changes - Software license related challenges - Storage Requirements - System Evolution (from data archiving, to data processing, to data on a map, to near-real-time products and maps) - Road map for the next 6 months (including how easily we re-used the snowDS code base to support the Airborne Snow Observatory Mission) Software in Use and their Software Licenses: IDL - Used for pre and post processing of data. Licensed under a proprietary software license held by Excelis. Apache OODT - Used for data management and workflow processing. Licensed under the Apache License Version 2. GDAL - Geospatial Data processing library used for data re-projection currently. Licensed under the X/MIT license. GeoServer - WMS Server. Licensed under the General Public License Version 2.0 Leaflet.js - Javascript web mapping library. Licensed under the Berkeley Software Distribution License. Python - Glue code and miscellaneous data processing support. Licensed under the Python Software Foundation License. Perl - Script wrapper for running the SCAG algorithm. Licensed under the General Public License Version 3. PHP - Front-end web application programming. Licensed under the PHP License Version 3.01

Identification of vibrational signatures from short chains of interlinked molecule-nanoparticle junctions obtained by inelastic electron tunnelling spectroscopy.

PubMed

Jafri, S H M; Löfås, H; Fransson, J; Blom, T; Grigoriev, A; Wallner, A; Ahuja, R; Ottosson, H; Leifer, K

2013-06-07

Short chains containing a series of metal-molecule-nanoparticle nanojunctions are a nano-material system with the potential to give electrical signatures close to those from single molecule experiments while enabling us to build portable devices on a chip. Inelastic electron tunnelling spectroscopy (IETS) measurements provide one of the most characteristic electrical signals of single and few molecules. In interlinked molecule-nanoparticle (NP) chains containing typically 5-7 molecules in a chain, the spectrum is expected to be a superposition of the vibrational signatures of individual molecules. We have established a stable and reproducible molecule-AuNP multi-junction by placing a few 1,8-octanedithiol (ODT) molecules onto a versatile and portable nanoparticle-nanoelectrode platform and measured for the first time vibrational molecular signatures at complex and coupled few-molecule-NP junctions. From quantum transport calculations, we model the IETS spectra and identify vibrational modes as well as the number of molecules contributing to the electron transport in the measured spectra.

Means of escape provisions and evacuation simulation of public building in Malaysia and Singapore

NASA Astrophysics Data System (ADS)

Samad, Muna Hanim Abdul; Taib, Nooriati; Ying, Choo Siew

2017-10-01

The Uniform Building By-law 1984 of Malaysia is the legal document governing fire safety requirements in buildings. Its prescriptive nature has made the requirements out dated from the viewpoint of current performance based approach in most developed countries. The means of escape provisions is a critical requirement to safeguard occupants' safety in fire especially in public buildings. As stipulated in the UBBL 1984, the means of escape provisions includes sufficient escape routes, travel distance, protection of escape routes, etc. designated as means to allow occupants to escape within a safe period of time. This research aims at investigating the effectiveness of those provisions in public buildings during evacuation process involving massive crowd during emergencies. This research includes a scenario-based study on evacuation processes using two software i.e. PyroSim, a crowd modelling software to conduct smoke study and Pathfinder to stimulate evacuation model of building in Malaysia and Singapore as comparative study. The results show that the buildings used as case study were designed according to Malaysian UBBL 1984 and Singapore Firecode, 2013 respectively provide relative safe means of escape. The simulations of fire and smoke and coupled with simulation of evacuation have demonstrated that although there are adequate exits designated according to fire requirements, the impact of the geometry of atriums on the behavior of fire and smoke have significant effect on escape time especially for unfamiliar user of the premises.

Study of fault tolerant software technology for dynamic systems

NASA Technical Reports Server (NTRS)

Caglayan, A. K.; Zacharias, G. L.

1985-01-01

The major aim of this study is to investigate the feasibility of using systems-based failure detection isolation and compensation (FDIC) techniques in building fault-tolerant software and extending them, whenever possible, to the domain of software fault tolerance. First, it is shown that systems-based FDIC methods can be extended to develop software error detection techniques by using system models for software modules. In particular, it is demonstrated that systems-based FDIC techniques can yield consistency checks that are easier to implement than acceptance tests based on software specifications. Next, it is shown that systems-based failure compensation techniques can be generalized to the domain of software fault tolerance in developing software error recovery procedures. Finally, the feasibility of using fault-tolerant software in flight software is investigated. In particular, possible system and version instabilities, and functional performance degradation that may occur in N-Version programming applications to flight software are illustrated. Finally, a comparative analysis of N-Version and recovery block techniques in the context of generic blocks in flight software is presented.

Analysis of Traffic Signals on a Software-Defined Network for Detection and Classification of a Man-in-the-Middle Attack

DTIC Science & Technology

2017-09-01

unique characteristics of reported anomalies in the collected traffic signals to build a classification framework. Other cyber events, such as a...Furthermore, we identify unique characteristics of reported anomalies in the collected traffic signals to build a classification framework. Other cyber...2]. The applications build flow rules using network topology information provided by the control plane [1]. Since the control plane is able to

Impact of external conditions on energy consumption in industrial halls

NASA Astrophysics Data System (ADS)

Żabnieńśka-Góra, Alina

2017-11-01

The energy demand for heating the halls buildings is high. The impact on this may have the technology of production, building construction and technology requirements (HVAC systems). The isolation of the external partitions, the location of the object in relation to the surrounding buildings and the degree of the interior insolation (windows and skylights) are important in the context of energy consumption. The article discusses the impact of external conditions, wind and sunlight on energy demand in the industrial hall. The building model was prepared in IDA ICE 4.0 simulation software. Model validation was done based on measurements taken in the analyzed building.

Protein mechanics: from single molecules to functional biomaterials.

PubMed

Li, Hongbin; Cao, Yi

2010-10-19

Elastomeric proteins act as the essential functional units in a wide variety of biomechanical machinery and serve as the basic building blocks for biological materials that exhibit superb mechanical properties. These proteins provide the desired elasticity, mechanical strength, resilience, and toughness within these materials. Understanding the mechanical properties of elastomeric protein-based biomaterials is a multiscale problem spanning from the atomistic/molecular level to the macroscopic level. Uncovering the design principles of individual elastomeric building blocks is critical both for the scientific understanding of multiscale mechanics of biomaterials and for the rational engineering of novel biomaterials with desirable mechanical properties. The development of single-molecule force spectroscopy techniques has provided methods for characterizing mechanical properties of elastomeric proteins one molecule at a time. Single-molecule atomic force microscopy (AFM) is uniquely suited to this purpose. Molecular dynamic simulations, protein engineering techniques, and single-molecule AFM study have collectively revealed tremendous insights into the molecular design of single elastomeric proteins, which can guide the design and engineering of elastomeric proteins with tailored mechanical properties. Researchers are focusing experimental efforts toward engineering artificial elastomeric proteins with mechanical properties that mimic or even surpass those of natural elastomeric proteins. In this Account, we summarize our recent experimental efforts to engineer novel artificial elastomeric proteins and develop general and rational methodologies to tune the nanomechanical properties of elastomeric proteins at the single-molecule level. We focus on general design principles used for enhancing the mechanical stability of proteins. These principles include the development of metal-chelation-based general methodology, strategies to control the unfolding hierarchy of multidomain elastomeric proteins, and the design of novel elastomeric proteins that exhibit stimuli-responsive mechanical properties. Moving forward, we are now exploring the use of these artificial elastomeric proteins as building blocks of protein-based biomaterials. Ultimately, we would like to rationally tailor mechanical properties of elastomeric protein-based materials by programming the molecular sequence, and thus nanomechanical properties, of elastomeric proteins at the single-molecule level. This step would help bridge the gap between single protein mechanics and material biomechanics, revealing how the mechanical properties of individual elastomeric proteins are translated into the properties of macroscopic materials.

Programmable and autonomous computing machine made of biomolecules

PubMed Central

Benenson, Yaakov; Paz-Elizur, Tamar; Adar, Rivka; Keinan, Ehud; Livneh, Zvi; Shapiro, Ehud

2013-01-01

Devices that convert information from one form into another according to a definite procedure are known as automata. One such hypothetical device is the universal Turing machine1, which stimulated work leading to the development of modern computers. The Turing machine and its special cases2, including finite automata3, operate by scanning a data tape, whose striking analogy to information-encoding biopolymers inspired several designs for molecular DNA computers4–8. Laboratory-scale computing using DNA and human-assisted protocols has been demonstrated9–15, but the realization of computing devices operating autonomously on the molecular scale remains rare16–20. Here we describe a programmable finite automaton comprising DNA and DNA-manipulating enzymes that solves computational problems autonomously. The automaton’s hardware consists of a restriction nuclease and ligase, the software and input are encoded by double-stranded DNA, and programming amounts to choosing appropriate software molecules. Upon mixing solutions containing these components, the automaton processes the input molecule via a cascade of restriction, hybridization and ligation cycles, producing a detectable output molecule that encodes the automaton’s final state, and thus the computational result. In our implementation 1012 automata sharing the same software run independently and in parallel on inputs (which could, in principle, be distinct) in 120 μl solution at room temperature at a combined rate of 109 transitions per second with a transition fidelity greater than 99.8%, consuming less than 10−10 W. PMID:11719800

Semiautomated model building for RNA crystallography using a directed rotameric approach.

PubMed

Keating, Kevin S; Pyle, Anna Marie

2010-05-04

Structured RNA molecules play essential roles in a variety of cellular processes; however, crystallographic studies of such RNA molecules present a large number of challenges. One notable complication arises from the low resolutions typical of RNA crystallography, which results in electron density maps that are imprecise and difficult to interpret. This problem is exacerbated by the lack of computational tools for RNA modeling, as many of the techniques commonly used in protein crystallography have no equivalents for RNA structure. This leads to difficulty and errors in the model building process, particularly in modeling of the RNA backbone, which is highly error prone due to the large number of variable torsion angles per nucleotide. To address this, we have developed a method for accurately building the RNA backbone into maps of intermediate or low resolution. This method is semiautomated, as it requires a crystallographer to first locate phosphates and bases in the electron density map. After this initial trace of the molecule, however, an accurate backbone structure can be built without further user intervention. To accomplish this, backbone conformers are first predicted using RNA pseudotorsions and the base-phosphate perpendicular distance. Detailed backbone coordinates are then calculated to conform both to the predicted conformer and to the previously located phosphates and bases. This technique is shown to produce accurate backbone structure even when starting from imprecise phosphate and base coordinates. A program implementing this methodology is currently available, and a plugin for the Coot model building program is under development.

Meet the Molecules in Chocolate: Informal Opportunities for Building Thematic Molecular Models with Children

ERIC Educational Resources Information Center

Amey, Jennifer R.; Fletcher, Matthew D.; Fletcher, Rachael V.; Jones, Alison; Roberts, Erica W.; Roberts, Ieuan O.

2008-01-01

We describe the development and use of a molecular model building activity with a chocolate theme, suitable for a public presentation of chemistry through interaction with visitors to science festivals and museums, and as a special classroom activity during science weeks, and so forth. (Contains 3 figures.)

Beyond Wiki to Judgewiki for Transparent Climate Change Decisions

NASA Astrophysics Data System (ADS)

Capron, M. E.

2008-12-01

Climate Change is like the prisoner's dilemma, a zero-sum game, or cheating in sports. Everyone and every country is tempted to selfishly maintain or advance their standard of living. The tremendous difference between standards of living amplifies the desire to opt out of Climate Change solutions adverse to economic competitiveness. Climate Change is also exceedingly complex. No one person, one organization, one country, or partial collection of countries has the capacity and the global support needed to make decisions on Climate Change solutions. There are thousands of potential actions, tens of thousands of known and unknown environmental and economic impacts. Some actions are belatedly found to be unsustainable beyond token volumes, corn ethanol or soy-biodiesel for example. Mankind can address human nature and complexity with a globally transparent information and decision process available to all 7 billion of us. We need a process that builds trust and simplifies complexity. Fortunately, we have the Internet for trust building communication and computers to simplify complexity. Mankind can produce new software tailored to the challenge. We would combine group information collection software (a wiki) with a decision-matrix (a judge), market forecasting, and video games to produce the tool mankind needs for trust building transparent decisions on Climate Change actions. The resulting software would be a judgewiki.

Laser electrospray mass spectrometry of adsorbed molecules at atmospheric pressure

NASA Astrophysics Data System (ADS)

Brady, John J.; Judge, Elizabeth J.; Simon, Kuriakose; Levis, Robert J.

2010-02-01

Atmospheric pressure mass analysis of solid phase biomolecules is performed using laser electrospray mass spectrometry (LEMS). A non-resonant femtosecond duration laser pulse vaporizes native samples at atmospheric pressure for subsequent electrospray ionization and transfer into a mass spectrometer. LEMS was used to detect a complex molecule (irinotecan HCl), a complex mixture (cold medicine formulation with active ingredients: acetaminophen, dextromethorphan HBr and doxylamine succinate), and a biological building block (deoxyguanosine) deposited on steel surfaces without a matrix molecule.

Single Molecule Electronics and Devices

PubMed Central

Tsutsui, Makusu; Taniguchi, Masateru

2012-01-01

The manufacture of integrated circuits with single-molecule building blocks is a goal of molecular electronics. While research in the past has been limited to bulk experiments on self-assembled monolayers, advances in technology have now enabled us to fabricate single-molecule junctions. This has led to significant progress in understanding electron transport in molecular systems at the single-molecule level and the concomitant emergence of new device concepts. Here, we review recent developments in this field. We summarize the methods currently used to form metal-molecule-metal structures and some single-molecule techniques essential for characterizing molecular junctions such as inelastic electron tunnelling spectroscopy. We then highlight several important achievements, including demonstration of single-molecule diodes, transistors, and switches that make use of electrical, photo, and mechanical stimulation to control the electron transport. We also discuss intriguing issues to be addressed further in the future such as heat and thermoelectric transport in an individual molecule. PMID:22969345

Modeling Molecules

NASA Technical Reports Server (NTRS)

2000-01-01

The molecule modeling method known as Multibody Order (N) Dynamics, or MBO(N)D, was developed by Moldyn, Inc. at Goddard Space Flight Center through funding provided by the SBIR program. The software can model the dynamics of molecules through technology which stimulates low-frequency molecular motions and properties, such as movements among a molecule's constituent parts. With MBO(N)D, a molecule is substructured into a set of interconnected rigid and flexible bodies. These bodies replace the computation burden of mapping individual atoms. Moldyn's technology cuts computation time while increasing accuracy. The MBO(N)D technology is available as Insight II 97.0 from Molecular Simulations, Inc. Currently the technology is used to account for forces on spacecraft parts and to perform molecular analyses for pharmaceutical purposes. It permits the solution of molecular dynamics problems on a moderate workstation, as opposed to on a supercomputer.

Evaluating Different Green School Building Designs for Albania: Indoor Thermal Comfort, Energy Use Analysis with Solar Systems

NASA Astrophysics Data System (ADS)

Dalvi, Ambalika Rajendra

Improving the conditions of schools in many parts of the world is gradually acquiring importance. The Green School movement is an integral part of this effort since it aims at improving indoor environmental conditions. This would in turn, enhance student- learning while minimizing adverse environmental impact through energy efficiency of comfort-related HVAC and lighting systems. This research, which is a part of a larger research project, aims at evaluating different school building designs in Albania in terms of energy use and indoor thermal comfort, and identify energy efficient options of existing schools. We start by identifying three different climate zones in Albania; Coastal (Durres), Hill/Pre-mountainous (Tirana), mountainous (Korca). Next, two prototypical school building designs are identified from the existing stock. Numerous scenarios are then identified for analysis which consists of combinations of climate zone, building type, building orientation, building upgrade levels, presence of renewable energy systems (solar photovoltaic and solar water heater). The existing building layouts, initially outlined in CAD software and then imported into a detailed building energy software program (eQuest) to perform annual simulations for all scenarios. The research also predicted indoor thermal comfort conditions of the various scenarios on the premise that windows could be opened to provide natural ventilation cooling when appropriate. This study also estimated the energy generated from solar photovoltaic systems and solar water heater systems when placed on the available roof area to determine the extent to which they are able to meet the required electric loads (plug and lights) and building heating loads respectively. The results showed that there is adequate indoor comfort without the need for mechanical cooling for the three climate zones, and that only heating is needed during the winter months.

Defect measurement and analysis of JPL ground software: a case study

NASA Technical Reports Server (NTRS)

Powell, John D.; Spagnuolo, John N., Jr.

2004-01-01

Ground software systems at JPL must meet high assurance standards while remaining on schedule due to relatively immovable launch dates for spacecraft that will be controlled by such systems. Toward this end, the Software Quality Improvement (SQI) project's Measurement and Benchmarking (M&B) team is collecting and analyzing defect data of JPL ground system software projects to build software defect prediction models. The aim of these models is to improve predictability with regard to software quality activities. Predictive models will quantitatively define typical trends for JPL ground systems as well as Critical Discriminators (CDs) to provide explanations for atypical deviations from the norm at JPL. CDs are software characteristics that can be estimated or foreseen early in a software project's planning. Thus, these CDs will assist in planning for the predicted degree to which software quality activities for a project are likely to deviation from the normal JPL ground system based on pasted experience across the lab.

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

Katipamula, Srinivas; Gowri, Krishnan; Hernandez, George

This paper describes one such reference process that can be deployed to provide continuous automated conditioned-based maintenance management for buildings that have BIM, a building automation system (BAS) and a computerized maintenance management software (CMMS) systems. The process can be deployed using an open source transactional network platform, VOLTTRON™, designed for distributed sensing and controls and supports both energy efficiency and grid services.

Socio-Cognitive Dynamics of Knowledge Building in the Work of 9- and 10-Year-Olds

ERIC Educational Resources Information Center

Zhang, Jianwei; Scardamalia, Marlene; Lamon, Mary; Messina, Richard; Reeve, Richard

2007-01-01

This study examines four months of online discourse of 22 Grade 4 students engaged in efforts to advance their understanding of optics. Their work is part of a school-wide knowledge building initiative, the essence of which is giving students collective responsibility for idea improvement. This goal is supported by software--Knowledge…

USE OF ROUGH SETS AND SPECTRAL DATA FOR BUILDING PREDICTIVE MODELS OF REACTION RATE CONSTANTS

EPA Science Inventory

A model for predicting the log of the rate constants for alkaline hydrolysis of organic esters has been developed with the use of gas-phase min-infrared library spectra and a rule-building software system based on the mathematical theory of rough sets. A diverse set of 41 esters ...

How to Break through Techno-Shock and Build Multi-Media Units.

ERIC Educational Resources Information Center

Sutz, Rachel; Warren, Maria W.; Williams, Holly

1998-01-01

Describes how three teachers learned about using Hyperstudio (presentation software), constructed a Web page, and created an original film as part of a unit on Florida writers. Recommends three major strategies for learning a new technology: choose the literary works, then the technology; build on your strengths; and learn to talk to the…

Probe-based measurement of lateral single-electron transfer between individual molecules

PubMed Central

Steurer, Wolfram; Fatayer, Shadi; Gross, Leo; Meyer, Gerhard

2015-01-01

The field of molecular electronics aims at using single molecules as functional building blocks for electronics components, such as switches, rectifiers or transistors. A key challenge is to perform measurements with atomistic control over the alignment of the molecule and its contacting electrodes. Here we use atomic force microscopy to examine charge transfer between weakly coupled pentacene molecules on insulating films with single-electron sensitivity and control over the atomistic details. We show that, in addition to the imaging capability, the probe tip can be used to control the charge state of individual molecules and to detect charge transfers to/from the tip, as well as between individual molecules. Our approach represents a novel route for molecular charge transfer studies with a host of opportunities, especially in combination with single atom/molecule manipulation and nanopatterning techniques. PMID:26387533

LEGOS: Object-based software components for mission-critical systems. Final report, June 1, 1995--December 31, 1997

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

NONE

1998-08-01

An estimated 85% of the installed base of software is a custom application with a production quantity of one. In practice, almost 100% of military software systems are custom software. Paradoxically, the marginal costs of producing additional units are near zero. So why hasn`t the software market, a market with high design costs and low productions costs evolved like other similar custom widget industries, such as automobiles and hardware chips? The military software industry seems immune to market pressures that have motivated a multilevel supply chain structure in other widget industries: design cost recovery, improve quality through specialization, and enablemore » rapid assembly from purchased components. The primary goal of the ComponentWare Consortium (CWC) technology plan was to overcome barriers to building and deploying mission-critical information systems by using verified, reusable software components (Component Ware). The adoption of the ComponentWare infrastructure is predicated upon a critical mass of the leading platform vendors` inevitable adoption of adopting emerging, object-based, distributed computing frameworks--initially CORBA and COM/OLE. The long-range goal of this work is to build and deploy military systems from verified reusable architectures. The promise of component-based applications is to enable developers to snap together new applications by mixing and matching prefabricated software components. A key result of this effort is the concept of reusable software architectures. A second important contribution is the notion that a software architecture is something that can be captured in a formal language and reused across multiple applications. The formalization and reuse of software architectures provide major cost and schedule improvements. The Unified Modeling Language (UML) is fast becoming the industry standard for object-oriented analysis and design notation for object-based systems. However, the lack of a standard real-time distributed object operating system, lack of a standard Computer-Aided Software Environment (CASE) tool notation and lack of a standard CASE tool repository has limited the realization of component software. The approach to fulfilling this need is the software component factory innovation. The factory approach takes advantage of emerging standards such as UML, CORBA, Java and the Internet. The key technical innovation of the software component factory is the ability to assemble and test new system configurations as well as assemble new tools on demand from existing tools and architecture design repositories.« less

Space Shuttle Usage of z/OS

NASA Technical Reports Server (NTRS)

Green, Jan

2009-01-01

This viewgraph presentation gives a detailed description of the avionics associated with the Space Shuttle's data processing system and its usage of z/OS. The contents include: 1) Mission, Products, and Customers; 2) Facility Overview; 3) Shuttle Data Processing System; 4) Languages and Compilers; 5) Application Tools; 6) Shuttle Flight Software Simulator; 7) Software Development and Build Tools; and 8) Fun Facts and Acronyms.

Model-It: A Case Study of Learner-Centered Software Design for Supporting Model Building.

ERIC Educational Resources Information Center

Jackson, Shari L.; Stratford, Steven J.; Krajcik, Joseph S.; Soloway, Elliot

Learner-centered software design (LCSD) guides the design of tasks, tools, and interfaces in order to support the unique needs of learners: growth, diversity and motivation. This paper presents a framework for LCSD and describes a case study of its application to the ScienceWare Model-It, a learner-centered tool to support scientific modeling and…

NoSQL Data Store Technologies

DTIC Science & Technology

2014-09-01

NoSQL Data Store Technologies John Klein, Software Engineering Institute Patrick Donohoe, Software Engineering Institute Neil Ernst...REPORT TYPE N/A 3. DATES COVERED 4. TITLE AND SUBTITLE NoSQL Data Store Technologies 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT...distribute data 4. Data Replication – determines how a NoSQL database facilitates reliable, high performance data replication to build

Intent Specifications: An Approach to Building Human-Centered Specifications

NASA Technical Reports Server (NTRS)

Leveson, Nancy G.

1999-01-01

This paper examines and proposes an approach to writing software specifications, based on research in systems theory, cognitive psychology, and human-machine interaction. The goal is to provide specifications that support human problem solving and the tasks that humans must perform in software development and evolution. A type of specification, called intent specifications, is constructed upon this underlying foundation.

Statistical Theory for the "RCT-YES" Software: Design-Based Causal Inference for RCTs. NCEE 2015-4011

ERIC Educational Resources Information Center

Schochet, Peter Z.

2015-01-01

This report presents the statistical theory underlying the "RCT-YES" software that estimates and reports impacts for RCTs for a wide range of designs used in social policy research. The report discusses a unified, non-parametric design-based approach for impact estimation using the building blocks of the Neyman-Rubin-Holland causal…

The Development and Evaluation of Software to Foster Professional Development in Educational Assessment

ERIC Educational Resources Information Center

Benton, Morgan C.

2008-01-01

This dissertation sought to answer the question: Is it possible to build a software tool that will allow teachers to write better multiple-choice questions? The thesis proceeded from the finding that the quality of teaching is very influential in the amount that students learn. A basic premise of this research, then, is that improving teachers…

The Design and Evaluation of Class Exercises as Active Learning Tools in Software Verification and Validation

ERIC Educational Resources Information Center

Wu, Peter Y.; Manohar, Priyadarshan A.; Acharya, Sushil

2016-01-01

It is well known that interesting questions can stimulate thinking and invite participation. Class exercises are designed to make use of questions to engage students in active learning. In a project toward building a community skilled in software verification and validation (SV&V), we critically review and further develop course materials in…

Adopting Open-Source Software Applications in U. S. Higher Education: A Cross-Disciplinary Review of the Literature

ERIC Educational Resources Information Center

van Rooij, Shahron Williams

2009-01-01

Higher Education institutions in the United States are considering Open Source software applications such as the Moodle and Sakai course management systems and the Kuali financial system to build integrated learning environments that serve both academic and administrative needs. Open Source is presumed to be more flexible and less costly than…

Open Source Software and Design-Based Research Symbiosis in Developing 3D Virtual Learning Environments: Examples from the iSocial Project

ERIC Educational Resources Information Center

Schmidt, Matthew; Galyen, Krista; Laffey, James; Babiuch, Ryan; Schmidt, Carla

2014-01-01

Design-based research (DBR) and open source software are both acknowledged as potentially productive ways for advancing learning technologies. These approaches have practical benefits for the design and development process and for building and leveraging community to augment and sustain design and development. This report presents a case study of…

Seismic performance for vertical geometric irregularity frame structures

NASA Astrophysics Data System (ADS)

Ismail, R.; Mahmud, N. A.; Ishak, I. S.

2018-04-01

This research highlights the result of vertical geometric irregularity frame structures. The aid of finite element analysis software, LUSAS was used to analyse seismic performance by focusing particularly on type of irregular frame on the differences in height floors and continued in the middle of the building. Malaysia’s building structures were affected once the earthquake took place in the neighbouring country such as Indonesia (Sumatera Island). In Malaysia, concrete is widely used in building construction and limited tension resistance to prevent it. Analysing structural behavior with horizontal and vertical static load is commonly analyses by using the Plane Frame Analysis. The case study of this research is to determine the stress and displacement in the seismic response under this type of irregular frame structures. This study is based on seven-storey building of Clinical Training Centre located in Sungai Buloh, Selayang, Selangor. Since the largest earthquake occurs in Acheh, Indonesia on December 26, 2004, the data was recorded and used in conducting this research. The result of stress and displacement using IMPlus seismic analysis in LUSAS Modeller Software under the seismic response of a formwork frame system states that the building is safe to withstand the ground and in good condition under the variation of seismic performance.

Design, Development and Pre-Flight Testing of the Communications, Navigation, and Networking Reconfigurable Testbed (Connect) to Investigate Software Defined Radio Architecture on the International Space Station

NASA Technical Reports Server (NTRS)

Over, Ann P.; Barrett, Michael J.; Reinhart, Richard C.; Free, James M.; Cikanek, Harry A., III

2011-01-01

The Communication Navigation and Networking Reconfigurable Testbed (CoNNeCT) is a NASA-sponsored mission, which will investigate the usage of Software Defined Radios (SDRs) as a multi-function communication system for space missions. A softwaredefined radio system is a communication system in which typical components of the system (e.g., modulators) are incorporated into software. The software-defined capability allows flexibility and experimentation in different modulation, coding and other parameters to understand their effects on performance. This flexibility builds inherent redundancy and flexibility into the system for improved operational efficiency, real-time changes to space missions and enhanced reliability/redundancy. The CoNNeCT Project is a collaboration between industrial radio providers and NASA. The industrial radio providers are providing the SDRs and NASA is designing, building and testing the entire flight system. The flight system will be integrated on the Express Logistics Carrier (ELC) on the International Space Station (ISS) after launch on the H-IIB Transfer Vehicle in 2012. This paper provides an overview of the technology research objectives, payload description, design challenges and pre-flight testing results.

Integrating open-source software applications to build molecular dynamics systems.

PubMed

Allen, Bruce M; Predecki, Paul K; Kumosa, Maciej

2014-04-05

Three open-source applications, NanoEngineer-1, packmol, and mis2lmp are integrated using an open-source file format to quickly create molecular dynamics (MD) cells for simulation. The three software applications collectively make up the open-source software (OSS) suite known as MD Studio (MDS). The software is validated through software engineering practices and is verified through simulation of the diglycidyl ether of bisphenol-a and isophorone diamine (DGEBA/IPD) system. Multiple simulations are run using the MDS software to create MD cells, and the data generated are used to calculate density, bulk modulus, and glass transition temperature of the DGEBA/IPD system. Simulation results compare well with published experimental and numerical results. The MDS software prototype confirms that OSS applications can be analyzed against real-world research requirements and integrated to create a new capability. Copyright © 2014 Wiley Periodicals, Inc.

New FEDS Software Helps You Design for Maximum Energy Efficiency, Minimum Cost

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

Gilbride, Theresa L.

2003-01-30

This article was written for the Partner Update a newsletter put out by Potomac Communications for DOE's Rebuild America program. The article describes the FEDS (Federal Energy Decision System) software, the official analytical tool of the Rebuild America program. This software, developed by PNNL with support from DOE, FEMP and Rebuild, helps government entities and contractors make informed decisions about which energy efficiency improvements are the most cost effective for their facilities. FEDS churns thru literally thousands of calculations accounting for energy uses, costs, and interactions from different types of HVAC systems, lighting types, insulation levels, building types, occupancy levelsmore » and times. FEDS crunchs the numbers so decision makers can get fast reliable answers on which alternatives are the best for their particular building. In this article, we're touting the improvements in the latest upgrade of FEDS, which is available free to Rebuild America partners. We tell partners what FEDS does, how to order it, and even where to get tech support and training.« less

cryoem-cloud-tools: A software platform to deploy and manage cryo-EM jobs in the cloud.

PubMed

Cianfrocco, Michael A; Lahiri, Indrajit; DiMaio, Frank; Leschziner, Andres E

2018-06-01

Access to streamlined computational resources remains a significant bottleneck for new users of cryo-electron microscopy (cryo-EM). To address this, we have developed tools that will submit cryo-EM analysis routines and atomic model building jobs directly to Amazon Web Services (AWS) from a local computer or laptop. These new software tools ("cryoem-cloud-tools") have incorporated optimal data movement, security, and cost-saving strategies, giving novice users access to complex cryo-EM data processing pipelines. Integrating these tools into the RELION processing pipeline and graphical user interface we determined a 2.2 Å structure of ß-galactosidase in ∼55 hours on AWS. We implemented a similar strategy to submit Rosetta atomic model building and refinement to AWS. These software tools dramatically reduce the barrier for entry of new users to cloud computing for cryo-EM and are freely available at cryoem-tools.cloud. Copyright © 2018. Published by Elsevier Inc.

Implementation of building information modeling in Malaysian construction industry

NASA Astrophysics Data System (ADS)

Memon, Aftab Hameed; Rahman, Ismail Abdul; Harman, Nur Melly Edora

2014-10-01

This study has assessed the implementation level of Building Information Modeling (BIM) in the construction industry of Malaysia. It also investigated several computer software packages facilitating BIM and challenges affecting its implementation. Data collection for this study was carried out using questionnaire survey among the construction practitioners. 95 completed forms of questionnaire received against 150 distributed questionnaire sets from consultant, contractor and client organizations were analyzed statistically. Analysis findings indicated that the level of implementation of BIM in the construction industry of Malaysia is very low. Average index method employed to assess the effectiveness of various software packages of BIM highlighted that Bentley construction, AutoCAD and ArchiCAD are three most popular and effective software packages. Major challenges to BIM implementation are it requires enhanced collaboration, add work to a designer, interoperability and needs enhanced collaboration. For improving the level of implementing BIM in Malaysian industry, it is recommended that a flexible training program of BIM for all practitioners must be created.

Conformation-based signal transfer and processing at the single-molecule level

NASA Astrophysics Data System (ADS)

Li, Chao; Wang, Zhongping; Lu, Yan; Liu, Xiaoqing; Wang, Li

2017-11-01

Building electronic components made of individual molecules is a promising strategy for the miniaturization and integration of electronic devices. However, the practical realization of molecular devices and circuits for signal transmission and processing at room temperature has proven challenging. Here, we present room-temperature intermolecular signal transfer and processing using SnCl2Pc molecules on a Cu(100) surface. The in-plane orientations of the molecules are effectively coupled via intermolecular interaction and serve as the information carrier. In the coupled molecular arrays, the signal can be transferred from one molecule to another in the in-plane direction along predesigned routes and processed to realize logical operations. These phenomena enable the use of molecules displaying intrinsic bistable states as complex molecular devices and circuits with novel functions.

Managing computer-controlled operations

NASA Technical Reports Server (NTRS)

Plowden, J. B.

1985-01-01

A detailed discussion of Launch Processing System Ground Software Production is presented to establish the interrelationships of firing room resource utilization, configuration control, system build operations, and Shuttle data bank management. The production of a test configuration identifier is traced from requirement generation to program development. The challenge of the operational era is to implement fully automated utilities to interface with a resident system build requirements document to eliminate all manual intervention in the system build operations. Automatic update/processing of Shuttle data tapes will enhance operations during multi-flow processing.

Improving STEM Education and Workforce Development by the Inclusion of Research Experiences in the Curriculum at SWC

DTIC Science & Technology

2016-06-08

server environment. While the college’s two Cisco blade -servers are located in separate buildings, these 1. REPORT DATE (DD-MM-YYYY) 4. TITLE AND...college’s two Cisco blade -servers are located in separate buildings, these units now work as one unit. Critical databases and software packages are...server environment. While the college’s two Cisco blade -servers are located in separate buildings, these units now work as one unit. Critical

Building Computer-Based Experiments in Psychology without Programming Skills.

PubMed

Ruisoto, Pablo; Bellido, Alberto; Ruiz, Javier; Juanes, Juan A

2016-06-01

Research in Psychology usually requires to build and run experiments. However, although this task has required scripting, recent computer tools based on graphical interfaces offer new opportunities in this field for researchers with non-programming skills. The purpose of this study is to illustrate and provide a comparative overview of two of the main free open source "point and click" software packages for building and running experiments in Psychology: PsychoPy and OpenSesame. Recommendations for their potential use are further discussed.

Point clouds in BIM

NASA Astrophysics Data System (ADS)

Antova, Gergana; Kunchev, Ivan; Mickrenska-Cherneva, Christina

2016-10-01

The representation of physical buildings in Building Information Models (BIM) has been a subject of research since four decades in the fields of Construction Informatics and GeoInformatics. The early digital representations of buildings mainly appeared as 3D drawings constructed by CAD software, and the 3D representation of the buildings was only geometric, while semantics and topology were out of modelling focus. On the other hand, less detailed building representations, with often focus on ‘outside’ representations were also found in form of 2D /2,5D GeoInformation models. Point clouds from 3D laser scanning data give a full and exact representation of the building geometry. The article presents different aspects and the benefits of using point clouds in BIM in the different stages of a lifecycle of a building.

Warning: Projects May Be Closer than They Appear

NASA Technical Reports Server (NTRS)

Africa, Colby

2004-01-01

I had been working for two years as the technical product manager for a large software company, when their partner company gave me a call. They needed good software engineers to customize a new version of software, and they thought I was their guy. They told me what they wanted to do to the software, and they even showed me some prototypes. Their idea was to take the basic software tool that the large company was producing and make it more accessible to the customer. They would do this by building in flexibility based on user skill level and organizational maturity. I thought that was a fascinating approach, and I bought into it in a big way. I decided to leave my job and join up with the smaller company as their director of software engineering.

The Supertree Toolkit 2: a new and improved software package with a Graphical User Interface for supertree construction.

PubMed

Hill, Jon; Davis, Katie E

2014-01-01

Building large supertrees involves the collection, storage, and processing of thousands of individual phylogenies to create large phylogenies with thousands to tens of thousands of taxa. Such large phylogenies are useful for macroevolutionary studies, comparative biology and in conservation and biodiversity. No easy to use and fully integrated software package currently exists to carry out this task. Here, we present a new Python-based software package that uses well defined XML schema to manage both data and metadata. It builds on previous versions by 1) including new processing steps, such as Safe Taxonomic Reduction, 2) using a user-friendly GUI that guides the user to complete at least the minimum information required and includes context-sensitive documentation, and 3) a revised storage format that integrates both tree- and meta-data into a single file. These data can then be manipulated according to a well-defined, but flexible, processing pipeline using either the GUI or a command-line based tool. Processing steps include standardising names, deleting or replacing taxa, ensuring adequate taxonomic overlap, ensuring data independence, and safe taxonomic reduction. This software has been successfully used to store and process data consisting of over 1000 trees ready for analyses using standard supertree methods. This software makes large supertree creation a much easier task and provides far greater flexibility for further work.

Managing Scientific Software Complexity with Bocca and CCA

DOE PAGES

Allan, Benjamin A.; Norris, Boyana; Elwasif, Wael R.; ...

2008-01-01

In high-performance scientific software development, the emphasis is often on short time to first solution. Even when the development of new components mostly reuses existing components or libraries and only small amounts of new code must be created, dealing with the component glue code and software build processes to obtain complete applications is still tedious and error-prone. Component-based software meant to reduce complexity at the application level increases complexity to the extent that the user must learn and remember the interfaces and conventions of the component model itself. To address these needs, we introduce Bocca, the first tool to enablemore » application developers to perform rapid component prototyping while maintaining robust software-engineering practices suitable to HPC environments. Bocca provides project management and a comprehensive build environment for creating and managing applications composed of Common Component Architecture components. Of critical importance for high-performance computing (HPC) applications, Bocca is designed to operate in a language-agnostic way, simultaneously handling components written in any of the languages commonly used in scientific applications: C, C++, Fortran, Python and Java. Bocca automates the tasks related to the component glue code, freeing the user to focus on the scientific aspects of the application. Bocca embraces the philosophy pioneered by Ruby on Rails for web applications: start with something that works, and evolve it to the user's purpose.« less

Concept of software interface for BCI systems

NASA Astrophysics Data System (ADS)

Svejda, Jaromir; Zak, Roman; Jasek, Roman

2016-06-01

Brain Computer Interface (BCI) technology is intended to control external system by brain activity. One of main part of such system is software interface, which carries about clear communication between brain and either computer or additional devices connected to computer. This paper is organized as follows. Firstly, current knowledge about human brain is briefly summarized to points out its complexity. Secondly, there is described a concept of BCI system, which is then used to build an architecture of proposed software interface. Finally, there are mentioned disadvantages of sensing technology discovered during sensing part of our research.

Enhancements to the EPANET-RTX (Real-Time Analytics) ...

EPA Pesticide Factsheets

Technical brief and software The U.S. Environmental Protection Agency (EPA) developed EPANET-RTX as a collection of object-oriented software libraries comprising the core data access, data transformation, and data synthesis (real-time analytics) components of a real-time hydraulic and water quality modeling system. While EPANET-RTX uses the hydraulic and water quality solvers of EPANET, the object libraries are a self-contained set of building blocks for software developers. “Real-time EPANET” promises to change the way water utilities, commercial vendors, engineers, and the water community think about modeling.

LIDAR Point Cloud Data Extraction and Establishment of 3D Modeling of Buildings

NASA Astrophysics Data System (ADS)

Zhang, Yujuan; Li, Xiuhai; Wang, Qiang; Liu, Jiang; Liang, Xin; Li, Dan; Ni, Chundi; Liu, Yan

2018-01-01

This paper takes the method of Shepard’s to deal with the original LIDAR point clouds data, and generate regular grid data DSM, filters the ground point cloud and non ground point cloud through double least square method, and obtains the rules of DSM. By using region growing method for the segmentation of DSM rules, the removal of non building point cloud, obtaining the building point cloud information. Uses the Canny operator to extract the image segmentation is needed after the edges of the building, uses Hough transform line detection to extract the edges of buildings rules of operation based on the smooth and uniform. At last, uses E3De3 software to establish the 3D model of buildings.

Evolution of the ATLAS Nightly Build System

NASA Astrophysics Data System (ADS)

Undrus, A.

2012-12-01

The ATLAS Nightly Build System is a major component in the ATLAS collaborative software organization, validation, and code approval scheme. For over 10 years of development it has evolved into a factory for automatic release production and grid distribution. The 50 multi-platform branches of ATLAS releases provide vast opportunities for testing new packages, verification of patches to existing software, and migration to new platforms and compilers for ATLAS code that currently contains 2200 packages with 4 million C++ and 1.4 million python scripting lines written by about 1000 developers. Recent development was focused on the integration of ATLAS Nightly Build and Installation systems. The nightly releases are distributed and validated and some are transformed into stable releases used for data processing worldwide. The ATLAS Nightly System is managed by the NICOS control tool on a computing farm with 50 powerful multiprocessor nodes. NICOS provides the fully automated framework for the release builds, testing, and creation of distribution kits. The ATN testing framework of the Nightly System runs unit and integration tests in parallel suites, fully utilizing the resources of multi-core machines, and provides the first results even before compilations complete. The NICOS error detection system is based on several techniques and classifies the compilation and test errors according to their severity. It is periodically tuned to place greater emphasis on certain software defects by highlighting the problems on NICOS web pages and sending automatic e-mail notifications to responsible developers. These and other recent developments will be presented and future plans will be described.

DUO: Spectra of diatomic molecules

NASA Astrophysics Data System (ADS)

Yurchenko, Sergei N.; Lodi, Lorenzo; Tennyson, Jonathan; Stolyarov, Andrey V.

2016-05-01

Duo computes rotational, rovibrational and rovibronic spectra of diatomic molecules. The software, written in Fortran 2003, solves the Schrödinger equation for the motion of the nuclei for the simple case of uncoupled, isolated electronic states and also for the general case of an arbitrary number and type of couplings between electronic states. Possible couplings include spin-orbit, angular momenta, spin-rotational and spin-spin. Introducing the relevant couplings using so-called Born-Oppenheimer breakdown curves can correct non-adiabatic effects.

The Production Data Approach for Full Lifecycle Management

NASA Astrophysics Data System (ADS)

Schopf, J.

2012-04-01

The amount of data generated by scientists is growing exponentially, and studies have shown [Koe04] that un-archived data sets have a resource half-life that is only a fraction of those resources that are electronically archived. Most groups still lack standard approaches and procedures for data management. Arguably, however, scientists know something about building software. A recent article in Nature [Mer10] stated that 45% of research scientists spend more time now developing software than they did 5 years ago, and 38% spent at least 1/5th of their time developing software. Fox argues [Fox10] that a simple release of data is not the correct approach to data curation. In addition, just as software is used in a wide variety of ways never initially envisioned by its developers, we're seeing this even to a greater extent with data sets. In order to address the need for better data preservation and access, we propose that data sets should be managed in a similar fashion to building production quality software. These production data sets are not simply published once, but go through a cyclical process, including phases such as design, development, verification, deployment, support, analysis, and then development again, thereby supporting the full lifecycle of a data set. The process involved in academically-produced software changes over time with respect to issues such as how much it is used outside the development group, but factors in aspects such as knowing who is using the code, enabling multiple developers to contribute to code development with common procedures, formal testing and release processes, developing documentation, and licensing. When we work with data, either as a collection source, as someone tagging data, or someone re-using it, many of the lessons learned in building production software are applicable. Table 1 shows a comparison of production software elements to production data elements. Table 1: Comparison of production software and production data. Production Software Production Data End-user considerations End-user considerations Multiple Coders: Repository with check-in procedures Coding standards Multiple producers/collectors Local archive with check-in procedure Metadata Standards Formal testing Formal testing Bug tracking and fixes Bug tracking and fixes, QA/QC Documentation Documentation Formal Release Process Formal release process to external archive License Citation/usage statement The full presentation of this abstract will include a detailed discussion of these issues so that researchers can produce usable and accessible data sets as a first step toward reproducible science. By creating production-quality data sets, we extend the potential of our data, both in terms of usability and usefulness to ourselves and other researchers. The more we treat data with formal processes and release cycles, the more relevant and useful it can be to the scientific community.

Nanogap structures for molecular nanoelectronics

PubMed Central

2012-01-01

This study is focused on the realization of nanodevices for nano and molecular electronics, based on molecular interactions in a metal-molecule-metal (M-M-M) structure. In an M-M-M system, the electronic function is a property of the structure and can be characterized through I/V measurements. The contact between the metals and the molecule was obtained by gold nanogaps (with a dimension of less than 10 nm), produced with the electromigration technique. The nanogap fabrication was controlled by a custom hardware and the related software system. The studies were carried out through experiments and simulations of organic molecules, in particular oligothiophenes. PMID:22321736

Nestly--a framework for running software with nested parameter choices and aggregating results.

PubMed

McCoy, Connor O; Gallagher, Aaron; Hoffman, Noah G; Matsen, Frederick A

2013-02-01

The execution of a software application or pipeline using various combinations of parameters and inputs is a common task in bioinformatics. In the absence of a specialized tool to organize, streamline and formalize this process, scientists must write frequently complex scripts to perform these tasks. We present nestly, a Python package to facilitate running tools with nested combinations of parameters and inputs. nestly provides three components. First, a module to build nested directory structures corresponding to choices of parameters. Second, the nestrun script to run a given command using each set of parameter choices. Third, the nestagg script to aggregate results of the individual runs into a CSV file, as well as support for more complex aggregation. We also include a module for easily specifying nested dependencies for the SCons build tool, enabling incremental builds. Source, documentation and tutorial examples are available at http://github.com/fhcrc/nestly. nestly can be installed from the Python Package Index via pip; it is open source (MIT license).

And so Ad Infinitum: The Search for Quark and Lepton Substructure

ERIC Educational Resources Information Center

Lincoln, Don

2018-01-01

The saga of the search for the ultimate constituents of matter has long been one of finding a seemingly fundamental structure that, in turn, was found to be made of even smaller building blocks. Matter is made of molecules. Molecules are in turn made of atoms, which are themselves made of electrons and atomic nuclei. The nucleus consists of…

Rules of thumb to increase the software quality through testing

NASA Astrophysics Data System (ADS)

Buttu, M.; Bartolini, M.; Migoni, C.; Orlati, A.; Poppi, S.; Righini, S.

2016-07-01

The software maintenance typically requires 40-80% of the overall project costs, and this considerable variability mostly depends on the software internal quality: the more the software is designed and implemented to constantly welcome new changes, the lower will be the maintenance costs. The internal quality is typically enforced through testing, which in turn also affects the development and maintenance costs. This is the reason why testing methodologies have become a major concern for any company that builds - or is involved in building - software. Although there is no testing approach that suits all contexts, we infer some general guidelines learned during the Development of the Italian Single-dish COntrol System (DISCOS), which is a project aimed at producing the control software for the three INAF radio telescopes (the Medicina and Noto dishes, and the newly-built SRT). These guidelines concern both the development and the maintenance phases, and their ultimate goal is to maximize the DISCOS software quality through a Behavior-Driven Development (BDD) workflow beside a continuous delivery pipeline. We consider different topics and patterns; they involve the proper apportion of the tests (from end-to-end to low-level tests), the choice between hardware simulators and mockers, why and how to apply TDD and the dependency injection to increase the test coverage, the emerging technologies available for test isolation, bug fixing, how to protect the system from the external resources changes (firmware updating, hardware substitution, etc.) and, eventually, how to accomplish BDD starting from functional tests and going through integration and unit tests. We discuss pros and cons of each solution and point out the motivations of our choices either as a general rule or narrowed in the context of the DISCOS project.

Modeling software systems by domains

NASA Technical Reports Server (NTRS)

Dippolito, Richard; Lee, Kenneth

1992-01-01

The Software Architectures Engineering (SAE) Project at the Software Engineering Institute (SEI) has developed engineering modeling techniques that both reduce the complexity of software for domain-specific computer systems and result in systems that are easier to build and maintain. These techniques allow maximum freedom for system developers to apply their domain expertise to software. We have applied these techniques to several types of applications, including training simulators operating in real time, engineering simulators operating in non-real time, and real-time embedded computer systems. Our modeling techniques result in software that mirrors both the complexity of the application and the domain knowledge requirements. We submit that the proper measure of software complexity reflects neither the number of software component units nor the code count, but the locus of and amount of domain knowledge. As a result of using these techniques, domain knowledge is isolated by fields of engineering expertise and removed from the concern of the software engineer. In this paper, we will describe kinds of domain expertise, describe engineering by domains, and provide relevant examples of software developed for simulator applications using the techniques.

Intelligent Agents for Design and Synthesis Environments: My Summary

NASA Technical Reports Server (NTRS)

Norvig, Peter

1999-01-01

This presentation gives a summary of intelligent agents for design synthesis environments. We'll start with the conclusions, and work backwards to justify them. First, an important assumption is that agents (whatever they are) are good for software engineering. This is especially true for software that operates in an uncertain, changing environment. The "real world" of physical artifacts is like that: uncertain in what we can measure, changing in that things are always breaking down, and we must interact with non-software entities. The second point is that software engineering techniques can contribute to good design. There may have been a time when we wanted to build simple artifacts containing little or no software. But modern aircraft and spacecraft are complex, and rely on a great deal of software. So better software engineering leads to better designed artifacts, especially when we are designing a series of related artifacts and can amortize the costs of software development. The third point is that agents are especially useful for design tasks, above and beyond their general usefulness for software engineering, and the usefulness of software engineering to design.

Tuning of Terahertz Resonances of Pyridyl Benzamide Derivatives by Electronegative Atom Substitution

NASA Astrophysics Data System (ADS)

Dash, Jyotirmayee; Ray, Shaumik; Devi, Nirmala; Basutkar, Nitin; Gonnade, Rajesh G.; Ambade, Ashootosh V.; Pesala, Bala

2018-05-01

N-(pyridin-2-yl) benzamide (Ph2AP)-based organic molecules with prominent terahertz (THz) signatures (less than 5 THz) have been synthesized. The THz resonances are tuned by substituting the most electronegative atom, fluorine, at ortho (2F-Ph2AP), meta (3F-Ph2AP), and para (4F-Ph2AP) positions in a Ph2AP molecule. Substitution of fluorine helps in varying the charge distribution of the atoms forming hydrogen bond and hence strength of the hydrogen bond is varied which helps in tuning the THz resonances. The tuning of lower THz resonances of 2F-Ph2AP, 3F-Ph2AP, and 4F-Ph2AP has been explained in terms of compliance constant (relaxed force constant). Four-molecule cluster simulations have been carried out using Gaussian09 software to calculate the compliance constant of the hydrogen bonds. Crystal structure simulations of the above molecules using CRYSTAL14 software have been carried out to understand the origin of THz resonances. It has been observed that THz resonances are shifted to higher frequencies with stronger hydrogen bonds. The study shows that 3F-Ph2AP and 4F-Ph2AP have higher hydrogen bond strength and hence the THz resonances originating due to stretching of intermolecular hydrogen bonds have been shifted to higher frequencies compared to 2F-Ph2AP. The methodology presented here will help in designing novel organic molecules by substituting various electronegative atoms in order to achieve prominent THz resonances.

Enhanced simulator software for image validation and interpretation for multimodal localization super-resolution fluorescence microscopy

NASA Astrophysics Data System (ADS)

Erdélyi, Miklós; Sinkó, József; Gajdos, Tamás.; Novák, Tibor

2017-02-01

Optical super-resolution techniques such as single molecule localization have become one of the most dynamically developed areas in optical microscopy. These techniques routinely provide images of fixed cells or tissues with sub-diffraction spatial resolution, and can even be applied for live cell imaging under appropriate circumstances. Localization techniques are based on the precise fitting of the point spread functions (PSF) to the measured images of stochastically excited, identical fluorescent molecules. These techniques require controlling the rate between the on, off and the bleached states, keeping the number of active fluorescent molecules at an optimum value, so their diffraction limited images can be detected separately both spatially and temporally. Because of the numerous (and sometimes unknown) parameters, the imaging system can only be handled stochastically. For example, the rotation of the dye molecules obscures the polarization dependent PSF shape, and only an averaged distribution - typically estimated by a Gaussian function - is observed. TestSTORM software was developed to generate image stacks for traditional localization microscopes, where localization meant the precise determination of the spatial position of the molecules. However, additional optical properties (polarization, spectra, etc.) of the emitted photons can be used for further monitoring the chemical and physical properties (viscosity, pH, etc.) of the local environment. The image stack generating program was upgraded by several new features, such as: multicolour, polarization dependent PSF, built-in 3D visualization, structured background. These features make the program an ideal tool for optimizing the imaging and sample preparation conditions.

Visually impaired researchers get their hands on quantum chemistry: application to a computational study on the isomerization of a sterol.

PubMed

Lounnas, Valère; Wedler, Henry B; Newman, Timothy; Schaftenaar, Gijs; Harrison, Jason G; Nepomuceno, Gabriella; Pemberton, Ryan; Tantillo, Dean J; Vriend, Gert

2014-11-01

In molecular sciences, articles tend to revolve around 2D representations of 3D molecules, and sighted scientists often resort to 3D virtual reality software to study these molecules in detail. Blind and visually impaired (BVI) molecular scientists have access to a series of audio devices that can help them read the text in articles and work with computers. Reading articles published in this journal, though, is nearly impossible for them because they need to generate mental 3D images of molecules, but the article-reading software cannot do that for them. We have previously designed AsteriX, a web server that fully automatically decomposes articles, detects 2D plots of low molecular weight molecules, removes meta data and annotations from these plots, and converts them into 3D atomic coordinates. AsteriX-BVI goes one step further and converts the 3D representation into a 3D printable, haptic-enhanced format that includes Braille annotations. These Braille-annotated physical 3D models allow BVI scientists to generate a complete mental model of the molecule. AsteriX-BVI uses Molden to convert the meta data of quantum chemistry experiments into BVI friendly formats so that the entire line of scientific information that sighted people take for granted-from published articles, via printed results of computational chemistry experiments, to 3D models-is now available to BVI scientists too. The possibilities offered by AsteriX-BVI are illustrated by a project on the isomerization of a sterol, executed by the blind co-author of this article (HBW).

Visually impaired researchers get their hands on quantum chemistry: application to a computational study on the isomerization of a sterol

NASA Astrophysics Data System (ADS)

Lounnas, Valère; Wedler, Henry B.; Newman, Timothy; Schaftenaar, Gijs; Harrison, Jason G.; Nepomuceno, Gabriella; Pemberton, Ryan; Tantillo, Dean J.; Vriend, Gert

2014-11-01

In molecular sciences, articles tend to revolve around 2D representations of 3D molecules, and sighted scientists often resort to 3D virtual reality software to study these molecules in detail. Blind and visually impaired (BVI) molecular scientists have access to a series of audio devices that can help them read the text in articles and work with computers. Reading articles published in this journal, though, is nearly impossible for them because they need to generate mental 3D images of molecules, but the article-reading software cannot do that for them. We have previously designed AsteriX, a web server that fully automatically decomposes articles, detects 2D plots of low molecular weight molecules, removes meta data and annotations from these plots, and converts them into 3D atomic coordinates. AsteriX-BVI goes one step further and converts the 3D representation into a 3D printable, haptic-enhanced format that includes Braille annotations. These Braille-annotated physical 3D models allow BVI scientists to generate a complete mental model of the molecule. AsteriX-BVI uses Molden to convert the meta data of quantum chemistry experiments into BVI friendly formats so that the entire line of scientific information that sighted people take for granted—from published articles, via printed results of computational chemistry experiments, to 3D models—is now available to BVI scientists too. The possibilities offered by AsteriX-BVI are illustrated by a project on the isomerization of a sterol, executed by the blind co-author of this article (HBW).

What makes computational open source software libraries successful?

NASA Astrophysics Data System (ADS)

Bangerth, Wolfgang; Heister, Timo

2013-01-01

Software is the backbone of scientific computing. Yet, while we regularly publish detailed accounts about the results of scientific software, and while there is a general sense of which numerical methods work well, our community is largely unaware of best practices in writing the large-scale, open source scientific software upon which our discipline rests. This is particularly apparent in the commonly held view that writing successful software packages is largely the result of simply ‘being a good programmer’ when in fact there are many other factors involved, for example the social skill of community building. In this paper, we consider what we have found to be the necessary ingredients for successful scientific software projects and, in particular, for software libraries upon which the vast majority of scientific codes are built today. In particular, we discuss the roles of code, documentation, communities, project management and licenses. We also briefly comment on the impact on academic careers of engaging in software projects.

Comparison of calculation and simulation of evacuation in real buildings

NASA Astrophysics Data System (ADS)

Szénay, Martin; Lopušniak, Martin

2018-03-01

Each building must meet requirements for safe evacuation in order to prevent casualties. Therefore methods for evaluation of evacuation are used when designing buildings. In the paper, calculation methods were tested on three real buildings. The testing used methods of evacuation time calculation pursuant to Slovak standards and evacuation time calculation using the buildingExodus simulation software. If calculation methods have been suitably selected taking into account the nature of evacuation and at the same time if correct values of parameters were entered, we will be able to obtain almost identical times of evacuation in comparison with real results obtained from simulation. The difference can range from 1% to 27%.

An expert system for prediction of chemical toxicity

USGS Publications Warehouse

Hickey, James P.; Aldridge, Andrew J.; Passino-Reader, Dora R.; Frank, Anthony M.

1992-01-01

The National Fisheries Research Center- Great Lakes has developed an interactive computer program that uses the structure of an organic molecule to predict its acute toxicity to four aquatic species. The expert system software, written in the muLISP language, identifies the skeletal structures and substituent groups of an organic molecule from a user-supplied standard chemical notation known as a SMILES string, and then generates values for four solvatochromic parameters. Multiple regression equations relate these parameters to the toxicities (expressed as log10LC50s and log10EC50s, along with 95% confidence intervals) for four species. The system is demonstrated by prediction of toxicity for anilide-type pesticides to the fathead minnow (Pimephales promelas). This software is designed for use on an IBM-compatible personal computer by personnel with minimal toxicology background for rapid estimation of chemical toxicity. The system has numerous applications, with much potential for use in the pharmaceutical industry

Localization-based super-resolution imaging meets high-content screening.

PubMed

Beghin, Anne; Kechkar, Adel; Butler, Corey; Levet, Florian; Cabillic, Marine; Rossier, Olivier; Giannone, Gregory; Galland, Rémi; Choquet, Daniel; Sibarita, Jean-Baptiste

2017-12-01

Single-molecule localization microscopy techniques have proven to be essential tools for quantitatively monitoring biological processes at unprecedented spatial resolution. However, these techniques are very low throughput and are not yet compatible with fully automated, multiparametric cellular assays. This shortcoming is primarily due to the huge amount of data generated during imaging and the lack of software for automation and dedicated data mining. We describe an automated quantitative single-molecule-based super-resolution methodology that operates in standard multiwell plates and uses analysis based on high-content screening and data-mining software. The workflow is compatible with fixed- and live-cell imaging and allows extraction of quantitative data like fluorophore photophysics, protein clustering or dynamic behavior of biomolecules. We demonstrate that the method is compatible with high-content screening using 3D dSTORM and DNA-PAINT based super-resolution microscopy as well as single-particle tracking.

Lean and Efficient Software: Whole-Program Optimization of Executables

DTIC Science & Technology

2015-09-30

libraries. Many levels of library interfaces—where some libraries are dynamically linked and some are provided in binary form only—significantly limit...software at build time. The opportunity: Our objective in this project is to substantially improve the performance, size, and robustness of binary ...executables by using static and dynamic binary program analysis techniques to perform whole-program optimization directly on compiled programs

The Role of Standards in Cloud-Computing Interoperability

DTIC Science & Technology

2012-10-01

services are not shared outside the organization. CloudStack, Eucalyptus, HP, Microsoft, OpenStack , Ubuntu, and VMWare provide tools for building...center requirements • Developing usage models for cloud ven- dors • Independent IT consortium OpenStack http://www.openstack.org • Open-source...software for running private clouds • Currently consists of three core software projects: OpenStack Compute (Nova), OpenStack Object Storage (Swift

Anatomy of BioJS, an open source community for the life sciences.

PubMed

Yachdav, Guy; Goldberg, Tatyana; Wilzbach, Sebastian; Dao, David; Shih, Iris; Choudhary, Saket; Crouch, Steve; Franz, Max; García, Alexander; García, Leyla J; Grüning, Björn A; Inupakutika, Devasena; Sillitoe, Ian; Thanki, Anil S; Vieira, Bruno; Villaveces, José M; Schneider, Maria V; Lewis, Suzanna; Pettifer, Steve; Rost, Burkhard; Corpas, Manuel

2015-07-08

BioJS is an open source software project that develops visualization tools for different types of biological data. Here we report on the factors that influenced the growth of the BioJS user and developer community, and outline our strategy for building on this growth. The lessons we have learned on BioJS may also be relevant to other open source software projects.

A Proven Methodology for Developing Secure Software and Applying It to Ground Systems

NASA Technical Reports Server (NTRS)

Bailey, Brandon

2016-01-01

Part Two expands upon Part One in an attempt to translate the methodology for ground system personnel. The goal is to build upon the methodology presented in Part One by showing examples and details on how to implement the methodology. Section 1: Ground Systems Overview; Section 2: Secure Software Development; Section 3: Defense in Depth for Ground Systems; Section 4: What Now?

Development of an Integrated Process, Modeling and Simulation Platform for Performance-Based Design of Low-Energy and High IEQ Buildings

ERIC Educational Resources Information Center

Chen, Yixing

2013-01-01

The objective of this study was to develop a "Virtual Design Studio (VDS)": a software platform for integrated, coordinated and optimized design of green building systems with low energy consumption, high indoor environmental quality (IEQ), and high level of sustainability. The VDS is intended to assist collaborating architects,…

To Build on Appleworks and the Apple II, or Not--Seven Points to Guide Your Decision.

ERIC Educational Resources Information Center

Chesebrough, David E.

1993-01-01

Discusses seven factors to consider in deciding whether or not to build on AppleWorks and Apple II technology now that Apple Computer is developing little new software for the system. Factors include the impact of change on users and the existence of mail-order support services, which are listed in a sidebar. (KRN)

Development of an audio-based virtual gaming environment to assist with navigation skills in the blind.

PubMed

Connors, Erin C; Yazzolino, Lindsay A; Sánchez, Jaime; Merabet, Lotfi B

2013-03-27

Audio-based Environment Simulator (AbES) is virtual environment software designed to improve real world navigation skills in the blind. Using only audio based cues and set within the context of a video game metaphor, users gather relevant spatial information regarding a building's layout. This allows the user to develop an accurate spatial cognitive map of a large-scale three-dimensional space that can be manipulated for the purposes of a real indoor navigation task. After game play, participants are then assessed on their ability to navigate within the target physical building represented in the game. Preliminary results suggest that early blind users were able to acquire relevant information regarding the spatial layout of a previously unfamiliar building as indexed by their performance on a series of navigation tasks. These tasks included path finding through the virtual and physical building, as well as a series of drop off tasks. We find that the immersive and highly interactive nature of the AbES software appears to greatly engage the blind user to actively explore the virtual environment. Applications of this approach may extend to larger populations of visually impaired individuals.

Supporting Building Portfolio Investment and Policy Decision Making through an Integrated Building Utility Data Platform

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

Aziz, Azizan; Lasternas, Bertrand; Alschuler, Elena

The American Recovery and Reinvestment Act stimulus funding of 2009 for smart grid projects resulted in the tripling of smart meters deployment. In 2012, the Green Button initiative provided utility customers with access to their real-time1 energy usage. The availability of finely granular data provides an enormous potential for energy data analytics and energy benchmarking. The sheer volume of time-series utility data from a large number of buildings also poses challenges in data collection, quality control, and database management for rigorous and meaningful analyses. In this paper, we will describe a building portfolio-level data analytics tool for operational optimization, businessmore » investment and policy assessment using 15-minute to monthly intervals utility data. The analytics tool is developed on top of the U.S. Department of Energy’s Standard Energy Efficiency Data (SEED) platform, an open source software application that manages energy performance data of large groups of buildings. To support the significantly large volume of granular interval data, we integrated a parallel time-series database to the existing relational database. The time-series database improves on the current utility data input, focusing on real-time data collection, storage, analytics and data quality control. The fully integrated data platform supports APIs for utility apps development by third party software developers. These apps will provide actionable intelligence for building owners and facilities managers. Unlike a commercial system, this platform is an open source platform funded by the U.S. Government, accessible to the public, researchers and other developers, to support initiatives in reducing building energy consumption.« less

The development and technology transfer of software engineering technology at NASA. Johnson Space Center

NASA Technical Reports Server (NTRS)

Pitman, C. L.; Erb, D. M.; Izygon, M. E.; Fridge, E. M., III; Roush, G. B.; Braley, D. M.; Savely, R. T.

1992-01-01

The United State's big space projects of the next decades, such as Space Station and the Human Exploration Initiative, will need the development of many millions of lines of mission critical software. NASA-Johnson (JSC) is identifying and developing some of the Computer Aided Software Engineering (CASE) technology that NASA will need to build these future software systems. The goal is to improve the quality and the productivity of large software development projects. New trends are outlined in CASE technology and how the Software Technology Branch (STB) at JSC is endeavoring to provide some of these CASE solutions for NASA is described. Key software technology components include knowledge-based systems, software reusability, user interface technology, reengineering environments, management systems for the software development process, software cost models, repository technology, and open, integrated CASE environment frameworks. The paper presents the status and long-term expectations for CASE products. The STB's Reengineering Application Project (REAP), Advanced Software Development Workstation (ASDW) project, and software development cost model (COSTMODL) project are then discussed. Some of the general difficulties of technology transfer are introduced, and a process developed by STB for CASE technology insertion is described.

Structural and vibrational investigations of a neurotransmitter molecule: Serotonin (5-hydroxy tryptamine)

NASA Astrophysics Data System (ADS)

Jha, Omkant; Yadav, R. A.

2016-11-01

Structural and vibrational studies have been carried out for the most stable conformer of serotonin (5-HT) at the DFT/B3LYP/6-311++G** level using the Gaussian 09 software. In light of the computed vibrational parameters the observed IR and Raman frequencies have been analyzed. To help assign the vibrational fundamentals the GAR2PED software has been used to compute PEDs. Several of the fundamentals are drastically changed in going from indole to serotonin. The two NH bonds of the NH2 group are slightly different possibly due to bonding of the two H atoms of the NH2 group with different atoms. The rocking and wagging modes of the NH2 groups show mixing with the other modes while the remaining four modes are pure group modes. The Kekule phenyl ring stretching mode is found to remain almost unchanged. The HOMO-LUMO energy gap supports to pharmacological active property of the serotonin molecule. The HOMO and LUMO study suggests the existence of charge transfer within the molecule. The NBO analysis has been carried out to gather information regarding the proper and improper hydrogen bonds.

Comparative evaluation of several docking tools for docking small molecule ligands to DC-SIGN.

PubMed

Jug, Gregor; Anderluh, Marko; Tomašič, Tihomir

2015-06-01

Five docking tools, namely AutoDock, FRED, CDOCKER, FlexX and GOLD, have been critically examined, with the aim of selecting those most appropriate for use as docking tools for docking molecules to the lectin dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin (DC-SIGN). This lectin has been selected for its rather non-druggable binding site, which enables complex interactions that guide the binding of the core monosaccharide. Since optimal orientation is crucial for forming coordination bonds, it was important to assess whether the selected docking tools could reproduce the optimal binding conformation for several oligosaccharides that are known to bind DC-SIGN. Our results show that even widely used docking programs have certain limitations when faced with a rather shallow and featureless binding site, as is the case of DC-SIGN. The FRED docking software (OpenEye Scientific Software, Inc.) was found to score as the best tool for docking ligands to DC-SIGN. The performance of FRED was further assessed on another lectin, Langerin. We have demonstrated that this validated docking protocol could be used for docking to other lectins similar to DC-SIGN.

Structural and vibrational study of a neurotransmitter molecule: Dopamine [4-(2-aminoethyl) benzene-1,2-diol].

PubMed

Jha, Omkant; Yadav, T K; Yadav, R A

2018-01-15

Structural and vibrational studies for the most stable conformer of dopamine {4-(2-Aminoethyl) benzene-1, 2-diol} have been carried out at the DFT/B3LYP/6-311++G** level using the Gaussian 09 software. The IR and Raman spectra have been recorded and analyzed in light of the computed vibrational parameters using the DFT and the PEDs computed with the help of the GAR2PED software. Some of the fundamentals have considerably changed frequencies in going from benzene to dopamine. Except the rocking and wagging modes of the NH 2 group the other four modes are pure group modes. The rocking and wagging modes of the NH 2 group show mixing with the other modes. The two OH stretching vibrations are highly localized modes. The Kekule phenyl ring stretching mode is found to remain almost unchanged. The HOMO-LUMO study suggests the existence of charge transfer within the molecule and the energy gap supports the pharmacological active property of the dopamine molecule. The NBO analysis has been carried out to understand the proper and improper hydrogen bonding. Copyright © 2017. Published by Elsevier B.V.

Expert system verification and validation study: ES V/V Workshop

NASA Technical Reports Server (NTRS)

French, Scott; Hamilton, David

1992-01-01

The primary purpose of this document is to build a foundation for applying principles of verification and validation (V&V) of expert systems. To achieve this, some V&V as applied to conventionally implemented software is required. Part one will discuss the background of V&V from the perspective of (1) what is V&V of software and (2) V&V's role in developing software. Part one will also overview some common analysis techniques that are applied when performing V&V of software. All of these materials will be presented based on the assumption that the reader has little or no background in V&V or in developing procedural software. The primary purpose of part two is to explain the major techniques that have been developed for V&V of expert systems.

Software architecture and engineering for patient records: current and future.

PubMed

Weng, Chunhua; Levine, Betty A; Mun, Seong K

2009-05-01

During the "The National Forum on the Future of the Defense Health Information System," a track focusing on "Systems Architecture and Software Engineering" included eight presenters. These presenters identified three key areas of interest in this field, which include the need for open enterprise architecture and a federated database design, net centrality based on service-oriented architecture, and the need for focus on software usability and reusability. The eight panelists provided recommendations related to the suitability of service-oriented architecture and the enabling technologies of grid computing and Web 2.0 for building health services research centers and federated data warehouses to facilitate large-scale collaborative health care and research. Finally, they discussed the need to leverage industry best practices for software engineering to facilitate rapid software development, testing, and deployment.

Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard.

PubMed

Terwilliger, Thomas C; Grosse-Kunstleve, Ralf W; Afonine, Pavel V; Moriarty, Nigel W; Zwart, Peter H; Hung, Li Wei; Read, Randy J; Adams, Paul D

2008-01-01

The PHENIX AutoBuild wizard is a highly automated tool for iterative model building, structure refinement and density modification using RESOLVE model building, RESOLVE statistical density modification and phenix.refine structure refinement. Recent advances in the AutoBuild wizard and phenix.refine include automated detection and application of NCS from models as they are built, extensive model-completion algorithms and automated solvent-molecule picking. Model-completion algorithms in the AutoBuild wizard include loop building, crossovers between chains in different models of a structure and side-chain optimization. The AutoBuild wizard has been applied to a set of 48 structures at resolutions ranging from 1.1 to 3.2 A, resulting in a mean R factor of 0.24 and a mean free R factor of 0.29. The R factor of the final model is dependent on the quality of the starting electron density and is relatively independent of resolution.

A Roadmap for HEP Software and Computing R&D for the 2020s

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

Alves, Antonio Augusto, Jr; et al.

Particle physics has an ambitious and broad experimental programme for the coming decades. This programme requires large investments in detector hardware, either to build new facilities and experiments, or to upgrade existing ones. Similarly, it requires commensurate investment in the R&D of software to acquire, manage, process, and analyse the shear amounts of data to be recorded. In planning for the HL-LHC in particular, it is critical that all of the collaborating stakeholders agree on the software goals and priorities, and that the efforts complement each other. In this spirit, this white paper describes the R&D activities required to preparemore » for this software upgrade.« less

227 Views of RNA: Is RNA Unique in Its Chemical Isomer Space?

PubMed Central

Meringer, Markus; Goodwin, Jay

2015-01-01

Abstract Ribonucleic acid (RNA) is one of the two nucleic acids used by extant biochemistry and plays a central role as the intermediary carrier of genetic information in transcription and translation. If RNA was involved in the origin of life, it should have a facile prebiotic synthesis. A wide variety of such syntheses have been explored. However, to date no one-pot reaction has been shown capable of yielding RNA monomers from likely prebiotically abundant starting materials, though this does not rule out the possibility that simpler, more easily prebiotically accessible nucleic acids may have preceded RNA. Given structural constraints, such as the ability to form complementary base pairs and a linear covalent polymer, a variety of structural isomers of RNA could potentially function as genetic platforms. By using structure-generation software, all the potential structural isomers of the ribosides (BC5H9O4, where B is nucleobase), as well as a set of simpler minimal analogues derived from them, that can potentially serve as monomeric building blocks of nucleic acid–like molecules are enumerated. Molecules are selected based on their likely stability under biochemically relevant conditions (e.g., moderate pH and temperature) and the presence of at least two functional groups allowing the monomers to be incorporated into linear polymers. The resulting structures are then evaluated by using molecular descriptors typically applied in quantitative structure–property relationship (QSPR) studies and predicted physicochemical properties. Several databases have been queried to determine whether any of the computed isomers had been synthesized previously. Very few of the molecules that emerge from this structure set have been previously described. We conclude that ribonucleosides may have competed with a multitude of alternative structures whose potential proto-biochemical roles and abiotic syntheses remain to be explored. Key Words: Evolution—Chemical evolution—Exobiology—Prebiotic chemistry—RNA world. Astrobiology 15, 538–558. PMID:26200431

Chip-based microtrap arrays for cold polar molecules

NASA Astrophysics Data System (ADS)

Hou, Shunyong; Wei, Bin; Deng, Lianzhong; Yin, Jianping

2017-12-01

Compared to the atomic chip, which has been a powerful platform to perform an astonishing range of applications from rapid Bose-Einstein condensate (BEC) production to the atomic clock, the molecular chip is only in its infant stages. Recently a one-dimensional electric lattice was demonstrated to trap polar molecules on a chip. This excellent work opens up the way to building a molecular chip laboratory. Here we propose a two-dimensional (2D) electric lattice on a chip with concise and robust structure, which is formed by arrays of squared gold wires. Arrays of microtraps that originate in the microsize electrodes offer a steep gradient and thus allow for confining both light and heavy polar molecules. Theoretical analysis and numerical calculations are performed using two types of sample molecules, N D3 and SrF, to justify the possibility of our proposal. The height of the minima of the potential wells is about 10 μm above the surface of the chip and can be easily adjusted in a wide range by changing the voltages applied on the electrodes. These microtraps offer intriguing perspectives for investigating cold molecules in periodic potentials, such as quantum computing science, low-dimensional physics, and some other possible applications amenable to magnetic or optical lattice. The 2D adjustable electric lattice is expected to act as a building block for a future gas-phase molecular chip laboratory.

OpenEIS. Users Guide

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

Kim, Woohyun; Lutes, Robert G.; Katipamula, Srinivas

This document is a users guide for OpenEIS, a software code designed to provide standard methods for authoring, sharing, testing, using and improving algorithms for operational building energy efficiency.

Anya Petersen | NREL

Science.gov Websites

application architecture, energy informatics, scalable acquisition of sensor data, and software tools for engaging occupants in building energy performance. Prior to joining NREL, Anya developed custom business

Commercial Building Energy Asset Score

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

This software (Asset Scoring Tool) is designed to help building owners and managers to gain insight into the as-built efficiency of their buildings. It is a web tool where users can enter their building information and obtain an asset score report. The asset score report consists of modeled building energy use (by end use and by fuel type), building systems (envelope, lighting, heating, cooling, service hot water) evaluations, and recommended energy efficiency measures. The intended users are building owners and operators who have limited knowledge of building energy efficiency. The scoring tool collects minimum building data (~20 data entries) frommore » users and build a full-scale energy model using the inference functionalities from Facility Energy Decision System (FEDS). The scoring tool runs real-time building energy simulation using EnergyPlus and performs life-cycle cost analysis using FEDS. An API is also under development to allow the third-party applications to exchange data with the web service of the scoring tool.« less

Global structure of forked DNA in solution revealed by high-resolution single-molecule FRET.

PubMed

Sabir, Tara; Schröder, Gunnar F; Toulmin, Anita; McGlynn, Peter; Magennis, Steven W

2011-02-09

Branched DNA structures play critical roles in DNA replication, repair, and recombination in addition to being key building blocks for DNA nanotechnology. Here we combine single-molecule multiparameter fluorescence detection and molecular dynamics simulations to give a general approach to global structure determination of branched DNA in solution. We reveal an open, planar structure of a forked DNA molecule with three duplex arms and demonstrate an ion-induced conformational change. This structure will serve as a benchmark for DNA-protein interaction studies.

Watching the Solvation of Atoms in Liquids One Solvent Molecule at a Time

NASA Astrophysics Data System (ADS)

Bragg, Arthur E.; Glover, William J.; Schwartz, Benjamin J.

2010-06-01

We use mixed quantum-classical molecular dynamics simulations and ultrafast transient hole-burning spectroscopy to build a molecular-level picture of the motions of solvent molecules around Na atoms in liquid tetrahydrofuran. We find that even at room temperature, the solvation of Na atoms occurs in discrete steps, with the number of solvent molecules nearest the atom changing one at a time. This explains why the rate of solvent relaxation differs for different initial nonequilibrium states, and reveals how the solvent helps determine the identity of atomic species in liquids.

Robust excitons inhabit soft supramolecular nanotubes

PubMed Central

Eisele, Dörthe M.; Arias, Dylan H.; Fu, Xiaofeng; Bloemsma, Erik A.; Steiner, Colby P.; Jensen, Russell A.; Rebentrost, Patrick; Eisele, Holger; Tokmakoff, Andrei; Lloyd, Seth; Nelson, Keith A.; Nicastro, Daniela; Knoester, Jasper; Bawendi, Moungi G.

2014-01-01

Nature's highly efficient light-harvesting antennae, such as those found in green sulfur bacteria, consist of supramolecular building blocks that self-assemble into a hierarchy of close-packed structures. In an effort to mimic the fundamental processes that govern nature’s efficient systems, it is important to elucidate the role of each level of hierarchy: from molecule, to supramolecular building block, to close-packed building blocks. Here, we study the impact of hierarchical structure. We present a model system that mirrors nature’s complexity: cylinders self-assembled from cyanine-dye molecules. Our work reveals that even though close-packing may alter the cylinders’ soft mesoscopic structure, robust delocalized excitons are retained: Internal order and strong excitation-transfer interactions—prerequisites for efficient energy transport—are both maintained. Our results suggest that the cylindrical geometry strongly favors robust excitons; it presents a rational design that is potentially key to nature’s high efficiency, allowing construction of efficient light-harvesting devices even from soft, supramolecular materials. PMID:25092336

Terahertz spectral characteristics of two kinds of important functional oligosaccharides

NASA Astrophysics Data System (ADS)

Li, Ge; Liu, Wei; Wang, Wenai

2018-01-01

The absorption spectra of two kinds of important functional oligosaccharides were firstly acquired based on Fourier transform infrared spectroscopy in the range of 0.15-10THz. The simulation results of their infrared spectra were given based on Gaussian software, which were in good agreement with the experiment results. The rotation spectra and some perssad vibration spectra of these molecules were analyzed, and their absorption peaks were exactly identified. The components information was obtained by comparing the simulation results of different molecules.

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.

De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks.

PubMed

Schneider, G; Lee, M L; Stahl, M; Schneider, P

2000-07-01

An evolutionary algorithm was developed for fragment-based de novo design of molecules (TOPAS, TOPology-Assigning System). This stochastic method aims at generating a novel molecular structure mimicking a template structure. A set of approximately 25,000 fragment structures serves as the building block supply, which were obtained by a straightforward fragmentation procedure applied to 36,000 known drugs. Eleven reaction schemes were implemented for both fragmentation and building block assembly. This combination of drug-derived building blocks and a restricted set of reaction schemes proved to be a key for the automatic development of novel, synthetically tractable structures. In a cyclic optimization process, molecular architectures were generated from a parent structure by virtual synthesis, and the best structure of a generation was selected as the parent for the subsequent TOPAS cycle. Similarity measures were used to define 'fitness', based on 2D-structural similarity or topological pharmacophore distance between the template molecule and the variants. The concept of varying library 'diversity' during a design process was consequently implemented by using adaptive variant distributions. The efficiency of the design algorithm was demonstrated for the de novo construction of potential thrombin inhibitors mimicking peptide and non-peptide template structures.

Vision Based Localization in Urban Environments

NASA Technical Reports Server (NTRS)

McHenry, Michael; Cheng, Yang; Matthies, Larry

2005-01-01

As part of DARPA's MARS2020 program, the Jet Propulsion Laboratory developed a vision-based system for localization in urban environments that requires neither GPS nor active sensors. System hardware consists of a pair of small FireWire cameras and a standard Pentium-based computer. The inputs to the software system consist of: 1) a crude grid-based map describing the positions of buildings, 2) an initial estimate of robot location and 3) the video streams produced by each camera. At each step during the traverse the system: captures new image data, finds image features hypothesized to lie on the outside of a building, computes the range to those features, determines an estimate of the robot's motion since the previous step and combines that data with the map to update a probabilistic representation of the robot's location. This probabilistic representation allows the system to simultaneously represent multiple possible locations, For our testing, we have derived the a priori map manually using non-orthorectified overhead imagery, although this process could be automated. The software system consists of two primary components. The first is the vision system which uses binocular stereo ranging together with a set of heuristics to identify features likely to be part of building exteriors and to compute an estimate of the robot's motion since the previous step. The resulting visual features and the associated range measurements are software component, a particle-filter based localization system. This system uses the map and the then fed to the second primary most recent results from the vision system to update the estimate of the robot's location. This report summarizes the design of both the hardware and software and will include the results of applying the system to the global localization of a robot over an approximately half-kilometer traverse across JPL'S Pasadena campus.

Methodology to build medical ontology from textual resources.

PubMed

Baneyx, Audrey; Charlet, Jean; Jaulent, Marie-Christine

2006-01-01

In the medical field, it is now established that the maintenance of unambiguous thesauri goes through ontologies. Our research task is to help pneumologists code acts and diagnoses with a software that represents medical knowledge through a domain ontology. In this paper, we describe our general methodology aimed at knowledge engineers in order to build various types of medical ontologies based on terminology extraction from texts. The hypothesis is to apply natural language processing tools to textual patient discharge summaries to develop the resources needed to build an ontology in pneumology. Results indicate that the joint use of distributional analysis and lexico-syntactic patterns performed satisfactorily for building such ontologies.

Urban weather data and building models for the inclusion of the urban heat island effect in building performance simulation.

PubMed

Palme, M; Inostroza, L; Villacreses, G; Lobato, A; Carrasco, C

2017-10-01

This data article presents files supporting calculation for urban heat island (UHI) inclusion in building performance simulation (BPS). Methodology is used in the research article "From urban climate to energy consumption. Enhancing building performance simulation by including the urban heat island effect" (Palme et al., 2017) [1]. In this research, a Geographical Information System (GIS) study is done in order to statistically represent the most important urban scenarios of four South-American cities (Guayaquil, Lima, Antofagasta and Valparaíso). Then, a Principal Component Analysis (PCA) is done to obtain reference Urban Tissues Categories (UTC) to be used in urban weather simulation. The urban weather files are generated by using the Urban Weather Generator (UWG) software (version 4.1 beta). Finally, BPS is run out with the Transient System Simulation (TRNSYS) software (version 17). In this data paper, four sets of data are presented: 1) PCA data (excel) to explain how to group different urban samples in representative UTC; 2) UWG data (text) to reproduce the Urban Weather Generation for the UTC used in the four cities (4 UTC in Lima, Guayaquil, Antofagasta and 5 UTC in Valparaíso); 3) weather data (text) with the resulting rural and urban weather; 4) BPS models (text) data containing the TRNSYS models (four building models).

Semi-Automatic Modelling of Building FAÇADES with Shape Grammars Using Historic Building Information Modelling

NASA Astrophysics Data System (ADS)

Dore, C.; Murphy, M.

2013-02-01

This paper outlines a new approach for generating digital heritage models from laser scan or photogrammetric data using Historic Building Information Modelling (HBIM). HBIM is a plug-in for Building Information Modelling (BIM) software that uses parametric library objects and procedural modelling techniques to automate the modelling stage. The HBIM process involves a reverse engineering solution whereby parametric interactive objects representing architectural elements are mapped onto laser scan or photogrammetric survey data. A library of parametric architectural objects has been designed from historic manuscripts and architectural pattern books. These parametric objects were built using an embedded programming language within the ArchiCAD BIM software called Geometric Description Language (GDL). Procedural modelling techniques have been implemented with the same language to create a parametric building façade which automatically combines library objects based on architectural rules and proportions. Different configurations of the façade are controlled by user parameter adjustment. The automatically positioned elements of the façade can be subsequently refined using graphical editing while overlaying the model with orthographic imagery. Along with this semi-automatic method for generating façade models, manual plotting of library objects can also be used to generate a BIM model from survey data. After the 3D model has been completed conservation documents such as plans, sections, elevations and 3D views can be automatically generated for conservation projects.

Total mass difference statistics algorithm: a new approach to identification of high-mass building blocks in electrospray ionization Fourier transform ion cyclotron mass spectrometry data of natural organic matter.

PubMed

Kunenkov, Erast V; Kononikhin, Alexey S; Perminova, Irina V; Hertkorn, Norbert; Gaspar, Andras; Schmitt-Kopplin, Philippe; Popov, Igor A; Garmash, Andrew V; Nikolaev, Evgeniy N

2009-12-15

The ultrahigh-resolution Fourier transform ion cyclotron resonance (FTICR) mass spectrum of natural organic matter (NOM) contains several thousand peaks with dozens of molecules matching the same nominal mass. Such a complexity poses a significant challenge for automatic data interpretation, in which the most difficult task is molecular formula assignment, especially in the case of heavy and/or multielement ions. In this study, a new universal algorithm for automatic treatment of FTICR mass spectra of NOM and humic substances based on total mass difference statistics (TMDS) has been developed and implemented. The algorithm enables a blind search for unknown building blocks (instead of a priori known ones) by revealing repetitive patterns present in spectra. In this respect, it differs from all previously developed approaches. This algorithm was implemented in designing FIRAN-software for fully automated analysis of mass data with high peak density. The specific feature of FIRAN is its ability to assign formulas to heavy and/or multielement molecules using "virtual elements" approach. To verify the approach, it was used for processing mass spectra of sodium polystyrene sulfonate (PSS, M(w) = 2200 Da) and polymethacrylate (PMA, M(w) = 3290 Da) which produce heavy multielement and multiply-charged ions. Application of TMDS identified unambiguously monomers present in the polymers consistent with their structure: C(8)H(7)SO(3)Na for PSS and C(4)H(6)O(2) for PMA. It also allowed unambiguous formula assignment to all multiply-charged peaks including the heaviest peak in PMA spectrum at mass 4025.6625 with charge state 6- (mass bias -0.33 ppm). Application of the TMDS-algorithm to processing data on the Suwannee River FA has proven its unique capacities in analysis of spectra with high peak density: it has not only identified the known small building blocks in the structure of FA such as CH(2), H(2), C(2)H(2)O, O but the heavier unit at 154.027 amu. The latter was identified for the first time and assigned a formula C(7)H(6)O(4) consistent with the structure of dihydroxyl-benzoic acids. The presence of these compounds in the structure of FA has so far been numerically suggested but never proven directly. It was concluded that application of the TMDS-algorithm opens new horizons in unfolding molecular complexity of NOM and other natural products.

Assistant for Specifying Quality Software (ASQS) Mission Area Analysis

DTIC Science & Technology

1990-12-01

somewhat arbitrary, it was a reasonable and fast approach for partitioning the mission and software domains. The MAD builds on work done by Boeing Aerospace...Reliability ++ Reliability +++ Response 2: NO Discussion: A NO response implies intermittent burns -- most likely to perform attitude control functions...Propulsion Reliability +++ Reliability ++ 4-15 4.8.3 Query BT.3 Query: For intermittent thruster firing requirements, will the average burn time be less than

Managing Variation in Services in a Software Product Line Context

DTIC Science & Technology

2010-05-01

Oriented Domain Analysis ( FODA ) Feasibility Study (CMU/SEI-90-TR-021, ADA235785). Software Engineering Institute, Carnegie Mellon University, 1990...the systems in the product line, and a plan for building the systems. Product line scope and product line analysis define the boundaries and...systems, as well as expected ways in which they may vary. Product line analysis applies established modeling techniques to engineer the common and

Building a Trusted Path for Applications Using COTS Components

DTIC Science & Technology

2004-11-01

against attacks by malicious software. Trojan horse programs, i.e., programs with additional hidden, often malicious, functions, are more and more...cannot be imitated by untrusted software." Wiseman et al. (1988) propose a user interface for the SMITE system to prevent Trojan horses from...input, two of which can also be used for the hologram service. 7.0 CONCLUSION Trojan horse programs, i.e., programs with additional hidden, often

Building simulation: Ten challenges

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

Hong, Tianzhen; Langevin, Jared; Sun, Kaiyu

Buildings consume more than one-third of the world’s primary energy. Reducing energy use and greenhouse-gas emissions in the buildings sector through energy conservation and efficiency improvements constitutes a key strategy for achieving global energy and environmental goals. Building performance simulation has been increasingly used as a tool for designing, operating and retrofitting buildings to save energy and utility costs. However, opportunities remain for researchers, software developers, practitioners and policymakers to maximize the value of building performance simulation in the design and operation of low energy buildings and communities that leverage interdisciplinary approaches to integrate humans, buildings, and the power gridmore » at a large scale. This paper presents ten challenges that highlight some of the most important issues in building performance simulation, covering the full building life cycle and a wide range of modeling scales. In conclusion, the formulation and discussion of each challenge aims to provide insights into the state-of-the-art and future research opportunities for each topic, and to inspire new questions from young researchers in this field.« less

Building simulation: Ten challenges

DOE PAGES

Hong, Tianzhen; Langevin, Jared; Sun, Kaiyu

2018-04-12

Buildings consume more than one-third of the world’s primary energy. Reducing energy use and greenhouse-gas emissions in the buildings sector through energy conservation and efficiency improvements constitutes a key strategy for achieving global energy and environmental goals. Building performance simulation has been increasingly used as a tool for designing, operating and retrofitting buildings to save energy and utility costs. However, opportunities remain for researchers, software developers, practitioners and policymakers to maximize the value of building performance simulation in the design and operation of low energy buildings and communities that leverage interdisciplinary approaches to integrate humans, buildings, and the power gridmore » at a large scale. This paper presents ten challenges that highlight some of the most important issues in building performance simulation, covering the full building life cycle and a wide range of modeling scales. In conclusion, the formulation and discussion of each challenge aims to provide insights into the state-of-the-art and future research opportunities for each topic, and to inspire new questions from young researchers in this field.« less

Open Energy Information System version 2.0

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

OpenEIS was created to provide standard methods for authoring, sharing, testing, using, and improving algorithms for operational building energy efficiency with building managers and building owners. OpenEIS is designed as a no-cost/low-cost solution that will propagate the fault detection and diagnostic (FDD) solutions into the marketplace by providing state- of- the-art analytical and diagnostic algorithms. As OpenEIS penetrates the market, demand by control system manufacturers and integrators serving small and medium commercial customers will help push these types of commercial software tool offerings into the broader marketplace.

Draco,Version 6.x.x

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

Thompson, Kelly; Budge, Kent; Lowrie, Rob

2016-03-03

Draco is an object-oriented component library geared towards numerically intensive, radiation (particle) transport applications built for parallel computing hardware. It consists of semi-independent packages and a robust build system. The packages in Draco provide a set of components that can be used by multiple clients to build transport codes. The build system can also be extracted for use in clients. Software includes smart pointers, Design-by-Contract assertions, unit test framework, wrapped MPI functions, a file parser, unstructured mesh data structures, a random number generator, root finders and an angular quadrature component.

Simulation of an active solar energy system integrated in a passive building in order to obtain system efficiency

NASA Astrophysics Data System (ADS)

Ceacaru, Mihai C.

2012-11-01

In this work we present a simulation of an active solar energy system. This system belongs to the first passive office building (2086 square meters) in Romania and it is used for water heating consumption. This office building was opened in February 2009 and was built based on passive house design solutions. For this simulation, we use Solar Water Heating module, which belongs to the software RETSCREEN and this simulation is done for several cities in Romania. Results obtained will be compared graphically.

Building Information Model: advantages, tools and adoption efficiency

NASA Astrophysics Data System (ADS)

Abakumov, R. G.; Naumov, A. E.

2018-03-01

The paper expands definition and essence of Building Information Modeling. It describes content and effects from application of Information Modeling at different stages of a real property item. Analysis of long-term and short-term advantages is given. The authors included an analytical review of Revit software package in comparison with Autodesk with respect to: features, advantages and disadvantages, cost and pay cutoff. A prognostic calculation is given for efficiency of adoption of the Building Information Modeling technology, with examples of its successful adoption in Russia and worldwide.

ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines

PubMed Central

Wolfinger, Michael T.; Fallmann, Jörg; Eggenhofer, Florian; Amman, Fabian

2015-01-01

Recent achievements in next-generation sequencing (NGS) technologies lead to a high demand for reuseable software components to easily compile customized analysis workflows for big genomics data. We present ViennaNGS, an integrated collection of Perl modules focused on building efficient pipelines for NGS data processing. It comes with functionality for extracting and converting features from common NGS file formats, computation and evaluation of read mapping statistics, as well as normalization of RNA abundance. Moreover, ViennaNGS provides software components for identification and characterization of splice junctions from RNA-seq data, parsing and condensing sequence motif data, automated construction of Assembly and Track Hubs for the UCSC genome browser, as well as wrapper routines for a set of commonly used NGS command line tools. PMID:26236465

Inductive knowledge acquisition experience with commercial tools for space shuttle main engine testing

NASA Technical Reports Server (NTRS)

Modesitt, Kenneth L.

1990-01-01

Since 1984, an effort has been underway at Rocketdyne, manufacturer of the Space Shuttle Main Engine (SSME), to automate much of the analysis procedure conducted after engine test firings. Previously published articles at national and international conferences have contained the context of and justification for this effort. Here, progress is reported in building the full system, including the extensions of integrating large databases with the system, known as Scotty. Inductive knowledge acquisition has proven itself to be a key factor in the success of Scotty. The combination of a powerful inductive expert system building tool (ExTran), a relational data base management system (Reliance), and software engineering principles and Computer-Assisted Software Engineering (CASE) tools makes for a practical, useful and state-of-the-art application of an expert system.

Open Source and Design Thinking at NASA: A Vision for Future Software

NASA Technical Reports Server (NTRS)

Trimble, Jay

2017-01-01

NASA Mission Control Software for the Visualization of data has historically been closed, accessible only to small groups of flight controllers, often bound to a specific mission discipline such as flight dynamics, health and status or mission planning. Open Mission Control Technologies (MCT) provides new capability for NASA mission controllers and, by being fully open source, opens up NASA software for the visualization of mission data to broader communities inside and outside of NASA. Open MCT is the product of a design thinking process within NASA, using participatory design and design sprints to build a product that serves users.